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Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures
Abstract
Networks of tryptophan (Trp)─an aromatic amino acid with strong fluorescence response─are ubiquitous in biological systems, forming diverse architectures in transmembrane proteins, cytoskeletal filaments, subneuronal elements, photoreceptor complexes, virion capsids, and other cellular structures. We analyze the cooperative effects induced by ultraviolet (UV) excitation of several biologically relevant Trp mega-networks, thus giving insights into novel mechanisms for cellular signaling and control. Our theoretical analysis in the single-excitation manifold predicts the formation of strongly superradiant states due to collective interactions among organized arrangements of up to >10^5 Trp UV-excited transition dipoles in microtubule architectures, which leads to an enhancement of the fluorescence quantum yield (QY) that is confirmed by our experiments. We demonstrate the observed consequences of this superradiant behavior in the fluorescence QY for hierarchically organized tubulin structures, which increases in different geometric regimes at thermal equilibrium before saturation, highlighting the effect’s persistence in the presence of disorder. Our work thus showcases the many orders of magnitude across which the brightest (hundreds of femtoseconds) and darkest (tens of seconds) states can coexist in these Trp lattices.
... Superradiant effects in the ultraviolet region of the electromagnetic spectrum have been studied for biosystems [2][3][4] and emerge largely due to collective light-matter interactions involving tryptophan (Trp), which is a strongly fluorescent amino acid found in many proteins. It has many notable photophysical properties, such as its strong ultraviolet absorption, significant absorption-emission Stokes shift, and large transition dipole moment. ...
... Coherent quantum phenomena arising from organized networks of chromophores in protein scaffolds have been shown to play a role in the efficiency of photosynthetic complexes [6][7][8][9][10] and of other light-harvesting structures (see [2,[11][12][13][14] and references therein). More recently, superradiant states have been experimentally confirmed in tryptophan net-works of microtubules (MTs) and theoretically predicted in centrioles 1 and neuronal axon bundles [3]. In this work, we study the role of superradiance in a wider class of neuroprotein polymers, including cytoskeletal filaments and pathological aggregates, thereby demonstrating the generalizability of our prior experimental results and theoretical predictions for a novel group of chromophore architectures with significant implications for a host of neurodegenerative and other complex diseases. ...
... The quantum yield dampening by only 3.08% when the static disorder is five times that of room temperature demonstrates its robustness. Such quantum yield robustness to static disorder has recently been experimentally confirmed for microtubules at room temperature [3] (also see Figs. S6 and S7 of [3] for theoretical predictions of the enormous superradiant enhancements for axonal microtubule bundles, and of the quantum yield robustness for centrioles, respectively). ...
We study here the collective quantum optical effect of superradiance in neuroprotein architectures. This phenomenon arises from the interaction of the electromagnetic field with an organized network of tryptophan chromophores, where each can be effectively modeled as a two-level quantum emitter. Building on our prior experimental confirmation of single-photon superradiance in microtubules, we predict that bright superradiant states will also emerge in simulated actin filament bundles and amyloid fibrils, which manifests in the form of high quantum yields that are robust to static disorder up to five times that of room temperature. For microtubules and amyloid fibrils, the quantum yield is enhanced with increasing system size, contrary to the conventional expectations of quantum effects in a thermally equilibrated environment. We conduct our analyses using a non-Hermitian Hamiltonian derived from the Lindblad equation for an open quantum system that describes the interaction of a chromophore network with the electromagnetic field, in the single-photon limit. Our detailed quantum yield predictions in realistic neuroprotein structures -- including analysis of the potential information-processing applications of correlated superradiant and subradiant states at divergent timescales -- provide motivation for a range of in vitro experiments to confirm these quantum enhancements, which can serve in vivo as a mechanism for dissipating or downconverting high-energy UV metabolic photon emissions in intensely oxidative pathological environments, including those found in Alzheimer's disease and related dementias.
... Tryptophans in microtubules might be adopted as information processors. Babcock et al. suggested mega-networks of tryptophans in microtubules involving super-radiant states of tryptophan, where super-radiance can survive even at thermal equilibrium [42]. Super-radiant emission can realize the information transfer in a similar way to that for two separated quantum dots establishing photonic information processing in an experimental study [43]. ...
We aim to derive a super-radiance solution of coherent light and sound waves involving water degrees of freedom in the environment of a microtubule. We introduce a Lagrangian density functional of quantum electrodynamics with non-relativistic charged bosons as a model of quantum brain dynamics (QBD) involving water molecular conformational states and photon fields. We also introduce the model of charged boson fields (water degrees of freedom) coupled with phonons. Both optical and acoustic super-radiance solutions are derived in our approach. An acoustic super-radiance mechanism involving information transfer is proposed as an additional candidate to solve the binding problem and to achieve acoustic holography. Our results can be applied to achieve holographic memory storage and information processing in QBD.
... They argue that the specificity of energy transfer mechanisms in microtubules is determined by the internal nature of the interactions of these amino acids, as well as the influence of the external environment (Shirmonvsky & Chizhov, 2023). Those quantum effects were also observed in a biological organism (Babcock, et al., 2024). ...
The aim of this work is to show more consciously and tangibly how and under which conditions we can optimally develop our inner potential. The work defines a mathematical model that is intended to show the dynamics of individuation a priori on the individual and collective level and describes the individual associated variables in detail and speculatively. The work also proposes a new paradigm that complements psychology with quantum physics. Two hypothetical courses are described: under which conditions an individual grows and regresses over time. The work concludes with an ethical dilemma about what it means to be and remain a human being who can control his animal instincts and what we should normatively align our individual growth with throughout our lives and which of two options artificial intelligences choose in the ethical dilemma. The work is intended to serve to derive insights on the individual and collective level to be able to progress productively. The work is a conglomerate of well-founded research, personal thoughts, intuitions, observations, social analyses with the best of conscience and should nevertheless always be viewed with a critical eye and healthy doubt, true to the motto: Habe Mut, dich deines eigenen Verstandes zu bedienen.
... We also speculate that this could, with the emerging evidence of quantum effects in biology, and the very large fields created by mitochondria, hint at the existence of field-based homeostasis and organisation. Furthermore a link between ordered structure and quantum properties have been previously made for other biological structures such as microtubules and DNA 31,32 . It is suggested that the ordered nature of tryptophans in microtubules allow for super radiance whereby an incoming photon has the same probability of exciting not just one tryptophan but the ordered collection. ...
