1
|
Ouedraogo D, Souffrant M, Yao XQ, Hamelberg D, Gadda G. Non-active Site Residue in Loop L4 Alters Substrate Capture and Product Release in d-Arginine Dehydrogenase. Biochemistry 2023; 62:1070-1081. [PMID: 36795942 PMCID: PMC9996824 DOI: 10.1021/acs.biochem.2c00697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Numerous studies demonstrate that enzymes undergo multiple conformational changes during catalysis. The malleability of enzymes forms the basis for allosteric regulation: residues located far from the active site can exert long-range dynamical effects on the active site residues to modulate catalysis. The structure of Pseudomonas aeruginosa d-arginine dehydrogenase (PaDADH) shows four loops (L1, L2, L3, and L4) that span the substrate and the FAD-binding domains. Loop L4 comprises residues 329-336, spanning over the flavin cofactor. The I335 residue on loop L4 is ∼10 Å away from the active site and ∼3.8 Å from N(1)-C(2)═O atoms of the flavin. In this study, we used molecular dynamics and biochemical techniques to investigate the effect of the mutation of I335 to histidine on the catalytic function of PaDADH. Molecular dynamics showed that the conformational dynamics of PaDADH are shifted to a more closed conformation in the I335H variant. In agreement with an enzyme that samples more in a closed conformation, the kinetic data of the I335H variant showed a 40-fold decrease in the rate constant of substrate association (k1), a 340-fold reduction in the rate constant of substrate dissociation from the enzyme-substrate complex (k2), and a 24-fold decrease in the rate constant of product release (k5), compared to that of the wild-type. Surprisingly, the kinetic data are consistent with the mutation having a negligible effect on the reactivity of the flavin. Altogether, the data indicate that the residue at position 335 has a long-range dynamical effect on the catalytic function in PaDADH.
Collapse
Affiliation(s)
- Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| |
Collapse
|
2
|
Gao S, Klinman JP. Functional roles of enzyme dynamics in accelerating active site chemistry: Emerging techniques and changing concepts. Curr Opin Struct Biol 2022; 75:102434. [PMID: 35872562 PMCID: PMC9901422 DOI: 10.1016/j.sbi.2022.102434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 02/08/2023]
Abstract
With the growing acceptance of the contribution of protein conformational ensembles to enzyme catalysis and regulation, research in the field of protein dynamics has shifted toward an understanding of the atomistic properties of protein dynamical networks and the mechanisms and time scales that control such behavior. A full description of an enzymatic reaction coordinate is expected to extend beyond the active site and include site-specific networks that communicate with the protein/water interface. Advances in experimental tools for the spatial resolution of thermal activation pathways are being complemented by biophysical methods for visualizing dynamics in real time. An emerging multidimensional model integrates the impacts of bound substrate/effector on the distribution of protein substates that are in rapid equilibration near room temperature with reaction-specific protein embedded heat transfer conduits.
Collapse
Affiliation(s)
- Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, CA, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, United States. https://twitter.com/S_H_Gao
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, CA, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, United States; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, United States.
| |
Collapse
|
3
|
Diffracted X-ray Tracking Method for Measuring Intramolecular Dynamics of Membrane Proteins. Int J Mol Sci 2022; 23:ijms23042343. [PMID: 35216461 PMCID: PMC8880040 DOI: 10.3390/ijms23042343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins change their conformations in response to chemical and physical stimuli and transmit extracellular signals inside cells. Several approaches have been developed for solving the structures of proteins. However, few techniques can monitor real-time protein dynamics. The diffracted X-ray tracking method (DXT) is an X-ray-based single-molecule technique that monitors the internal motion of biomolecules in an aqueous solution. DXT analyzes trajectories of Laue spots generated from the attached gold nanocrystals with a two-dimensional axis by tilting (θ) and twisting (χ). Furthermore, high-intensity X-rays from synchrotron radiation facilities enable measurements with microsecond-timescale and picometer-spatial-scale intramolecular information. The technique has been applied to various membrane proteins due to its superior spatiotemporal resolution. In this review, we introduce basic principles of DXT, reviewing its recent and extended applications to membrane proteins and living cells, respectively.
Collapse
|
4
|
Qu G, Sun Z. In Silico Prediction Methods for Site-Saturation Mutagenesis. Methods Mol Biol 2022; 2397:49-69. [PMID: 34813059 DOI: 10.1007/978-1-0716-1826-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Directed enzyme evolution has proven to be a powerful means to endow biocatalysts with novel catalytic repertoires. Apart from completely random gene mutagenesis, site-directed or site-saturation mutagenesis requires a semi-rational selection of the amino acid positions or the substituted residues, which can dramatically reduce the screening efforts in protein engineering. To this end, in silico prediction methods play a pivotal role in targeting site-saturation mutagenesis. In this chapter, we provide two distinct computational methods, (a) conformational dynamics-guided design and (b) protein-ligand interaction fingerprinting analysis, to identify specific positions for site-saturation mutagenesis toward manipulating substrate specificity/stereoselectivity of an alcohol dehydrogenase, and improving activity of a carboxylic acid reductase, respectively.
