1
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Rahimi M, Taghdir M, Abasi Joozdani F. Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease. Sci Rep 2023; 13:14179. [PMID: 37648682 PMCID: PMC10469195 DOI: 10.1038/s41598-023-40818-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 protease families to illustrate the significance of examining the dynamic behaviors and molecular motions for an entire understanding of their dynamics-structure-function relationships. Using computer simulations and principal component analysis approaches, the dynamics data obtained revealed that: (i) The flap regions are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease; (ii) There are dynamic structural regions in some proteins that contribute to the biological function and allostery of proteins via appropriate flexibility. These regions are a clear sign of the evolution of conformational dynamics of proteins, which we call dynamozones. The flap regions are one of the most important dynamozones members that are critical for HIV-1 protease function. Due to the existence of other members of dynamozones in different proteins, we propose to consider dynamozones as a footprint of the evolution of the conformational dynamics of proteins.
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Affiliation(s)
- Mohammad Rahimi
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran.
| | - Farzane Abasi Joozdani
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
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2
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Gaur NK, Ghosh B, Goyal VD, Kulkarni K, Makde RD. Evolutionary conservation of protein dynamics: insights from all-atom molecular dynamics simulations of 'peptidase' domain of Spt16. J Biomol Struct Dyn 2023; 41:1445-1457. [PMID: 34971347 DOI: 10.1080/07391102.2021.2021990] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Protein function is encoded in its sequence, manifested in its three-dimensional structure, and facilitated by its dynamics. Studies have suggested that protein structures with higher sequence similarity could have more similar patterns of dynamics. However, such studies of protein dynamics within and across protein families typically rely on coarse-grained models, or approximate metrics like crystallographic B-factors. This study uses µs scale molecular dynamics (MD) simulations to explore the conservation of dynamics among homologs of ∼50 kDa N-terminal module of Spt16 (Spt16N). Spt16N from Saccharomyces cerevisiae (Sc-Spt16N) and three of its homologs with 30-40% sequence identities were available in the PDB. To make our data-set more comprehensive, the crystal structure of an additional homolog (62% sequence identity with Sc-Spt16N) was solved at 1.7 Å resolution. Cumulative MD simulations of 6 µs were carried out on these Spt16N structures and on two additional protein structures with varying degrees of similarity to it. The simulations revealed that correlation in patterns of backbone fluctuations vary linearly with sequence identity. This trend could not be inferred using crystallographic B-factors. Further, normal mode analysis suggested a similar pattern of inter-domain (inter-lobe) motions not only among Spt16N homologs, but also in the M24 peptidase structure. On the other hand, MD simulation results highlighted conserved motions that were found unique for Spt16N protein, this along with electrostatics trends shed light on functional aspects of Spt16N.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neeraj K Gaur
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India.,Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Biplab Ghosh
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Venuka Durani Goyal
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Kiran Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
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3
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Lemay-St-Denis C, Doucet N, Pelletier JN. Integrating dynamics into enzyme engineering. Protein Eng Des Sel 2022; 35:6842866. [PMID: 36416215 DOI: 10.1093/protein/gzac015] [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] [Received: 06/21/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 11/24/2022] Open
Abstract
Enzyme engineering has become a widely adopted practice in research labs and industry. In parallel, the past decades have seen tremendous strides in characterizing the dynamics of proteins, using a growing array of methodologies. Importantly, links have been established between the dynamics of proteins and their function. Characterizing the dynamics of an enzyme prior to, and following, its engineering is beginning to inform on the potential of 'dynamic engineering', i.e. the rational modification of protein dynamics to alter enzyme function. Here we examine the state of knowledge at the intersection of enzyme engineering and protein dynamics, describe current challenges and highlight pioneering work in the nascent area of dynamic engineering.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Nicolas Doucet
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, QC, Canada
| | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
- Chemistry Department, Université de Montréal, Montreal, QC, Canada
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4
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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.
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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
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5
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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.
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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
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6
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Schober AF, Mathis AD, Ingle C, Park JO, Chen L, Rabinowitz JD, Junier I, Rivoire O, Reynolds KA. A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism. Cell Rep 2020; 27:3359-3370.e7. [PMID: 31189117 DOI: 10.1016/j.celrep.2019.05.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 04/05/2019] [Accepted: 05/09/2019] [Indexed: 11/29/2022] Open
Abstract
Enzyme function and evolution are influenced by the larger context of a metabolic pathway. Deleterious mutations or perturbations in one enzyme can often be compensated by mutations to others. We used comparative genomics and experiments to examine evolutionary interactions with the essential metabolic enzyme dihydrofolate reductase (DHFR). Analyses of synteny and co-occurrence across bacterial species indicate that DHFR is coupled to thymidylate synthase (TYMS) but relatively independent from the rest of folate metabolism. Using quantitative growth rate measurements and forward evolution in Escherichia coli, we demonstrate that the two enzymes adapt as a relatively independent unit in response to antibiotic stress. Metabolomic profiling revealed that TYMS activity must not exceed DHFR activity to prevent the depletion of reduced folates and the accumulation of the intermediate dihydrofolate. Comparative genomics analyses identified >200 gene pairs with similar statistical signatures of modular co-evolution, suggesting that cellular pathways may be decomposable into small adaptive units.
