1
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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 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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Chalopin Y. GPCR Signaling: A Study of the Interplay Between Structure, Energy, and Function. Proteins 2024. [PMID: 39095933 DOI: 10.1002/prot.26724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/26/2024] [Accepted: 06/12/2024] [Indexed: 08/04/2024]
Abstract
G protein-coupled receptors (GPCRs) exemplify sophisticated allosteric communication, transducing extracellular signals through ligand-induced structural rearrangements that resonate through the molecular scaffold. Despite extensive study, the biophysical underpinnings of how conformational changes spread remain unclear. This work employs a novel physics-based framework to characterize the role of energy dissipation in directing intramolecular signaling pathways. By modeling each residue as a network of coupled oscillators, we generate a localization landscape depicting the vibrational energy distribution throughout the protein scaffold. Quantifying directional energy flux between residues reveals distinct pathways for energy and information transfer, illuminating sequences of allosteric communication. Our analysis of CB1 and CCR5 crystal structures unveils an anisotropic pattern of energy dissipation aligning with key functional dynamics, such as activation-related conformational changes. These anisotropic patterns of vibrational energy flow constitute pre-configured channels for allosteric signaling. Elucidating the relationship between structural topology and energy dissipation patterns provides key insights into the thermodynamic drivers of conformational signaling. This methodology significantly advances our mechanistic understanding of allostery in GPCRs and presents a broadly applicable approach for rationally dissecting allosteric communication pathways, with potential implications for structure-based drug design targeting these critical receptors.
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Affiliation(s)
- Yann Chalopin
- Structures, Properties and Modeling of Solids Laboratory Physics Department, CentraleSupélec/National Center for the Scientific Research, University of Paris-Saclay, Gif-sur-Yvette, France
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3
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Karvelis E, Swanson C, Tidor B. Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity. ACS Catal 2024; 14:10491-10509. [PMID: 39050899 PMCID: PMC11264209 DOI: 10.1021/acscatal.4c01446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/16/2024] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
The task of adapting enzymes for specific applications is often hampered by our incomplete ability to tune and tailor catalytic functions, particularly when seeking increased activity. Here, we develop and demonstrate a rational approach to address this challenge, applied to ketol-acid reductoisomerase (KARI), which has uses in industrial-scale isobutanol production. While traditional structure-based computational enzyme redesign strategies typically focus on the enzyme-bound ground state (GS) and transition state (TS), we postulated that additionally treating the underlying dynamics of complete turnover events that connect and pass through both states could further elucidate the structural properties affecting catalysis and help identify mutations that lead to increased catalytic activity. To examine the dynamics of substrate conversion with atomistic detail, we adapted and applied computational methods based on path sampling techniques to gather thousands of QM/MM simulations of attempted substrate turnover events by KARI: both productive (reactive) and unproductive (nonreactive) attempts. From these data, machine learning models were constructed and used to identify specific conformational features (interatomic distances, angles, and torsions) associated with successful, productive catalysis. Multistate protein redesign techniques were then used to select mutations that stabilized reactive-like structures over nonreactive-like ones while also meeting additional criteria consistent with enhanced specific activity. This procedure resulted in eight high-confidence enzyme mutants with a significant improvement in calculated specific activity relative to wild type (WT), with the fastest variant's increase in calculated k cat being (2 ± 1) × 104-fold. Collectively, these results suggest that introducing mutations designed to increase the population of reaction-promoting conformations of the enzyme-substrate complex before it reaches the barrier can provide an effective approach to engineering improved enzyme catalysts.
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Affiliation(s)
- Elijah Karvelis
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chloe Swanson
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bruce Tidor
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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4
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Read BJ, Mitchell JBO, da Silva RG. Allosteric activation unveils protein-mass modulation of ATP phosphoribosyltransferase product release. Commun Chem 2024; 7:77. [PMID: 38582930 PMCID: PMC10998830 DOI: 10.1038/s42004-024-01165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
Heavy-isotope substitution into enzymes slows down bond vibrations and may alter transition-state barrier crossing probability if this is coupled to fast protein motions. ATP phosphoribosyltransferase from Acinetobacter baumannii is a multi-protein complex where the regulatory protein HisZ allosterically enhances catalysis by the catalytic protein HisGS. This is accompanied by a shift in rate-limiting step from chemistry to product release. Here we report that isotope-labelling of HisGS has no effect on the nonactivated reaction, which involves negative activation heat capacity, while HisZ-activated HisGS catalytic rate decreases in a strictly mass-dependent fashion across five different HisGS masses, at low temperatures. Surprisingly, the effect is not linked to the chemical step, but to fast motions governing product release in the activated enzyme. Disruption of a specific enzyme-product interaction abolishes the isotope effects. Results highlight how altered protein mass perturbs allosterically modulated thermal motions relevant to the catalytic cycle beyond the chemical step.
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Affiliation(s)
- Benjamin J Read
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - John B O Mitchell
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK.
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5
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Balasubramani SG, Korchagina K, Schwartz S. Transition Path Sampling Study of Engineered Enzymes That Catalyze the Morita-Baylis-Hillman Reaction: Why Is Enzyme Design so Difficult? J Chem Inf Model 2024; 64:2101-2111. [PMID: 38451822 PMCID: PMC10963169 DOI: 10.1021/acs.jcim.4c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
It is hoped that artificial enzymes designed in laboratories can be efficient alternatives to chemical catalysts that have been used to synthesize organic molecules. However, the design of artificial enzymes is challenging and requires a detailed molecular-level analysis to understand the mechanism they promote in order to design efficient variants. In this study, we computationally investigate the mechanism of proficient Morita-Baylis-Hillman enzymes developed using a combination of computational design and directed evolution. The powerful transition path sampling method coupled with in-depth post-processing analysis has been successfully used to elucidate the different chemical pathways, transition states, protein dynamics, and free energy barriers of reactions catalyzed by such laboratory-optimized enzymes. This research provides an explanation for how different chemical modifications in an enzyme affect its catalytic activity in ways that are not predictable by static design algorithms.
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Affiliation(s)
- Sree Ganesh Balasubramani
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, Arizona 85721, United States
| | - Kseniia Korchagina
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, Arizona 85721, United States
| | - Steven Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, Arizona 85721, United States
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6
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Beach A, Adhikari P, Singh G, Song M, DeGroot N, Lu Y. Structural Effects on the Temperature Dependence of Hydride Kinetic Isotope Effects of the NADH/NAD + Model Reactions in Acetonitrile: Charge-Transfer Complex Tightness Is a Key. J Org Chem 2024; 89:3184-3193. [PMID: 38364859 PMCID: PMC10913049 DOI: 10.1021/acs.joc.3c02562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
It has recently frequently been found that the kinetic isotope effect (KIE) is independent of temperature (T) in H-tunneling reactions in enzymes but becomes dependent on T in their mutants. Many enzymologists found that the trend is related to different donor-acceptor distances (DADs) at tunneling-ready states (TRSs), which could be sampled by protein dynamics. That is, a more rigid system of densely populated short DADs gives rise to a weaker T dependence of KIEs. Theoreticians have attempted to develop H-tunneling theories to explain the observations, but none have been universally accepted. It is reasonable to assume that the DAD sampling concept, if it exists, applies to the H-transfer reactions in solution, as well. In this work, we designed NADH/NAD+ model reactions to investigate their structural effects on the T dependence of hydride KIEs in acetonitrile. Hammett correlations together with N-CH3/CD3 secondary KIEs were used to provide the electronic structure of the TRSs and thus the rigidity of their charge-transfer complexation vibrations. In all three pairs of reactions, a weaker T dependence of KIEs always corresponds to a steeper Hammett slope on the substituted hydride acceptors. It was found that a tighter/rigid charge-transfer complexation system corresponds with a weaker T dependence of KIEs, consistent with the observations in enzymes.