Collapse
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| |
Collapse
|
5
|
Li J, Lin J, Kohen A, Singh P, Francis K, Cheatum CM. Evolution of Optimized Hydride Transfer Reaction and Overall Enzyme Turnover in Human Dihydrofolate Reductase. Biochemistry 2021; 60:3822-3828. [PMID: 34875176 PMCID: PMC8697555 DOI: 10.1021/acs.biochem.1c00558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Evolution of dihydrofolate
reductase (DHFR) has been studied using
the enzyme from Escherichia coli DHFR
(ecDHFR) as a model, but less studies have used the enzyme from Homo sapiens DHFR (hsDHFR). Each enzyme maintains
a short and narrow distribution of hydride donor-acceptor distances
(DAD) at the tunneling ready state (TRS). Evolution of the enzyme
was previously studied in ecDHFR where three key sites were identified
as important to the catalyzed reaction. The corresponding sites in
hsDHFR are F28, 62-PEKN, and 26-PPLR. Each of these sites was studied
here through the creation of mutant variants of the enzyme and measurements
of the temperature dependence of the intrinsic kinetic isotope effects
(KIEs) on the reaction. F28 is mutated first to M (F28M) and then
to the L of the bacterial enzyme (F28L). The KIEs of the F28M variant
are larger and more temperature-dependent than wild-type (WT), suggesting
a broader and longer average DAD at the TRS. To more fully mimic ecDHFR,
we also study a triple mutant of the human enzyme (F32L-PP26N-PEKN62G).
Remarkably, the intrinsic KIEs, while larger in magnitude, are temperature-independent
like the WT enzymes. We also construct deletion mutations of hsDHFR
removing both the 62-PEKN and 26-PPLR sequences. The results mirror
those described previously for insertion mutants of ecDHFR. Taken
together, these results suggest a balancing act during DHFR evolution
between achieving an optimal TRS for hydride transfer and preventing
product inhibition arising from the different intercellular pools
of NADPH and NADP+ in prokaryotic and eukaryotic cells.
Collapse
Affiliation(s)
- Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Jennifer Lin
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Kevin Francis
- Texas A&M University-Kingsville, Kingsville, Texas 78363, United States
| | | |
Collapse
|
6
|
Xin X, Li C, Gao D, Wang D. Catalytic Descriptors to Investigate Catalytic Power in the Reaction of Haloalkane Dehalogenase Enzyme with 1,2-Dichloroethane. Int J Mol Sci 2021; 22:ijms22115854. [PMID: 34072602 PMCID: PMC8197811 DOI: 10.3390/ijms22115854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Enzymes play a fundamental role in many biological processes. We present a theoretical approach to investigate the catalytic power of the haloalkane dehalogenase reaction with 1,2-dichloroethane. By removing the three main active-site residues one by one from haloalkane dehalogenase, we found two reactive descriptors: one descriptor is the distance difference between the breaking bond and the forming bond, and the other is the charge difference between the transition state and the reactant complex. Both descriptors scale linearly with the reactive barriers, with the three-residue case having the smallest barrier and the zero-residue case having the largest. The results demonstrate that, as the number of residues increases, the catalytic power increases. The predicted free energy barriers using the two descriptors of this reaction in water are 23.1 and 24.2 kcal/mol, both larger than the ones with any residues, indicating that the water solvent hinders the reactivity. Both predicted barrier heights agree well with the calculated one at 25.2 kcal/mol using a quantum mechanics and molecular dynamics approach, and also agree well with the experimental result at 26.0 kcal/mol. This study shows that reactive descriptors can also be used to describe and predict the catalytic performance for enzyme catalysis.
Collapse
|
7
|
Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
Collapse
Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| |
Collapse
|
8
|
Duff MR, Redzic JS, Ryan LP, Paukovich N, Zhao R, Nix JC, Pitts TM, Agarwal P, Eisenmesser EZ. Structure, dynamics and function of the evolutionarily changing biliverdin reductase B family. J Biochem 2021; 168:191-202. [PMID: 32246827 DOI: 10.1093/jb/mvaa039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/19/2020] [Indexed: 11/14/2022] Open
Abstract
Biliverdin reductase B (BLVRB) family members are general flavin reductases critical in maintaining cellular redox with recent findings revealing that BLVRB alone can dictate cellular fate. However, as opposed to most enzymes, the BLVRB family remains enigmatic with an evolutionarily changing active site and unknown structural and functional consequences. Here, we applied a multi-faceted approach that combines X-ray crystallography, NMR and kinetics methods to elucidate the structural and functional basis of the evolutionarily changing BLVRB active site. Using a panel of three BLVRB isoforms (human, lemur and hyrax) and multiple human BLVRB mutants, our studies reveal a novel evolutionary mechanism where coenzyme 'clamps' formed by arginine side chains at two co-evolving positions within the active site serve to slow coenzyme release (Positions 14 and 78). We find that coenzyme release is further slowed by the weaker binding substrate, resulting in relatively slow turnover numbers. However, different BLVRB active sites imposed by either evolution or mutagenesis exhibit a surprising inverse relationship between coenzyme release and substrate turnover that is independent of the faster chemical step of hydride transfer also measured here. Collectively, our studies have elucidated the role of the evolutionarily changing BLVRB active site that serves to modulate coenzyme release and has revealed that coenzyme release is coupled to substrate turnover.