Life may be expressed as the flow of electrons, protons, and other ions, resulting in large potential difference. It is also highly photo-sensitive, as a large proportion of the redox capable molecules it relies on are chromophoric. It is thus suggestive that a key organelle in eukaryotes, the mitochondrion, constantly adapt their morphology as part of the homeostatic process. Studying unstained in vivo nano-scale structure in live cells is technically very challenging. One option is to study a central electron carrier in metabolism, reduced nicotinamide adenine dinucleotide (NADH), which is fluorescent and mostly located within mitochondria. Using one and two-photon absorption (340–360 nm and 730 nm, respectively), fluorescence lifetime imaging and anisotropy spectroscopy of NADH in solution and in live cells, we show that mitochondria do indeed appear to be aligned and exhibit high anisotropy (asymmetric directionality). Aqueous solution of NADH showed an anisotropy of ~ 0.20 compared to fluorescein or coumarin of < 0.1 and 0.04 in water respectively and as expected for small organic molecules. The anisotropy of NADH also increased further to 0.30 in the presence of proteins and 0.42 in glycerol (restricted environment) following two-photon excitation, suggesting more ordered structures. Two-photon NADH fluorescence imaging of Michigan Cancer Foundation-7 (MCF7) also showed strong anisotropy of 0.25 to 0.45. NADH has a quantum yield of fluorescence of 2% compared to more than 40% for photoionisation (electron generation), when exposed to light at 360 nm and below. The consequence of such highly ordered and directional NADH patterns with respect to electron ejection upon ultra-violet (UV) excitation could be very informative—especially in relation to ascertaining the extent of quantum effects in biology, including electron and photonic cascade, communication and modulation of effects such as spin and tunnelling.
Molecular chirality has long been monitored in the frequency domain in the ultraviolet, visible, and infrared regimes. Recently developed time-domain approaches can detect time-dependent chiral dynamics by enhancing intrinsically weak chiral signals. Even-order nonlinear signals in chiral molecules have gained attention thanks to their existence in the electric dipole approximation, without relying on the weaker higher-order multipole interactions. We illustrate the optimization of temporal polarization pulse-shaping in various frequency ranges (infrared/optical and optical/X ray) to enhance chiral nonlinear signals. These signals can be recast as an overlap integral of matter and field pseudoscalars which contain the relevant chiral information. Simulations are carried out for second- and fourth-order nonlinear spectroscopies in L-tryptophan.
The article represents the TGD view about experimental findings related to microtubules, in particular the most recent findings strongly suggesting mesoscale quantum coherence for microtubular system and actually much more general mesoscale systems in living matter.
Aim
Emergentism as an ontology of consciousness leaves unanswered the question as to its mechanism. I aim to solve the body–mind problem by explaining how conscious organisms emerged on an evolutionary basis at various times in accordance with an accepted scientific principle through a mechanism that cannot be understood, in principle.
Proposal
The reason for this cloak of secrecy is found in a seeming contradiction in the behavior of information with respect to the first two laws of thermodynamics. Information, the microstate of particles within an isolated system’s macrostate, can, like first-law energy, be neither created nor destroyed, yet the information in the system, like second-law entropy, will inevitably increase. To explain information increasing without being created, Laplace’s demon is invoked, able to predict where each particle is destined. This doesn’t work for emerging events like consciousness, which are unpredictable. This can be understood in terms of the derivation of entropy, and the emergence of classical physics, from the Relativistic Transactional Interpretation of Quantum Mechanics. I propose that the increased entropy in a time-irreversible, unpredictable (emergent) isolated system requires the simultaneous deletion of information concerning the steps, or calculations, involved.
Conclusion
Thus, the steps leading to consciousness are immediately destroyed and must remain a mystery. Implications include that entropy, not panpsychism, is the universal principle generative of consciousness, that our being conscious proves that we are not predetermined, and that consciousness requires assuming an “entropy debt” that can only be repaid by living organisms, prohibiting the emergence of conscious machines.
Microtubules are self-assembling biological helical nanotubes made of the protein tubulin that are essential for cell motility, cell architecture, cell division, molecular signaling, and intracellular trafficking. It has been hypothesized that this hollow molecular nanostructure may support optical transitions in photoexcited tryptophan, tyrosine, or phenylalanine amino acid lattices to function as a light-harvester in similar fashion as photosynthetic units; this ability coupled with its shape is analogous to a quantum wire. In support of this, recent experimental work demonstrates that electronic energy can diffuse across microtubules in a manner that cannot be explained by conventional Förster theory making them effective light harvesters. Here we present theoretical work of energy transfer between amino acids in tubulin via dipole excitations in the presence and absence of a chemical perturbation. Results demonstrate the potential for chemical manipulation of the optical properties of aromatic amino acid lattices in microtubule protein structures.
Microtubules and actin filaments are protein polymers that play a variety of energy conversion roles in the biological cell. While these polymers are being increasingly harnessed for mechanochemical roles both inside and outside physiological conditions, their capabilities for photonic energy conversion are not well understood. In this Perspective, we first introduce the reader to the photophysical properties of protein polymers, examining light harvesting by their constituent aromatic residues. We then discuss both the opportunities and the challenges in interfacing protein biochemistry with photophysics. We also review the literature reporting the response of microtubules and actin filaments to infrared light, illustrating the potential of these polymers to these polymers serve as targets for photobiomodulation. Finally, we present broad challenges and questions in the field of protein biophotonics. Understanding how protein polymers interact with light will pioneer both biohybrid device fabrication and light-based therapeutics.
The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Physical Review X 8, 031061 (2018)] have revealed the presence of a pronounced mode at ∼0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2σ) from such collective behavior, illustrating how photoexcitation can alter specific THz vibrational modes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can give rise to a multiscale response involving two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fröohlich condensates that are fundamentally determined by nonlinear interactions in biology.
The repeating arrangement of tubulin dimers confers great mechanical strength to microtubules, which are used as scaffolds for intracellular macromolecular transport in cells and exploited in biohybrid devices. The crystalline order in a microtubule, with lattice constants short enough to allow energy transfer between amino acid chromophores, is similar to synthetic structures designed for light harvesting. After photoexcitation, can these amino acid chromophores transfer excitation energy along the microtubule like a natural or artificial light-harvesting system? Here, we use tryptophan autofluorescence lifetimes to probe energy hopping between aromatic residues in tubulin and microtubules. By studying how the quencher concentration alters tryptophan autofluorescence lifetimes, we demonstrate that electronic energy can diffuse over 6.6 nm in microtubules. We discover that while diffusion lengths are influenced by tubulin polymerization state (free tubulin versus tubulin in the microtubule lattice), they are not significantly altered by the average number of protofilaments (13 versus 14). We also demonstrate that the presence of the anesthetics etomidate and isoflurane reduce exciton diffusion. Energy transport as explained by conventional Förster theory (accommodating for interactions between tryptophan and tyrosine residues) does not sufficiently explain our observations. Our studies indicate that microtubules are, unexpectedly, effective light harvesters.