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Affiliation(s)
- Amanda Beach
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Pratichhya Adhikari
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Grishma Singh
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Meimei Song
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Nicholas DeGroot
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
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7
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Hill TD, Basnet S, Lepird HH, Rightnowar BW, Moran SD. Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy. J Chem Phys 2023; 159:165101. [PMID: 37870142 PMCID: PMC10597647 DOI: 10.1063/5.0167991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.
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Affiliation(s)
| | - Sunil Basnet
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Hannah H. Lepird
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Blaze W. Rightnowar
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Sean D. Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
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8
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Brown M, Schramm VL. Decreased Transition-State Analogue Affinity in Isotopically Heavy MTAN with Increased Catalysis. Biochemistry 2023; 62:2928-2933. [PMID: 37788145 PMCID: PMC10636763 DOI: 10.1021/acs.biochem.3c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase from Helicobacter pylori (HpMTAN) demonstrated faster chemistry when expressed as an isotopically heavy protein, with 2H, 13C, and 15N replacing the bulk of normal isotopes. The inverse heavy enzyme isotope effect has been attributed to improved enzyme-reactant interactions causing more frequent transition-state formation ( Proc. Natl. Acad. Sci. U.S.A. 2021, 118, e2109118118). Transition-state analogues stabilize the transient dynamic geometry of the transition state and inform on transition-state dynamics. Here, a slow-onset, tight-binding transition-state analogue of HpMTAN is characterized with heavy and light enzymes. Dissociation constants for the initial encounter complex (Ki) and for the tightly bound complex after slow-onset inhibition (Ki*) with hexylthio-DADMe-Immucillin-A (HTDIA) gave Ki values for light and heavy HpMTAN = 52 ± 10 and 85 ± 13 pM and Ki* values = 5.9 ± 0.3 and 10.0 ± 1.2 pM, respectively. HTDIA dissociates from heavy HpMTAN at 0.063 ± 0.002 min-1, faster than that from light HpMTAN at 0.032 ± 0.004 min-1. These values are consistent with transition-state formation by an improved catalytic site dynamic search and inconsistent with catalytic efficiency proportional to tight binding of the transition state.
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Affiliation(s)
- Morais Brown
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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9
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Markin CJ, Mokhtari DA, Du S, Doukov T, Sunden F, Cook JA, Fordyce PM, Herschlag D. Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology. Proc Natl Acad Sci U S A 2023; 120:e2219074120. [PMID: 37428919 PMCID: PMC10629569 DOI: 10.1073/pnas.2219074120] [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: 11/08/2022] [Accepted: 06/14/2023] [Indexed: 07/12/2023] Open
Abstract
Using high-throughput microfluidic enzyme kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the alkaline phosphatase PafA on binding affinity for two transition state analogs (TSAs), vanadate and tungstate. As predicted by catalytic models invoking transition state complementary, mutations to active site and active-site-contacting residues had highly similar impacts on catalysis and TSA binding. Unexpectedly, most mutations to more distal residues that reduced catalysis had little or no impact on TSA binding and many even increased tungstate affinity. These disparate effects can be accounted for by a model in which distal mutations alter the enzyme's conformational landscape, increasing the occupancy of microstates that are catalytically less effective but better able to accommodate larger transition state analogs. In support of this ensemble model, glycine substitutions (rather than valine) were more likely to increase tungstate affinity (but not more likely to impact catalysis), presumably due to increased conformational flexibility that allows previously disfavored microstates to increase in occupancy. These results indicate that residues throughout an enzyme provide specificity for the transition state and discriminate against analogs that are larger only by tenths of an Ångström. Thus, engineering enzymes that rival the most powerful natural enzymes will likely require consideration of distal residues that shape the enzyme's conformational landscape and fine-tune active-site residues. Biologically, the evolution of extensive communication between the active site and remote residues to aid catalysis may have provided the foundation for allostery to make it a highly evolvable trait.
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Affiliation(s)
- Craig J. Markin
- Department of Biochemistry, Stanford University, Stanford, CA94305
| | | | - Siyuan Du
- Department of Biochemistry, Stanford University, Stanford, CA94305
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Light Source, Stanford Linear Accelerator Centre National Accelerator Laboratory, Menlo Park, CA94025
| | - Fanny Sunden
- Department of Biochemistry, Stanford University, Stanford, CA94305
| | - Jordan A. Cook
- Department of Biochemistry, Stanford University, Stanford, CA94305
| | - Polly M. Fordyce
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- Chan Zuckerberg Biohub, San Francisco, CA94110
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
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10
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Antoniou D, Zoi I, Schwartz SD. Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling. Methods Enzymol 2023; 685:319-340. [PMID: 37245906 PMCID: PMC10228753 DOI: 10.1016/bs.mie.2023.03.005] [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: 05/30/2023]
Abstract
Despite initial resistance, it has been increasingly accepted that protein dynamics plays a role in enzymatic catalysis. There have been two lines of research. Some works study slow conformational motions that are not coupled to the reaction coordinate, but guide the system towards catalytically competent conformations. Understanding at the atomistic level how this is accomplished has remained elusive except for a few systems. In this review we focus on fast sub-picosecond motions that are coupled to the reaction coordinate. The use of Transition Path Sampling has allowed us an atomistic description of how these rate-promoting vibrational motions are incorporated in the reaction mechanism. We will also show how we used insights from rate-promoting motions in protein design.
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Affiliation(s)
- Dimitri Antoniou
- Department of Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Ioanna Zoi
- Department of Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Steven D Schwartz
- Department of Biochemistry, University of Arizona, Tucson, AZ, United States.
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11
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Chalopin Y, Cramer SP, Arragain S. Phonon-assisted electron-proton transfer in [FeFe] hydrogenases: Topological role of clusters. Biophys J 2023; 122:1557-1567. [PMID: 36960530 PMCID: PMC10147833 DOI: 10.1016/j.bpj.2023.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/27/2023] [Accepted: 03/16/2023] [Indexed: 03/25/2023] Open
Abstract
[FeFe] hydrogenases are enzymes that have acquired a unique capacity to synthesize or consume molecular hydrogen (H2). This function relies on a complex catalytic mechanism involving the active site and two distinct electron and proton transfer networks working in concert. By an analysis based on terahertz vibrations of [FeFe] hydrogenase structure, we are able to predict and identify the existence of rate-promoting vibrations at the catalytic site and the coupling with functional residues involved in reported electron and proton transfer networks. Our findings suggest that the positioning of the cluster is influenced by the response of the scaffold to thermal fluctuations, which in turn drives the formation of networks for electron transfer through phonon-assisted mechanisms. Thus, we address the problem of linking the molecular structure to the catalytic function through picosecond dynamics, while raising the functional gain brought by the cofactors or clusters, using the concept of fold-encoded localized vibrations.
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Affiliation(s)
- Yann Chalopin
- Laboratoire d'Energétique Macroscopique et Moléculaire, Combustion (EM2C), CNRS/CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France.
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12
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Demchenko AP. Proton transfer reactions: from photochemistry to biochemistry and bioenergetics. BBA ADVANCES 2023. [DOI: 10.1016/j.bbadva.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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13
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Eberhart ME, Wilson TR, Johnston NW, Alexandrova AN. Geometry of Charge Density as a Reporter on the Role of the Protein Scaffold in Enzymatic Catalysis: Electrostatic Preorganization and Beyond. J Chem Theory Comput 2023; 19:694-704. [PMID: 36562645 DOI: 10.1021/acs.jctc.2c01060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Enzymes host active sites inside protein macromolecules, which have diverse, often incredibly complex, and atom-expensive structures. It is an outstanding question what the role of these expensive scaffolds might be in enzymatic catalysis. Answering this question is essential to both enzymology and the design of artificial enzymes with proficiencies that will match those of the best natural enzymes. Protein rigidifying the active site, contrasted with the dynamics and vibrational motion promoting the reaction, as well as long-range electrostatics (also known as electrostatic preorganization) were all proposed as central contributions of the scaffold to the catalysis. Here, we show that all these effects inevitably produce changes in the quantum mechanical electron density in the active site, which in turn defines the reactivity. The phenomena are therefore fundamentally inseparable. The geometry of the electron density-a scalar field characterized by a number of mathematical features such as critical points-is a rigorous and convenient descriptor of enzymatic catalysis and a reporter on the role of the protein. We show how this geometry can be analyzed, linked to the reaction barriers, and report in particular on intramolecular electric fields in enzymes. We illustrate these tools on the studies of electrostatic preorganization in several representative enzyme classes, both natural and artificial. We highlight the forward-looking aspects of the approach.
