1
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Gao S, Wu XT, Zhang W, Richardson T, Barrow SL, Thompson-Kucera CA, Iavarone AT, Klinman JP. Temporal Resolution of Activity-Related Solvation Dynamics in the TIM Barrel Enzyme Murine Adenosine Deaminase. ACS Catal 2024; 14:4554-4567. [PMID: 39099600 PMCID: PMC11296675 DOI: 10.1021/acscatal.3c02687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Murine adenosine deaminase (mADA) is a prototypic system for studying the thermal activation of active site chemistry within the TIM barrel family of enzyme reactions. Previous temperature-dependent hydrogen deuterium exchange studies under various conditions have identified interconnected thermal networks for heat transfer from opposing protein-solvent interfaces to active site residues in mADA. One of these interfaces contains a solvent exposed helix-loop-helix moiety that presents the hydrophobic face of its long α-helix to the backside of bound substrate. Herein we pursue the time and temperature dependence of solvation dynamics at the surface of mADA, for comparison to established kinetic parameters that represent active site chemistry. We first created a modified protein devoid of native tryptophans with close to native kinetic behavior. Single site-specific tryptophan mutants were back inserted into each of the four positions where native tryptophans reside. Measurements of nanosecond fluorescence relaxation lifetimes and Stokes shift decays, that reflect time dependent environmental reoroganization around the photo-excited state of Trp*, display minimal temperature dependences. These regions serve as controls for the behavior of a new single tryptophan inserted into a solvent exposed region near the helix-loop-helix moiety located behind the bound substrate, Lys54Trp. This installed Trp displays a significantly elevated value for Ea ( k Stokes shift ) ; further, when Phe61 within the long helix positioned behind bound substrate is replaced by a series of aliphatic hydrophobic side chains, the trends in Ea ( k Stokes shift ) mirror the earlier reported impact of the same series of function-altering hydrophobic side chains on the activation energy of catalysis, Ea ( k cat ) .The reported experimental findings implicate a solvent initiated and rapid (>ns) protein restructuring that contributes to the enthalpic activation barrier to catalysis in mADA.
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Affiliation(s)
- Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Xin Ting Wu
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Tyre Richardson
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Samuel L. Barrow
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Christian A. Thompson-Kucera
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Anthony T. Iavarone
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
| | - Judith P. Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
- California Institute for Quantitative Biosciences, and University of California, Berkeley, Berkeley, California, 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, United States
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2
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Zaragoza JPT, Offenbacher AR, Hu S, Gee CL, Firestein ZM, Minnetian N, Deng Z, Fan F, Iavarone AT, Klinman JP. Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase. Proc Natl Acad Sci U S A 2023; 120:e2211630120. [PMID: 36867685 PMCID: PMC10013837 DOI: 10.1073/pnas.2211630120] [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: 07/06/2022] [Accepted: 01/27/2023] [Indexed: 03/05/2023] Open
Abstract
The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen-deuterium exchange experiments to define a catalytically-linked, radiating cone of aliphatic side chains that connects an active site iron center of SLO to the protein-solvent interface. Employing eight variants of SLO that have been appended with a fluorescent probe at the identified surface loop, nanosecond fluorescence Stokes shifts have been measured. We report a remarkable identity of the energies of activation (Ea) for the Stokes shifts decay rates and the millisecond C-H bond cleavage step that is restricted to side chain mutants within an identified thermal network. These findings implicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, the presented data implicate a thermally initiated, cooperative protein reorganization that occurs on a timescale faster than nanosecond and represents the enthalpic barrier to the reaction of SLO.