Collapse
Affiliation(s)
- Michael R Duff
- Biochemistry & Cellular and Molecular Biology Department, University of Tennessee, 1311 Cumberland Ave., Knoxville, TN 37996, USA
| | - Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Lucas P Ryan
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Natasia Paukovich
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Todd M Pitts
- Division of Medical Oncology, School of Medicine, University of Colorado, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Pratul Agarwal
- Biochemistry & Cellular and Molecular Biology Department, University of Tennessee, 1311 Cumberland Ave., Knoxville, TN 37996, USA
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, 12801 E 17th Ave., Aurora, CO 80045, USA
| |
Collapse
|
9
|
Acceleration of catalysis in dihydrofolate reductase by transient, site-specific photothermal excitation. Proc Natl Acad Sci U S A 2021; 118:2014592118. [PMID: 33468677 DOI: 10.1073/pnas.2014592118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have studied the role of protein dynamics in chemical catalysis in the enzyme dihydrofolate reductase (DHFR), using a pump-probe method that employs pulsed-laser photothermal heating of a gold nanoparticle (AuNP) to directly excite a local region of the protein structure and transient absorbance to probe the effect on enzyme activity. Enzyme activity is accelerated by pulsed-laser excitation when the AuNP is attached close to a network of coupled motions in DHFR (on the FG loop, containing residues 116-132, or on a nearby alpha helix). No rate acceleration is observed when the AuNP is attached away from the network (distal mutant and His-tagged mutant) with pulsed excitation, or for any attachment site with continuous wave excitation. We interpret these results within an energy landscape model in which transient, site-specific addition of energy to the enzyme speeds up the search for reactive conformations by activating motions that facilitate this search.
Collapse
|
10
|
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.
Collapse
|
11
|
Redzic JS, Duff MR, Blue A, Pitts TM, Agarwal P, Eisenmesser EZ. Modulating Enzyme Function via Dynamic Allostery within Biliverdin Reductase B. Front Mol Biosci 2021; 8:691208. [PMID: 34095235 PMCID: PMC8173106 DOI: 10.3389/fmolb.2021.691208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/30/2021] [Indexed: 11/17/2022] Open
Abstract
The biliverdin reductase B (BLVRB) class of enzymes catalyze the NADPH-dependent reduction of multiple flavin substrates and are emerging as critical players in cellular redox regulation. However, the role of dynamics and allostery have not been addressed, prompting studies here that have revealed a position 15 Å away from the active site within human BLVRB (T164) that is inherently dynamic and can be mutated to control global micro-millisecond motions and function. By comparing the inherent dynamics through nuclear magnetic resonance (NMR) relaxation approaches of evolutionarily distinct BLVRB homologues and by applying our previously developed Relaxation And Single Site Multiple Mutations (RASSMM) approach that monitors both the functional and dynamic effects of multiple mutations to the single T164 site, we have discovered that the most dramatic mutagenic effects coincide with evolutionary changes and these modulate coenzyme binding. Thus, evolutionarily changing sites distal to the active site serve as dynamic "dials" to globally modulate motions and function. Despite the distal dynamic and functional coupling modulated by this site, micro-millisecond motions span an order of magnitude in their apparent kinetic rates of motions. Thus, global dynamics within BLVRB are a collection of partially coupled motions tied to catalytic function.
Collapse
Affiliation(s)
- Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Denver, CO, United States
| | - Michael R Duff
- Biochemistry and Cellular and Molecular Biology Department, University of Tennessee, Knoxville, TN, United States
| | - Ashley Blue
- National High Magnetic Field Laboratory, Tallahassee, FL, United States
| | - Todd M Pitts
- Division of Medical Oncology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Pratul Agarwal
- Department of Physiological Sciences and High Performance Computing Center, Oklahoma State University, Stillwater, OK, United States
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Denver, CO, United States
| |
Collapse
|
12
|
Zamora RA, Ramirez-Sarmiento CA, Castro-Fernández V, Villalobos P, Maturana P, Herrera-Morande A, Komives EA, Guixé V. Tuning of Conformational Dynamics Through Evolution-Based Design Modulates the Catalytic Adaptability of an Extremophilic Kinase. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ricardo A. Zamora
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Cesar A. Ramirez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile. Avenida Vicuña Mackenna 4860, Macul, Santiago 6904411, Chile
| | - Víctor Castro-Fernández
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Pablo Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Pablo Maturana
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Alejandra Herrera-Morande
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| | - Elizabeth A. Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92092-0378, United States
| | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile
| |
Collapse
|
13
|
Site-Specific Tryptophan Labels Reveal Local Microsecond-Millisecond Motions of Dihydrofolate Reductase. Molecules 2020; 25:molecules25173819. [PMID: 32842574 PMCID: PMC7503464 DOI: 10.3390/molecules25173819] [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: 07/24/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Many enzymes are known to change conformations during their catalytic cycle, but the role of these protein motions is not well understood. Escherichia coli dihydrofolate reductase (DHFR) is a small, flexible enzyme that is often used as a model system for understanding enzyme dynamics. Recently, native tryptophan fluorescence was used as a probe to study micro- to millisecond dynamics of DHFR. Yet, because DHFR has five native tryptophans, the origin of the observed conformational changes could not be assigned to a specific region within the enzyme. Here, we use DHFR mutants, each with a single tryptophan as a probe for temperature jump fluorescence spectroscopy, to further inform our understanding of DHFR dynamics. The equilibrium tryptophan fluorescence of the mutants shows that each tryptophan is in a different environment and that wild-type DHFR fluorescence is not a simple summation of all the individual tryptophan fluorescence signatures due to tryptophan–tryptophan interactions. Additionally, each mutant exhibits a two-phase relaxation profile corresponding to ligand association/dissociation convolved with associated conformational changes and a slow conformational change that is independent of ligand association and dissociation, similar to the wild-type enzyme. However, the relaxation rate of the slow phase depends on the location of the tryptophan within the enzyme, supporting the conclusion that the individual tryptophan fluorescence dynamics do not originate from a single collective motion, but instead report on local motions throughout the enzyme.