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Affiliation(s)
- Andrew F Schober
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrew D Mathis
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christine Ingle
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junyoung O Park
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Li Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Ivan Junier
- Centre National de la Recherche Scientifique, Université Grenoble Alpes, TIMC-IMAG, F-38000 Grenoble, France
| | - Olivier Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, F-75005 Paris, France
| | - Kimberly A Reynolds
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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7
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Crean RM, Gardner JM, Kamerlin SCL. Harnessing Conformational Plasticity to Generate Designer Enzymes. J Am Chem Soc 2020; 142:11324-11342. [PMID: 32496764 PMCID: PMC7467679 DOI: 10.1021/jacs.0c04924] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Indexed: 02/08/2023]
Abstract
Recent years have witnessed an explosion of interest in understanding the role of conformational dynamics both in the evolution of new enzymatic activities from existing enzymes and in facilitating the emergence of enzymatic activity de novo on scaffolds that were previously non-catalytic. There are also an increasing number of examples in the literature of targeted engineering of conformational dynamics being successfully used to alter enzyme selectivity and activity. Despite the obvious importance of conformational dynamics to both enzyme function and evolvability, many (although not all) computational design approaches still focus either on pure sequence-based approaches or on using structures with limited flexibility to guide the design. However, there exist a wide variety of computational approaches that can be (re)purposed to introduce conformational dynamics as a key consideration in the design process. Coupled with laboratory evolution and more conventional existing sequence- and structure-based approaches, these techniques provide powerful tools for greatly expanding the protein engineering toolkit. This Perspective provides an overview of evolutionary studies that have dissected the role of conformational dynamics in facilitating the emergence of novel enzymes, as well as advances in computational approaches that allow one to target conformational dynamics as part of enzyme design. Harnessing conformational dynamics in engineering studies is a powerful paradigm with which to engineer the next generation of designer biocatalysts.
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Affiliation(s)
- Rory M. Crean
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Jasmine M. Gardner
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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8
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Pagano P, Guo Q, Ranasinghe C, Schroeder E, Robben K, Häse F, Ye H, Wickersham K, Aspuru-Guzik A, Major DT, Gakhar L, Kohen A, Cheatum CM. Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase. ACS Catal 2019; 9:11199-11206. [PMID: 33996196 PMCID: PMC8118594 DOI: 10.1021/acscatal.9b03345] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Thermal motions of enzymes have been invoked to explain the temperature dependence of kinetic isotope effects (KIE) in enzyme-catalyzed hydride transfers. Formate dehydrogenase (FDH) from Candida boidinii exhibits a temperature independent KIE that becomes temperature dependent upon mutation of hydrophobic residues in the active site. Ternary complexes of FDH that mimic the transition state structure allow investigation of how these mutations influence active-site dynamics. A combination of X-ray crystallography, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamic simulations characterize the structure and dynamics of the active site. FDH exhibits oscillatory frequency fluctuations on the picosecond timescale, and the amplitude of these fluctuations correlates with the temperature dependence of the KIE. Both the kinetic and dynamic phenomena can be reproduced computationally. These results provide experimental evidence for a connection between the temperature dependence of KIEs and motions of the active site in an enzyme-catalyzed reaction consistent with activated tunneling models of the hydride transfer reaction.
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Affiliation(s)
- Philip Pagano
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Qi Guo
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Chethya Ranasinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Evan Schroeder
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Kevin Robben
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Florian Häse
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Hepeng Ye
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Kyle Wickersham
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
- Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada
| | - Dan T. Major
- Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Lokesh Gakhar
- Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
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9
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The Structural Dynamics of Engineered β-Lactamases Vary Broadly on Three Timescales yet Sustain Native Function. Sci Rep 2019; 9:6656. [PMID: 31040324 PMCID: PMC6491436 DOI: 10.1038/s41598-019-42866-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/10/2019] [Indexed: 12/20/2022] Open
Abstract
Understanding the principles of protein dynamics will help guide engineering of protein function: altering protein motions may be a barrier to success or may be an enabling tool for protein engineering. The impact of dynamics on protein function is typically reported over a fraction of the full scope of motional timescales. If motional patterns vary significantly at different timescales, then only by monitoring motions broadly will we understand the impact of protein dynamics on engineering functional proteins. Using an integrative approach combining experimental and in silico methodologies, we elucidate protein dynamics over the entire span of fast to slow timescales (ps to ms) for a laboratory-engineered system composed of five interrelated β-lactamases: two natural homologs and three laboratory-recombined variants. Fast (ps-ns) and intermediate (ns-µs) dynamics were mostly conserved. However, slow motions (µs-ms) were few and conserved in the natural homologs yet were numerous and widely dispersed in their recombinants. Nonetheless, modified slow dynamics were functionally tolerated. Crystallographic B-factors from high-resolution X-ray structures were partly predictive of the conserved motions but not of the new slow motions captured in our solution studies. Our inspection of protein dynamics over a continuous range of timescales vividly illustrates the complexity of dynamic impacts of protein engineering as well as the functional tolerance of an engineered enzyme system to new slow motions.