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Affiliation(s)
- Mark E Eberhart
- Department of Chemistry, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Timothy R Wilson
- Department of Chemistry, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Nathaniel W Johnston
- Department of Chemistry, and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Anastassia N Alexandrova
- Department of Chemistry, and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
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14
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Frost CF, Balasubramani SG, Antoniou D, Schwartz SD. Connecting Conformational Motions to Rapid Dynamics in Human Purine Nucleoside Phosphorylase. J Phys Chem B 2023; 127:144-150. [PMID: 36538016 PMCID: PMC9873402 DOI: 10.1021/acs.jpcb.2c07243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The influence of protein motions on enzyme catalysis remains a topic of active discussion. Protein motions occur across a variety of time scales, from vibrational fluctuations in femtoseconds, to collective motions in milliseconds. There have been numerous studies that show conformational motions may assist in catalysis, protein folding, and substrate specificity. It is also known through transition path sampling studies that rapid promoting vibrations contribute to enzyme catalysis. Human purine nucleoside phosphorylase (PNP) is one enzyme that contains both an important conformational motion and a rapid promoting vibration. The slower motion in this enzyme is associated with a loop motion, that when open allows substrate entry and product release but closes over the active site during catalysis. We examine the differences between an unconstrained PNP structure and a PNP structure with constraints on the loop motion. To investigate possible coupling between the slow and fast protein dynamics, we employed transition path sampling, reaction coordinate identification, electric field calculations, and free energy calculations reported here.
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Affiliation(s)
- Clara F Frost
- University of Arizona, Department of Chemistry & Biochemistry, Tucson, Arizona85721, United States
| | | | - Dimitri Antoniou
- University of Arizona, Department of Chemistry & Biochemistry, Tucson, Arizona85721, United States
| | - Steven D Schwartz
- University of Arizona, Department of Chemistry & Biochemistry, Tucson, Arizona85721, United States
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15
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Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation. Nat Commun 2022; 13:7607. [PMID: 36494361 PMCID: PMC9734150 DOI: 10.1038/s41467-022-34960-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisGS while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisGS Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisGS with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisGS interface lying ~20 Å away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisGS to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisGS. In the Arg56Ala-HisGS mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein-protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.
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16
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Adhikari P, Song M, Bai M, Rijal P, DeGroot N, Lu Y. Solvent Effects on the Temperature Dependence of Hydride Kinetic Isotope Effects: Correlation to the Donor-Acceptor Distances. J Phys Chem A 2022; 126:7675-7686. [PMID: 36228057 DOI: 10.1021/acs.jpca.2c06065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein structural effects on the temperature (T) dependence of kinetic isotope effects (KIEs) in H-tunneling reactions have recently been used to discuss about the role of enzyme thermal motions in catalysis. Frequently observed nearly T-independent KIEs in the wild-type enzymes and T-dependent KIEs in variants suggest that H-tunneling in the former is assisted by the naturally evolved protein constructive vibrations that help sample short donor-acceptor distances (DADs) needed. This explanation that correlates the T-dependence of KIEs with DAD sampling has been highly debated as simulations following other H-tunneling models sometimes gave alternative explanations. In this paper, solvent effects on the T-dependence of KIEs of two hydride tunneling reactions of NADH/NAD+ analogues (represented by ΔEa = EaD - EaH) were determined in attempts to replicate the observations in enzymes and test the protein vibration-assisted DAD sampling concept. Effects of selected aprotic solvents on the DADPRC's of the productive reactant complexes (PRCs) and the DADTRS's of the activated tunneling ready states (TRSs) were obtained through computations and analyses of the kinetic data, including 2° KIEs, respectively. A weaker T-dependence of KIEs (i.e., smaller ΔEa) was found in a more polar aprotic solvent in which the system has a shorter average DADPRC and DADTRS. Further results show that a charge-transfer (CT) complexation made of a stronger donor/acceptor gives rise to a smaller ΔEa. Overall, the shorter and less broadly distributed DADs resulting from the stronger CT complexation vibrations give rise to a smaller ΔEa. Our results appear to support the explanation that links the T-dependence of KIEs to the donor-acceptor rigidity in enzymes.
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Affiliation(s)
- Pratichhya Adhikari
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Meimei Song
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Mingxuan Bai
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Pratap Rijal
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Nicholas DeGroot
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
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17
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Abstract
Many enzymes that show a large specificity in binding the enzymatic transition state with a higher affinity than the substrate utilize substrate binding energy to drive protein conformational changes to form caged substrate complexes. These protein cages provide strong stabilization of enzymatic transition states. Using part of the substrate binding energy to drive the protein conformational change avoids a similar strong stabilization of the Michaelis complex and irreversible ligand binding. A seminal step in the development of modern enzyme catalysts was the evolution of enzymes that couple substrate binding to a conformational change. These include enzymes that function in glycolysis (triosephosphate isomerase), the biosynthesis of lipids (glycerol phosphate dehydrogenase), the hexose monophosphate shunt (6-phosphogluconate dehydrogenase), and the mevalonate pathway (isopentenyl diphosphate isomerase), catalyze the final step in the biosynthesis of pyrimidine nucleotides (orotidine monophosphate decarboxylase), and regulate the cellular levels of adenine nucleotides (adenylate kinase). The evolution of enzymes that undergo ligand-driven conformational changes to form active protein-substrate cages is proposed to proceed by selection of variants, in which the selected side chain substitutions destabilize a second protein conformer that shows compensating enhanced binding interactions with the substrate. The advantages inherent to enzymes that incorporate a conformational change into the catalytic cycle provide a strong driving force for the evolution of flexible protein folds such as the TIM barrel. The appearance of these folds represented a watershed event in enzyme evolution that enabled the rapid propagation of enzyme activities within enzyme superfamilies.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, New York 14260-3000, United States
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18
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Balasubramani SG, Schwartz SD. Transition Path Sampling Based Calculations of Free Energies for Enzymatic Reactions: The Case of Human Methionine Adenosyl Transferase and Plasmodium vivax Adenosine Deaminase. J Phys Chem B 2022; 126:5413-5420. [PMID: 35830574 PMCID: PMC9444332 DOI: 10.1021/acs.jpcb.2c03251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transition path sampling (TPS) is widely used for the calculations of reaction rates, transition state structures, and reaction coordinates of condensed phase systems. Here we discuss a scheme for the calculation of free energies using the ensemble of TPS reactive trajectories in combination with a window-based sampling technique for enzyme-catalyzed reactions. We calculate the free energy profiles of the reactions catalyzed by the human methionine S-adenosyltransferase (MAT2A) enzyme and the Plasmodium vivax adenosine deaminase (pvADA) enzyme to assess the accuracy of this method. MAT2A catalyzes the formation of S-adenosine-l-methionine following a SN2 mechanism, and using our method, we estimate the free energy barrier for this reaction to be 16 kcal mol-1, which is in excellent agreement with the experimentally measured activation energy of 17.27 kcal mol-1. Furthermore, for the pvADA enzyme-catalyzed reaction we estimate a free energy barrier of 21 kcal mol-1, and the calculated free energy profile is similar to that predicted from experimental observations. Calculating free energies by employing our simple method within TPS provides significant advantages over methods such as umbrella sampling because it is free from any applied external bias, is accurate compared to experimental measurements, and has a reasonable computational cost.