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Affiliation(s)
- Jan Paulo T. Zaragoza
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Adam R. Offenbacher
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, East Carolina University, Greenville, NC27858
| | - Shenshen Hu
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Christine L. Gee
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA94720
| | | | - Natalie Minnetian
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Zhenyu Deng
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Flora Fan
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
| | - Judith P. Klinman
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA94720
- Department of Chemistry, University of California Berkeley, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA94720
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3
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Gao S, Zhang W, Barrow SL, Iavarone AT, Klinman JP. Temperature-dependent hydrogen deuterium exchange shows impact of analog binding on adenosine deaminase flexibility but not embedded thermal networks. J Biol Chem 2022; 298:102350. [PMID: 35933011 PMCID: PMC9483566 DOI: 10.1016/j.jbc.2022.102350] [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: 04/04/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
The analysis of hydrogen deuterium exchange by mass spectrometry as a function of temperature and mutation (TDHDX-MS) has emerged as a generic and efficient tool for the spatial resolution of protein networks that are proposed to function in the thermal activation of catalysis. In this work, we extend TDHDX from apo-enzyme structures to protein-ligand complexes. Using adenosine deaminase as a prototype, we compared the impacts of a substrate analog (1-deaza-adenosine or DAA) and a very tight-binding inhibitor/transition state analog (pentostatin) at single and multiple temperatures. At a single temperature, we observed different HDX-MS properties for the two ligands, as expected from their 106-fold differences in strength of binding. By contrast, analogous patterns for TDHDX-MS emerge in the presence of both DAA and pentostatin, indicating similar impacts of either ligand on the enthalpic barriers for local protein unfolding. We extended TDHDX to a function-altering mutant of adenosine deaminase in the presence of pentostatin and revealed a protein thermal network that is highly similar to that previously reported for the apo-enzyme (Gao et al., 2020, JACS 142, 19936-19949). Finally, we discuss the differential impacts of pentostatin binding on overall protein flexibility vs. site-specific thermal transfer pathways in the context of models for substrate-induced changes to a distributed protein conformational landscape that act in synergy with embedded protein thermal networks to achieve efficient catalysis.
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Affiliation(s)
- Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Samuel L Barrow
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Anthony T Iavarone
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94720, United States; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, United States.
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4
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Dong M. A Minireview on Temperature Dependent Protein Conformational Sampling. Protein J 2021; 40:545-553. [PMID: 34181188 DOI: 10.1007/s10930-021-10012-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2021] [Indexed: 12/01/2022]
Abstract
In this minireview we discuss the role of the more subtle conformational change-protein conformational sampling and connect it to the classic relationship of protein structure and function. The theory of pre-existing functional states of protein are discussed in context of alternate protein conformational sampling. Last, we discuss how temperature, ligand binding and mutations affect the protein conformational sampling mode which is linked to the protein function regulation. The review includes several protein systems that showed temperature dependent protein conformational sampling. We also specifically included two enzyme systems, thermophilic alcohol dehydrogenase (ht-ADH) and thermolysin which we previously studied when discussing temperature dependent protein conformational sampling.
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Affiliation(s)
- Ming Dong
- Department of Chemistry, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC, 27410, USA.
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5
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Ghosh AK, Schramm VL. Protein Mass-Modulated Effects in Alkaline Phosphatase. Biochemistry 2021; 60:118-124. [PMID: 33410323 PMCID: PMC8340299 DOI: 10.1021/acs.biochem.0c00917] [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: 11/30/2022]
Abstract
Recent experimental studies engaging isotopically substituted protein (heavy protein) have revealed that many, but not all, enzymatic systems exhibit altered chemical steps in response to an altered mass. The results have been interpreted as femtosecond protein dynamics at the active site being linked (or not) to transition-state barrier crossing. An altered enzyme mass can influence several kinetic parameters (kcat, Km, and kchem) in amounts of ≤30% relative to light enzymes. An early report on deuterium-labeled Escherichia coli alkaline phosphatase (AP) showed an unusually large enzyme kinetic isotope effect on kcat. We examined steady-state and chemical step properties of native AP, [2H]AP, and [2H,13C,15N]AP to characterize the role of heavy enzyme protein dynamics in reactions catalyzed by AP. Both [2H]- and [2H,13C,15N]APs showed unaltered steady-state and single-turnover rate constants. These findings characterize AP as one of the enzymes in which mass-dependent catalytic site dynamics is dominated by reactant-linked atomic motions. Two catalytic site zinc ions activate the oxygen nucleophiles in the catalytic site of AP. The mass of the zinc ions is unchanged in light and heavy APs. They are essentially linked to catalysis and provide a possible explanation for the loss of linkage between catalysis and protein mass in these enzymes.
