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Son A, Kim W, Park J, Lee W, Lee Y, Choi S, Kim H. Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics. Int J Mol Sci 2024; 25:9725. [PMID: 39273672 PMCID: PMC11395565 DOI: 10.3390/ijms25179725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 09/06/2024] [Accepted: 09/07/2024] [Indexed: 09/15/2024] Open
Abstract
Protein dynamics play a crucial role in biological function, encompassing motions ranging from atomic vibrations to large-scale conformational changes. Recent advancements in experimental techniques, computational methods, and artificial intelligence have revolutionized our understanding of protein dynamics. Nuclear magnetic resonance spectroscopy provides atomic-resolution insights, while molecular dynamics simulations offer detailed trajectories of protein motions. Computational methods applied to X-ray crystallography and cryo-electron microscopy (cryo-EM) have enabled the exploration of protein dynamics, capturing conformational ensembles that were previously unattainable. The integration of machine learning, exemplified by AlphaFold2, has accelerated structure prediction and dynamics analysis. These approaches have revealed the importance of protein dynamics in allosteric regulation, enzyme catalysis, and intrinsically disordered proteins. The shift towards ensemble representations of protein structures and the application of single-molecule techniques have further enhanced our ability to capture the dynamic nature of proteins. Understanding protein dynamics is essential for elucidating biological mechanisms, designing drugs, and developing novel biocatalysts, marking a significant paradigm shift in structural biology and drug discovery.
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Affiliation(s)
- Ahrum Son
- Department of Molecular Medicine, Scripps Research, San Diego, CA 92037, USA
| | - Woojin Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Jongham Park
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Wonseok Lee
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Yerim Lee
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Seongyun Choi
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Hyunsoo Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- Protein AI Design Institute, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- SCICS, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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2
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Gao S, Wu XT, Zhang W, Richardson T, Barrow SL, Thompson-Kucera CA, Iavarone AT, Klinman JP. Temporal Resolution of Activity-Related Solvation Dynamics in the TIM Barrel Enzyme Murine Adenosine Deaminase. ACS Catal 2024; 14:4554-4567. [PMID: 39099600 PMCID: PMC11296675 DOI: 10.1021/acscatal.3c02687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Murine adenosine deaminase (mADA) is a prototypic system for studying the thermal activation of active site chemistry within the TIM barrel family of enzyme reactions. Previous temperature-dependent hydrogen deuterium exchange studies under various conditions have identified interconnected thermal networks for heat transfer from opposing protein-solvent interfaces to active site residues in mADA. One of these interfaces contains a solvent exposed helix-loop-helix moiety that presents the hydrophobic face of its long α-helix to the backside of bound substrate. Herein we pursue the time and temperature dependence of solvation dynamics at the surface of mADA, for comparison to established kinetic parameters that represent active site chemistry. We first created a modified protein devoid of native tryptophans with close to native kinetic behavior. Single site-specific tryptophan mutants were back inserted into each of the four positions where native tryptophans reside. Measurements of nanosecond fluorescence relaxation lifetimes and Stokes shift decays, that reflect time dependent environmental reoroganization around the photo-excited state of Trp*, display minimal temperature dependences. These regions serve as controls for the behavior of a new single tryptophan inserted into a solvent exposed region near the helix-loop-helix moiety located behind the bound substrate, Lys54Trp. This installed Trp displays a significantly elevated value for Ea ( k Stokes shift ) ; further, when Phe61 within the long helix positioned behind bound substrate is replaced by a series of aliphatic hydrophobic side chains, the trends in Ea ( k Stokes shift ) mirror the earlier reported impact of the same series of function-altering hydrophobic side chains on the activation energy of catalysis, Ea ( k cat ) .The reported experimental findings implicate a solvent initiated and rapid (>ns) protein restructuring that contributes to the enthalpic activation barrier to catalysis in mADA.
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Affiliation(s)
- Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Xin Ting Wu
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Tyre Richardson
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Samuel L. Barrow
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Christian A. Thompson-Kucera
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Anthony T. Iavarone
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Judith P. Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, United States
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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4
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Yahalom A, Shaked H, Ruthstein S, Chill JH. Inherent Minor Conformer of Bordetella Effector BteA Directs Chaperone-Mediated Unfolding. J Am Chem Soc 2022; 144:11553-11557. [PMID: 35749268 DOI: 10.1021/jacs.2c04122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The pathogen Bordetella pertussis uses a type-3 secretion system (T3SS) to inject its cytotoxic effector BteA into the host cell via a designated needle structure. Prior to injection BteA is bound to its cognate chaperone BtcA presumed to assist in effector unfolding en route to needle passage. We utilized NMR and EPR spectroscopy to uncover the molecular mechanism of BtcA-mediated unfolding of BteA. BtcA induces a global structural change in the effector, which adopts a more extended and partially unfolded conformation. EPR distance measurements further show that the structured helical-bundle form of free BteA exists in conformational equilibrium with a lowly populated minor species. The nature of this equilibrium was probed using NMR relaxation dispersion experiments. At 283 K structural effects are most pronounced for a contiguous surface spanning the A- and B-helices of BteA, extending at 303 K to a second surface including the D- and E-helices. Residues perturbed in the minor conformation coincide with those exhibiting a BtcA-induced increase in flexibility, identifying this conformation as the BtcA-bound form of the effector. Our findings hint at a conformational-selectivity mechanism for the chaperone interaction with the effector, a paradigm that may be common to effector-chaperones secretion complexes in this family of pathogens.