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Affiliation(s)
- Sree Ganesh Balasubramani
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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19
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Rapp C, Nidetzky B. Hydride Transfer Mechanism of Enzymatic Sugar Nucleotide C2 Epimerization Probed with a Loose-Fit CDP-Glucose Substrate. ACS Catal 2022; 12:6816-6830. [PMID: 35747200 PMCID: PMC9207888 DOI: 10.1021/acscatal.2c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/12/2022] [Indexed: 11/29/2022]
Abstract
![]()
Transient oxidation–reduction
through hydride transfer with
tightly bound NAD coenzyme is used by a large class of sugar nucleotide
epimerases to promote configurational inversion of carbon stereocenters
in carbohydrate substrates. A requirement for the epimerases to coordinate
hydride abstraction and re-addition with substrate rotation in the
binding pocket poses a challenge for dynamical protein conformational
selection linked to enzyme catalysis. Here, we studied the thermophilic
C2 epimerase from Thermodesulfatator atlanticus (TaCPa2E) in combination with a slow CDP-glucose
substrate (kcat ≈ 1.0 min–1; 60 °C) to explore the sensitivity of the enzymatic hydride
transfer toward environmental fluctuations affected by temperature
(20–80 °C). We determined noncompetitive primary kinetic
isotope effects (KIE) due to 2H at the glucose C2 and showed
that a normal KIE on the kcat (Dkcat) reflects isotope sensitivity of
the hydrogen abstraction to enzyme-NAD+ in a rate-limiting
transient oxidation. The Dkcat peaked at 40 °C was 6.1 and decreased to 2.1 at low (20 °C)
and 3.3 at high temperature (80 °C). The temperature profiles
for kcat with the 1H and 2H substrate showed a decrease in the rate below a dynamically
important breakpoint (∼40 °C), suggesting an equilibrium
shift to an impaired conformational landscape relevant for catalysis
in the low-temperature region. Full Marcus-like model fits of the
rate and KIE profiles provided evidence for a high-temperature reaction
via low-frequency conformational sampling associated with a broad
distribution of hydride donor–acceptor distances (long-distance
population centered at 3.31 ± 0.02 Å), only poorly suitable
for quantum mechanical tunneling. Collectively, dynamical characteristics
of TaCPa2E-catalyzed hydride transfer during transient
oxidation of CDP-glucose reveal important analogies to mechanistically
simpler enzymes such as alcohol dehydrogenase and dihydrofolate reductase.
A loose-fit substrate (in TaCPa2E) resembles structural
variants of these enzymes by extensive dynamical sampling to balance
conformational flexibility and catalytic efficiency.
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Affiliation(s)
- Christian Rapp
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria
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20
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Wu S, Ma A. Mechanism for the rare fluctuation that powers protein conformational change. J Chem Phys 2022; 156:054119. [PMID: 35135246 PMCID: PMC8824576 DOI: 10.1063/5.0077444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/17/2022] [Indexed: 11/14/2022] Open
Abstract
Most functional processes of biomolecules are rare events. Key to a rare event is the rare fluctuation that enables the energy activation process that precedes and powers crossing of the activation barrier. However, the physical nature of this rare fluctuation and how it enables energy activation and subsequently barrier crossing are unknown. We developed a novel metric, the reaction capacity pC, that rigorously defines the beginning and parameterizes the progress of energy activation. This enabled us to identify the rare fluctuation as a special phase-space condition that is necessary and sufficient for initiating systematic energy flow from the non-reaction coordinates into the reaction coordinates. The energy activation of a prototype biomolecular isomerization reaction is dominated by kinetic energy transferring into and accumulating in the reaction coordinates, administered by inertial forces alone. This mechanism for energy activation is fundamentally different from the mechanism suggested by Kramers theory.
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Affiliation(s)
- Shanshan Wu
- Richard Loan and Hill Department of Biomedical Engineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA
| | - Ao Ma
- Richard Loan and Hill Department of Biomedical Engineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA
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21
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Schafer JW, Chen X, Schwartz SD. Engineered Tryptophan Synthase Balances Equilibrium Effects and Fast Dynamic Effects. ACS Catal 2022; 12:913-922. [PMID: 35719741 PMCID: PMC9202816 DOI: 10.1021/acscatal.1c03913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Creating efficient and stable enzymes for catalysis in pharmaceutical and industrial laboratories is an important research goal. Arnold et al. used directed evolution to engineer a natural tryptophan synthase to create a mutant that is operable under laboratory conditions without the need for a natural allosteric effector. The use of directed evolution allows researchers to improve enzymes without understanding the structure-activity relationship. Here, we present a transition path sampling study of a key chemical transformation in the tryptophan synthase catalytic cycle. We observed that while directed evolution does mimic the natural allosteric effect from a stability perspective, fast protein dynamics associated with chemistry has been dramatically altered. This work provides further evidence of the role of protein dynamics in catalysis and clearly demonstrates the multifaceted complexity of mutations associated with protein engineering. This study also demonstrates a fascinating contrast between allosteric and stand-alone functions at the femtosecond time scale.
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Affiliation(s)
- Joseph W Schafer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xi Chen
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
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22
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Chalopin Y, Sparfel J. Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins. Front Mol Biosci 2022; 8:736376. [PMID: 35004841 PMCID: PMC8733615 DOI: 10.3389/fmolb.2021.736376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
Proteins are among the most complex molecular structures, which have evolved to develop broad functions, such as energy conversion and transport, information storage and processing, communication, and regulation of chemical reactions. However, the mechanisms by which these dynamical entities coordinate themselves to perform biological tasks remain hotly debated. Here, a physical theory is presented to explain how functional dynamical behavior possibly emerge in complex/macro molecules, thanks to the effect that we term bilocalization of thermal vibrations. More specifically, our approach allows us to understand how structural irregularities lead to a partitioning of the energy of the vibrations into two distinct sets of molecular domains, corresponding to slow and fast motions. This shape-encoded spectral allocation, associated to the genetic sequence, provides a close access to a wide reservoir of dynamical patterns, and eventually allows the emergence of biological functions by natural selection. To illustrate our approach, the SPIKE protein structure of SARS-COV2 is considered.
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Affiliation(s)
- Yann Chalopin
- Laboratoire EM2C-CNRS and CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Julien Sparfel
- Laboratoire EM2C-CNRS and CentraleSupélec, University of Paris-Saclay, Gif-sur-Yvette, France
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23
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Tvaroška I. Glycosyltransferases as targets for therapeutic intervention in cancer and inflammation: molecular modeling insights. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-021-02026-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Brown M, Zoi I, Antoniou D, Namanja-Magliano HA, Schwartz SD, Schramm VL. Inverse heavy enzyme isotope effects in methylthioadenosine nucleosidases. Proc Natl Acad Sci U S A 2021; 118:e2109118118. [PMID: 34580228 PMCID: PMC8501826 DOI: 10.1073/pnas.2109118118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 11/18/2022] Open
Abstract
Heavy enzyme isotope effects occur in proteins substituted with 2H-, 13C-, and 15N-enriched amino acids. Mass alterations perturb femtosecond protein motions and have been used to study the linkage between fast motions and transition-state barrier crossing. Heavy enzymes typically show slower rates for their chemical steps. Heavy bacterial methylthioadenosine nucleosidases (MTANs from Helicobactor pylori and Escherichia coli) gave normal isotope effects in steady-state kinetics, with slower rates for the heavy enzymes. However, both enzymes revealed rare inverse isotope effects on their chemical steps, with faster chemical steps in the heavy enzymes. Computational transition-path sampling studies of H. pylori and E. coli MTANs indicated closer enzyme-reactant interactions in the heavy MTANs at times near the transition state, resulting in an improved reaction coordinate geometry. Specific catalytic interactions more favorable for heavy MTANs include improved contacts to the catalytic water nucleophile and to the adenine leaving group. Heavy bacterial MTANs depart from other heavy enzymes as slowed vibrational modes from the heavy isotope substitution caused improved barrier-crossing efficiency. Improved sampling frequency and reactant coordinate distances are highlighted as key factors in MTAN transition-state stabilization.