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Affiliation(s)
- Ananda K Ghosh
- 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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6
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Liu F, Zhang J. Nano-second protein dynamics of key residue at Position 38 in catechol-O-methyltransferase system: a time-resolved fluorescence study. J Biochem 2020; 168:417-425. [DOI: 10.1093/jb/mvaa063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/17/2020] [Indexed: 02/02/2023] Open
Abstract
AbstractHuman catechol-O-methyltransferase, a key enzyme related to neurotransmitter metabolism, catalyses a methyl transfer from S-adenosylmethionine to catechol. Although extensive studies aim to understand the enzyme mechanisms, the connection of protein dynamics and enzyme catalysis is still not clear. Here, W38in (Trp143Phe) and W38in/Y68A (Trp143Phe with Tyr68Ala) mutants were carried out to study the relationship of dynamics and catalysis in nano-second timescale using time-resolved fluorescence lifetimes and Stokes shifts in various solvents. The comprehensive data implied the mutant W38in/Y68A with lower activity is more rigid than the ‘WT’−W38in, suggesting the importance of flexibility at residue 38 to maintain the optimal catalysis.
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Affiliation(s)
- Fan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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7
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Zhang J, Balsbaugh JL, Gao S, Ahn NG, Klinman JP. Hydrogen deuterium exchange defines catalytically linked regions of protein flexibility in the catechol O-methyltransferase reaction. Proc Natl Acad Sci U S A 2020; 117:10797-10805. [PMID: 32371482 PMCID: PMC7245127 DOI: 10.1073/pnas.1917219117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Human catechol O-methyltransferase (COMT) has emerged as a model for understanding enzyme-catalyzed methyl transfer from S-adenosylmethionine (AdoMet) to small-molecule catecholate acceptors. Mutation of a single residue (tyrosine 68) behind the methyl-bearing sulfonium of AdoMet was previously shown to impair COMT activity by interfering with methyl donor-acceptor compaction within the activated ground state of the wild type enzyme [J. Zhang, H. J. Kulik, T. J. Martinez, J. P. Klinman, Proc. Natl. Acad. Sci. U.S.A. 112, 7954-7959 (2015)]. This predicts the involvement of spatially defined protein dynamical effects that further tune the donor/acceptor distance and geometry as well as the electrostatics of the reactants. Here, we present a hydrogen/deuterium exchange (HDX)-mass spectrometric study of wild type and mutant COMT, comparing temperature dependences of HDX against corresponding kinetic and cofactor binding parameters. The data show that the impaired Tyr68Ala mutant displays similar breaks in Arrhenius plots of both kinetic and HDX properties that are absent in the wild type enzyme. The spatial resolution of HDX below a break point of 15-20 °C indicates changes in flexibility across ∼40% of the protein structure that is confined primarily to the periphery of the AdoMet binding site. Above 20 °C, Tyr68Ala behaves more like WT in HDX, but its rate and enthalpic barrier remain significantly altered. The impairment of catalysis by Tyr68Ala can be understood in the context of a mutationally induced alteration in protein motions that becomes manifest along and perpendicular to the primary group transfer coordinate.
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Affiliation(s)
- Jianyu Zhang
- Department of Chemistry, University of California, Berkeley, CA 94720
- The California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Jeremy L Balsbaugh
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309
| | - Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, CA 94720
- The California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309;
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, CA 94720;
- The California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
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8
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Abstract
This first serious attempt at an autobiographical accounting has forced me to sit still long enough to compile my thoughts about a long personal and scientific journey. I especially hope that my trajectory will be of interest and perhaps beneficial to much younger women who are just getting started in their careers. To paraphrase from Virginia Woolf's writings in A Room of One's Own at the beginning of the 20th century, "for most of history Anonymous was a Woman." However, Ms. Woolf is also quoted as saying "nothing has really happened until it has been described," a harbinger of the enormous historical changes that were about to be enacted and recorded by women in the sciences and other disciplines. The progress in my chosen field of study-the chemical basis of enzyme action-has also been remarkable, from the first description of an enzyme's 3D structure to a growing and deep understanding of the origins of enzyme catalysis.