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10
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Asciutto EK, Pochapsky TC. Some Surprising Implications of NMR-directed Simulations of Substrate Recognition and Binding by Cytochrome P450 cam (CYP101A1). J Mol Biol 2018; 430:1295-1310. [PMID: 29596916 DOI: 10.1016/j.jmb.2018.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 02/05/2023]
Abstract
Cytochrome P450cam (CYP101A1) catalyzes the stereospecific 5-exo hydroxylation of d-camphor by molecular oxygen. Previously, residual dipolar couplings measured for backbone amide 1H-15N correlations in both substrate-free and bound forms of CYP101A1 were used as restraints in soft annealing molecular dynamic simulations in order to identify average conformations of the enzyme with and without substrate bound. Multiple substrate-dependent conformational changes remote from the enzyme active site were identified, and site-directed mutagenesis and activity assays confirmed the importance of these changes in substrate recognition. The current work makes use of perturbation response scanning (PRS) and umbrella sampling molecular dynamic of the residual dipolar coupling-derived CYP101A1 structures to probe the roles of remote structural features in enforcing the regio- and stereospecific nature of the hydroxylation reaction catalyzed by CYP101A1. An improper dihedral angle Ψ was defined and used to maintain substrate orientation in the CYP101A1 active site, and it was observed that different values of Ψ result in different PRS response maps. Umbrella sampling methods show that the free energy of the system is sensitive to Ψ, and bound substrate forms an important mechanical link in the transmission of mechanical coupling through the enzyme structure. Finally, a qualitative approach to interpreting PRS maps in terms of the roles of secondary structural features is proposed.
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Affiliation(s)
- Eliana K Asciutto
- School of Science and Technology, UNSAM and CONICET, Campus Migueletes, 25 de Mayo y Francia, Buenos Aires, Argentina
| | - Thomas C Pochapsky
- Department of Chemistry and Rosenstiel Basic Biomedical Sciences Research Institute, MS 015, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA.
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11
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Chen X, Schwartz SD. Directed Evolution as a Probe of Rate Promoting Vibrations Introduced via Mutational Change. Biochemistry 2018; 57:3289-3298. [PMID: 29553716 DOI: 10.1021/acs.biochem.8b00185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this article, we study with transition path sampling and reaction coordinate analysis how directed evolution in the Kemp eliminase family of artificial enzymes makes differential use of rapid rate promoting vibrations as a component of their chemical mechanism. Even though this family was initially created by placing the expected active site in a fixed protein matrix, we find a shift from largely static to more dynamic active sites that make use of donor-acceptor compression as the evolutionary process proceeds. We see that this introduction of dynamics significantly shifts the order of processes in the reaction. We also suggest that the lack of "design for dynamics" may help explain the relatively low proficiency of such designed enzymes.
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Affiliation(s)
- Xi Chen
- Department of Chemistry and Biochemistry , University of Arizona , 1306 East University Boulevard , Tucson , Arizona 85721 , United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry , University of Arizona , 1306 East University Boulevard , Tucson , Arizona 85721 , United States
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12
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Świderek K, Arafet K, Kohen A, Moliner V. Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer. J Chem Theory Comput 2017; 13:1375-1388. [PMID: 28192669 PMCID: PMC5371049 DOI: 10.1021/acs.jctc.6b01032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these processes. In this paper, the hydride-transfer step catalyzed by thymidylate synthase (TSase) is studied by examining hybrid quantum mechanics/molecular mechanics (QM/MM) potentials via multiple semiempirical methods and the M06-2X hybrid density functional. Calculations of protium and tritium transfer in these reactions across a range of temperatures allowed calculation of the temperature dependence of kinetic isotope effects (KIE). Dynamics and quantum-tunneling effects are revealed to have little effect on the reaction rate, but are significant in determining the KIEs and their temperature dependence. A good agreement with experiments is found, especially when computed for RM1/MM simulations. The small temperature dependence of quantum tunneling corrections and the quasiclassical contribution term cancel each other, while the recrossing transmission coefficient seems to be temperature-independent over the interval of 5-40 °C.
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Affiliation(s)
- Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castelló, Spain
- Institute of Applied Radiation Chemistry, Lodz University of Technology , 90-924 Lodz, Poland
| | - Kemel Arafet
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castelló, Spain
| | - Amnon Kohen
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castelló, Spain
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13
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Luk LYP, Loveridge EJ, Allemann RK. Protein motions and dynamic effects in enzyme catalysis. Phys Chem Chem Phys 2016; 17:30817-27. [PMID: 25854702 DOI: 10.1039/c5cp00794a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The role of protein motions in promoting the chemical step of enzyme catalysed reactions remains a subject of considerable debate. Here, a unified view of the role of protein dynamics in dihydrofolate reductase catalysis is described. Recently the role of such motions has been investigated by characterising the biophysical properties of isotopically substituted enzymes through a combination of experimental and computational analyses. Together with previous work, these results suggest that dynamic coupling to the chemical coordinate is detrimental to catalysis and may have been selected against during DHFR evolution. The full catalytic power of Nature's catalysts appears to depend on finely tuning protein motions in each step of the catalytic cycle.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
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14
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Guo Q, Gakhar L, Wickersham K, Francis K, Vardi-Kilshtain A, Major DT, Cheatum CM, Kohen A. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii. Biochemistry 2016; 55:2760-71. [PMID: 27100912 DOI: 10.1021/acs.biochem.6b00181] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD(+)) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 × 10(-7) (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented.