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Affiliation(s)
- Morais Brown
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Ioanna Zoi
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Dimitri Antoniou
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | | | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461;
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25
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Schmidt-Engler JM, von Berg S, Bredenbeck J. Temperature-Dependent Low-Frequency Modes in the Active Site of Bovine Carbonic Anhydrase II Probed by 2D-IR Spectroscopy. J Phys Chem Lett 2021; 12:7777-7782. [PMID: 34374547 DOI: 10.1021/acs.jpclett.1c01453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Enzyme catalysis achieves tremendous rate accelerations. Enzyme reaction centers provide a constraint geometry that preferentially binds an activated form of the substrate and thus lowers the energy barrier. However, this transition state picture neglects the flexibility of proteins and its role in enzymatic catalysis. Especially for proton transfer reactions, it has been suggested that motions of the protein modulate the donor-acceptor distance and prepare a tunneling-ready state. We report the detection of frequency fluctuations of an azide anion (N3-) bound in the active site of the protein carbonic anhydrase II, where a low-frequency mode of the protein has been proposed to facilitate proton transfer over two water molecules during the catalyzed reaction. 2D-IR spectroscopy resolves an underdamped low-frequency mode at about 1 THz (30 cm-1). We find its frequency to be viscosity- and temperature-dependent and to decrease by 6 cm-1 between 230 and 320 K, reporting the softening of the mode's potential.
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Affiliation(s)
- Julian M Schmidt-Engler
- Institute of Biophysics, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
| | - Sarah von Berg
- Institute of Biophysics, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
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26
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Reilley DJ, Wang J, Dokholyan NV, Alexandrova AN. Titr-DMD-A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework. J Chem Theory Comput 2021; 17:4538-4549. [PMID: 34165292 PMCID: PMC10662685 DOI: 10.1021/acs.jctc.1c00338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The pH-dependence of enzyme fold stability and catalytic activity is a fundamentally dynamic, structural property which is difficult to study. The challenges and expense of investigating dynamic, atomic scale behavior experimentally means that computational methods, particularly constant pH molecular dynamics (CpHMD), are well situated tools for this. However, these methods often struggle with affordable sampling of sufficiently long time scales while also obtaining accurate pKa prediction and verifying the structures they generate. We introduce Titr-DMD, an affordable CpHMD method that combines the quasi-all-atom coarse-grained discrete molecular dynamics (DMD) method for conformational sampling with Propka for pKa prediction, to circumvent these issues. The combination enables rapid sampling on limited computational resources, while simulations are still performed on the atomic scale. We benchmark the method on a set of proteins with experimentally attested pKa and on the pH triggered conformational change in a staphylococcal nuclease mutant, a rare experimental study of such behavior. Our results show Titr-DMD to be an effective and inexpensive method to study pH-coupled protein dynamics.
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Affiliation(s)
- David J Reilley
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
- California NanoSystems Institute, Los Angeles, California 90095-1569, United States
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27
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Manuchehrfar F, Li H, Tian W, Ma A, Liang J. Exact Topology of the Dynamic Probability Surface of an Activated Process by Persistent Homology. J Phys Chem B 2021; 125:4667-4680. [PMID: 33938737 DOI: 10.1021/acs.jpcb.1c00904] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To gain insight into the reaction mechanism of activated processes, we introduce an exact approach for quantifying the topology of high-dimensional probability surfaces of the underlying dynamic processes. Instead of Morse indexes, we study the homology groups of a sequence of superlevel sets of the probability surface over high-dimensional configuration spaces using persistent homology. For alanine-dipeptide isomerization, a prototype of activated processes, we identify locations of probability peaks and connecting ridges, along with measures of their global prominence. Instead of a saddle point, the transition state ensemble (TSE) of conformations is at the most prominent probability peak after reactants/products, when proper reaction coordinates are included. Intuition-based models, even those exhibiting a double-well, fail to capture the dynamics of the activated process. Peak occurrence, prominence, and locations can be distorted upon subspace projection. While principal component analysis accounts for conformational variance, it inflates the complexity of the surface topology and destroys the dynamic properties of the topological features. In contrast, TSE emerges naturally as the most prominent peak beyond the reactant/product basins, when projected to a subspace of minimum dimension containing the reaction coordinates. Our approach is general and can be applied to investigate the topology of high-dimensional probability surfaces of other activated processes.
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Affiliation(s)
- Farid Manuchehrfar
- Center for Bioinformatics and Quantiative Biology and Department of Bioengneering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Huiyu Li
- Center for Bioinformatics and Quantiative Biology and Department of Bioengneering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Wei Tian
- Center for Bioinformatics and Quantiative Biology and Department of Bioengneering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Ao Ma
- Center for Bioinformatics and Quantiative Biology and Department of Bioengneering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Jie Liang
- Center for Bioinformatics and Quantiative Biology and Department of Bioengneering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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28
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Abstract
This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.
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29
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Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles. Proc Natl Acad Sci U S A 2020; 117:33204-33215. [PMID: 33376217 DOI: 10.1073/pnas.2011350117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme's reaction cycle. To examine positioning and motions and test catalytic proposals, we collected "room temperature" X-ray crystallography data for Pseudomonas putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Ensemble analyses indicated limited change through KSI's reaction cycle. Active site positioning was on the 1- to 1.5-Å scale, and was not exceptional compared to noncatalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI's general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active-site motions. Most generally, this ensemble perspective extends traditional structure-function relationships, providing the basis for a new era of "ensemble-function" interrogation of enzymes.
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30
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Stewman SF, Tsui KK, Ma A. Dynamic Instability from Non-equilibrium Structural Transitions on the Energy Landscape of Microtubule. Cell Syst 2020; 11:608-624.e9. [PMID: 33086051 DOI: 10.1016/j.cels.2020.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 09/12/2019] [Accepted: 09/25/2020] [Indexed: 11/30/2022]
Abstract
Microtubules are the backbone of the cytoskeleton and vital to numerous cellular processes. The central dogma of microtubules is that all their functions are driven by dynamic instability, but its mechanism has remained unresolved for over 30 years because of conceptual difficulties inherent in the dominant GTP-cap framework. We present a physically rigorous structural mechanochemical model: dynamic instability is driven by non-equilibrium transitions between the bent (B), straight (S), and curved (C) forms of tubulin monomers and longitudinal interfaces in the two-dimensional lattice of microtubule. All the different phenomena (growth, shortening, catastrophe, rescue, and pausing) are controlled by the kinetic pathways for B↔S↔C transitions and corresponding energy landscapes. Different kinetics at minus end are due to different B↔S↔C pathways imposed by the polarity of microtubule lattice. This model enables us to reproduce all the observed phenomena of dynamic instability of purified tubulins in kinetic simulations.
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Affiliation(s)
- Shannon F Stewman
- Department of Bioengineering, the University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
| | - Kenneth K Tsui
- Department of Bioengineering, the University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
| | - Ao Ma
- Department of Bioengineering, the University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA.