The natural black-brown pigment eumelanin protects humans from high-energy UV photons by absorbing and rapidly dissipating their energy before proteins and DNA are damaged. The extremely weak fluorescence of eumelanin points toward nonradiative relaxation on the timescale of picoseconds or shorter. However, the extreme chemical and physical complexity of eumelanin masks its photoprotection mechanism. We sought to determine the electronic and structural relaxation pathways in eumelanin using three complementary ultrafast optical spectroscopy methods: fluorescence, transient absorption, and stimulated Raman spectroscopies. We show that photoexcitation of chromophores across the UV-visible spectrum rapidly generates a distribution of visible excitation energies via ultrafast internal conversion among neighboring coupled chromophores, and then all these excitations relax on a timescale of ∼4 ps without transferring their energy to other chromophores. Moreover, these picosecond dynamics are shared by the monomeric building block, 5,6-dihydroxyindole-2-carboxylic acid. Through a series of solvent and pH-dependent measurements complemented by quantum chemical modeling, we show that these ultrafast dynamics are consistent with the partial excited-state proton transfer from the catechol hydroxy groups to the solvent. The use of this multispectroscopic approach allows the minimal functional unit in eumelanin and the role of exciton coupling and excited-state proton transfer to be determined, and ultimately reveals the mechanism of photoprotection in eumelanin. This knowledge has potential for use in the design of new soft optical components and organic sunscreens.
Microtubule targeting agents (MTAs) have been exploited mainly as anti-cancer drugs
because of their impact on cellular division and angiogenesis. Additionally, microtubules (MTs) are key structures for intracellular transport, which is frequently hijacked during viral infection. We have analyzed the antiviral activity of clinically used MTAs in the infection of DNA and RNA viruses, including SARS-CoV-2, to find that MT destabilizer agents show a higher impact than stabilizers in the viral infections tested, and FDA-approved anti-helminthic benzimidazoles were among the most active compounds. In order to understand the reasons for the observed antiviral activity, we studied the impact of these compounds in motor proteins-mediated intracellular transport. To do so, we used labeled peptide tools, finding that clinically available MTAs impaired the movement
linked to MT motors in living cells. However, their effect on viral infection lacked a clear correlation to their effect in motor-mediated transport, denoting the complex use of the cytoskeleton by viruses. Finally, we further delved into the molecular mechanism of action of Mebendazole by combining biochemical and structural studies to obtain crystallographic high-resolution information of the Mebendazole-tubulin complex, which provided insights into the mechanisms of differential toxicity between helminths and mammalians.
Photoreceptors are a class of light-sensing proteins with critical biological functions. UVR8 is the only identified UV photoreceptor in plants and its dimer dissociation upon UV sensing activates UV-protective processes. However, the dissociation mechanism is still poorly understood. Here, by integrating extensive mutations, ultrafast spectroscopy, and computational calculations, we find that the funneled excitation energy in the interfacial tryptophan (Trp) pyramid center drives a directional Trp-Trp charge separation in 80 ps and produces a critical transient Trp anion, enabling its ultrafast charge neutralization with a nearby positive arginine residue in 17 ps to destroy a key salt bridge. A domino effect is then triggered to unzip the strong interfacial interactions, which is facilitated through flooding the interface by channel and interfacial water molecules. These detailed dynamics reveal a unique molecular mechanism of UV-induced dimer monomerization.
The cytoskeleton is a dynamic network of proteins, including actin, microtubules, and their associated motor proteins, that enables essential cellular processes such as motility, division, and growth. While actomyosin networks are extensively studied, how interactions between actin and microtubules, ubiquitous in the cytoskeleton, influence actomyosin activity remains an open question. Here, we create a network of co-entangled actin and microtubules driven by myosin II. We combine dynamic differential microscopy, particle image velocimetry, and particle tracking to show that both actin and microtubules undergo ballistic contraction with unexpectedly indistinguishable characteristics. This contractility is distinct from faster disordered motion and rupturing that active actin networks exhibit. Our results suggest that microtubules enable self-organized myosin-driven contraction by providing flexural rigidity and enhanced connectivity to actin networks. Beyond the immediate relevance to cytoskeletal dynamics, our results shed light on the design of active materials that can be precisely tuned by the network composition.
Plants utilize a UV-B (280 to 315 nm) photoreceptor UVR8 (UV RESISTANCE LOCUS 8) to sense environmental UV levels and regulate gene expression to avoid harmful UV effects. Uniquely, UVR8 uses intrinsic tryptophan for UV-B perception with a homodimer structure containing 26 structural tryptophan residues. However, besides 8 tryptophans at the dimer interface to form two critical pyramid perception centers, the other 18 tryptophans’ functional role is unknown. Here, using ultrafast fluorescence spectroscopy, computational methods and extensive mutations, we find that all 18 tryptophans form light-harvesting networks and funnel their excitation energy to the pyramid centers to enhance light-perception efficiency. We determine the timescales of all elementary tryptophan-to-tryptophan energy-transfer steps in picoseconds to nanoseconds, in excellent agreement with quantum computational calculations, and finally reveal a significant leap in light-perception quantum efficiency from 35% to 73%. This photoreceptor is the first system discovered so far, to be best of our knowledge, using natural amino-acid tryptophans to form networks for both light harvesting and light perception.
The maintenance of axons for the lifetime of an organism requires an axonal cytoskeleton that is robust but also flexible to adapt to mechanical challenges and to support plastic changes of axon morphology. Furthermore, cytoskeletal organization has to adapt to axons of dramatically different dimensions, and to their compartment-specific requirements in the axon initial segment, in the axon shaft, at synapses or in growth cones. To understand how the cytoskeleton caters to these different demands, this review summarizes five decades of electron microscopic studies. It focuses on the organization of microtubules and neurofilaments in axon shafts in both vertebrate and invertebrate neurons, as well as the axon initial segments of vertebrate motor- and interneurons. Findings from these ultrastructural studies are being interpreted here on the basis of our contemporary molecular understanding. They strongly suggest that axon architecture in animals as diverse as arthropods and vertebrates is dependent on loosely cross-linked bundles of microtubules running all along axons, with only minor roles played by neurofilaments.
A comparison between the single particle spectrum of the discrete Bardeen-Cooper-Schrieffer (BCS) model, used for small superconducting grains, and the spectrum of a paradigmatic model of Single Excitation Superradiance (SES) is presented. They are both characterized by an equally spaced energy spectrum (Picket Fence) where all the levels are coupled between each other by a constant coupling which is real for the BCS model and purely imaginary for the SES model. While the former corresponds to the discrete BCS-model describing the coupling of Cooper pairs in momentum space and it induces a Superconductive regime, the latter describes the coupling of single particle energy levels to a common decay channel and it induces a Superradiant transition. We show that the transition to a Superradiant regime can be connected to the emergence of an imaginary energy gap, similarly to the transition to a Superconductive regime where a real energy gap emerges. Despite their different physical origin, it is possible to show that both the Superradiant and the Superconducting gaps have the same magnitude in the large gap limit. Nevertheless, some differences appear: while the critical coupling at which the Superradiant gap appears is independent of the system size N, for the Superconductivity gap it scales as (ln N)⁻¹, which is the expected BCS result. The presence of a gap in the imaginary energy axis between the Superradiant and the Subradiant states shares many similarities with the “standard” gap on the real energy axis: the superradiant state is protected against disorder from the imaginary gap as well as the superconducting ground state is protected by the real energy gap. Moreover we connect the origin of the gapped phase to the long-range nature of the coupling between the energy levels.