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Affiliation(s)
- Qi Guo
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Lokesh Gakhar
- Protein Crystallography Facility and Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Kyle Wickersham
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Kevin Francis
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Alexandra Vardi-Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 5290002, Israel
| | - Dan T Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 5290002, Israel
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
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15
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Ruiz-Pernía JJ, Behiry E, Luk LYP, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Minimization of dynamic effects in the evolution of dihydrofolate reductase. Chem Sci 2016; 7:3248-3255. [PMID: 29997817 PMCID: PMC6006479 DOI: 10.1039/c5sc04209g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/02/2016] [Indexed: 11/22/2022] Open
Abstract
Protein isotope labeling is a powerful technique to probe functionally important motions in enzyme catalysis and can be applied to investigate the conformational dynamics of proteins. Previous investigations have indicated that dynamic coupling is detrimental to catalysis by dihydrofolate reductase (DHFR) from the mesophile Escherichia coli (EcDHFR). Comparison of DHFRs from organisms adapted to survive at a wide range of temperatures suggests that dynamic coupling in DHFR catalysis has been minimized during evolution; it arises from reorganizational motions needed to facilitate charge transfer events. Contrary to the behaviour observed for the DHFR from the moderate thermophile Geobacillus stearothermophilus (BsDHFR), the chemical transformation catalyzed by the cold-adapted bacterium Moritella profunda (MpDHFR) is only weakly affected by protein isotope substitutions at low temperatures, but the isotopically substituted enzyme is a substantially inferior catalyst at higher, non-physiological temperatures. QM/MM studies revealed that this behaviour is caused by the enzyme's structural sensitivity to temperature changes, which enhances unfavorable dynamic coupling at higher temperatures by promoting additional recrossing trajectories on the transition state dividing surface. We postulate that these motions are minimized by fine-tuning DHFR flexibility through optimization of the free energy surface of the reaction, such that a nearly static reaction-ready configuration with optimal electrostatic properties is maintained under physiological conditions.
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Affiliation(s)
- J Javier Ruiz-Pernía
- Departament de Química Física i Analítica , Universitat Jaume I , 12071 Castelló , Spain .
| | - Enas Behiry
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - Louis Y P Luk
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - E Joel Loveridge
- School of Chemistry & Cardiff Catalysis Institute , 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 .
| | - Rudolf K Allemann
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
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16
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Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- Sackler Institute
of Molecular Medicine, Department of Human Genetics and Molecular
Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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17
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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.
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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
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18
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Abeysinghe T, Hong B, Wang Z, Kohen A. Preserved hydride transfer mechanism in evolutionarily divergent thymidylate synthases. CURRENT TOPICS IN BIOCHEMICAL RESEARCH 2016; 17:19-30. [PMID: 28018055 PMCID: PMC5172458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Thymidylate synthase (TSase) catalyzes a hydride transfer in the last step of the de novo biosynthesis of the DNA nucleotide thymine. We compared two isozymes, namely, TSase from Escherichia coli (ecTSase) and TSase from Bacillus subtilis (bsTSase) that represent a case of divergent evolution. Interestingly, a highly conserved histidine (H147 of ecTSase) was proposed to serve a critical role in catalysis, but in bsTSase it is naturally substituted by valine (Val). Yet, bsTSase is more active than ecTSase, and the intrinsic kinetic isotope effects (KIEs) of both are temperature-independent, suggesting a similarly well-organized transition state (TS) for the catalyzed hydride transfer. To examine the role of that histidine (His) in TSase catalysis, we examined the kinetics of H147V ecTSase, which "bridges" between these two TSases. In contrast to both wild-type TSases, the single mutation results in deficient catalysis. The mutation leads to intrinsic KIEs that are temperature-dependent, indicating a substantial imperfection in its TS. The findings reveal two important features: a direct role of H147 in the hydride transfer step catalyzed by the ecTSase and the evolutionary compensation for its deficiency in bsTSase via extensive polymorphism across the protein. Very different active site residues are observed for these evolutionarily divergent isozymes, which result in a well-organized TS for both. It is suggested that evolutionary pressure compensated for the H to V substitution at the active site of bsTSase by polymorphism leading to a well-organized TS in both enzymes.
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Affiliation(s)
- Thelma Abeysinghe
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Baoyu Hong
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
- Genentech, South San Francisco, CA 94080, USA
| | - Zhen Wang
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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19
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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.
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Affiliation(s)
- Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA, USA
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20
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Effects of Non-Natural Amino Acid Incorporation into the Enzyme Core Region on Enzyme Structure and Function. Int J Mol Sci 2015; 16:22735-53. [PMID: 26402667 PMCID: PMC4613333 DOI: 10.3390/ijms160922735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/02/2015] [Accepted: 09/14/2015] [Indexed: 11/17/2022] Open
Abstract
Techniques to incorporate non-natural amino acids (NNAAs) have enabled biosynthesis of proteins containing new building blocks with unique structures, chemistry, and reactivity that are not found in natural amino acids. It is crucial to understand how incorporation of NNAAs affects protein function because NNAA incorporation may perturb critical function of a target protein. This study investigates how the site-specific incorporation of NNAAs affects catalytic properties of an enzyme. A NNAA with a hydrophobic and bulky sidechain, 3-(2-naphthyl)-alanine (2Nal), was site-specifically incorporated at six different positions in the hydrophobic core of a model enzyme, murine dihydrofolate reductase (mDHFR). The mDHFR variants with a greater change in van der Waals volume upon 2Nal incorporation exhibited a greater reduction in the catalytic efficiency. Similarly, the steric incompatibility calculated using RosettaDesign, a protein stability calculation program, correlated with the changes in the catalytic efficiency.