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31
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Ben Bdira F, Waudby CA, Volkov AN, Schröder SP, AB E, Codée JDC, Overkleeft HS, Aerts JMFG, Ingen H, Ubbink M. Dynamics of Ligand Binding to a Rigid Glycosidase**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Christopher A. Waudby
- Institute of Structural and Molecular Biology University College London and Birkbeck College London WC1E 6BT UK
| | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology Pleinlaan 2 1050 Brussels Belgium
- Jean Jeener NMR Centre VUB Pleinlaan 2 1050 Brussels Belgium
| | - Sybrin P. Schröder
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Eiso AB
- ZoBio BV BioPartner 2 building J.H. Oortweg 19 2333 CH Leiden The Netherlands
| | - Jeroen D. C. Codée
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hugo Ingen
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
- Present address: NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
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32
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Ben Bdira F, Waudby CA, Volkov AN, Schröder SP, AB E, Codée JDC, Overkleeft HS, Aerts JMFG, van Ingen H, Ubbink M. Dynamics of Ligand Binding to a Rigid Glycosidase*. Angew Chem Int Ed Engl 2020; 59:20508-20514. [PMID: 32533782 PMCID: PMC7693232 DOI: 10.1002/anie.202003236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/29/2020] [Indexed: 11/09/2022]
Abstract
The single-domain GH11 glycosidase from Bacillus circulans (BCX) is involved in the degradation of hemicellulose, which is one of the most abundant renewable biomaterials in nature. We demonstrate that BCX in solution undergoes minimal structural changes during turnover. NMR spectroscopy results show that the rigid protein matrix provides a frame for fast substrate binding in multiple conformations, accompanied by slow conversion, which is attributed to an enzyme-induced substrate distortion. A model is proposed in which the rigid enzyme takes advantage of substrate flexibility to induce a conformation that facilitates the acyl formation step of the hydrolysis reaction.
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Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Christopher A. Waudby
- Institute of Structural and Molecular BiologyUniversity College London and Birkbeck CollegeLondonWC1E 6BTUK
| | - Alexander N. Volkov
- VIB-VUB Center for Structural BiologyPleinlaan 21050BrusselsBelgium
- Jean Jeener NMR CentreVUBPleinlaan 21050BrusselsBelgium
| | - Sybrin P. Schröder
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Eiso AB
- ZoBio BVBioPartner 2 buildingJ.H. Oortweg 192333 CHLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hugo van Ingen
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
- Present address: NMR Spectroscopy Research GroupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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33
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Chalopin Y. The physical origin of rate promoting vibrations in enzymes revealed by structural rigidity. Sci Rep 2020; 10:17465. [PMID: 33060716 PMCID: PMC7566648 DOI: 10.1038/s41598-020-74439-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Enzymes are the most efficient catalysts known to date. However, decades of research have failed to fully explain the catalytic power of enzymes, and most of the current attempts to uncloak the details of atomic motions at active sites remain incomplete. Here, a straightforward manner for understanding the interplay between the complex or irregular enzyme topology and dynamical effects at catalytic sites is introduced, by revealing how fast localized vibrations form spontaneously in the stiffest parts of the scaffold. While shedding light on a physical mechanism that allowed the selection of the picosecond (ps) timescale to increase the catalytic proficiency, this approach exposes the functional importance of localized motions as a by-product of the stability-function tradeoff in enzyme evolution. From this framework of analysis—directly accessible from available diffraction data—experimental strategies for engineering the catalytic rate in enzymatic proteins are proposed.
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Affiliation(s)
- Yann Chalopin
- Laboratoire EM2C, CNRS & CentraleSupelec, University of Paris-Saclay, 91190, Gif-sur-Yvette, France.
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34
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Agarwal PK, Bernard DN, Bafna K, Doucet N. Enzyme dynamics: Looking beyond a single structure. ChemCatChem 2020; 12:4704-4720. [PMID: 33897908 PMCID: PMC8064270 DOI: 10.1002/cctc.202000665] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 12/23/2022]
Abstract
Conventional understanding of how enzymes function strongly emphasizes the role of structure. However, increasing evidence clearly indicates that enzymes do not remain fixed or operate exclusively in or close to their native structure. Different parts of the enzyme (from individual residues to full domains) undergo concerted motions on a wide range of time-scales, including that of the catalyzed reaction. Information obtained on these internal motions and conformational fluctuations has so far uncovered and explained many aspects of enzyme mechanisms, which could not have been understood from a single structure alone. Although there is wide interest in understanding enzyme dynamics and its role in catalysis, several challenges remain. In addition to technical difficulties, the vast majority of investigations are performed in dilute aqueous solutions, where conditions are significantly different than the cellular milieu where a large number of enzymes operate. In this review, we discuss recent developments, several challenges as well as opportunities related to this topic. The benefits of considering dynamics as an integral part of the enzyme function can also enable new means of biocatalysis, engineering enzymes for industrial and medicinal applications.
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Affiliation(s)
- Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma 74078
- Arium BioLabs, 2519 Caspian Drive, Knoxville, Tennessee 37932
| | - David N. Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
| | - Khushboo Bafna
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, 1045 Avenue de la Médecine, Université Laval, Québec, QC, G1V 0A6, Canada
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35
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Chen X, Schwartz SD. Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction. ACS OMEGA 2020; 5:23468-23480. [PMID: 32954200 PMCID: PMC7496013 DOI: 10.1021/acsomega.0c03472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Morphinone reductase (MR) is an important model system for studying the contribution of protein motions to H-transfer reactions. In this research, we used quantum mechanical/molecular mechanics (QM/MM) simulation together with transition path sampling (TPS) simulation to study two important topics of current research on MR: the existence of multiple catalytic reaction pathways and the involvement of fast protein motions in the catalytic process. We have discovered two reaction pathways for the wild type and three reaction pathways for the N189A mutant. With the committor distribution analysis method, we found reaction coordinates for all five reaction pathways. Only one wild-type reaction pathway has a rate-promoting vibration from His186, while all of the other four pathways do not involve any protein motions in their catalytic process through the transition state. The rate-promoting vibration in the wild-type MR, which comes from a direction perpendicular to the donor-acceptor axis, functions to decrease the donor-acceptor distance by causing a subtle "out-of-plane" motion of a donor atom. By comparing reaction pathways between the two enzymes, we concluded that the major effect of the N189A point mutation is to increase the active site volume by altering the active site backbone and eliminating the Asn189 side chain. This effect causes a different NADH geometry at the reactant state, which very well explains the different reaction mechanisms between the two enzymes, as well as the disappearance of the His186 rate-promoting vibrations in the N189A mutant. The unfavorable geometry of the NADH pyridine ring induced by the N189A point mutation is the potential cause of multiple reaction pathways in N189A mutants.
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36
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Li H, Ma A. Kinetic energy flows in activated dynamics of biomolecules. J Chem Phys 2020; 153:094109. [DOI: 10.1063/5.0020275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Huiyu Li
- Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA
| | - Ao Ma
- Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA
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37
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Zhang J, Borrelli R, Tanimura Y. Proton tunneling in a two-dimensional potential energy surface with a non-linear system–bath interaction: Thermal suppression of reaction rate. J Chem Phys 2020; 152:214114. [DOI: 10.1063/5.0010580] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Jiaji Zhang
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Raffaele Borrelli
- DISAFA, University of Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, Italy
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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38
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Kim K, Plapp BV. Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer. Biochemistry 2020; 59:862-879. [PMID: 31994873 DOI: 10.1021/acs.biochem.9b01074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous studies showed that the L57F and F93W alcohol dehydrogenases catalyze the oxidation of benzyl alcohol with some quantum mechanical hydrogen tunneling, whereas the V203A enzyme has diminished tunneling. Here, steady-state kinetics for the L57F and F93W enzymes were studied, and microscopic rate constants for the ordered bi-bi mechanism were estimated from simulations of transient kinetics for the S48T, F93A, S48T/F93A, F93W, and L57F enzymes. Catalytic efficiencies for benzyl alcohol oxidation (V1/EtKb) vary over a range of ∼100-fold for the less active enzymes up to the L57F enzyme and are mostly associated with the binding of alcohol rather than the rate constants for hydride transfer. In contrast, catalytic efficiencies for benzaldehyde reduction (V2/EtKp) are ∼500-fold higher for the L57F enzyme than for the less active enzymes and are mostly associated with the rate constants for hydride transfer. Atomic-resolution structures (1.1 Å) for the F93W and L57F enzymes complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol are almost identical to previous structures for the wild-type, S48T, and V203A enzymes. Least-squares refinement with SHELXL shows that the nicotinamide ring is slightly strained in all complexes and that the apparent donor-acceptor distances from C4N of NAD to C7 of pentafluorobenzyl alcohol range from 3.28 to 3.49 Å (±0.02 Å) and are not correlated with the rate constants for hydride transfer or hydrogen tunneling. How the substitutions affect the dynamics of reorganization during hydrogen transfer and the extent of tunneling remain to be determined.