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Affiliation(s)
- Judith P Klinman
- Department of Chemistry, Department of Molecular and Cell Biology, and California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA;
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9
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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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10
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Zaragoza JPT, Nguy A, Minnetian N, Deng Z, Iavarone AT, Offenbacher AR, Klinman JP. Detecting and Characterizing the Kinetic Activation of Thermal Networks in Proteins: Thermal Transfer from a Distal, Solvent-Exposed Loop to the Active Site in Soybean Lipoxygenase. J Phys Chem B 2019; 123:8662-8674. [PMID: 31580070 PMCID: PMC6944211 DOI: 10.1021/acs.jpcb.9b07228] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rate-limiting chemical reaction catalyzed by soybean lipoxygenase (SLO) involves quantum mechanical tunneling of a hydrogen atom from substrate to its active site ferric-hydroxide cofactor. SLO has emerged as a prototypical system for linking the thermal activation of a protein scaffold to the efficiency of active site chemistry. Significantly, hydrogen-deuterium exchange-mass spectrometry (HDX-MS) experiments on wild type and mutant forms of SLO have uncovered trends in the enthalpic barriers for HDX within a solvent-exposed loop (positions 317-334) that correlate well with trends in the corresponding enthalpic barriers for kcat. A model for this behavior posits that collisions between water and loop 317-334 initiate thermal activation at the protein surface that is then propagated 15-34 Å inward toward the reactive carbon of substrate in proximity to the iron catalyst. In this study, we have prepared protein samples containing cysteine residues either at the tip of the loop 317-334 (Q322C) or on a control loop, 586-603 (S596C). Chemical modification of cysteines with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (Badan, BD) provides site-specific probes for the measurement of fluorescence relaxation lifetimes and Stokes shift decays as a function of temperature. Computational studies indicate that surface water structure is likely to be largely preserved in each sample. While both loops exhibit temperature-independent fluorescence relaxation lifetimes as do the Stokes shifts for S596C-BD, the activation enthalpy for the nanosecond solvent reorganization at Q322C-BD (Ea(ksolv) = 2.8(0.9) kcal/mol)) approximates the enthalpy of activation for catalytic C-H activation (Ea(kcat) = 2.3(0.4) kcal/mol). This study establishes and validates the methodology for measuring rates of rapid local motions at the protein/solvent interface of SLO. These new findings, when combined with previously published correlations between protein motions and the rate-limiting hydride transfer in a thermophilic alcohol dehydrogenase, provide experimental evidence for thermally induced "protein quakes" as the origin of enthalpic barriers in catalysis.
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Affiliation(s)
- Jan Paulo T. Zaragoza
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Andy Nguy
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Natalie Minnetian
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Zhenyu Deng
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Adam R. Offenbacher
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
| | - Judith P. Klinman
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, United States
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11
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Pinney MM, Natarajan A, Yabukarski F, Sanchez DM, Liu F, Liang R, Doukov T, Schwans JP, Martinez TJ, Herschlag D. Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein. J Am Chem Soc 2018; 140:9827-9843. [DOI: 10.1021/jacs.8b01596] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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12
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Behiry EM, Ruiz-Pernia JJ, Luk L, Tuñón I, Moliner V, Allemann RK. Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Enas M. Behiry
- School of Chemistry; Cardiff University; Park Place Cardiff CF10 3AT UK
| | | | - Louis Luk
- School of Chemistry; Cardiff University; Park Place Cardiff CF10 3AT UK
| | - Iñaki Tuñón
- Departament de Química Física; Universitat de València; 46100 Burjassot Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica; Universitat Jaume I; 12071 Castelló Spain
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13
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Behiry EM, Ruiz‐Pernia JJ, Luk L, Tuñón I, Moliner V, Allemann RK. Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State. Angew Chem Int Ed Engl 2018; 57:3128-3131. [PMID: 29341402 PMCID: PMC5861672 DOI: 10.1002/anie.201712826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Indexed: 11/10/2022]
Abstract
The origin of substrate preference in promiscuous enzymes was investigated by enzyme isotope labelling of the alcohol dehydrogenase from Geobacillus stearothermophilus (BsADH). At physiological temperature, protein dynamic coupling to the reaction coordinate was insignificant. However, the extent of dynamic coupling was highly substrate-dependent at lower temperatures. For benzyl alcohol, an enzyme isotope effect larger than unity was observed, whereas the enzyme isotope effect was close to unity for isopropanol. Frequency motion analysis on the transition states revealed that residues surrounding the active site undergo substantial displacement during catalysis for sterically bulky alcohols. BsADH prefers smaller substrates, which cause less protein friction along the reaction coordinate and reduced frequencies of dynamic recrossing. This hypothesis allows a prediction of the trend of enzyme isotope effects for a wide variety of substrates.