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21
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Singh P, Francis K, Kohen A. Network of remote and local protein dynamics in dihydrofolate reductase catalysis. ACS Catal 2015; 5:3067-3073. [PMID: 27182453 DOI: 10.1021/acscatal.5b00331] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics calculations and bionformatic studies of dihydrofolate reductase (DHFR) have suggested a network of coupled motions across the whole protein that is correlated to the reaction coordinate. Experimental studies demonstrated that distal residues G121, M42 and F125 in E. coli DHFR participate in that network. The missing link in our understanding of DHFR catalysis is the lack of a mechanism by which such remote residues can affect the catalyzed chemistry at the active site. Here, we present a study of the temperature dependence of intrinsic kinetic isotope effects (KIEs) that indicates synergism between a remote residue in that dynamic network, G121, and the active site's residue I14. The intrinsic KIEs for the I14A-G121V double mutant showed steeper temperature dependence (ΔEa(T-H)) than expected from comparison of the wild type and two single mutants. That effect was non-additive, i.e., ΔEa(T-H)G121V +ΔEa(T-H) I14A < ΔEa(T-H) double mutant, which indicates a synergism between the two residues. This finding links the remote residues in the network under investigation to the enzyme's active site, providing a mechanism by which these residues can be coupled to the catalyzed chemistry. This experimental evidence validates calculations proposing that both remote and active site residues constitute a network of coupled promoting motions correlated to the bond activation step (C-H→C hydride transfer in this case). Additionally, the effect of I14A and G121V mutations on single turnover rates was additive rather than synergistic. Although single turnover rate measurements are more readily available and thus more popular than assessing intrinsic kinetic isotope effects, the current finding demonstrates that for these rates, which in DHFR reflect several microscopic rate constants, can fall short of revealing the nature of the C-H bond activation per se.
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Affiliation(s)
- Priyanka Singh
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Kevin Francis
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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22
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Abeysinghe T, Kohen A. Role of long-range protein dynamics in different thymidylate synthase catalyzed reactions. Int J Mol Sci 2015; 16:7304-19. [PMID: 25837629 PMCID: PMC4425018 DOI: 10.3390/ijms16047304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 02/01/2023] Open
Abstract
Recent studies of Escherichia coli thymidylate synthase (ecTSase) showed that a highly conserved residue, Y209, that is located 8 Å away from the reaction site, plays a key role in the protein’s dynamics. Those crystallographic studies indicated that Y209W mutant is a structurally identical but dynamically altered relative to the wild type (WT) enzyme, and that its turnover catalytic rate governed by a slow hydride-transfer has been affected. The most challenging test of an examination of a fast chemical conversion that precedes the rate-limiting step has been achieved here. The physical nature of both fast and slow C-H bond activations have been compared between the WT and mutant by means of observed and intrinsic kinetic isotope effects (KIEs) and their temperature dependence. The findings indicate that the proton abstraction step has not been altered as much as the hydride transfer step. Additionally, the comparison indicated that other kinetic steps in the TSase catalyzed reaction were substantially affected, including the order of the substrate binding. Enigmatically, although Y209 is H-bonded to 3'-OH of 2'-deoxyuridine-5'-monophosphate (dUMP), its altered dynamics is more pronounced on the binding of the remote cofactor, (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4folate), revealing the importance of long-range dynamics of the enzymatic complex and its catalytic function.
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Affiliation(s)
- Thelma Abeysinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA.
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA.
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23
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Schulenburg C, Stark Y, Künzle M, Hilvert D. Comparative laboratory evolution of ordered and disordered enzymes. J Biol Chem 2015; 290:9310-20. [PMID: 25697360 DOI: 10.1074/jbc.m115.638080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Indexed: 11/06/2022] Open
Abstract
Intrinsically disordered proteins are ubiquitous in nature. To assess potential evolutionary advantages and disadvantages of structural disorder under controlled laboratory conditions, we directly compared the evolvability of weakly active ordered and disordered variants of dihydrofolate reductase by genetic selection. The circularly permuted Escherichia coli enzyme, which exists as a molten globule in the absence of ligands, and a well folded deletion mutant of the Bacillus stearothermophilus enzyme served as starting points. Both scaffolds evolved at similar rates and to similar extents, reaching near-native activity after three rounds of mutagenesis and selection. Surprisingly, however, the starting structural properties of the two scaffolds changed only marginally during optimization. Although the ordered and disordered proteins accumulated distinct sets of mutations, the changes introduced likely improved catalytic efficiency indirectly in both cases by bolstering the network of dynamic conformational fluctuations that productively couple into the reaction coordinate.