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Fröhlich discovered the remarkable condensation of polar vibrations into the lowest frequency mode when the system is pumped externally. For a full understanding of the Fröhlich condensate one needs to go beyond the mean field level to describe critical behavior as well as quantum fluctuations. The energy redistribution among vibrational modes with nonlinearity included is shown to be essential for realizing the condensate and the phonon-number distribution, revealing the transition from quasithermal to super-Poissonian statistics with the pump. We further study the spectroscopic properties of the Fröhlich condensate, which are especially revealed by the narrow linewidth. This gives the long-lived coherence and the collective motion of the condensate. Finally, we show that the proteins such as bovine serum albumin and lysozyme are most likely the candidates for observing such collective modes in THz regime by means of Raman or infrared spectroscopy.
Microtubules are biological protein polymers with critical and diverse functions. Their structures share some similarities with photosynthetic antenna complexes, particularly in the ordered arrangement of photoactive molecules with large transition dipole moments. As the role of photoexcitations in microtubules remains an open question, here we analyze tryptophan molecules, the amino acid building block of microtubules with the largest transition dipole strength. By taking their positions and dipole orientations from realistic models capable of reproducing tubulin experimental spectra, and using a Hamiltonian widely employed in quantum optics to describe light-matter interactions, we show that such molecules arranged in their native microtubule configuration exhibit a superradiant lowest exciton state, which represents an excitation fully extended on the chromophore lattice. We also show that such a superradiant state emerges due to supertransfer coupling between the lowest exciton states of smaller blocks of the microtubule. In the dynamics we find that the spreading of excitation is ballistic in the absence of external sources of disorder and strongly dependent on initial conditions. The velocity of photoexcitation spreading is shown to be enhanced by the supertransfer effect with respect to the velocity one would expect from the strength of the nearest-neighbor coupling between tryptophan molecules in the microtubule. Finally, such structures are shown to have an enhanced robustness to static disorder when compared to geometries that include only short-range interactions. These cooperative effects (superradiance and supertransfer) may induce ultra-efficient photoexcitation absorption and could enhance excitonic energy transfer in microtubules over long distances under physiological conditions. © 2019 The Author(s). Published by IOP Publishing Ltd on behalf of the Institute of Physics and Deutsche Physikalische Gesellschaft.
We describe the activation of out-of-equilibrium collective oscillations of a macromolecule as a classical phonon condensation phenomenon. If a macromolecule is modeled as an open system—that is, it is subjected to an external energy supply and is in contact with a thermal bath to dissipate the excess energy—the internal nonlinear couplings among the normal modes make the system undergo a nonequilibrium phase transition when the energy input rate exceeds a threshold value. This transition takes place between a state where the energy is incoherently distributed among the normal modes and a state where the input energy is channeled into the lowest-frequency mode entailing a coherent oscillation of the entire molecule. The model put forward in the present work is derived as the classical counterpart of a quantum model proposed a long time ago by Fröhlich in an attempt to explain the huge speed of enzymatic reactions. We show that such a phenomenon is actually possible. Two different and complementary THz near-field spectroscopic techniques—a plasmonic rectenna and a microwire near-field probe—have been used in two different labs to eliminate artifacts. By considering an aqueous solution of a model protein, the bovine serum albumin, we find that this protein displays a remarkable absorption feature around 0.314 THz, when driven in a stationary out-of-thermal equilibrium state by means of optical pumping. The experimental outcomes are in very good qualitative agreement with the theory developed in the first part of the paper and in excellent quantitative agreement with the theoretical result, allowing us to identify the observed spectral feature with a collective oscillation of the entire molecule.
Oxidative stress is a pathological hallmark of neurodegenerative tauopathic disorders such as Alzheimer's disease and Parkinson's disease-related dementia, which are characterized by altered forms of the microtubule-associated protein (MAP) tau. MAP tau is a key protein in stabilizing the microtubule architecture that regulates neuron morphology and synaptic strength. The precise role of reactive oxygen species (ROS) in the tauopathic disease process, however, is poorly understood. It is known that the production of ROS by mitochondria can result in ultraweak photon emission (UPE) within cells. One likely absorber of these photons is the microtubule cytoskeleton, as it forms a vast network spanning neurons, is highly co-localized with mitochondria, and shows a high density of aromatic amino acids. Functional microtubule networks may traffic this ROS-generated endogenous photon energy for cellular signaling, or they may serve as dissipaters/conduits of such energy. Experimentally, after in vitro exposure to exogenous photons, microtubules have been shown to reorient and reorganize in a dose-dependent manner with the greatest effect being observed around 280 nm, in the tryptophan and tyrosine absorption range. In this paper, recent modeling efforts based on ambient temperature experiment are presented, showing that tubulin polymers can feasibly absorb and channel these photoexcitations via resonance energy transfer, on the order of dendritic length scales. Since microtubule networks are compromised in tauopathic diseases, patients with these illnesses would be unable to support effective channeling of these photons for signaling or dissipation. Consequent emission surplus due to increased UPE production or decreased ability to absorb and transfer may lead to increased cellular oxidative damage, thus hastening the neurodegenerative process.
Atoms interact with each other through the electromagnetic field, creating collective states that can radiate faster or slower than a single atom, i.e. super- and sub-radiance. The generation and control of such states by engineering the dipolar interactions between atoms can enable new tools for atomic-based technologies. Atom-atom interactions in free space are limited in range, since the amplitude of the radiated field decreases inversely with distance. When the field is confined to one dimension it propagates unaltered, allowing infinite-range interactions. Here we present the first report of infinite-range interactions between atomic dipoles mediated by an optical waveguide. This is evidenced by the collective radiative decay of a single-photon distributed between distant atoms. We use cold $^{87}$Rb atoms in the vicinity of a single-mode optical nanofiber (ONF) that coherently exchange evanescently coupled photons through the ONF mode. In particular, we observe super-radiance of a few atoms separated by hundreds of resonant wavelengths. This effect is not possible for atoms separated by more than a wavelength interacting through free space. The same platform allows us to measure sub-radiance, a rarely observed effect, presenting a novel tool for quantum optics. This result constitutes a proof-of-principle for collective behavior of macroscopically delocalized atomic states, a crucial element for new proposals in quantum information and many-body physic. Given the application of one-dimensional waveguides in photonic-based quantum technologies, we envision infinite-range interactions as the natural next step towards interconnecting quantum systems on scales suitable for practical applications
Quantum biology is the study of quantum effects on biochemical mechanisms and biological function. We show that the biological production of reactive oxygen species (ROS) in live cells can be influenced by coherent electron spin dynamics, providing a new example of quantum biology in cellular regulation. ROS partitioning appears to be mediated during the activation of molecular oxygen (O2) by reduced flavoenzymes, forming spin-correlated radical pairs (RPs). We find that oscillating magnetic fields at Zeeman resonance alter relative yields of cellular superoxide (O2•-) and hydrogen peroxide (H2O2) ROS products, indicating coherent singlet-triplet mixing at the point of ROS formation. Furthermore, the orientation-dependence of magnetic stimulation, which led to specific changes in ROS levels, increased either mitochondrial respiration and glycolysis rates. Our results reveal quantum effects in live cell cultures that bridge atomic and cellular levels by connecting ROS partitioning to cellular bioenergetics.