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Affiliation(s)
- Enas M. Behiry
- School of ChemistryCardiff UniversityPark PlaceCardiffCF10 3ATUK
| | | | - Louis Luk
- School of ChemistryCardiff UniversityPark PlaceCardiffCF10 3ATUK
| | - Iñaki Tuñón
- Departament de Química FísicaUniversitat de València46100BurjassotSpain
| | - Vicent Moliner
- Departament de Química Física i AnalíticaUniversitat Jaume I12071CastellóSpain
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14
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Shanmuganatham KK, Wallace RS, Ting-I Lee A, Plapp BV. Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Protein Sci 2018; 27:750-768. [PMID: 29271062 DOI: 10.1002/pro.3370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 01/06/2023]
Abstract
The dynamics of enzyme catalysis range from the slow time scale (∼ms) for substrate binding and conformational changes to the fast time (∼ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysis by alcohol dehydrogenase was tested by substituting five different, conserved amino acid residues that are distal from the active site and located in the hinge region for the conformational change or in hydrophobic clusters. X-ray crystallography shows that the structures for the G173A, V197I, I220 (V, L, or F), V222I, and F322L enzymes complexed with NAD+ and an analogue of benzyl alcohol are almost identical, except for small perturbations at the sites of substitution. The enzymes have very similar kinetic constants for the oxidation of benzyl alcohol and reduction of benzaldehyde as compared to the wild-type enzyme, and the rates of conformational changes are not altered. Less conservative substitutions of these amino acid residues, such as G173(V, E, K, or R), V197(G, S, or T), I220(G, S, T, or N), and V222(G, S, or T) produced unstable or poorly expressed proteins, indicating that the residues are critical for global stability. The enzyme scaffold accommodates conservative substitutions of distal residues, and there is no evidence that fast, global dynamics significantly affect the rate constants for hydride transfers. In contrast, other studies show that proximal residues significantly participate in catalysis.
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Affiliation(s)
- Karthik K Shanmuganatham
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Diagnostic Virology Laboratory, USDA, Ames, IA, 50010
| | - Rachel S Wallace
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Ann Ting-I Lee
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,No 92, Jing Mao 1st Rd., Taichung, Taiwan, 406, Republic of China
| | - Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109
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15
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Vaughn MB, Zhang J, Spiro TG, Dyer RB, Klinman JP. Activity-Related Microsecond Dynamics Revealed by Temperature-Jump Förster Resonance Energy Transfer Measurements on Thermophilic Alcohol Dehydrogenase. J Am Chem Soc 2018; 140:900-903. [PMID: 29323490 DOI: 10.1021/jacs.7b12369] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previous studies of a thermophilic alcohol dehydrogenase (ht-ADH) demonstrated a range of discontinuous transitions at 30 °C that include catalysis, kinetic isotope effects, protein hydrogen-deuterium exchange rates, and intrinsic fluorescence properties. Using the Förster resonance energy transfer response from a Trp-NADH donor-acceptor pair in T-jump studies of ht-ADH, we now report microsecond protein motions that can be directly related to active site chemistry. Two distinctive transients are observed: a slow, kinetic process lacking a temperature break, together with a faster transient that is only detectable above 30 °C. The latter establishes a link between enzyme activity and microsecond protein motions near the cofactor binding site, in a region distinct from a previously detected protein network that communicates with the substrate binding site. Though evidence of direct dynamical links between microsecond protein motions and active site bond cleavage events is extremely rare, these studies highlight the potential of T-jump measurements to uncover such properties.