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Affiliation(s)
- Cindy Schulenburg
- From the Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
| | - Yvonne Stark
- From the Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
| | - Matthias Künzle
- From the Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
| | - Donald Hilvert
- From the Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
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24
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Abstract
![]()
The role of the enzyme’s dynamic motions
in catalysis is at the center of heated contemporary debates among
both theoreticians and experimentalists. Resolving these apparent
disputes is of both intellectual and practical importance: incorporation
of enzyme dynamics could be critical for any calculation of enzymatic
function and may have profound implications for structure-based drug
design and the design of biomimetic catalysts. Analysis of the
literature suggests that while part of the dispute may reflect substantial
differences between theoretical approaches, much of the debate is
semantic. For example, the term “protein dynamics” is
often used by some researchers when addressing motions that are in
thermal equilibrium with their environment, while other researchers
only use this term for nonequilibrium events. The last cases are those
in which thermal energy is “stored” in a specific protein
mode and “used” for catalysis before it can dissipate
to its environment (i.e., “nonstatistical dynamics”).
This terminology issue aside, a debate has arisen among theoreticians
around the roles of nonstatistical vs statistical dynamics in catalysis.
However, the author knows of no experimental findings available today
that examined this question in enzyme catalyzed reactions. Another
source of perhaps nonsubstantial argument might stem from the varying
time scales of enzymatic motions, which range from seconds to femtoseconds.
Motions at different time scales play different roles in the many
events along the catalytic cascade (reactant binding, reprotonation
of reactants, structural rearrangement toward the transition state,
product release, etc.). In several cases, when various experimental
tools have been used to probe catalytic events at differing time scales,
illusory contradictions seem to have emerged. In this Account, recent
attempts to sort the merits of those questions are discussed along
with possible future directions. A possible summary of current
studies could be that enzyme, substrate, and solvent dynamics contribute
to enzyme catalyzed reactions in several ways: first via mutual “induced-fit”
shifting of their conformational ensemble upon binding; then via thermal
search of the conformational space toward the reaction’s transition-state
(TS) and the rare event of the barrier crossing toward products, which
is likely to be on faster time scales then the first and following
events; and finally via the dynamics associated with products release,
which are rate-limiting for many enzymatic reactions. From a chemical
perspective, close to the TS, enzymatic systems seem to stiffen, restricting
motions orthogonal to the chemical coordinate and enabling dynamics
along the reaction coordinate to occur selectively. Studies of how
enzymes evolved to support those efficient dynamics at various time
scales are still in their infancy, and further experiments and calculations
are needed to reveal these phenomena in both enzymes and uncatalyzed
reactions.
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Affiliation(s)
- Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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25
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Bhabha G, Biel JT, Fraser JS. Keep on moving: discovering and perturbing the conformational dynamics of enzymes. Acc Chem Res 2015; 48:423-30. [PMID: 25539415 PMCID: PMC4334266 DOI: 10.1021/ar5003158] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CONSPECTUS: Because living organisms are in constant motion, the word "dynamics" can hold many meanings to biologists. Here we focus specifically on the conformational changes that occur in proteins and how studying these protein dynamics may provide insights into enzymatic catalysis. Advances in integrating techniques such as X-ray crystallography, nuclear magnetic resonance, and electron cryomicroscopy (cryo EM) allow us to model the dominant structures and exchange rates for many proteins and protein complexes. For proteins amenable to atomic resolution techniques, the major questions shift from simply describing the motions to discovering their role in function. Concurrently, there is an increasing need for using perturbations to test predictive models of dynamics-function relationships. Examples are the catalytic cycles of dihydrofolate reductase (DHFR) and cyclophilin A (CypA). In DHFR, mutations that alter the ability of the active site to sample productive higher energy states on the millisecond time scale reduce the rate of hydride transfer significantly. Recently identified rescue mutations restore function, but the mechanism by which they do so remains unclear. The exact role of any changes in the dynamics remains an open question. For CypA, a network of side chains that exchange between two conformations is critical for catalysis. Mutations that lock the network in one state also reduce catalytic activity. A further understanding of enzyme dynamics of well-studied enzymes such as dihydrofolate reductase and cyclophilin A will lead to improvement in ability to modulate the functions of computationally designed enzymes and large macromolecular machines. In designed enzymes, directed evolution experiments increase catalytic rates. Detailed X-ray studies suggest that these mutations likely limit the conformational space explored by residues in the active site. For proteins where atomic resolution information is currently inaccessible, other techniques such as cryo-EM and high-resolution single molecule microscopy continue to advance. Understanding the conformational dynamics of larger systems such as protein machines will likely become more accessible and provide new opportunities to rationally modulate protein function.
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Affiliation(s)
- Gira Bhabha
- Department
of Cellular and Molecular Pharmacology and the Howard Hughes Medical
Institute, University of California, San Francisco, California 94158, United States
| | - Justin T. Biel
- Biophysics Graduate Group, University of California, San Francisco, California 94158, United States
| | - James S. Fraser
- Department of Bioengineering and Therapeutic
Science and California Institute for Quantitative Biology, University of California, San Francisco, California 94158, United States
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26
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Hanoian P, Liu CT, Hammes-Schiffer S, Benkovic S. Perspectives on electrostatics and conformational motions in enzyme catalysis. Acc Chem Res 2015; 48:482-9. [PMID: 25565178 PMCID: PMC4334233 DOI: 10.1021/ar500390e] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Enzymes
are essential for all living organisms, and their effectiveness as
chemical catalysts has driven more than a half century of research
seeking to understand the enormous rate enhancements they provide.