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Affiliation(s)
- Keehyuk Kim
- Department of Biochemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
| | - Bryce V Plapp
- Department of Biochemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
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39
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Pagano P, Guo Q, Ranasinghe C, Schroeder E, Robben K, Häse F, Ye H, Wickersham K, Aspuru-Guzik A, Major DT, Gakhar L, Kohen A, Cheatum CM. Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase. ACS Catal 2019; 9:11199-11206. [PMID: 33996196 PMCID: PMC8118594 DOI: 10.1021/acscatal.9b03345] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Thermal motions of enzymes have been invoked to explain the temperature dependence of kinetic isotope effects (KIE) in enzyme-catalyzed hydride transfers. Formate dehydrogenase (FDH) from Candida boidinii exhibits a temperature independent KIE that becomes temperature dependent upon mutation of hydrophobic residues in the active site. Ternary complexes of FDH that mimic the transition state structure allow investigation of how these mutations influence active-site dynamics. A combination of X-ray crystallography, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamic simulations characterize the structure and dynamics of the active site. FDH exhibits oscillatory frequency fluctuations on the picosecond timescale, and the amplitude of these fluctuations correlates with the temperature dependence of the KIE. Both the kinetic and dynamic phenomena can be reproduced computationally. These results provide experimental evidence for a connection between the temperature dependence of KIEs and motions of the active site in an enzyme-catalyzed reaction consistent with activated tunneling models of the hydride transfer reaction.
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Affiliation(s)
- Philip Pagano
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Qi Guo
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Chethya Ranasinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Evan Schroeder
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Kevin Robben
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Florian Häse
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Hepeng Ye
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Kyle Wickersham
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
- Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada
| | - Dan T. Major
- Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Lokesh Gakhar
- Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
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40
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Ranasinghe C, Pagano P, Sapienza PJ, Lee AL, Kohen A, Cheatum CM. Isotopic Labeling of Formate Dehydrogenase Perturbs the Protein Dynamics. J Phys Chem B 2019; 123:10403-10409. [PMID: 31696711 DOI: 10.1021/acs.jpcb.9b08426] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isotope substitution of enzymes has become a means of addressing the participation of protein motions in enzyme-catalyzed reactions. The idea is that only the enzyme mass will be altered and not the electrostatics, so that the protein dynamics are essentially the same but at lower frequencies because of the mass change. In this study, we variably label all carbon atoms in formate dehydrogenase (FDH) with 13C, all nitrogen atoms with 15N, and all nonexchangeable hydrogen atoms with deuterium and investigate the impact that isotopic substitution has on the dynamics at the active site by two-dimensional infrared spectroscopy and compare with the measurements of the temperature dependence of the intrinsic kinetic isotope effects (KIEs). We show that 15N labeling of FDH has the largest effect and makes the active site more heterogeneous, whereas the addition of nonexchangeable deuterium appears to have the opposite effect of 15N on active-site dynamics, resulting in a behavior similar to that of native FDH. Nevertheless, the temperature dependence of the KIEs shows a monotonic trend with protein mass that does not correspond with the changes in dynamics. These results suggest that isotope labeling has more than just a mass effect on enzyme dynamics and may influence electrostatics in ways that complicate the interpretation of the protein isotope effect.
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Affiliation(s)
- Chethya Ranasinghe
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242-1727 , United States
| | - Philip Pagano
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242-1727 , United States
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Andrew L Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Amnon Kohen
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242-1727 , United States
| | - Christopher M Cheatum
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242-1727 , United States
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41
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Egawa T, Deng H, Chang E, Callender R. Effect of Protein Isotope Labeling on the Catalytic Mechanism of Lactate Dehydrogenase. J Phys Chem B 2019; 123:9801-9808. [PMID: 31644296 DOI: 10.1021/acs.jpcb.9b08656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate how isotopic labeling of the enzyme lactate dehydrogenase (LDH) affects its function. LDH is of special interest because there exists a line of residues spanning the protein that are involved in the transition state (TS) of the chemical reaction coordinate (so-called promoting vibration). Hence, studies have been carried out on this protein (as well as others) using labeled protein (so-called heavy protein) along with measurements of single turnover kcat yielding a KIE (=kcatlight/kcatheavy) aimed at understanding the effect of labeling generally and more specifically this line of residues. Here, it is shown that 13C, 15N, and 2H atom labeling of hhLDH (human heart) affects its internal structure which in turn affects its dynamics and catalytic mechanism. Spectral studies employing advanced FTIR difference spectroscopy show that the height of the electronic potential surface of the TS is lowered (probably by ground state destabilization) by labeling. Moreover, laser-induced T-jump relaxation kinetic spectroscopy shows that the microsecond to millisecond nuclear motions internal to the protein are affected by labeling. While the effects are small, they are sufficient to contribute to the observed KIE values as well or even more than promoting vibration effects.
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Affiliation(s)
- Tsuyoshi Egawa
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
| | - Hua Deng
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
| | - Eric Chang
- Department of Chemistry and Physical Sciences , Pace University , New York , New York 10038 , United States
| | - Robert Callender
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
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42
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Machado MR, Zeida A, Darré L, Pantano S. From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field. Interface Focus 2019; 9:20180085. [PMID: 31065347 PMCID: PMC6501346 DOI: 10.1098/rsfs.2018.0085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2019] [Indexed: 12/11/2022] Open
Abstract
Modern molecular and cellular biology profits from astonishing resolution structural methods, currently even reaching the whole cell level. This is encompassed by the development of computational methods providing a deep view into the structure and dynamics of molecular processes happening at very different scales in time and space. Linking such scales is of paramount importance when aiming at far-reaching biological questions. Computational methods at the interface between classical and coarse-grained resolutions are gaining momentum with several research groups dedicating important efforts to their development and tuning. An overview of such methods is addressed herein, with special emphasis on the SIRAH force field for coarse-grained and multi-scale simulations. Moreover, we provide proof of concept calculations on the implementation of a multi-scale simulation scheme including quantum calculations on a classical fine-grained/coarse-grained representation of double-stranded DNA. This opens the possibility to include the effect of large conformational fluctuations in chromatin segments on, for instance, the reactivity of particular base pairs within the same simulation framework.
