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Schematic representation of polypeptide chains with isotactic (a), syndiotactic (b) and heterotactic (c) structures. d The hydrogen bond registry between inter peptide bonds of polypeptide structures
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Natural proteins are concatenated amino acids with definite handedness or chirality, with their spatial orientation being preferentially left handed or L-chiral. This paper discusses the biophysics of stereo-chemical perturbation to proteins using D-(α) amino acid and its utility as an additional design alphabet while scripting novel protein struct...
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Context 1
... of combined L-and D-stereochemical nature the polymer structure may be of either stereoregular or stereoirregular in nature. If the stereocentres in a stereo- regular polymer are of alternately enantiomeric nature, the polymer is called as 'syndiotactic', and if the stereocentres are randomly distributed, it is called 'heterotactic' or 'atactic' (Fig. 2a-c). Made of asymmetric amino acids of always L-chiral stereochemical structure, proteins are ste- reoregular 'isotactic' polymers of 'homochiral' ...
Context 2
... most ubiquitous definition of secondary structure is in the topological patterns of inter-peptide hydrogen bonds, i.e., the sequential separation between the acceptor (n) and donor (n ± i) residues (n to n ± i or succinctly n ± i) of a Creating novel protein scripts beyond natural alphabets 249 hydrogen bond (Fig. 2d). The hydrogen bond topologies are stereospecific (Eisenberg 2003). The topologies are predominantly n ? i type in polypeptides of isotactic ste- reochemistry, but may be both n ? i and n-i type in syn- diotactic or heterotactic polypeptides. The short ranged n ? 2 type hydrogen bonds charac- terize the b turns, which may be of L-or ...
Context 3
... to B L /B D regions of /, w space (Fig. 3), the region of extended conformation for poly L-chains. Unlike poly L-chiral helices, the / L , w L and / D , w D values differ slightly for a syndiotactic helix, and the difference deter- mines the screw sense of the helix. The helix is with a registry of alternating n ? 7 and n -5 type hydrogen bonds ( Fig. 2d) and occurs in Gramicidin A, a microbial polypeptide of syndiotactic stereochemistry (Szabo and Urry 1979;Urry 1971;Wallace 1998Wallace , 2000). Extended conformation of isotactic stereochemistry, in mutually hydrogen-bonded parallel or antiparallel arrangement, characterize the b sheet motifs of proteins, in which the hydrogen bond ...
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The fact that biologically relevant molecules exist only as one of the two enantiomers is a fascinating example of complete symmetry breaking of chirality and has long intrigued our curiosity. The origin of this selective chirality has remained a fundamental enigma with regard to the origin of life since the time of Pasteur, 160 years ago. The symm...
The fact that biologically relevant molecules exist only as one of the two enantiomers is a fascinating example of complete symmetry breaking of chirality and has long intrigued our curiosity. The origin of this selective chirality has remained a fundamental enigma with regard to the origin of life since the time of Pasteur, 160 years ago. The symm...
A series of discotic tricarboxyamides with varied amino acid side arm functionality and their HCl responsive diverse self-assembly behavior and formation of dynamic polymer is studied. Discotic trisamide 1 obtained from Boc protected L-Lys self-assembled into a long fibrillar aggregate-like supramolecular P helical polymer. However, on addition of...
Citations
... A well-defined solution structure of TP4-γ was obtained, with backbone RMSD values of 0.08 ± 0.03 Å to the mean coordinates and 0.72 ± 0.09 Å for all heavy atoms. The backbone torsion angles for all L-amino acids were located in the most favored or additionally allowed regions of the Ramachandran plot, and torsion angles for all D-amino acids were in allowed regions as well [34]. An ensemble of 20 energy minimized structures with the lowest target function is shown in Supporting Fig. S3. ...
... Theoretically, we hypothesize that during interactions of RGD or NGR peptides with their targets, there is a possibility of 'Gly' being in any plausible conformation in Ramachandran map. Achiral nature of Cα carbon atom and no side-chains helps Glycine to occupy 57% region of Ramachandran plot (R-plot) whereas, the other amino acids are restricted to a meager 21% [53]. This means that Glycine can access both L-chiral and D-chiral amino acid basins of the Ramachandran map. ...