Collapse
|
14
|
Proteins-Based Nanocatalysts for Energy Conversion Reactions. Top Curr Chem (Cham) 2020; 378:43. [PMID: 32562011 DOI: 10.1007/s41061-020-00306-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/10/2020] [Indexed: 10/24/2022]
Abstract
In recent years, the incorporation of molecular enzymes into nanostructured frameworks to create efficient energy conversion biomaterials has gained increasing interest as a promising strategy owing to both the dynamic behavior of proteins for their electrocatalytic function and the unique properties of the synergistic interactions between proteins and nanosized materials. Herein, we review the impact of proteins on energy conversion fields and the contribution of proteins to the improved activity of the resulting nanocomposites. We address different strategies to fabricate protein-based nanocatalysts as well as current knowledge on the structure-function relationships of enzymes during the catalytic processes. Additionally, a comprehensive review of state-of-the-art bioelectrocatalytic materials for water-splitting reactions such as hydrogen evolution reaction (HER) and oxygen evolution reactions (OER) is afforded. Finally, we briefly envision opportunities to develop a new generation of electrocatalysts towards the electrochemical reduction of N2 to NH3 using theoretical tools to built nature-inspired nitrogen reduction reaction catalysts.
Collapse
|
15
|
Johannissen LO, Iorgu AI, Scrutton NS, Hay S. What are the signatures of tunnelling in enzyme-catalysed reactions? Faraday Discuss 2020; 221:367-378. [DOI: 10.1039/c9fd00044e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computed tunnelling contributions and correlations between apparent activation enthalpy and entropy are explored for the interpretation of enzyme-catalysed H-transfer reactions.
Collapse
Affiliation(s)
- Linus O. Johannissen
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Andreea I. Iorgu
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Sam Hay
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| |
Collapse
|
16
|
Li J, Fortunato G, Lin J, Agarwal PK, Kohen A, Singh P, Cheatum CM. Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase. Biochemistry 2019; 58:3861-3868. [PMID: 31423766 PMCID: PMC7296831 DOI: 10.1021/acs.biochem.9b00460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Understanding protein motions and their role in enzymatic reactions is an important and timely topic in enzymology. Protein motions that are involved in the chemical step of catalysis are particularly intriguing but difficult to identify. A global network of coupled residues in Escherichia coli dihydrofolate reductase (E. coli DHFR), which assists in catalyzing the chemical step, has previously been demonstrated through quantum mechanical/molecular mechanical and molecular dynamics simulations as well as bioinformatic analyses. A few specific residues (M42, G121, F125, and I14) were shown to function synergistically with measurements of single-turnover rates and the temperature dependence of intrinsic kinetic isotope effects (KIEsint) of site-directed mutants. This study hypothesizes that the global network of residues involved in the chemical step is evolutionarily conserved and probes homologous residues of the potential global network in human DHFR through measurements of the temperature dependence of KIEsint and computer simulations based on the empirical valence bond method. We study mutants M53W and S145V. Both of these remote residues are homologous to network residues in E. coli DHFR. Non-additive isotope effects on activation energy are observed between M53 and S145, indicating their synergistic effect on the chemical step in human DHFR, which suggests that both of these residues are part of a network affecting the chemical step in enzyme catalysis. This finding supports the hypothesis that human and E. coli DHFR share similar networks, consistent with evolutionary preservation of such networks.
Collapse
Affiliation(s)
- Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | | | - Jennifer Lin
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | - Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | | |
Collapse
|
17
|
Stadler AM, Schneidewind J, Zamponi M, Knieps-Grünhagen E, Gholami S, Schwaneberg U, Rivalta I, Garavelli M, Davari MD, Jaeger KE, Krauss U. Ternary Complex Formation and Photoactivation of a Photoenzyme Results in Altered Protein Dynamics. J Phys Chem B 2019; 123:7372-7384. [PMID: 31380636 DOI: 10.1021/acs.jpcb.9b06608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interplay between protein dynamics and catalysis remains a fundamental question in enzymology. We here investigate the ns-timescale dynamics of a light-dependent NADPH:protochlorophyllide oxidoreductase (LPOR), a photoenzyme crucial for chlorophyll synthesis. LPORs catalyze the light-triggered trans addition of a hydride and a proton across the C17═C18 double bond of the chlorophyll precursor protochlorophyllide (Pchlide). Because of the lack of an LPOR structure, the global structural and dynamic consequences of LPOR/Pchlide/NADPH ternary complex formation remain elusive. Moreover, photoactivation of LPORs by low-light preillumination is controversially discussed as unequivocal proof for this phenomenon is lacking. By employing quasielastic neutron spectroscopy (QENS), we show that the formation of the ternary holoprotein complex as well as photoactivation lead to progressive rigidification of the protein. These findings are supported by thermostability measurements, which reveal different melting behavior and thermostabilities for the apo- and holoprotein ternary complexes. Molecular dynamics simulations in good agreement with the experimental QENS results suggest that the increased flexibility observed for the apoprotein stems from structural fluctuations of the NADPH and Pchlide substrate binding sites of the enzyme. On the basis of our results, in conjunction with activity and stability measurements, we provide independent proof for LPOR photoactivation, defined as a process that modifies the protein structure and dynamics, resulting in an increased substrate turnover. Our findings advance the structural and dynamic understanding of LPORs and provide a first link between protein dynamics and catalysis for this enzyme class.