Neurons are terminally differentiated cells that use their microtubule arrays not for cell division but rather as architectural elements required for the elaboration of elongated axons and dendrites. In addition to acting as compression-bearing struts that provide for the shape of the neuron, microtubules also act as directional railways for organelle transport. The stability properties of neuronal microtubules are commonly discussed in the biomedical literature as crucial to the development and maintenance of the nervous system, and have recently gained attention as central to the etiology of neurodegenerative diseases. Drugs that affect microtubule stability are currently under investigation as potential therapies for disease and injury of the nervous system. There is often a lack of consistency, however, in how the issue of microtubule stability is discussed in the literature, and this can affect the design and interpretation of experiments as well as potential therapeutic regimens. Neuronal microtubules are considered to be more stable than microtubules in dividing cells. On average, this is true, but in addition to an abundant stable microtubule fraction in neurons, there is also an abundant labile microtubule fraction. Both are functionally important. Individual microtubules consist of domains that differ in their stability properties, and these domains can also differ markedly in their composition as well as how they interact with various microtubule-related proteins in the neuron. Myriad proteins and pathways have been discussed as potential contributors to microtubule stability in neurons. This article is protected by copyright. All rights reserved.
We analyze a one-dimensional ring structure composed of many two-level systems, in the limit where only one excitation is present. The two-level systems are coupled to a common environment, where the excitation can be lost, which induces super- and subradiant behavior, an example of cooperative quantum coherent effect. We consider time-independent random fluctuations of the excitation energies. This static disorder, also called inhomogeneous broadening in literature, induces Anderson localization and is able to quench superradiance. We identify two different regimes: (i) weak opening, in which superradiance is quenched at the same critical disorder at which the states of the closed system localize; (ii) strong opening, with a critical disorder strength proportional to both the system size and the degree of opening, displaying robustness of cooperativity to disorder. Relevance to photosynthetic complexes is discussed.
We analyze a one-dimensional ring structure composed of many two-level systems, in the limit where only one excitation is present. The two-level systems are coupled to a common environment, where the excitation can be lost, which induces super- and subradiant behavior. Moreover, each two-level system is coupled to another independent environment, modeled by a classical white noise, simulating a dephasing bath and described by the Haken-Strobl master equation. Single-exciton superradiance, an example of a cooperative quantum coherent effect, is destroyed at a critical dephasing strength proportional to the system size, showing robustness of cooperativity to the action of the dephasing environment. We also show that the coupling to a common decay channel contrasts with the action of dephasing, driving the entanglement decay to slow down on increasing the system size. Moreover, after a projective measurement which finds the excitation in the system, the entanglement reaches a stationary value, independent of the initial conditions.
Centrioles are among the largest protein-based structures found in most cell types, measuring approximately 250 nm in diameter and approximately 500 nm long in vertebrate cells. Here, we briefly review ultrastructural observations about centrioles and associated structures. At the core of most centrioles is a microtubule scaffold formed from a radial array of nine triplet microtubules. Beyond the microtubule triplets of the centriole, we discuss the critically important cartwheel structure and the more enigmatic luminal density, both found on the inside of the centriole. Finally, we discuss the connectors between centrioles, and the distal and subdistal appendages outside of the microtubule scaffold that reflect centriole age and impart special functions to the centriole. Most of the work we review has been done with electron microscopy or electron tomography of resin-embedded samples, but we also highlight recent work performed with cryoelectron microscopy, cryotomography and subvolume averaging. Significant opportunities remain in the description of centriolar structure, both in mapping of component proteins within the structure and in determining the effect of mutations on components that contribute to the structure and function of the centriole.
We theoretically investigate the radiative dynamics of molecular aggregates with physical dimensions much smaller than an optical wavelength. The fluorescence decay rate of a one-dimensional aggregate consisting of N electronically coupled two-level molecules interacting with acoustic and optical lattice phonons is calculated. The linear dependence (superradiance) of the radiative decay rate on the aggregate size N is shown to be quenched by exciton–phonon coupling. An increase of aggregate size N eventually leads to a convergent, size independent decay rate, which is N* times faster than the monomer decay rate. The coherencesizeN* is generally a function of the exciton–phonon coupling strength, the phonon bandwidth, and the aggregate temperature. For low frequency phonons, a scaling law is obtained and an empirical relation for the temperature dependence N*∼T−1/3 is derived.
We present a refined model of the αβ-tubulin dimer to 3.5 Å resolution. An improved experimental density for the zinc-induced tubulin sheets was obtained by adding 114 electron diffraction patterns at 40-60 ° tilt and increasing the completeness of structure factor amplitudes to 84.7 %. The refined structure was obtained using maximum-likelihood including phase information from experimental images, and simulated annealing Cartesian refinement to an R-factor of 23.2 and free R-factor of 29.7. The current model includes residues α:2-34, α:61-439, β:2-437, one molecule of GTP, one of GDP, and one of taxol, as well as one magnesium ion at the non-exchangeable nucleotide site, and one putative zinc ion near the M-loop in the α-tubulin subunit. The acidic C-terminal tails could not be traced accurately, neither could the N-terminal loop including residues 35-60 in the α-subunit. There are no major changes in the overall fold of tubulin with respect to the previous structure, testifying to the quality of the initial experimental phases. The overall geometry of the model is, however, greatly improved, and the position of side-chains, especially those of exposed polar/charged groups, is much better defined. Three short protein sequence frame shifts were detected with respect to the non-refined structure. In light of the new model we discuss details of the tubulin structure such as nucleotide and taxol binding sites, lateral contacts in zinc-sheets, and the significance of the location of highly conserved residues.
The role of microtubules in cellular pathways of UV-B signaling in plants as well as in related structural cell response become into focus of few last publications. As microtubules in plant cell reorient/reorganize (become randomized, fragmented or depolymerized) in a response to direct UV-B exposure, these cytoskeletal components could be involved into UV-B signaling pathways as highly responsive players. In the current addendum, indirect UV-B-induced microtubules reorganization in cells of shielded Arabidopsis thaliana (GFP-MAP4) primary roots and the correspondence of microtubules depolymerization with the typical hallmarks of the programmed cell death in Nicotiana tabacum BY-2 (GFP-MBD) cells are discussed.
We report here a complete study of solvation dynamics of tryptophan in bulk water with femtosecond resolution and present an accurate method for the construction of its solvation correlation function. The water dynamics was observed in one hundred picosecond (∼108 ps) at lipid–water interfaces while in buffer and salt/buffer solutions it becomes faster in tens of picoseconds (∼7–20 ps). These water motions are being elucidated on the femtosecond to subnanosecond (or longer) time scale for their different biological functions, such as global structural stability of membranes through well-ordered interfacial water structures and efficient recognition of molecules (and ions) by membrane proteins through ultrafast water displacement.