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Affiliation(s)
- Morgan B Vaughn
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | | | - Thomas G Spiro
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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16
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Klinman JP, Offenbacher AR, Hu S. Origins of Enzyme Catalysis: Experimental Findings for C-H Activation, New Models, and Their Relevance to Prevailing Theoretical Constructs. J Am Chem Soc 2017; 139:18409-18427. [PMID: 29244501 PMCID: PMC5812730 DOI: 10.1021/jacs.7b08418] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The physical basis for enzymatic rate accelerations is a subject of great fundamental interest and of direct relevance to areas that include the de novo design of green catalysts and the pursuit of new drug regimens. Extensive investigations of C-H activating systems have provided considerable insight into the relationship between an enzyme's overall structure and the catalytic chemistry at its active site. This Perspective highlights recent experimental data for two members of distinct, yet iconic C-H activation enzyme classes, lipoxygenases and prokaryotic alcohol dehydrogenases. The data necessitate a reformulation of the dominant textbook definition of biological catalysis. A multidimensional model emerges that incorporates a range of protein motions that can be parsed into a combination of global stochastic conformational thermal fluctuations and local donor-acceptor distance sampling. These motions are needed to achieve a high degree of precision with regard to internuclear distances, geometries, and charges within the active site. The available model also suggests a physical framework for understanding the empirical enthalpic barrier in enzyme-catalyzed processes. We conclude by addressing the often conflicting interface between computational and experimental chemists, emphasizing the need for computation to predict experimental results in advance of their measurement.
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Affiliation(s)
- Judith P Klinman
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
| | - Adam R Offenbacher
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
| | - Shenshen Hu
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
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17
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Seyedi S, Matyushov DV. Ergodicity breaking of iron displacement in heme proteins. SOFT MATTER 2017; 13:8188-8201. [PMID: 29082406 DOI: 10.1039/c7sm01561e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by the softening of the force constant for atomic/molecular displacements by electrostatic and van der Waals forces from the protein-water thermal bath. Displacement softening passes through a nonergodic dynamical transition when the relaxation time of the force-force correlation function enters, with increasing temperature, the instrumental observation window. Two crossover temperatures are identified. The lower crossover, presently connected to the glass transition, is related to the dynamical unfreezing of rotations of water molecules within nanodomains polarized by charged surface residues of the protein. The higher crossover temperature, usually assigned to the dynamical transition, marks the onset of water translations. All crossovers are ergodicity breaking transitions depending on the corresponding observation windows. Allowing stretched exponential relaxation of the protein-water thermal bath significantly improves the theory-experiment agreement when applied to solid protein samples studied by Mössbauer spectroscopy.
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Affiliation(s)
- Salman Seyedi
- Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287, USA
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18
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Longbotham JE, Hardman SJO, Görlich S, Scrutton NS, Hay S. Untangling Heavy Protein and Cofactor Isotope Effects on Enzyme-Catalyzed Hydride Transfer. J Am Chem Soc 2016; 138:13693-13699. [PMID: 27676389 DOI: 10.1021/jacs.6b07852] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
"Heavy" (isotopically labeled) enzyme isotope effects offer a direct experimental probe of the role of protein vibrations on enzyme-catalyzed reactions. Here we have developed a strategy to generate isotopologues of the flavoenzyme pentaerythritol tetranitrate reductase (PETNR) where the protein and/or intrinsic flavin mononucleotide (FMN) cofactor are isotopically labeled with 2H, 15N, and 13C. Both the protein and cofactor contribute to the enzyme isotope effect on the reductive hydride transfer reaction, but their contributions are not additive and may partially cancel each other out. However, the isotope effect specifically arising from the FMN suggests that vibrations local to the active site play a role in the hydride transfer chemistry, while the protein-only "heavy enzyme" effect demonstrates that protein vibrations contribute to catalysis in PETNR. In all cases, enthalpy-entropy compensation plays a major role in minimizing the magnitude of "heavy enzyme" isotope effects. Fluorescence lifetime measurements of the intrinsic flavin mononucleotide show marked differences between "light" and "heavy" enzymes on the nanosecond-picosecond time scale, suggesting relevant time scale(s) for those vibrations implicated in the "heavy enzyme" isotope effect on the PETNR reaction.