Collapse
Affiliation(s)
| | | | - Michaela Zamponi
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) , Forschungszentrum Jülich GmbH , Lichtenbergstr. 1 , 85748 Garching , Germany
| | | | - Samira Gholami
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
| | - Ulrich Schwaneberg
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , D-52074 Aachen , Germany.,DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52056 Aachen , Germany
| | - Ivan Rivalta
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182 , F-69342 Lyon , France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy.,École Normale Supérieure de Lyon, CNRS, Laboratoire de Chimie UMR 5182, Université de Lyon , 46 Allée d'Italie , F-69364 Lyon Cedex 07 , France
| | - Mehdi D Davari
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , D-52074 Aachen , Germany
| | - Karl-Erich Jaeger
- IBG-1: Biotechnologie , Forschungszentrum Jülich GmbH , D-52425 Jülich , Germany
| | | |
Collapse
|
18
|
Liu B, Qu G, Li J, Fan W, Ma J, Xu Y, Nie Y, Sun Z. Conformational Dynamics‐Guided Loop Engineering of an Alcohol Dehydrogenase: Capture, Turnover and Enantioselective Transformation of Difficult‐to‐Reduce Ketones. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900249] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Beibei Liu
- School of Biotechnology, Key laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi 214122 People's Republic of China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Ge Qu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Jun‐Kuan Li
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science and EngineeringTianjin University Tianjin 300072 People's Republic of China
| | - Wenchao Fan
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Jun‐An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science and EngineeringTianjin University Tianjin 300072 People's Republic of China
| | - Yan Xu
- School of Biotechnology, Key laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi 214122 People's Republic of China
| | - Yao Nie
- School of Biotechnology, Key laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi 214122 People's Republic of China
| | - Zhoutong Sun
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| |
Collapse
|
19
|
Roca M, Ruiz-Pernía JJ, Castillo R, Oliva M, Moliner V. Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase. Phys Chem Chem Phys 2018; 20:25722-25737. [PMID: 30280169 DOI: 10.1039/c8cp04244f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The origin of the catalytic power of enzymes has been a question of debate for a long time. In this regard, the possible contribution of protein dynamics in enzymatic catalysis has become one of the most controversial topics. In the present work, the hydride transfer step in the formate dehydrogenase (FDH EC 1.2.1.2) enzyme is studied by means of molecular dynamic (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials in order to explore any correlation between dynamics, tunnelling effects and the rate constant. The temperature dependence of the kinetic isotope effects (KIEs), which is one of the few tests that can be studied by experiments and simulations to shed light on this debate, has been computed and the results have been compared with previous experimental data. The classical mechanical free energy barrier and the number of recrossing trajectories seem to be temperature-independent while the quantum vibrational corrections and the tunnelling effects are slightly temperature-dependent over the interval of 5-45 °C. The computed primary KIEs are in very good agreement with previous experimental data, being almost temperature-independent within the standard deviations. The modest dependence on the temperature is due to just the quantum vibrational correction contribution. These results, together with the analysis of the evolution of the collective variables such as the electrostatic potential or the electric field created by the protein on the key atoms involved in the reaction, confirm that while the protein is well preorganised, some changes take place along the reaction that favour the hydride transfer and the product release. Coordinates defining these movements are, in fact, part of the real reaction coordinate.
Collapse
Affiliation(s)
- Maite Roca
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | | | - Raquel Castillo
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Mónica Oliva
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| |
Collapse
|
20
|
Nagae T, Yamada H, Watanabe N. High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP . Acta Crystallogr D Struct Biol 2018; 74:895-905. [PMID: 30198899 PMCID: PMC6130465 DOI: 10.1107/s2059798318009397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/29/2018] [Indexed: 11/10/2022] Open
Abstract
A high-pressure crystallographic study was conducted on Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ in crystal forms containing both the open and closed conformations of the M20 loop under high-pressure conditions of up to 800 MPa. At pressures between 270 and 500 MPa the crystal form containing the open conformation exhibited a phase transition from P21 to C2. Several structural changes in ecDHFR were observed at high pressure that were also accompanied by structural changes in the NADP+ cofactor and the hydration structure. In the crystal form with the closed conformation the M20 loop moved as the pressure changed, with accompanying conformational changes around the active site, including NADP+ and folate. These movements were consistent with the suggested hypothesis that movement of the M20 loop was necessary for ecDHFR to catalyze the reaction. In the crystal form with the open conformation the nicotinamide ring of the NADP+ cofactor undergoes a large flip as an intermediate step in the reaction, despite being in a crystalline state. Furthermore, observation of the water molecules between Arg57 and folate elucidated an early step in the substrate-binding pathway. These results demonstrate the possibility of using high-pressure protein crystallography as a method to capture high-energy substates or transient structures related to the protein reaction cycle.
