Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning

From Wiley via Jisc Publications RouterHistory: received 2020-08-05, rev-recd 2021-01-21, accepted 2021-02-23, pub-electronic 2021-03-03, pub-print 2021-08Article version: VoRPublication status: PublishedFunder: Biotechnology and Biological Sciences Research Council; Id: http://dx.doi.org/10.13039/501100000268; Grant(s): BB/M017702/1Abstract: Molecular dynamics (MD) simulations are a popular method of studying protein structure and function, but are unable to reliably sample all relevant conformational space in reasonable computational timescales. A range of enhanced sampling methods are available that can improve conformational sampling, but these do not offer a complete solution. We present here a proof‐of‐principle method of combining MD simulation with machine learning to explore protein conformational space. An autoencoder is used to map snapshots from MD simulations onto a user‐defined conformational landscape defined by principal components analysis or specific structural features, and we show that we can predict, with useful accuracy, conformations that are not present in the training data. This method offers a new approach to the prediction of new low energy/physically realistic structures of conformationally dynamic proteins and allows an alternative approach to enhanced sampling of MD simulations

Design and evolution of enzymes for the Morita-Baylis-Hillman reaction

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Interplay between chromophore binding and domain assembly by the B₁₂-dependent photoreceptor protein, CarH.

From Europe PMC via Jisc Publications RouterHistory: ppub 2021-05-01, epub 2021-05-05Publication status: PublishedFunder: Biotechnology and Biological Sciences Research Council; Grant(s): BB/L002655/1, BB/L016486/1, BB/M011208/1Organisms across the natural world respond to their environment through the action of photoreceptor proteins. The vitamin B12-dependent photoreceptor, CarH, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids to protect against photo-oxidative stress. The binding of B12 to CarH monomers in the dark results in the formation of a homo-tetramer that complexes with DNA; B12 photochemistry results in tetramer dissociation, releasing DNA for transcription. Although the details of the response of CarH to light are beginning to emerge, the biophysical mechanism of B12-binding in the dark and how this drives domain assembly is poorly understood. Here - using a combination of molecular dynamics simulations, native ion mobility mass spectrometry and time-resolved spectroscopy - we reveal a complex picture that varies depending on the availability of B12. When B12 is in excess, its binding drives structural changes in CarH monomers that result in the formation of head-to-tail dimers. The structural changes that accompany these steps mean that they are rate-limiting. The dimers then rapidly combine to form tetramers. Strikingly, when B12 is scarcer, as is likely in nature, tetramers with native-like structures can form without a B12 complement to each monomer, with only one apparently required per head-to-tail dimer. We thus show how a bulky chromophore such as B12 shapes protein/protein interactions and in turn function, and how a protein can adapt to a sub-optimal availability of resources. This nuanced picture should help guide the engineering of B12-dependent photoreceptors as light-activated tools for biomedical applications

Structural basis of terephthalate recognition by solute binding protein TphC

From Springer Nature via Jisc Publications RouterHistory: received 2021-03-24, accepted 2021-10-06, registration 2021-10-12, pub-electronic 2021-10-29, online 2021-10-29, collection 2021-12Publication status: PublishedFunder: Commonwealth Scholarship Commission (CSC); doi: https://doi.org/10.13039/501100000867; Grant(s): INCN-2018-57Funder: RCUK | Engineering and Physical Sciences Research Council (EPSRC); doi: https://doi.org/10.13039/501100000266; Grant(s): EP/M013219/1, EP/023755/1Funder: RCUK | Biotechnology and Biological Sciences Research Council (BBSRC); doi: https://doi.org/10.13039/501100000268; Grant(s): BB/M011208/1, BB/M011208/1, BB/P01738X/1Abstract: Biological degradation of Polyethylene terephthalate (PET) plastic and assimilation of the corresponding monomers ethylene glycol and terephthalate (TPA) into central metabolism offers an attractive route for bio-based molecular recycling and bioremediation applications. A key step is the cellular uptake of the non-permeable TPA into bacterial cells which has been shown to be dependent upon the presence of the key tphC gene. However, little is known from a biochemical and structural perspective about the encoded solute binding protein, TphC. Here, we report the biochemical and structural characterisation of TphC in both open and TPA-bound closed conformations. This analysis demonstrates the narrow ligand specificity of TphC towards aromatic para-substituted dicarboxylates, such as TPA and closely related analogues. Further phylogenetic and genomic context analysis of the tph genes reveals homologous operons as a genetic resource for future biotechnological and metabolic engineering efforts towards circular plastic bio-economy solutions