The use of standards for the measurement of photoluminescence quantum yields (QYs) in dilute solutions is reviewed. Only three standards can be considered well estab-lished. Another group of six standards has been investigated by several independent researchers. A large group of standards is frequently used in recent literature, but the valid-ity of these is less certain. The needs for future development comprise: (i) confirmation of the validity of the QY values of many commonly used standard materials, preferably in the form of SI traceable standards; (ii) extension of the set of standard materials to the UV and near-IR spectral ranges; and (iii) good standards or robust protocols for the measurements of low QYs.
The Arabidopsis thaliana protein UVR8 is a photoreceptor for ultraviolet-B. Upon ultraviolet-B irradiation, UVR8 undergoes an immediate switch from homodimer to monomer, which triggers a signalling pathway for ultraviolet protection. The mechanism by which UVR8 senses ultraviolet-B remains largely unknown. Here we report the crystal structure of UVR8 at 1.8 Å resolution, revealing a symmetric homodimer of seven-bladed β-propeller that is devoid of any external cofactor as the chromophore. Arginine residues that stabilize the homodimeric interface, principally Arg 286 and Arg 338, make elaborate intramolecular cation-π interactions with surrounding tryptophan amino acids. Two of these tryptophans, Trp 285 and Trp 233, collectively serve as the ultraviolet-B chromophore. Our structural and biochemical analyses identify the molecular mechanism for UVR8-mediated ultraviolet-B perception, in which ultraviolet-B radiation results in destabilization of the intramolecular cation-π interactions, causing disruption of the critical intermolecular hydrogen bonds mediated by Arg 286 and Arg 338 and subsequent dissociation of the UVR8 homodimer.
Centrosomes are microtubule-organizing centres of animal cells. They influence the morphology of the microtubule cytoskeleton, function as the base for the primary cilium and serve as a nexus for important signalling pathways. At the core of a typical centrosome are two cylindrical microtubule-based structures termed centrioles, which recruit a matrix of associated pericentriolar material. Cells begin the cell cycle with exactly one centrosome, and the duplication of centrioles is constrained such that it occurs only once per cell cycle and at a specific site in the cell. As a result of this duplication mechanism, the two centrioles differ in age and maturity, and thus have different functions; for example, the older of the two centrioles can initiate the formation of a ciliary axoneme. We discuss spatial aspects of the centrosome duplication cycle, the mechanism of centriole assembly and the possible consequences of the inherent asymmetry of centrioles and centrosomes.
Solvent polarity and the local environment have profound effects on the emission spectral properties of fluorophores. The effects of solvent polarity are one origin of the Stokes shift, which is one of the earliest observations in fluorescence. Emission spectra are easily measured, resulting in numerous publications on emission spectra of fluorophores in different solvents, and when bound to proteins, membranes, and nucleic acids. One common use of solvent effects is to determine the polarity of the probe binding site on the macromolecule. This is accomplished by comparison of the emission spectra and/or quantum yields when the flu-orophore is bound to the macromolecule or dissolved in solvents of different polarity. However, there are many additional instances where solvent effects are used. Suppose a fluorescent ligand binds to a protein or membrane. Binding is usually accompanied by spectral shift or change in quantum yield due to the different environment for the bound ligand. Alternatively, the ligand may induce a spectral shift in the intrinsic or extrinsic protein fluorescence. In either case the spectral changes can be used to measure the extent of binding. The effects of solvent and environment on fluorescence spectra are complex, and are due to several factors in addition to solvent polarity. The factors that affect fluorescence emission spectra and quantum yields include:
Ultrafast transient absorption spectroscopy of wild-type bacteriorhodopsin (WT bR) and 2 tryptophan mutants (W86F and W182F) is performed with visible light excitation (pump) and UV probe. The aim is to investigate the photoinduced change in the charge distribution with 50-fs time resolution by probing the effects on the tryptophan absorption bands. A systematic, quantitative comparison of the transient absorption of the 3 samples is carried out. The main result is the absence in the W86F mutant of a transient induced absorption band observed at approximately 300-310 nm in WT bR and W182F. A simple model describing the dipolar interaction of the retinal moiety with the 2 tryptophan residues of interest allows us to reproduce the dominant features of the transient signals observed in the 3 samples at ultrashort pump-probe delays. In particular, we show that Trp(86) undergoes a significant Stark shift induced by the transient retinal dipole moment. The corresponding transient signal can be isolated by direct subtraction of experimental data obtained for WT bR and W86F. It shows an instantaneous rise, followed by a decay over approximately 500 fs corresponding to the isomerization time. Interestingly, it does not decay back to zero, thus revealing a change in the local electrostatic environment that remains long after isomerization, in the K intermediate state of the protein cycle. The comparison of WT bR and W86F also leads to a revised interpretation of the overall transient UV absorption of bR.
Neurons develop a highly polarized morphology consisting of dendrites and a long axon. Both axons and dendrites contain microtubules and microtubule-associated proteins (MAPs) with characteristic structures. Among MAPs, MAP2 is specifically expressed in dendrites whereas MAP2C and tau are abundant in the axon. But the influence of MAP2, MAP2C and tau on the organization of microtubule domains in dendrites versus axons is unknown. Both MAP2 and tau induce microtubule bundle formation in fibroblasts after transfection of complementary DNAs, and a long process resembling an axon is extended in Sf9 cells infected with recombinant baculovirus expressing tau. We have now expressed MAP2 and MAP2C in Sf9 cells in order to compare their morphology and the arrangement of their microtubules to that found in Sf9 cells expressing tau. We report here that the spacing between microtubules depends on the MAP expressed: in cells expressing MAP2, the distance is similar to that found in dendrites, whereas the spacing between microtubules in cells expressing MAP2C or tau is similar to that found in axons.
In the knowledge that human ultra-weak photon emission (UPE) is mainly due to the metabolic oxidative stress processes that the skin cells undergo in the presence of reactive oxygen species (ROS), external stressors (like UV radiation), but also internal stressors (like diseases or brain activity) might strongly influence the UPE. This manuscript revises the scientific advances focused on the influence of internal factors on the human UPE. According to literature, the UPE seems to be influenced by some diseases (including diabetes, hemiparesis, protoporphyria, or a typical cold), and even by the cerebral intention/relaxation (brain activity/meditation). These allow to consider UPE as a natural and promising non-invasive spectroscopic tool for helping during the diagnosis of a variety of illnesses or stress- / mood-state disorders. Nonetheless, further research is required for answering some still unresolved controversial points.
Future scalable photonic quantum information processing relies on the ability of integrating multiple interacting quantum emitters into a single chip. Quantum dots provide ideal on-chip quantum light sources. However, achieving quantum interaction between multiple quantum dots on-a-chip is a challenging task due to the randomness in their frequency and position, requiring local tuning technique and long-range quantum interaction. Here, we demonstrate quantum interactions between distant two quantum dots on a nanophotonic waveguide. We achieve a photon-mediated long-range interaction by integrating the quantum dots to the same optical mode of a nanophotonic waveguide and overcome spectral mismatch by incorporating on-chip thermal tuners. We observe their quantum interactions of the form of super-radiant emission, where the two dots collectively emit faster than each dot individually. Creating super-radiant emission from integrated quantum emitters could enable compact chip-integrated photonic structures that exhibit long-range quantum interactions. Therefore, these results represent a major step towards establishing photonic quantum information processors composed of multiple interacting quantum emitters on a semiconductor chip.