Collapse
Affiliation(s)
- Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Hiroyuki Yamada
- Venture Business Laboratory, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Nobuhisa Watanabe
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
- Venture Business Laboratory, Nagoya University, Chikusa, Nagoya 464-8603, Japan
- Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| |
Collapse
|
21
|
Mhashal AR, Pshetitsky Y, Eitan R, Cheatum CM, Kohen A, Major DT. Effect of Asp122 Mutation on the Hydride Transfer in E. coli DHFR Demonstrates the Goldilocks of Enzyme Flexibility. J Phys Chem B 2018; 122:8006-8017. [PMID: 30040418 DOI: 10.1021/acs.jpcb.8b05556] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF) in the presence of NADPH. The key hydride transfer step in the reaction is facilitated by a combination of enzyme active site preorganization and correlated protein motions in the Michaelis-Menten (E:NADPH:DHF) complex. The present theoretical study employs mutagenesis to examine the relation between structural and functional properties of the enzyme. We mutate Asp122 in Escherichia coli DHFR, which is a conserved amino acid in the DHFR family. The consequent effect of the mutation on enzyme catalysis is examined from an energetic, structural and short-time dynamic perspective. Our investigations suggest that the structural and short-time dynamic perturbations caused by Asp122X mutations (X = Asn, Ser, Ala) are along the reaction coordinate and lower the rate of hydride transfer. Importantly, analysis of the correlated and principle component motions in the enzyme suggest that the mutation alters the coupled motions that are present in the wild-type enzyme. In the case of D122N and D122S, the mutations inhibit coupled motion, whereas in the case of D122A, the mutation enhances coupled motion, although all mutations result in similar rate reduction. These results emphasize a Goldilocks principle of enzyme flexibility, that is, enzymes should neither be too rigid nor too flexible.
Collapse
Affiliation(s)
- Anil R Mhashal
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Yaron Pshetitsky
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Reuven Eitan
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Christopher M Cheatum
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - Amnon Kohen
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| |
Collapse
|
22
|
Campbell EC, Correy GJ, Mabbitt PD, Buckle AM, Tokuriki N, Jackson CJ. Laboratory evolution of protein conformational dynamics. Curr Opin Struct Biol 2018; 50:49-57. [DOI: 10.1016/j.sbi.2017.09.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
|
23
|
Carro J, Martínez-Júlvez M, Medina M, Martínez AT, Ferreira P. Protein dynamics promote hydride tunnelling in substrate oxidation by aryl-alcohol oxidase. Phys Chem Chem Phys 2018; 19:28666-28675. [PMID: 29043303 DOI: 10.1039/c7cp05904c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The temperature dependence of hydride transfer from the substrate to the N5 of the FAD cofactor during the reductive half-reaction of Pleurotus eryngii aryl-alcohol oxidase (AAO) is assessed here. Kinetic isotope effects on both the pre-steady state reduction of the enzyme and its steady-state kinetics, with differently deuterated substrates, suggest an environmentally-coupled quantum-mechanical tunnelling process. Moreover, those kinetic data, along with the crystallographic structure of the enzyme in complex with a substrate analogue, indicate that AAO shows a pre-organized active site that would only require the approaching of the hydride donor and acceptor for the tunnelled transfer to take place. Modification of the enzyme's active-site architecture by replacement of Tyr92, a residue establishing hydrophobic interactions with the substrate analogue in the crystal structure, in the Y92F, Y92L and Y92W variants resulted in different temperature dependence patterns that indicated a role of this residue in modulating the transfer reaction.
Collapse
Affiliation(s)
- Juan Carro
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain.
| | | | | | | | | |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Sharma B, Jamdar SN, Ghosh B, Yadav P, Kumar A, Kundu S, Goyal VD, Makde RD. Active site gate of M32 carboxypeptidases illuminated by crystal structure and molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1406-1415. [PMID: 28844748 DOI: 10.1016/j.bbapap.2017.07.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 01/09/2023]
Abstract
Enzyme gates are important dynamic features that regulate function. Study of these features is critical for understanding of enzyme mechanism. In this study, the active-site gate of M32 carboxypeptidases (M32CP) is illuminated. Only a handful of members of this family have been structurally and functionally characterized and various aspects of their activity and mechanism are yet not clarified. Here, crystal structure of putative M32CP from Deinococcus radiodurans (M32dr) was solved to 2.4Å resolution. Enzymatic assays confirmed its identity as a carboxypeptidase. Open and relatively closed conformations observed in the structure provided supporting evidence for previously hypothesized hinge motion in this family of enzymes. Molecular dynamics simulations of 1.5μs displayed distinct open and closed conformations revealing amplitude of the motion to be beyond what was observed in the crystal structure. Hinge region and anchoring region of this shell-type gate were identified. A small displacement of 3Å and a helical tilt of 9° propagated by the hinge region translates into a 10Å motion at the top of the gate. The dynamics of the gate was supported by our mutagenesis experiment involving formation of disulphide bond across helices of the gate. The nearly inactive mutant enzyme showed 65-fold increase in the enzymatic activity in presence of reducing agent. Further, while a previously proposed structural basis would have led to its classification in subfamily II, experimentally observed substrate length restriction places M32dr in subfamily I of M32CPs.