Nevertheless, a complete understanding of the factors that govern
the rate enhancements and selectivities of enzymes remains elusive,
due to the extraordinary complexity and cooperativity that are the
hallmarks of these biomolecules. We have used a combination of site-directed
mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear
magnetic resonance (NMR), vibrational and fluorescence spectroscopies,
resonance energy transfer, and computer simulations to study the implications
of conformational motions and electrostatic interactions on enzyme
catalysis in the enzyme dihydrofolate reductase (DHFR). We have
demonstrated that modest equilibrium conformational changes are functionally
related to the hydride transfer reaction. Results obtained for mutant
DHFRs illustrated that reductions in hydride transfer rates are correlated
with altered conformational motions, and analysis of the evolutionary
history of DHFR indicated that mutations appear to have occurred to
preserve both the hydride transfer rate and the associated conformational
changes. More recent results suggested that differences in local electrostatic
environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination
of primary and solvent kinetic isotope effects, we demonstrated that
the reaction mechanism is consistent across a broad pH range, and
computer simulations suggested that deprotonation of the active site
Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into
the ecDHFR active site provided an experimental tool
for interrogating these microenvironments and for investigating changes
in electrostatics along the DHFR catalytic cycle. Complementary molecular
dynamics simulations in conjunction with mixed quantum mechanical/molecular
mechanical calculations accurately reproduced the vibrational frequency
shifts in these probes and provided atomic-level insight into the
residues influencing these changes. Our findings indicate that conformational
and electrostatic changes are intimately related and functionally
essential. This approach can be readily extended to the study of other
enzyme systems to identify more general trends in the relationship
between conformational fluctuations and electrostatic interactions.
These results are relevant to researchers seeking to design novel
enzymes as well as those seeking to develop therapeutic agents that
function as enzyme inhibitors.
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Affiliation(s)
- Philip Hanoian
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - C. Tony Liu
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Stephen Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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27
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Liu CT, Francis K, Layfield JP, Huang X, Hammes-Schiffer S, Kohen A, Benkovic SJ. Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: temporal order and the roles of Asp27 and Tyr100. Proc Natl Acad Sci U S A 2014; 111:18231-6. [PMID: 25453098 PMCID: PMC4280594 DOI: 10.1073/pnas.1415940111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) has become a model for understanding enzyme catalysis, and yet several details of its mechanism are still unresolved. Specifically, the mechanism of the chemical step, the hydride transfer reaction, is not fully resolved. We found, unexpectedly, the presence of two reactive ternary complexes [enzyme:NADPH:7,8-dihydrofolate (E:NADPH:DHF)] separated by one ionization event. Furthermore, multiple kinetic isotope effect (KIE) studies revealed a stepwise mechanism in which protonation of the DHF precedes the hydride transfer from the nicotinamide cofactor (NADPH) for both reactive ternary complexes of the WT enzyme. This mechanism was supported by the pH- and temperature-independent intrinsic KIEs for the C-H→C hydride transfer between NADPH and the preprotonated DHF. Moreover, we showed that active site residues D27 and Y100 play a synergistic role in facilitating both the proton transfer and subsequent hydride transfer steps. Although D27 appears to have a greater effect on the overall rate of conversion of DHF to tetrahydrofolate, Y100 plays an important electrostatic role in modulating the pKa of the N5 of DHF to enable the preprotonation of DHF by an active site water molecule.
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Affiliation(s)
- C Tony Liu
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Kevin Francis
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242; and
| | - Joshua P Layfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801-3364
| | - Xinyi Huang
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801-3364
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242; and
| | - Stephen J Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802;
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28
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Luk LYP, Ruiz-Pernía JJ, Dawson WM, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant. J Am Chem Soc 2014; 136:17317-23. [PMID: 25396728 DOI: 10.1021/ja5102536] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Catalysis by dihydrofolate reductase from the moderately thermophilic bacterium Geobacillus stearothermophilus (BsDHFR) was investigated by isotope substitution of the enzyme. The enzyme kinetic isotope effect for hydride transfer was close to unity at physiological temperatures but increased with decreasing temperatures to a value of 1.65 at 5 °C. This behavior is opposite to that observed for DHFR from Escherichia coli (EcDHFR), where the enzyme kinetic isotope effect increased slightly with increasing temperature. These experimental results were reproduced in the framework of variational transition-state theory that includes a dynamical recrossing coefficient that varies with the mass of the protein. Our simulations indicate that BsDHFR has greater flexibility than EcDHFR on the ps-ns time scale, which affects the coupling of the environmental motions of the protein to the chemical coordinate and consequently to the recrossing trajectories on the reaction barrier. The intensity of the dynamic coupling in DHFRs is influenced by compensatory temperature-dependent factors, namely the enthalpic barrier needed to achieve an ideal transition-state configuration with minimal nonproductive trajectories and the protein disorder that disrupts the electrostatic preorganization required to stabilize the transition state. Together with our previous studies of other DHFRs, the results presented here provide a general explanation why protein dynamic effects vary between enzymes. Our theoretical treatment demonstrates that these effects can be satisfactorily reproduced by including a transmission coefficient in the rate constant calculation, whose dependence on temperature is affected by the protein flexibility.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry and ∥Cardiff Catalysis Institute, School of Chemistry, Cardiff University , Park Place, Cardiff, CF10 3AT, United Kingdom
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29
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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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30
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Francis K, Kohen A. Protein motions and the activation of the CH bond catalyzed by dihydrofolate reductase. Curr Opin Chem Biol 2014; 21:19-24. [PMID: 24742825 PMCID: PMC4149937 DOI: 10.1016/j.cbpa.2014.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 03/03/2014] [Accepted: 03/05/2014] [Indexed: 11/28/2022]
Abstract
The role of protein motions in enzymatic CH→C transfer is an area of great contemporary debate. An effective tool in probing such a role is the temperature dependence of the intrinsic kinetic isotope effects for the enzyme-catalyzed reaction. The outcome of those experiments is interpreted within the context of phenomenological Marcus-like models of hydrogen tunneling. The current review focuses on recent studies of dihydrofolate reductase (DHFR) and how the role of protein motions in the catalyzed reaction has been demonstrated. The motions in DHFR are controlled by local effects of active site residues, global effects involving remote residues across the enzyme and appear to be preserved during the evolution of the enzyme from bacteria to human.