Poly-peptide molecules have shown promising applications in drug delivery and tumor targeting. A series of tumor homing peptides were designed by exhaustively sampling low energy geometrical basins of amino acids at specific sites of a peptide molecule to induce a conformational lock. This peptide library was pruned to a limited set of eight molecules, employing electrostatic interactions, docking, and molecular dynamics simulations. These designed and optimized peptides were synthesized and tested on various cell lines, including breast cancer (MDA-MB-231), cervical cancer (HeLa), osteosarcoma (U2-OS), and non-cancerous mammary epithelial cells (MCF-10A) using confocal microscopy and flow cytometry. Peptides show differential uptake in cancerous MDA-MB-231, HeLa, U2-OS, and non-cancerous MCF-10A cells. Confocal imaging verified their ability to penetrate even in 3D tumorospheres of MDA-MB-231 cells. Further, experiments of mitochondrial membrane potential depolarization and Caspase-3 activation confirmed that their cytotoxic effects are by apoptosis. Homing ability of the designed peptides in in vivo system and fluorescence imaging with clinical samples of human origin have further confirmed that the in vitro studies are qualitatively identical and quantitatively comparable in their ability to selectively recognize tumor cells. Overall, we present a roadmap for the functional programming of peptide-based homing and penetrating molecules that can perform selective tumor targeting.
... www.nature.com/scientificreports/ entire protein universe, nonetheless, is made of only one of them (poly L-chiral or isotactic), which means (2 n − 1) is yet to be explored, and experiments in this direction may have a huge impact in biomaterials research 18,19 . Chiral engineering of peptide backbone was first utilized by Ghadiri and coworkers. ...
We present design and antibacterial studies of stereochemically diversified antimicrobial peptides against multidrug-resistant bacterial pathogens. Syndiotactic polypeptides are polymers of alternating L and D amino acids with LDLD or DLDL backbone stereochemical sequence, which can form stable gramicidin like helical conformations. We designed, synthesized and characterized eight model molecular systems with varied electrostatic fingerprints, modulated through calibrated sequence positioning. Six out of eight model systems showed very impressive antimicrobial activity against three difficult to treat bacterial species, Gentamicin resistant MRSA, E. coli and Mycobacterium. More importantly, the designed LDLD peptides were equally potent in serum, an important drawback of poly L peptide sequences due to enzyme mediated degradation and ion sensitivity. Further, we tested the activity of the designed peptides against drug-resistant clinical isolates of Staphylococcus aureus and Escherichia coli. Molecular dynamics simulation studies suggest formation of an assembly of individual peptides, preceding the membrane interaction and deformation. The activity estimates are comparable with the available peptide based antimicrobials, and are also highly specific and less toxic as per standard estimates. Incorporation of D amino-acids can significantly expand the peptide design space, which can in turn manifest in future biomaterial designs, especially antimicrobials.
... Protein molecules found in nature are polymers of amino acids with definite handedness or chirality, with their spatial orientation being preferentially left-handed or L-chiral. 1,2 Of late, this disproportionate or rather complete excess of L-amino acids is argued to be preordained and eventually turned out to be one of the most powerful arguments of creationists who believe that species on earth are not formed by evolution but by "intelligent design". 3 Tacticity is a relative term in stereochemistry, which deals with the arrangement of adjacent chiral centers within a given polymeric molecule. ...
... 4,5 If we can hypothetically add one more variable as "stereochemistry of amino acids" in the backbone, by adding Damino acids at "n" sequence positions, the number of stereoisomeric diversities increases exponentially from 1 n to 2 n , but the entire protein universe is made of just only one of them, which implies that (2 n − 1) is yet to be explored. 2 The origin of this apparent stereochemical filtration in protein biogenesis remains unclear; however, its consequence on peptide assemblies can be investigated and explored for the future design of bioinspired materials. 6 Our primary interest is to use the backbone stereochemistry as an additional variable, exploring novel architectures in the 2 n − 1 design space available for novel peptide-based molecular constructs. ...
Diversification of chain stereochemistry offers a tremendous increase in protein design space. We have designed a minimal fluorescent protein, pregnant with β-(1-azulenyl)-l-alanine in the hydrophobic core of a heterotactic protein scaffold, employing automated design tools such as automated repetitive simulated annealing molecular dynamics and IDeAS. The de novo designed heterochiral protein can be selectively excited at 342 nm, quite distant from the intrinsic fluorophore, and emits in the blue region. The structure and stability of the designed proteins were evaluated by established spectroscopic and calorimetric methods.