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Affiliation(s)
- James E Longbotham
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Samantha J O Hardman
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Stefan Görlich
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nigel S Scrutton
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
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19
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Meadows CW, Balakrishnan G, Kier BL, Spiro TG, Klinman JP. Temperature-Jump Fluorescence Provides Evidence for Fully Reversible Microsecond Dynamics in a Thermophilic Alcohol Dehydrogenase. J Am Chem Soc 2015. [PMID: 26223665 PMCID: PMC4970856 DOI: 10.1021/jacs.5b04413] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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Protein
dynamics on the microsecond (μs) time scale were
investigated by temperature-jump fluorescence spectroscopy as a function
of temperature in two variants of a thermophilic alcohol dehydrogenase:
W87F and W87F:H43A. Both mutants exhibit a fast, temperature-independent
μs decrease in fluorescence followed by a slower full recovery
of the initial fluorescence. The results, which rule out an ionizing
histidine as the origin of the fluorescence quenching, are discussed
in the context of a Trp49-containing dimer interface that acts as
a conduit for thermally activated structural change within the protein
interior.
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Affiliation(s)
| | - Gurusamy Balakrishnan
- ∥Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Brandon L Kier
- ∥Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Thomas G Spiro
- ∥Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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20
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Zhang J, Kulik HJ, Martinez TJ, Klinman JP. Mediation of donor-acceptor distance in an enzymatic methyl transfer reaction. Proc Natl Acad Sci U S A 2015; 112:7954-9. [PMID: 26080432 PMCID: PMC4491759 DOI: 10.1073/pnas.1506792112] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Enzymatic methyl transfer, catalyzed by catechol-O-methyltransferase (COMT), is investigated using binding isotope effects (BIEs), time-resolved fluorescence lifetimes, Stokes shifts, and extended graphics processing unit (GPU)-based quantum mechanics/molecular mechanics (QM/MM) approaches. The WT enzyme is compared with mutants at Tyr68, a conserved residue that is located behind the reactive sulfur of cofactor. Small (>1) BIEs are observed for an S-adenosylmethionine (AdoMet)-binary and abortive ternary complex containing 8-hydroxyquinoline, and contrast with previously reported inverse (<1) kinetic isotope effects (KIEs). Extended GPU-based computational studies of a ternary complex containing catecholate show a clear trend in ground state structures, from noncanonical bond lengths for WT toward solution values with mutants. Structural and dynamical differences that are sensitive to Tyr68 have also been detected using time-resolved Stokes shift measurements and molecular dynamics. These experimental and computational results are discussed in the context of active site compaction that requires an ionization of substrate within the enzyme ternary complex.
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Affiliation(s)
- Jianyu Zhang
- Department of Chemistry, University of California, Berkeley, CA 94720; California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Heather J Kulik
- Department of Chemistry, University of California, Berkeley, CA 94720; Photon Ultrafast Laser Science and Engineering Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Todd J Martinez
- Photon Ultrafast Laser Science and Engineering Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, CA 94720; California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
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21
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Abstract
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The grand challenge in enzymology is to define
and understand all of the parameters that contribute to enzymes’
enormous rate accelerations. The property of hydrogen tunneling in
enzyme reactions has moved the focus of research away from an exclusive
focus on transition state stabilization toward the importance of the
motions of the heavy atoms of the protein, a role for reduced barrier
width in catalysis, and the sampling of a protein conformational landscape
to achieve a family of protein substates that optimize enzyme–substrate
interactions and beyond. This Account focuses on a thermophilic
alcohol dehydrogenase for which the chemical step of hydride transfer
is rate determining across a wide range of experimental conditions.
The properties of the chemical coordinate have been probed using kinetic
isotope effects, indicating a transition in behavior below 30 °C
that distinguishes nonoptimal from optimal C–H activation.