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Affiliation(s)
- Kevin Francis
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, United States
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, United States.
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31
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Luk LP, Loveridge EJ, Allemann RK. Different dynamical effects in mesophilic and hyperthermophilic dihydrofolate reductases. J Am Chem Soc 2014; 136:6862-5. [PMID: 24779446 PMCID: PMC4046772 DOI: 10.1021/ja502673h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Indexed: 01/18/2023]
Abstract
The role of protein dynamics in the reaction catalyzed by dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) has been examined by enzyme isotope substitution ((15)N, (13)C, (2)H). In contrast to all other enzyme reactions investigated previously, including DHFR from Escherichia coli (EcDHFR), for which isotopic substitution led to decreased reactivity, the rate constant for the hydride transfer step is not affected by isotopic substitution of TmDHFR. TmDHFR therefore appears to lack the coupling of protein motions to the reaction coordinate that have been identified for EcDHFR catalysis. Clearly, dynamical coupling is not a universal phenomenon that affects the efficiency of enzyme catalysis.
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Affiliation(s)
- Louis
Y. P. Luk
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - E. Joel Loveridge
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
- Cardiff
Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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32
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Swiderek K, Ruiz-Pernía JJ, Moliner V, Tuñón I. Heavy enzymes--experimental and computational insights in enzyme dynamics. Curr Opin Chem Biol 2014; 21:11-8. [PMID: 24709164 DOI: 10.1016/j.cbpa.2014.03.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/14/2014] [Indexed: 11/18/2022]
Abstract
The role of protein motions in the chemical step of enzyme-catalyzed reactions is the subject of an open debate in the scientific literature. The systematic use of isotopically substituted enzymes has been revealed as a useful tool to quantify the role of these motions. According to the Born-Oppenheimer approximation, changing the mass of the protein does not change the forces acting on the system but alters the frequencies of the protein motions, which in turn can affect the rate constant. Experimental and theoretical studies carried out in this field are presented in this article and discussed in the framework of Transition State Theory.
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Affiliation(s)
- Katarzyna Swiderek
- Departamento de Química Física, Universitat de València, 46100 Burjassot, Spain; Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - J Javier Ruiz-Pernía
- Departamento de Química Física y Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Departamento de Química Física y Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de València, 46100 Burjassot, Spain.
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33
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Singh P, Sen A, Francis K, Kohen A. Extension and limits of the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. J Am Chem Soc 2014; 136:2575-82. [PMID: 24450297 PMCID: PMC3985941 DOI: 10.1021/ja411998h] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Enzyme catalysis
has been studied extensively, but the role of
enzyme dynamics in the catalyzed chemical conversion is still an enigma.
The enzyme dihydrofolate reductase (DHFR) is often used as a model
system to assess a network of coupled motions across the protein that
may affect the catalyzed chemical transformation. Molecular dynamics
simulations, quantum mechanical/molecular mechanical studies, and
bioinformatics studies have suggested the presence of a “global
dynamic network” of residues in DHFR. Earlier studies of two
DHFR distal mutants, G121V and M42W, indicated that these residues
affect the chemical step synergistically. While this finding was in
accordance with the concept of a network of functional motions across
the protein, two residues do not constitute a network. To better define
the extent and limits of the proposed network, the current work studied
two remote residues predicted to be part of the same network: W133
and F125. The effect of mutations in these residues on the nature
of the chemical step was examined via measurements of the temperature-dependence
of the intrinsic kinetic isotope effects (KIEs) and other kinetic
parameters, and double mutants were used to tie the findings to G121
and M42. The findings indicate that residue F125, which was implicated
by both calculations and bioinformatic methods, is a part of the same
global dynamic network as G121 and M42, while W133, implicated only
by bioinformatics, is not. These findings extend our understanding
of the proposed network and the relations between functional and genomic
couplings. Delineating that network illuminates the need to consider
remote residues and protein structural dynamics in the rational design
of drugs and of biomimetic catalysts.
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Affiliation(s)
- Priyanka Singh
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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