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Affiliation(s)
- Adi Yahalom
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Hadassa Shaked
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Sharon Ruthstein
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Jordan H Chill
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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Civera M, Moroni E, Sorrentino L, Vasile F, Sattin S. Chemical and Biophysical Approaches to Allosteric Modulation. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Monica Civera
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Elisabetta Moroni
- Istituto di Scienze e Tecnologie Chimiche Giulio Natta, SCITEC Via Mario Bianco 9 20131 Milan Italy
| | - Luca Sorrentino
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Francesca Vasile
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Sara Sattin
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
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6
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Winston DS, Boehr DD. Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity. Enzymes 2021; 49:149-193. [PMID: 34696831 DOI: 10.1016/bs.enz.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
All RNA viruses encode an RNA-dependent RNA polymerase (RdRp) responsible for genome replication. It is now recognized that enzymes in general, and RdRps specifically, are dynamic macromolecular machines such that their moving parts, including active site loops, play direct functional roles. While X-ray crystallography has provided deep insight into structural elements important for RdRp function, this methodology generally provides only static snapshots, and so is limited in its ability to report on dynamic fluctuations away from the lowest energy conformation. Nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations and other biophysical techniques have brought new insight into RdRp function by their ability to characterize the trajectories, kinetics and thermodynamics of conformational motions. In particular, these methodologies have identified coordinated motions among conserved structural motifs necessary for nucleotide selection and incorporation. Disruption of these motions through amino acid substitutions or inhibitor binding impairs RdRp function. Understanding and re-engineering these motions thus provides exciting new avenues for anti-viral strategies. This chapter outlines the basics of these methodologies, summarizes the dynamic motions observed in different RdRps important for nucleotide selection and incorporation, and illustrates how this information can be leveraged towards rational vaccine strain development and anti-viral drug design.
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Affiliation(s)
- Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States.
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Ben Imeddourene A, Zargarian L, Buckle M, Hartmann B, Mauffret O. Slow motions in A·T rich DNA sequence. Sci Rep 2020; 10:19005. [PMID: 33149183 PMCID: PMC7642443 DOI: 10.1038/s41598-020-75645-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/12/2020] [Indexed: 01/09/2023] Open
Abstract
In free B-DNA, slow (microsecond-to-millisecond) motions that involve equilibrium between Watson-Crick (WC) and Hoogsteen (HG) base-pairing expand the DNA dynamic repertoire that could mediate DNA-protein assemblies. R1ρ relaxation dispersion NMR methods are powerful tools to capture such slow conformational exchanges in solution using 13C/15 N labelled DNA. Here, these approaches were applied to a dodecamer containing a TTAAA element that was assumed to facilitate nucleosome formation. NMR data and inferred exchange parameters assign HG base pairs as the minor, transient conformers specifically observed in three successive A·T base pairs forming the TAA·TTA segment. The abundance of these HG A·T base pairs can be up to 1.2% which is high compared to what has previously been observed. Data analyses support a scenario in which the three adenines undergo non-simultaneous motions despite their spatial proximity, thus optimising the probability of having one HG base pair in the TAA·TTA segment. Finally, revisiting previous NMR data on H2 resonance linewidths on the basis of our results promotes the idea of there being a special propensity of A·T base pairs in TAA·TTA tracts to adopt HG pairing. In summary, this study provides an example of a DNA functional element submitted to slow conformational exchange. More generally, it strengthens the importance of the role of the DNA sequence in modulating its dynamics, over a nano- to milli-second time scale.
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Affiliation(s)
- A Ben Imeddourene
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - L Zargarian
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - M Buckle
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - B Hartmann
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - O Mauffret
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France.
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8
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Zhang M. Recent developments of methyl-labeling strategies in Pichia pastoris for NMR spectroscopy. Protein Expr Purif 2020; 166:105521. [DOI: 10.1016/j.pep.2019.105521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 11/26/2022]
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Abstract
The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety of spin relaxation parameters have been developed that provide quantitative information on interconversion kinetics, thermodynamic properties, and structural features of molecular states populated to a fraction of a percent at equilibrium and otherwise unobservable by other NMR approaches. The ongoing development of more sophisticated experimental techniques and the necessity to apply these methods to larger and more complex molecular systems engenders a corresponding need for theoretical advances describing such techniques and facilitating data analysis in applications. This review surveys current aspects of the theory of chemical exchange, as utilized in ZZ-exchange; Hahn and Carr-Purcell-Meiboom-Gill (CPMG) spin-echo; and R1ρ, chemical exchange saturation transfer (CEST), and dark state saturation transfer (DEST) spin-locking experiments. The review emphasizes theoretical results for kinetic topologies with more than two interconverting states, both to obtain compact analytical forms suitable for data analysis and to establish conditions for distinguishability between alternative kinetic schemes.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States.
| | - Hans Koss
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
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