Further, the introduction of single site mutants has the impact of
either enhancing or eliminating the temperature dependent transition
in catalysis. Biophysical probes, which include time dependent hydrogen/deuterium
exchange and fluorescent lifetimes and Stokes shifts, have also been
pursued. These studies allow the correlation of spatially resolved
transitions in protein motions with catalysis. It is now possible
to define a long-range network of protein motions in ht-ADH that extends
from a dimer interface to the substrate binding domain across to the
cofactor binding domain, over a distance of ca. 30 Å. The ongoing
challenge to obtaining spatial and temporal resolution of catalysis-linked
protein motions is discussed.
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Affiliation(s)
- Judith P. Klinman
- Department of Chemistry, Department of Molecular and Cell Biology, Institute of Quantitative Biology (QB3), University of California, Berkeley, California 94720, United States
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22
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Meadows C, Tsang JE, Klinman JP. Picosecond-resolved fluorescence studies of substrate and cofactor-binding domain mutants in a thermophilic alcohol dehydrogenase uncover an extended network of communication. J Am Chem Soc 2014; 136:14821-33. [PMID: 25314615 PMCID: PMC4210157 DOI: 10.1021/ja506667k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 01/18/2023]
Abstract
Time-resolved fluorescence dynamics are investigated in two mutants of a thermophilic alcohol dehydrogenase (ht-ADH): Y25A (at the dimer interface) and V260A (at the cofactor-binding domain). These residues, ca. 32 Å apart, are shown to exhibit opposing low-temperature effects on the hydride tunneling step. Using single-tryptophan constructs at the active site (Trp87) and a remote, surface-exposed site (Trp167), time-dependent Stokes shifts and collisional quenching data allow an analysis of intra-protein dynamical communication. A double mutant, Y25A:V260A, was also inserted into each single-Trp construct and analyzed accordingly. None of the mutations affect fluorescence lifetimes, Stokes shift relaxation rates, and quenching data for the surface-exposed Trp167 to an appreciable extent. By contrast, fluorescent probes of the active-site tryptophan 87 reveal distinctive forms of dynamical communication. Stokes shifts show that the distal Y25A increases active-site flexibility, V260A introduces a temperature-dependent equilibration process not previously reported by such measurements, and the double mutant (Y25A:V260A) eliminates the temperature-dependent transition sensed by the active-site tryptophan in the presence of V260A. Collisional quenching data at Trp87 further show a structural change in the active-site environment/solvation for V260A. In the aggregate, the temperature dependencies of the fluorescence data are distinct from the breaks in behavior previously reported for catalysis and hydrogen/deuterium exchange, attributed to time scales for the interconversion of protein conformational substates that are slower and more global than the local motions monitored within. An extended network of dynamical communication between the protein dimer surface and substrate- and cofactor-binding domains emerges from the flourescent data.
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Affiliation(s)
- Corey
W. Meadows
- Department of Chemistry, Department of Molecular and Cell
Biology, and the California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Jonathan E. Tsang
- Department of Chemistry, Department of Molecular and Cell
Biology, and the California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Judith P. Klinman
- Department of Chemistry, Department of Molecular and Cell
Biology, and the California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
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23
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Abstract
The role of evolutionary pressure on the chemical step catalyzed by enzymes is somewhat enigmatic, in part because chemistry is not rate-limiting for many optimized systems. Herein, we present studies that examine various aspects of the evolutionary relationship between protein dynamics and the chemical step in two paradigmatic enzyme families, dihydrofolate reductases and alcohol dehydrogenases. Molecular details of both convergent and divergent evolution are beginning to emerge. The findings suggest that protein dynamics across an entire enzyme can play a role in adaptation to differing physiological conditions. The growing tool kit of kinetics, kinetic isotope effects, molecular biology, biophysics, and bioinformatics provides means to link evolutionary changes in structure-dynamics function to the vibrational and conformational states of each protein.
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Affiliation(s)
- Judith P Klinman
- Department of Chemistry, Department of Molecular and Cell Biology, and the California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720 and.
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242-1294.
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