Coupled Motions Direct Electrons along Human Microsomal P450 Chains

Directional electron transfer through biological redox chains can be achieved by coupling reaction chemistry to conformational changes in individual redox enzymes

Computational Studies of Enzymic Hydrogen Tunnelling

The role of enzyme motions in hydrogen tunneling during catalysis is currently a very contentious subject. Experimental data, particularly of elevated kinetic isotope effects, has suggested a significant role for dynamics in the tunneling step. The importance of proton tunneling in the reaction catalysed by the heterotetrameric enzyme aromatic amine dehydrogenase (AADH) has been extensively studied both kinetically and computationally, and the availability of crystal structures for key reaction intenuediates makes this an ideal system for studying the involvement of dynamics in catalysis. Multinanosecond molecular dynamics simulations revealed that the motions of the reacting groups are not correlated with motions within the enzyme, and that the overall motions of the donor and acceptor atoms are not focused towards each other. Nevertheless, certain key motions are required to achieve tunnelinf, and these were identified from spectral density analysis as corresponding to a 165 cm- promoting vibration. This vibration is not part of a large network of vibrations, but is instead inherent within the substrate, as confinued by high-level frequency calculations of the isolated substrate. Comparing hybrid simulations of the heterotetramer and an isolated monomer of AADH revealed that this vibration is crucial for reducing the tunneling distance and the height of the barrier separating the reactant from product by moving the system up the potential energy surface. Numerical modelling of the experimental rates revealed that the promoting vibration is compatible with the reaction kinetics and compatible with the tunneling distance derived from a concomitant computational analysis, and that the presence or absence of such a vibration may not be easily identified experimentally. This represents the first example of a short-range oscillation acting as a promoting vibration, and opens the door to new experimental methods for studying enzymic tunneling and potentially for exploiting enzymes in biocatalysis by selectively exciting specific vibrational modes.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Computational studies of enzymic hydrogen tunnelling

The importance of proton tunnelling in the reaction catalysed by the heterotetrameric enzyme aromatic amine dehydrogenase (AADH) has been extensively studied both kinetically and computationally, and the availability of crystal structures for key reaction intermediates makes this an ideal system for studying the involvement of dynamics in catalysis. Multi-nanosecond molecular dynamics simulations revealed that the motions of the reacting groups are not correlated with motions within the enzyme, and that the overall motions of the donor and acceptor atoms are not focused towards each other. Nevertheless, certain key motions are required to achieve tunnelling, and these were identified from spectral density analysis as corresponding to a 165 cm-1 promoting vibration. This vibration is not part of a large network of vibrations, but is instead inherent within the substrate, as confirmed by high-level frequency calculations of the isolated substrate. Comparing hybrid simulations of the heterotetramer and an isolated monomer of AADH revealed that this vibration is crucial for reducing the tunnelling distance and the height of the barrier separating the reactant from product by moving the system up the potential energy surface. numerical modelling of the experimental rates revealed that the promoting vibration is compatible with the reaction kinetics and compatible with the tunnelling distance derived from a concomitant computational analysis, and that the presence or absence of such a vibration may not be easily identified experimentally. This represents the first example of a short-range oscillation acting as a promoting vibration, and opens the door to new experimental methods for studying enzymic tunnelling and potentially for exploiting enzymes in biocatalysis by selectively exciting specific vibrational modes