... 13 The uncertainty in adopting a specific fold further adds to the obstacles for designing CPPs with tailored functions. 14,15 To design peptides with tailored functions, it is vital to confine the peptide backbone architecture to a defined conformation; else, we have to wait for random hits with very minimal possibility of an informed and structured design paradigm getting established. 16 A stable template structure offers the possibility of optimizing design parameters like amphipathicity, topology, overall size, and sequence length. ...
Peptides have shown great potential in acting as template for developing versatile carrier platforms in nanomedicine, aimed at selective delivery of drugs to only pathological tissues saving its normal neighbors. Cell‐penetrating peptides (CPPs) are short oligomeric peptides capable of translocating across the cell membrane while simultaneously employing multiple mechanisms of entry. Most CPPs exist as disordered structures in solution and may adopt a helical conformation on interaction with cell membrane, vital to their penetrative capability. Herein, we report a series of cationic helical amphipathic peptides (CHAPs), which are topologically constrained to be helical. The peptides were tested against cervical and breast cancer cells for their cell penetration and drug delivery potential. The cellular uptake of CHAP peptides is independent of temperature and energy availability. The activity of the peptides is biocompatible in bovine serum. CHAPs delivered functional methotrexate (MTX) inside the cell as CHAP‐MTX conjugates. CHAP‐MTX conjugates were more toxic to cancer cells than MTX alone. However, the CHAP‐MTX conjugates were less toxic to HEK‐293 cells compared with the cancer cells suggesting higher affinity towards cancer cells. We attempted to constrain the conformation of the designed peptides as helical structures using 2‐amino isobutyric acid within the peptide sequence. This provides a template for inducing structural amphipathicity to the peptide sequence. Therefore, by providing a stable backbone architecture and secondary amphipathicity, we investigated the utility of our design paradigm to specifically design peptides with cell‐penetrating capability.
... Natural proteins and peptides are polymers 20 aminoacids in varying length and sequences, with almost all amino-acids exclusively L chiral (Durani 2008;Kumar and Ramakrishnan 2010). In polymer science, such an arrangement is termed as isotactic. ...
Tuberculosis is one of the leading causes of death, with an annual mortality rate of 2 million. The present treatment regimen for Mycobacterium species is strenuous, extending up to 12 months. Even then, rise of antibiotic resistance has limited the prognosis, with increased instances of multidrug resistant (MDR–TB) and extremely drug resistant (XDR–TB) cases reported. Peptide based antibiotics can be an effective solution due to their low toxicity, biocompatibility and predictable metabolism, but has not been employed due to their short plasma half life. In this brief communication, we demonstrate the bactericidal potency of cationic amphipathic peptides as an effective bactericidal agent against Mycobacterium smegmatis. Potency of stereo-engineered LDLD or DLDL peptides have been retained their potency, while their poly L variants rapidly lost their activity, when the experiment was repeated in human serum. To establish this as a design strategy, we further verified the results by repeating the experiment in a gram negative bacteria E. coli. One of the designed peptides were showing a minimum inhibitory concentration (MIC) value as low as 3.13 µM, suggesting the possibility of future development as a therapeutic peptide.
... Of late, design efforts have moved on to totally new functional folds beyond natural alphabets, folding into their global free energy minimum, optimized by molecular force fields at the design phase. Conventional peptide design only guarantees functional group constitution by opting specific amino acid sequence, and not their topology, because peptide molecules are very fluxional, and its conformation therefore is subjected to the external flux [1]. This is principally due to the isotactic (poly L) stereochemistry of naturally occurring peptide and protein backbone, where adoption of a conformation is a consequence of its amino-acid sequence, and this sequence-structure combination will eventually modulate its prescribed function [1]. ...
... Conventional peptide design only guarantees functional group constitution by opting specific amino acid sequence, and not their topology, because peptide molecules are very fluxional, and its conformation therefore is subjected to the external flux [1]. This is principally due to the isotactic (poly L) stereochemistry of naturally occurring peptide and protein backbone, where adoption of a conformation is a consequence of its amino-acid sequence, and this sequence-structure combination will eventually modulate its prescribed function [1]. Attempts of protein or peptide de novo design so far, have also been conservative, being mimics of natural protein folds, with few exceptions such as TOP7 and CC-Hept [2]. ...