Significance
This work resolves a long-standing controversy regarding the activation mechanism and photocycle of cryptochromes (CRYs), a broadly represented group of photosensors. We demonstrate a high degree of correspondence between the capability of the tryptophan (Trp) chain to photoreduce the flavin cofactor and biological activity. These results establish that the evolutionary pressure to conserve the Trp chain derives from maintaining a flavin photocycle that, in this case, entrains the fly circadian clock. Furthermore, we reengineer CRY to be more biologically photoresponsive by manipulating photoreduction by the Trp chain. As CRYs are important signaling molecules in animals, plants, and bacteria, and are increasingly used as optogenetic tools, the defined mechanism is relevant to many signaling processes and will enable novel applications.
From stomach ache to depression
Our gut hurts and we feel miserable. Such disparate phenomena are mechanistically connected, but how? Cervenka et al. review the many pathways taken by dietary tryptophan as it is metabolized into kynurenines. These metabolites distribute into homeostatic networks that integrate diverse aspects of mammalian physiology. Depending on physiological context, kynurenines influence health and disease states ranging from intestinal conditions to inflammation to cancer progression. Further, they can mediate the effects of exercise, mood, and neuronal excitability and, ultimately, communicate with the microbiota.
Science , this issue p. eaaf9794
The development of optical nanofibers (ONFs) and the study and control of their optical properties when coupling atoms to their electromagnetic modes has opened new possibilities for their use in quantum optics and quantum information science. These ONFs offer tight optical mode confinement (less than the wavelength of light) and diffraction-free propagation. The small cross section of the transverse field allows probing of linear and nonlinear spectroscopic features of atoms with exquisitely low power. The cooperativity—the figure of merit in many quantum optics and quantum information systems—tends to be large even for a single atom in the mode of an ONF, as it is proportional to the ratio of the atomic cross section to the electromagnetic mode cross section. ONFs offer a natural bus for information and for inter-atomic coupling through the tightly confined modes, which opens the possibility of one-dimensional many-body physics and interesting quantum interconnection applications. The presence of the ONF modifies the vacuum field, affecting the spontaneous emission rates of atoms in its vicinity. The high gradients in the radial intensity naturally provide the potential for trapping atoms around the ONF, allowing the creation of one-dimensional arrays of atoms. The same radial gradient in the transverse direction of the field is responsible for the existence of a large longitudinal component that introduces the possibility of spin–orbit coupling of the light and the atom, enabling the exploration of chiral quantum optics.
Non-Hermitian quantum mechanics (NHQM) is an important alternative to the standard (Hermitian) formalism of quantum mechanics, enabling the solution of otherwise difficult problems. The first book to present this theory, it is useful to advanced graduate students and researchers in physics, chemistry and engineering. NHQM provides powerful numerical and analytical tools for the study of resonance phenomena – perhaps one of the most striking events in nature. It is especially useful for problems whose solutions cause extreme difficulties within the structure of a conventional Hermitian framework. NHQM has applications in a variety of fields, including optics, where the refractive index is complex; quantum field theory, where the parity-time (PT) symmetry properties of the Hamiltonian are investigated; and atomic and molecular physics and electrical engineering, where complex potentials are introduced to simplify numerical calculations.
Using a reduced equation of motion for the density matrix which accounts for spontaneous emission and superradiance, we analyze the fluorescence and transient grating (TG) decays from a dilute, optically thin distribution of molecular aggregates. We find that the fluorescence is a limited form of superradiance, where cooperativity is restricted to the number N of two level systems which make up the aggregate. The dependence of the linear aggregate decay rate on the amount of inhomogeneous broadening, which is randomly distributed according to Gaussian line shape of width (1/e)2σ, is calculated. It is shown that σ must be comparable in magnitude to the nearest neighbor dipole–dipole coupling V and not the superradiant decay rate, in order to quench the superradiance.
Fretting About Electrons
The FRET technique (Fluorescence Resonance Energy Transfer) is widely used to probe structural dynamics in large macromolecules such as proteins. Essentially, the technique relies on photoexciting a donor chromophore and then watching for signs of energy transfer to an acceptor chromophore elsewhere in the framework. Consani et al. (p. 1586 , published online 7 February; see the Perspective by Winkler ) now show, using a sophisticated type of broadband time-resolved ultraviolet spectroscopy, that in myoglobin, an excited tryptophan residue relaxes by electron, rather than energy, transfer. The distinction is generally difficult to observe but has strong bearing on the applicability of FRET in this and analogous systems.
Fluorescence quantum yields (Q) for tyrosine, tryptophan, and phenylalanine in water at 23° determined by the comparative method using a quinine standard were found to be 0.14, 0.13, and 0.024, respectively. Similar values were obtained with phenol as the standard. The numbers are much lower than those literature values which have been widely used to calculate protein fluorescence quantum yields. Possible reasons for the discrepancies are discussed. The quantum yields of isomeric tyrosines and fluorophenylalanines are also reported.
Variation of intrinsic tryptophan (Trp) fluorescence intensity and lifetime in proteins is widely exploited to follow changes in protein structure such as folding/unfolding, substrate or ligand binding, and protein−protein interactions. Although a credible candidate for the source of weak Trp fluorescence in some proteins has long been believed to be electron transfer from excited Trp to an amide carbonyl group, recognition of when such a process should be exceptionally efficient has not been possible. Here we propose a reasonable basis for the 30-fold variation by the use of quantum mechanics−molecular mechanics simulations in which the energy of the lowest Trp ring-to-amide backbone charge transfer (CT) state is monitored during dynamics trajectories for 24 Trps in 17 proteins. The energy, fluctuations, and relaxation of high lying CT states are extremely sensitive to protein environment (local electric field direction and strength). Application of basic electron transfer theory with a single empirical electronic coupling reveals that the entire 30-fold range is explainable from local electric field effects on electron transfer to a nearby amide, although other acceptors may sometimes be responsible for a low yield. A key new concept uncovered in this work is that charged groups near the Trp can have profound effects on fluorescence lifetime and quantum yield, but location is critical. Negative (positive) charge will decrease (increase) quantum yield if closer to the indole ring than to the electron acceptor because these arrangements stabilize (destabilize) the CT state. If the charge is closer to the acceptor, the opposite will be true. A semiquantitative prediction using only the average energy gap and variance was achieved by using a universal electronic coupling constant and energy offset.
The conformational changes associated with the interaction of sodium laurate with the recombinant heme domain for cytochrome P-450BM3 have been investigated by steady-state and picosecond-time-resolved fluorescence spectroscopy. The steady-state quenching experiments show that while all the five tryptophan residues are accessible to acrylamide in the free enzyme as well as the enzyme. substrate complex, the number of tryptophan residues accessible to ionic quenchers decreases on interaction of the substrate with the enzyme. This indicates that some of the tryptophan residues move towards the core of the protein on interaction with the substrate. The number of tryptophan residues accessible to the solvent as determined by the calculation of the solvent-accessible area for the free enzyme agrees with the values obtained by the quenching experiments.