Collapse
Affiliation(s)
- Bhaskar Sharma
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Biplab Ghosh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Pooja Yadav
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.
| |
Collapse
|
27
|
Abstract
Enzyme isotope effects, or the kinetic effects of "heavy" enzymes, refer to the effect of isotopically labeled protein residues on the enzyme's activity or physical properties. These effects are increasingly employed in the examination of the possible contributions of protein dynamics to enzyme catalysis. One hypothesis assumed that isotopic substitution of all 12C, 14N, and nonexchangeable 1H by 13C, 15N, and 2H, would slow down protein picosecond to femtosecond dynamics without any effect on the system's electrostatics following the Born-Oppenheimer approximation. It was suggested that reduced reaction rates reported for several "heavy" enzymes accords with that hypothesis. However, numerous deviations from the predictions of that hypothesis were also reported. Current studies also attempt to test the role of individual residues by site-specific labeling or by labeling a pattern of residues on activity. It appears that in several systems the protein's fast dynamics are indeed reduced in "heavy" enzymes in a way that reduces the probability of barrier crossing of its chemical step. Other observations, however, indicated that slower protein dynamics are electrostatically altered in isotopically labeled enzymes. Interestingly, these effects appear to be system dependent, thus it might be premature to suggest a general role of "heavy" enzymes' effect on catalysis.
Collapse
|
28
|
Jones HBL, Wells SA, Prentice EJ, Kwok A, Liang LL, Arcus VL, Pudney CR. A complete thermodynamic analysis of enzyme turnover links the free energy landscape to enzyme catalysis. FEBS J 2017. [PMID: 28650586 DOI: 10.1111/febs.14152] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Our understanding of how enzymes work is coloured by static structure depictions where the enzyme scaffold is presented as either immobile, or in equilibrium between well-defined static conformations. Proteins, however, exhibit a large degree of motion over a broad range of timescales and magnitudes and this is defined thermodynamically by the enzyme free energy landscape (FEL). The role and importance of enzyme motion is extremely contentious. Much of the challenge is in the experimental detection of so called 'conformational sampling' involved in enzyme turnover. Herein we apply combined pressure and temperature kinetics studies to elucidate the full suite of thermodynamic parameters defining an enzyme FEL as it relates to enzyme turnover. We find that the key thermodynamic parameters governing vibrational modes related to enzyme turnover are the isobaric expansivity term and the change in heat capacity for enzyme catalysis. Variation in the enzyme FEL affects these terms. Our analysis is supported by a range of biophysical and computational approaches that specifically capture information on protein vibrational modes and the FEL (all atom flexibility calculations, red edge excitation shift spectroscopy and viscosity studies) that provide independent evidence for our findings. Our data suggest that restricting the enzyme FEL may be a powerful strategy when attempting to rationally engineer enzymes, particularly to alter thermal activity. Moreover, we demonstrate how rational predictions can be made with a rapid computational approach.
Collapse
Affiliation(s)
- Hannah B L Jones
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | - Stephen A Wells
- Department of Chemical Engineering, Faculty of Science, University of Bath, UK
| | - Erica J Prentice
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | - Anthony Kwok
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | - Liyin L Liang
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | - Vickery L Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | - Christopher R Pudney
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| |
Collapse
|
29
|
Ouedraogo D, Souffrant M, Vasquez S, Hamelberg D, Gadda G. Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase. Biochemistry 2017; 56:2477-2487. [DOI: 10.1021/acs.biochem.7b00098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Daniel Ouedraogo
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Sheena Vasquez
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| |
Collapse
|
30
|
Warshel A, Bora RP. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis. J Chem Phys 2017; 144:180901. [PMID: 27179464 DOI: 10.1063/1.4947037] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme's conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions.
Collapse
Affiliation(s)
- Arieh Warshel
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
| | - Ram Prasad Bora
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
| |
Collapse
|
31
|
Alotaibi M, Reyes BD, Le T, Luong P, Valafar F, Metzger RP, Fogel GB, Hecht D. Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution. J Mol Graph Model 2017; 71:135-153. [PMID: 27914300 PMCID: PMC5203806 DOI: 10.1016/j.jmgm.2016.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 10/04/2016] [Accepted: 10/10/2016] [Indexed: 12/15/2022]
Abstract
Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database. We used these alignments to compare active site and non-active site conservation in terms of amino acid residues, secondary structure and amino acid residue class. With respect to amino acid sequences and residue classes, active-site positions in both plasmid and chromosomal DHFR are significantly more conserved than non-active site positions. Secondary structure conservation was similar for active site and non-active site positions. Plasmid-encoded DHFR proteins have greater degree of sequence and residue class conservation, particularly in sequence positions associated with a network of concerted protein motions, than chromosomal-encoded DHFR proteins. These structure-based were used to build DHFR specific phylogenetic trees from which evidence for horizontal gene transfer was identified.
Collapse
Affiliation(s)
- Mona Alotaibi
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; King Saud University, P.O. Box 245714, Riyadh 11312, Saudi Arabia.
| | - Ben Delos Reyes
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Tin Le
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Phuong Luong
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Faramarz Valafar
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, CA 92182-7720, USA.
| | - Robert P Metzger
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA.
| | - Gary B Fogel
- Natural Selection, Inc., 6480 Weathers Place, Suite 350, San Diego, CA 92121, USA.
| | - David Hecht
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; Department of Chemistry, Southwestern College, 900 Otay Lakes Rd., Chula Vista, CA 91910, USA.
