Figure - available from: Scientific Reports
This content is subject to copyright. Terms and conditions apply.
Two-state exchange with 1:1 host–guest binding. Schemes for (a) chemical kinetics and (b) corresponding spin kinetics of a nucleus located at the host molecule.
Source publication
Nuclear magnetic resonance (NMR) lineshape analysis is a powerful tool for the study of chemical kinetics. Here we provide techniques for analysis of the relationship between experimentally observed spin kinetics (transitions between different environments A,B,⋯\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsf...
Similar publications
Nuclear magnetic resonance (NMR) lineshape analysis is a powerful tool for the study of chemical kinetics. Here we provide techniques for analysis of the relationship between experimentally observed spin kinetics and corresponding chemical kinetics. The advantages of using analytical solutions for two-, three- or generally N-state exchange lineshap...
Citations
... Under the conditions of the fast exchange between the two bound states ('dock' and the 'lock') they can be represented by an average state, and the binding approximated by a two-state model (Brezina, Hanykova et al. 2022) with the overall dissociation constant ′ and rate ′ represented by: ...
... This corresponds to ~15-fold decrease from the rate 1900 s -1 of the dock step, which is similar to the differences in the overall Kd values for the 11MACF/EBH-ΔC (only dock step) and 11MACF/EBH (both dock and lock steps). The proportional decrease corresponds to the fast exchange condition for the lock step (Brezina, Hanykova et al. 2022), with forward rate >> 2000 s -1 , estimated from the chemical shift differences. This rate is much higher than the dissociation rate of the dock step. ...
End Binding protein 1 (EB1) is a key component of the signalling networks located at the plus ends of microtubules. It incorporates an N-terminal microtubule binding CH domain and the C-terminal EBH domain that interacts with the SxIP-containing sequences of other microtubule plus end tracking proteins (+TIPs). By using a series of SxIP containing peptides derived from the microtubule-actin cross-linking factor, MACF, we show that the SxIP motif itself binds to EBH with low affinity, and the full interaction requires contribution of the post-SxIP residues. Based on the solution structure and dynamics of the EBH/MACF complex we proposed a two-step ‘dock-and-lock’ model for the EBH interaction with targets, where the SxIP motif initially binds to a partially-formed EBH pocket, which subsequently induces folding of the unstructured C-terminus and transition to the stable complex. We dissect contributions from different interactions into the binding and design MACF mutations of the post-SxIP region that enhance the affinity by two orders of magnitude, leading to a nanomolar interaction. We verify the enhanced recruitment of the mutated peptide to the dynamic plus ends of MTs in a live cell experiment. Our model explains EB1’s interaction with the SxIP-containing ligands and can be used to design of small molecule inhibitors that can block SxIP interaction with EB1.
... The rate constants for the 2B → 2A interconversion process (k 2B→2A ) were subsequently obtained by multiplying (k 2B→2A + k 2A→2B ) by the molar fraction of 2A. 40 The values of k 2B→2A obtained at different temperatures were analyzed using an Eyring plot according to eq 1, where k b and h are Boltzmann and Planck constants, respectively, R is the gas constant, and ΔH ‡ and ΔS ‡ are the activation enthalpy and activation entropy. 41 ...
Photoxenobactin E (1) is a natural product with an unusual thiocarboxylic acid terminus recently isolated from an entomopathogenic bacterium. The biosynthetic gene cluster associated with photoxenobactin E, and other reported derivatives, is very similar to that of piscibactin, the siderophore responsible for the iron uptake among bacteria of the Vibrionaceae family, including potential human pathogens. Here, the reisolation of 1 from the fish pathogen Vibrio anguillarum RV22 cultured under iron deprivation, its ability to chelate Ga(III), and the full NMR spectroscopic characterization of the Ga(III)-photoxenobactin E complex are presented. Our results show that Ga(III)-photoxenobactin E in solution exists in a thiol−thione tautomeric equilibrium, where Ga(III) is coordinated through the sulfur (thiol form) or oxygen (thione form) atoms of the thiocarboxylate group. This report represents the first NMR study of the chemical exchange between the thiol and thione forms associated with thiocarboxylate-Ga(III) coordination, including the kinetics of the interconversion process associated with this tautomeric exchange. These findings show significant implications for ligand design as they illustrate the potential of the thiocarboxylate group as a versatile donor for hard metal ions such as Ga(III).
... 14−18 Recently, this methodology has gained popularity, in part due to an inexpensive route to 5-fluoro tryptophan incorporation into proteins gradually replacing the traditional expression and growth in auxotrophic bacterial strains. 13,19−21 Together with numerical or analytical solutions of the modified Bloch-McConnell equations for multisite chemical exchange, 22,23 complex mechanistic information has been derived from dynamic NMR line shape analysis of organic and biochemical reactions. ...
The recent discovery of metamorphic proteins, which can switch between multiple conformations under native conditions, has challenged the well-established one sequence-one structure paradigm of protein folding. This is exemplified in the C-terminal domain of the multidomain transcription factor RfaH, which converts from an α-helical coiled-coil conformation in its autoinhibited state to a β-barrel conformation upon activation. Here, we use multisite line shape analysis of 19F NMR-monitored equilibrium chemical denaturation measurements of two 19F-labeled variants of full-length RfaH, to show that it folds/unfolds slowly on the NMR time scale, in an apparent all-or-none fashion at physiological pH and room temperature in the 3.3–4.8 M urea concentration range. The significant thermodynamic stability and slow unfolding rate (kinetic stability) are likely responsible for maintaining the closed autoinhibited state of RfaH, preventing spurious interactions with RNA polymerase (RNAP) when not functional. Our results provide a quantitative understanding of the folding-function relationship in the model fold-switching protein RfaH.
Biological phosphates can coordinate metal ions and their complexes are common in living systems. Dynamics of mutual oxygen atom exchange in the tetrahedral group in complexes has not been investigated. Here, we present a direct experimental proof of exchange (“phosphonate rotation”) in model Ln(III) complexes of monophosphonate H4dota analogue which alters phosphorus atom chirality of coordinated phosphonate monoester. Combination of macrocycle‐based isomerism with P‐based chirality leads to several diastereoisomers. (Non)‐coordinated oxygen atoms were distinguished through ¹⁷O‐labelled phosphonate group and their mutual exchange was followed by various NMR techniques and DFT calculations. The process is sterically demanding and occurs through bulky bidentate (κ²‐PO2)⁻ coordination and was observed only in twisted‐square antiprism (TSA) diastereoisomer of large Ln(III) ions. Its energy demands increase for smaller Ln(III) ions (²⁹⁸ΔG≠(exp./DFT)=51.8/52.1 and 61.0/71.5 kJ mol⁻¹ for La(III) and Eu(III), respectively). These results are helpful in design of such complexes as MRI CA and for protein paramagnetic NMR probes. It demonstrates usefulness of ¹⁷O NMR to study solution dynamics in complexes involving phosphorus acid derivatives and it may inspire use of this method to study dynamics of phosphoric acid derivatives (as e. g. phosphorus acid‐based inhibitors of metalloenzymes) in different areas of chemistry.