The time-resolved fluorescence studies carried out by means of the time-correlated single-photon-counting technique show that the fluorescence-decay curve is best fitted to a three-exponential model (0.2, 1.0 and 5.4 ns). Lifetime distributions, as recovered by the maximum-entropy method, agree with the discrete exponential model. The binding of the substrate does not lead to any significant change in the lifetime components of the enzyme, indicating that the tryptophan residues are possibly away from the substrate-binding domain. The decay-associated emission spectra and the magnitudes of amplitude of different lifetimes indicate that the shortest lifetime component (τ1) originates from the three tryptophan residues that are completely or partially accessible to the solvent, and τ2 originates from the tryptophan residues that are buried in the core of the enzyme and not accessible to the solvent. X-ray crystallographic data and solvent-acessible-area calculations have been used to identify these residues.
Protein folding kinetics is commonly monitored by changes in tryptophan (Trp) fluorescence intensity. Considerable recent discussion has centered on whether the fluorescence of the single Trp in the much-studied, fast-folding villin headpiece C-terminal domain (HP35) accurately reflects folding kinetics, given the general view that quenching is by a histidine cation (His(+)) one turn away in an α-helix (helix III) that forms early in the folding process, according to published MD simulations. To help answer this question, we ran 1.0 μs MD simulations on HP35 (N27H) and a faster-folding variant in its folded form at 300 K and used the coordinates and force field charges with quantum calculations to simulate fluorescence quenching caused by electron transfer to the local amide and to the His(+). The simulations demonstrate that quenching by His(+) in the fully formed helix III is possible only during certain Trp and His(+) rotamer and solvent conformations, the propensity of which is a variable that can allow Trp fluorescence to report the global folding rate, as recent experiments imply.
Tryptophan (Trp) fluorescence is potentially a powerful probe for studying the conformational ensembles of proteins in solution, as it is highly sensitive to the local electrostatic environment of the indole side chain. However, interpretation of the wavelength-dependent complex fluorescence decays of proteins has been stymied by controversy about two plausible origins of the typical multiple fluorescence lifetimes: multiple ground-state populations or excited-state relaxation. The latter naturally predicts the commonly observed wavelength-lifetime correlation between decay components, which associates short lifetimes with blue-shifted emission spectra and long lifetimes with red-shifted spectra. Here we show how multiple conformational populations also lead to the same strong wavelength-lifetime correlation in cyclic hexapeptides containing a single Trp residue. Fluorescence quenching in these peptides is due to electron transfer. Quantum mechanics-molecular mechanics simulations with 150-ps trajectories were used to calculate fluorescence wavelengths and lifetimes for the six canonical rotamers of seven hexapeptides in aqueous solution at room temperature. The simulations capture most of the unexpected diversity of the fluorescence properties of the seven peptides and reveal that rotamers having blue-shifted emission spectra, i.e., higher average energy, have an increased probability for quenching, i.e., shorter average lifetime, during large fluctuations in environment that bring the nonfluorescent charge transfer state and the fluorescing state into resonance. This general mechanism should also be operative in proteins that exhibit multiexponential fluorescence decays, where myriad other sources of conformational heterogeneity besides rotamers are possible.
We report on an ultrafast experimental and simulations study of the early relaxation events of photoexcited tryptophan in water. Experimentally, we used fluorescence up-conversion in both polychromatic and single wavelength detection modes in the 300-480 nm range with polarization dependence. We report on the time evolution of the Stokes shift, bandwidth, and anisotropy from tens of femtoseconds to picoseconds. These observables contain signatures of the simultaneous occurrence of intramolecular and solvent-molecule interactions, which we disentangle with the help of nonequilibrium molecular dynamics simulations. We also observe a breakdown of the linear response approximation to describe our results.
Phagokinetic tracks were used to determine the current direction of migration in 3T3 cells. Comparing this direction with the orientation of actin or tubulin-containing cellular structures by indirect immunofluorescence, the following results were obtained. First, the main actin-containing bundles were located at the bottom and tail end of 3T3 cells and ran parallel to the current or preceding direction of migration. Second, the 3 micrometer long rod-like structure (primary cilium), which contains tubulin and which has been observed by other investigators in transmission electron microscopy (Barnes, 1961; Sorokin, 1962; Wheatley, 1969) and in indirect immunofluorescence (Osborn and Weber, 1976), was oriented predominantly parallel to the substrate and to the current movement direction. It seems possible that the primary cilium has a role in the directional control of a migrating 3T3 cell, and that the main actin containing bundles act as substrate-attached rails along which the nucleus and bulk cytoplasm slide during displacement of the cells.
Weak luminescence was detected from oxygenated liquid cultures of the yeast Candida utilis during two stages of its growth cycle. The first period of emission occurred during the exponential phase of growth and comprised an ultraviolet band (270-390 nm; ca 19 photons s-1 cm-2 of culture surface) and a visible band (450-620 nm; ca 68 photons s-1 cm-2). The second period of emission occurred late in the stationary phase of growth and was comprised almost entirely of a visible region band (450-620 nm; 6.8 x 10(2) photons s-1 cm-2). No luminescence was observed when the yeast was grown anaerobically. These observations are compared with those previously obtained for two other yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe. The ratios of the intensities of the blue/red emissions in the stationary phase luminescences correlated with the ratio of the saturated/unsaturated lipid content for the three yeasts. This result provided further support for the claim that the stationary phase luminescence arises from the reactions associated with lipid peroxidation. A number of previously suggested sources of the exponential phase luminescence are discussed and rejected. Oxidative side reactions accompanying protein synthesis remain a possible source of that emission.
BHK cells were inoculated sparsely on one face ("sparse- or s-face") of a thin glass film whose opposite face was covered with a 2- to 3-day-old confluent layer of BHK cells ("confluent- or c-face"). After 7 hr of attaching and spreading in the absence of visible light, most of the cells on the s-face traversed with their long axes the direction of the whorls of the confluent cells on the c-face directly opposed. The effect was inhibited by a thin metal coating of the glass films. The results suggest that the cells were able to detect the orientation of others by signals that penetrated glass but not thin metallic films and, therefore, appeared to be carried by electromagnetic radiation. In contrast, the effect was not influenced by a thin coat of silicone on the glass, suggesting that the wavelength of this radiation is likely to be in the red to infrared range. The ability of cells to detect the direction of others by electromagnetic signals points to a rudimentary form of cellular "vision."
The spectral distributions of the luminescences emitted by the respiratory-deficient mutant of Saccharomyces cerevisiae and the normal yeast have been determined during the exponential phase of growth and during the stationary phase. The respiratory-deficient mutant gave a more intense emission in the visible region than did the normal yeast, but the UV intensities from the two yeasts did not differ greatly. These differences were explained in terms of higher O2- concentrations in the respiratory-deficient mutant which lead to enhanced visible region chemiluminescence from lipid peroxidation reactions.