... The structure of short peptides is primarily directed by short and long range electrostatic interactions of the backbone and sidechain [16]. In an earlier work, we have reported how in a folded short isotactic poly peptide like alpha helix, local electrostatic interactions are in conflict, with their dipoles pointing in the same direction, but harmonious in extended structures [1]. It is, however, difficult to design well-defined electrostatic zones in extended or coiled structures. ...
... Several antimicrobial peptides like gramicidin, valinomycin, and others have D-amino acids in their sequence, which makes them resistant to proteases and metabolically more stable. Further, it is observed that specific use of D-amino acids, unnatural amino acids, and dehydro amino acids in peptide design also favors a particular secondary structure [7]. Studies are reported where use of L-and D-amino acids in different combinations and proportions yielded molecules with enhanced activities [8]. ...
... Insilico, functionbased designs are also constructed by frolicking with molecule's electrostatic profiles, hydrogen bonds, conformations, tacticity etc. Tacticity is a relative term in stereochemistry, which deals with the arrangement of adjacent chiral centres within a given molecule especially polymers. Based on the arrangement, a polymer can be in isotactic, syndiotactic or heterotactic stereochemistry (Durani, 2008;Kumar and Ramakrishnan, 2010). An isotactic polypeptide sequence is characterised by having all amino acids in L-or Dstereochemistry, whereas a syndiotactic sequence is a stereoregular arrangement with alternate L-and D-amino acid or vice versa in succession and a heterotactic polymer is a random distribution of Land D-stereo-isomeric monomers (Fig. 3). ...
... Peptides and proteins are polymers of L-amino acids only and hence, isotactic in nature, with few exceptions. Typically, the conformational availability of any isotactic (poly-L or poly-D) polymer is restricted to 21% of Ramachandran map due to excluded volume effect (Kumar and Ramakrishnan, 2010) or steric collisions, among side-chains (Kuznetsova et al., 2015). A typical Ramachandran plot is a graphical representation of phi (4) and psi (j) dihedral angles depicting preferential conformation of any amino acid (Fig. 4). ...
Therapeutic activity of antibiotics is noteworthy, as they are used in the treatment of microbial infections. Regardless of their utility, there has been a steep decrease in the number of drug candidates due to antibiotic resistance, an inevitable consequence of noncompliance with the full therapeutic regimen. A variety of resistant species like MDR (Multi-Drug Resistant), XDR (Extensively Drug-Resistant) and PDR (Pan Drug-Resistant) species have evolved, but discovery pipeline has already shown signs of getting dried up. Therefore, the need for newer antibiotics is of utmost priority to combat the microbial infections of future times. Peptides have some interesting features like minimal side effect, high tolerability and selectivity towards specific targets, which would help them successfully comply with the stringent safety standards set for clinical trials. In this review, we attempt to present the state of the art in the discovery of peptide-based antimicrobials from a design perspective.
... Topology, also plays a key role in the geometrical evolution of a typical protein fold [1][2][3][4]. Topological variation in molecules with identical chemical structure can be provided by differences in their stereochemistry [5]. Ever since the historical discovery by Louis Pasteur in 1847, stereochemical variations and their possibilities are abundantly utilized while designing molecules at atomistic scale. ...
Topology is a key element in structure-activity relationship estimation while designing physiologically-active molecular constructs. Peptides may be a preferred choice for therapeutics, principally due to their biocompatibility, low toxicity and predictable metabolism. Peptide design only guarantees functional group constitution by opting specific amino acid sequence, and not their spatial orientation to bind and incite physiological response on chosen targets. This is principally because peptide conformation is subject to external flux, due to the isotactic stereochemistry of the peptide chain. Stereochemical engineering of peptide main chain offers the possibility of multiplying the structural space of a typical sequence to many orders of magnitude, and limiting the otherwise fluxional non-specific functional group dispensation in space by offering greater conformational rigidity. We put to test, this conceptual possibility already established in theoretical models, by designing amphipathic peptide systems and experimenting them on Gram-positive, Gram-negative and antibiotic-resistant bacteria. The unusual conformational rigidity and stability of syndiotactic peptides enable them to retain the designed electrostatic environment, while they encounter membrane surface. All the six designed systems exhibited bactericidal activity, pointing to the utility and specificity of stereo-engineered peptide systems for therapeutic applications. Overall, we hope that this work provides important insights and useful directives in designing novel peptide systems with antimicrobial activity, by expanding the design space, incorporating D-amino acid as an additional design variable.