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Affiliation(s)
- Matías R. Machado
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Leonardo Darré
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
- Institut Pasteur de Montevideo, Functional Genomics Unit, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
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43
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Czarnota S, Johannissen LO, Baxter NJ, Rummel F, Wilson AL, Cliff MJ, Levy CW, Scrutton NS, Waltho JP, Hay S. Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol- O-methyltransferase. ACS Catal 2019; 9:4394-4401. [PMID: 31080692 PMCID: PMC6503465 DOI: 10.1021/acscatal.9b00174] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/26/2019] [Indexed: 12/18/2022]
Abstract
Catechol-O-methyltransferase (COMT) is a model S-adenosyl-l-methionine (SAM) dependent methyl transferase, which catalyzes the methylation of catecholamine neurotransmitters such as dopamine in the primary pathway of neurotransmitter deactivation in animals. Despite extensive study, there is no consensus view of the physical basis of catalysis in COMT. Further progress requires experimental data that directly probes active site geometry, protein dynamics and electrostatics, ideally in a range of positions along the reaction coordinate. Here we establish that sinefungin, a fungal-derived inhibitor of SAM-dependent enzymes that possess transition state-like charge on the transferring group, can be used as a transition state analog of COMT when combined with a catechol. X-ray crystal structures and NMR backbone assignments of the ternary complexes of the soluble form of human COMT containing dinitrocatechol, Mg2+ and SAM or sinefungin were determined. Comparison and further analysis with the aid of density functional theory calculations and molecular dynamics simulations provides evidence for active site "compaction", which is driven by electrostatic stabilization between the transferring methyl group and "equatorial" active site residues that are orthogonal to the donor-acceptor (pseudo reaction) coordinate. We propose that upon catecholamine binding and subsequent proton transfer to Lys 144, the enzyme becomes geometrically preorganized, with little further movement along the donor-acceptor coordinate required for methyl transfer. Catalysis is then largely facilitated through stabilization of the developing charge on the transferring methyl group via "equatorial" H-bonding and electrostatic interactions orthogonal to the donor-acceptor coordinate.
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Affiliation(s)
- Sylwia Czarnota
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nicola J. Baxter
- Krebs
Institute for Biomolecular Research, Department of Molecular Biology
and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Felix Rummel
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Alex L. Wilson
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Matthew J. Cliff
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Colin W. Levy
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Jonathan P. Waltho
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Krebs
Institute for Biomolecular Research, Department of Molecular Biology
and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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44
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Deng H, Dyer RB, Callender R. Active-Site Glu165 Activation in Triosephosphate Isomerase and Its Deprotonation Kinetics. J Phys Chem B 2019; 123:4230-4241. [PMID: 31013084 DOI: 10.1021/acs.jpcb.9b02981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Triosephosphate isomerase (TIM) catalyzes the interconversion between dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (GAP) via an enediol(ate) intermediate. The active-site residue Glu165 serves as the catalytic base during catalysis. It abstracts a proton from C1 carbon of DHAP to form the reaction intermediate and donates a proton to C2 carbon of the intermediate to form product GAP. Our difference Fourier transform infrared spectroscopy studies on the yeast TIM (YeTIM)/phosphate complex revealed a C═O stretch band at 1706 cm-1 from the protonated Glu165 carboxyl group at pH 7.5, indicating that the p Ka of the catalytic base is increased by >3.0 pH units upon phosphate binding, and that the Glu165 carboxyl environment in the complex is still hydrophilic in spite of the increased p Ka. Hence, the results show that the binding of the phosphodianion group is part of the activation mechanism which involves the p Ka elevation of the catalytic base Glu165. The deprotonation kinetics of Glu165 in the μs to ms time range were determined via infrared (IR) T-jump studies on the YeTIM/phosphate and ("heavy enzyme") [U-13C,-15N]YeTIM/phosphate complexes. The slower deprotonation kinetics in the ms time scale is due to phosphate dissociation modulated by the loop motion, which slows down by enzyme mass increase to show a normal heavy enzyme kinetic isotope effect (KIE) ∼1.2 (i.e., slower rate in the heavy enzyme). The faster deprotonation kinetics in the tens of μs time scale is assigned to temperature-induced p Ka decrease, while phosphate is still bound, and it shows an inverse heavy enzyme KIE ∼0.89 (faster rate in the heavy enzyme). The IR static and T-jump spectroscopy provides atomic-level resolution of the catalytic mechanism because of its ability to directly observe the bond breaking/forming process.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx, New York 10461 , United States
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Robert Callender
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx, New York 10461 , United States
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Abstract
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The enormous rate accelerations observed
for many enzyme catalysts
are due to strong stabilizing interactions between the protein and
reaction transition state. The defining property of these catalysts
is their specificity for binding the transition state with a much
higher affinity than substrate. Experimental results are presented
which show that the phosphodianion-binding energy of phosphate monoester
substrates is used to drive conversion of their protein catalysts
from flexible and entropically rich ground states to stiff and catalytically
active Michaelis complexes. These results are generalized to other
enzyme-catalyzed reactions. The existence of many enzymes in flexible,
entropically rich, and inactive ground states provides a mechanism
for utilization of ligand-binding energy to mold these catalysts into
stiff and active forms. This reduces the substrate-binding energy
expressed at the Michaelis complex, while enabling the full and specific
expression of large transition-state binding energies. Evidence is
presented that the complexity of enzyme conformational changes increases
with increases in the enzymatic rate acceleration. The requirement
that a large fraction of the total substrate-binding energy be utilized
to drive conformational changes of floppy enzymes is proposed to favor
the selection and evolution of protein folds with multiple flexible
unstructured loops, such as the TIM-barrel fold. The effect of protein
motions on the kinetic parameters for enzymes that undergo ligand-driven
conformational changes is considered. The results of computational
studies to model the complex ligand-driven conformational change in
catalysis by triosephosphate isomerase are presented.
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Affiliation(s)
- John P Richard
- Department of Chemistry , SUNY, University at Buffalo , Buffalo , New York 14260-3000 , United States
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Iorgu AI, Baxter NJ, Cliff MJ, Levy C, Waltho JP, Hay S, Scrutton NS. Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes. ACS Catal 2018; 8:11589-11599. [PMID: 31119061 PMCID: PMC6516726 DOI: 10.1021/acscatal.8b02810] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/23/2018] [Indexed: 11/28/2022]
Abstract
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Many enzymes that
catalyze hydride transfer reactions work via
a mechanism dominated by quantum mechanical tunneling. The involvement
of fast vibrational modes of the reactive complex is often inferred
in these reactions, as in the case of the NAD(P)H-dependent pentaerythritol
tetranitrate reductase (PETNR). Herein, we interrogated the H-transfer
mechanism in PETNR by designing conservative (L25I and I107L) and
side chain shortening (L25A and I107A) PETNR variants and using a
combination of experimental approaches (stopped-flow rapid kinetics,
X-ray crystallography, isotope/temperature dependence studies of H-transfer
and NMR spectroscopy). X-ray data show subtle changes in the local
environment of the targeted side chains but no major structural perturbation
caused by mutagenesis of these two second sphere active site residues.
However, temperature dependence studies of H-transfer revealed a coenzyme-specific
and complex thermodynamic equilibrium between different reactive configurations
in PETNR–coenzyme complexes. We find that mutagenesis of these
second sphere “noncatalytic” residues affects differently
the reactivity of PETNR with NADPH and NADH coenzymes. We attribute
this to subtle, dynamic structural changes in the PETNR active site,
the effects of which impact differently in the nonequivalent reactive
geometries of PETNR−NADH and PETNR−NADPH complexes.
This inference is confirmed through changes observed in the NMR chemical
shift data for PETNR complexes with unreactive 1,4,5,6-tetrahydro-NAD(P)
analogues. We show that H-transfer rates can (to some extent) be buffered
through entropy–enthalpy compensation, but that use of integrated
experimental tools reveals hidden complexities that implicate a role
for dynamics in this relatively simple H-transfer reaction. Similar
approaches are likely to be informative in other enzymes to understand
the relative importance of (distal) hydrophobic side chains and dynamics
in controlling the rates of enzymatic H-transfer.
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Affiliation(s)
- Andreea I. Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicola J. Baxter
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Colin Levy
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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Affiliation(s)
- Valerie Vaissier Welborn
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California 94720, United States
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Jones HBL, Crean RM, Matthews C, Troya AB, Danson MJ, Bull SD, Arcus VL, van der Kamp MW, Pudney CR. Uncovering the Relationship between the Change in Heat Capacity for Enzyme Catalysis and Vibrational Frequency through Isotope Effect Studies. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Vickery L. Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton 3240, New Zealand
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
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