| |
Collapse
|
32
|
Hu S, Cattin‐Ortolá J, Munos JW, Klinman JP. Hydrostatic Pressure Studies Distinguish Global from Local Protein Motions in C−H Activation by Soybean Lipoxygenase‐1. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Shenshen Hu
- Department of ChemistryUniversity of California, California Institute for Quantitative Biosciences, University of California Berkeley CA 94720 USA
| | - Jérôme Cattin‐Ortolá
- Department of ChemistryUniversity of California, California Institute for Quantitative Biosciences, University of California Berkeley CA 94720 USA
- Department of Biochemistry, UW Box 357350 1705 NE Pacific St. Seattle WA 98195-7350 USA
| | - Jeffrey W. Munos
- Department of ChemistryUniversity of California, California Institute for Quantitative Biosciences, University of California Berkeley CA 94720 USA
- DuPont Industrial Biosciences 925 Page Mill Rd Palo Alto CA 94304 USA
| | - Judith P. Klinman
- Department of ChemistryUniversity of California, California Institute for Quantitative Biosciences, University of California Berkeley CA 94720 USA
- Department of Molecular and Cell BiologyUniversity of California Berkeley CA 94720 USA
| |
Collapse
|
33
|
Hu S, Cattin-Ortolá J, Munos JW, Klinman JP. Hydrostatic Pressure Studies Distinguish Global from Local Protein Motions in C-H Activation by Soybean Lipoxygenase-1. Angew Chem Int Ed Engl 2016; 55:9361-4. [PMID: 27348724 PMCID: PMC5040518 DOI: 10.1002/anie.201603592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 01/28/2023]
Abstract
The proposed contributions of distinct classes of local versus global protein motions during enzymatic bond making/breaking processes has been difficult to verify. We employed soybean lipoxygenase-1 as a model system to investigate the impact of high pressure at variable temperatures on the hydrogen-tunneling properties of the wild-type protein and three single-site mutants. For all variants, pressure dramatically elevates the enthalpies of activation for the C-H activation. In contrast, the primary kinetic isotope effects (KIEs) for C-H activation and their corresponding temperature dependencies remain unchanged up to ca. 700 bar. The differential impact of elevated hydrostatic pressure on the temperature dependencies of rate constants versus substrate KIEs provides direct evidence for two distinct classes of protein motions: local, isotope-dependent donor-acceptor distance-sampling modes, and a more global, isotope-independent search for productive protein conformational sub-states.
Collapse
Affiliation(s)
- Shenshen Hu
- Department of Chemistry, University of California, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Jérôme Cattin-Ortolá
- Department of Chemistry, University of California, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Department of Biochemistry, UW Box 357350, 1705 NE Pacific St., Seattle, WA, 98195-7350, USA
| | - Jeffrey W Munos
- Department of Chemistry, University of California, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- DuPont Industrial Biosciences, 925 Page Mill Rd, Palo Alto, CA, 94304, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
34
|
Abstract
Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions.
Collapse
Affiliation(s)
- P Singh
- University of Iowa, Iowa City, IA, United States
| | - Z Islam
- University of Iowa, Iowa City, IA, United States
| | - A Kohen
- University of Iowa, Iowa City, IA, United States.
| |
Collapse
|
35
|
Francis K, Sapienza PJ, Lee AL, Kohen A. The Effect of Protein Mass Modulation on Human Dihydrofolate Reductase. Biochemistry 2016; 55:1100-6. [PMID: 26813442 DOI: 10.1021/acs.biochem.5b00945] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) from Escherichia coli has long served as a model enzyme with which to elucidate possible links between protein dynamics and the catalyzed reaction. Such physical properties of its human counterpart have not been rigorously studied so far, but recent computer-based simulations suggest that these two DHFRs differ significantly in how closely coupled the protein dynamics and the catalyzed C-H → C hydride transfer step are. To test this prediction, two contemporary probes for studying the effect of protein dynamics on catalysis were combined here: temperature dependence of intrinsic kinetic isotope effects (KIEs), which are sensitive to the physical nature of the chemical step, and protein mass modulation, which slows down fast dynamics (femto- to picosecond time scale) throughout the protein. The intrinsic H/T KIEs of human DHFR, like those of E. coli DHFR, are shown to be temperature-independent in the range from 5 to 45 °C, indicating fast sampling of donor and acceptor distances (DADs) at the reaction's transition state (or tunneling ready state, TRS). Mass modulation of these enzymes through isotopic labeling with (13)C, (15)N, and (2)H at nonexchangeable hydrogens yields an 11% heavier enzyme. The additional mass has no effect on the intrinsic KIEs of the human enzyme. This finding indicates that the mass modulation of the human DHFR affects neither DAD distribution nor the DAD's conformational sampling dynamics. Furthermore, reduction in the enzymatic turnover number and the dissociation rate constant for the product indicate that the isotopic substitution affects kinetic steps that are not the catalyzed C-H → C hydride transfer. The findings are discussed in terms of fast dynamics and their role in catalysis, the comparison of calculations and experiments, and the interpretation of isotopically modulated heavy enzymes in general.
Collapse
Affiliation(s)
- Kevin Francis
- The Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Andrew L Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| |
Collapse
|
36
|
Abstract
Dihydrofolate reductase from
Escherichia coli (ecDHFR) serves as a model system for investigating the role of protein dynamics in enzyme catalysis. We discuss calculations predicting a network of dynamic motions that is coupled to the chemical step catalyzed by this enzyme. Kinetic studies testing these predictions are presented, and their potential use in better understanding the role of these dynamics in enzyme catalysis is considered. The cumulative results implicate motions across the entire protein in catalysis.
Collapse
Affiliation(s)
- Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA, USA
| |
Collapse
|