1
|
Affiliation(s)
- Matthias Heyden
- School of Molecular Sciences, Arizona State University, P.O. Box 871604, Tempe, Arizona 85287-1604, United States
| | - Dmitry V. Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
| |
Collapse
|
2
|
Abstract
The vibrational Stark effect in proteins yields line shifts indicative of strong internal electric fields up to a few volts per angstrom. These values are supported by numerical simulations of proteins. The simulations also show a significant breadth of field fluctuations translating to inhomogeneous broadening of vibrational lines. According to fluctuation-dissipation arguments, strong internal fields should lead to broad lines. Experimentally reported vibrational lines in proteins are, however, very narrow. This disconnect is explained here in terms of the insufficient (nonergodic) sampling of the protein's configurations on the lifetime of the vibrational probe. The slow component of the electric field fluctuations in proteins relaxes on the time scale of tens of nanoseconds and is dynamically frozen on the vibrational lifetime.
Collapse
Affiliation(s)
- Daniel R Martin
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, United States
| | - Dmitry V Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, United States
| |
Collapse
|
3
|
Wu Y, Fried SD, Boxer SG. A Preorganized Electric Field Leads to Minimal Geometrical Reorientation in the Catalytic Reaction of Ketosteroid Isomerase. J Am Chem Soc 2020; 142:9993-9998. [PMID: 32378409 DOI: 10.1021/jacs.0c00383] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrostatic interactions play a pivotal role in enzymatic catalysis and are increasingly modeled explicitly in computational enzyme design; nevertheless, they are challenging to measure experimentally. Using vibrational Stark effect (VSE) spectroscopy, we have measured electric fields inside the active site of the enzyme ketosteroid isomerase (KSI). These studies have shown that these fields can be unusually large, but it has been unclear to what extent they specifically stabilize the transition state (TS) relative to a ground state (GS). In the following, we use crystallography and computational modeling to show that KSI's intrinsic electric field is nearly perfectly oriented to stabilize the geometry of its reaction's TS. Moreover, we find that this electric field adjusts the orientation of its substrate in the ground state so that the substrate needs to only undergo minimal structural changes upon activation to its TS. This work provides evidence that the active site electric field in KSI is preorganized to facilitate catalysis and provides a template for how electrostatic preorganization can be measured in enzymatic systems.
Collapse
Affiliation(s)
- Yufan Wu
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Stephen D Fried
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| |
Collapse
|
4
|
Affiliation(s)
- Valerie Vaissier Welborn
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California 94720, United States
| |
Collapse
|
5
|
Derr JB, Tamayo J, Espinoza EM, Clark JA, Vullev VI. Dipole-induced effects on charge transfer and charge transport. Why do molecular electrets matter? CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0389] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Charge transfer (CT) and charge transport (CTr) are at the core of life-sustaining biological processes and of processes that govern the performance of electronic and energy-conversion devices. Electric fields are invaluable for guiding charge movement. Therefore, as electrostatic analogues of magnets, electrets have unexplored potential for generating local electric fields for accelerating desired CT processes and suppressing undesired ones. The notion about dipole-generated local fields affecting CT has evolved since the middle of the 20th century. In the 1990s, the first reports demonstrating the dipole effects on the kinetics of long-range electron transfer appeared. Concurrently, the development of molecular-level designs of electric junctions has led the exploration of dipole effects on CTr. Biomimetic molecular electrets such as polypeptide helices are often the dipole sources in CT systems. Conversely, surface-charge electrets and self-assembled monolayers of small polar conjugates are the preferred sources for modifying interfacial electric fields for controlling CTr. The multifaceted complexity of such effects on CT and CTr testifies for the challenges and the wealth of this field that still remains largely unexplored. This review outlines the basic concepts about dipole effects on CT and CTr, discusses their evolution, and provides accounts for their future developments and impacts.
Collapse
Affiliation(s)
- James B. Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Jesse Tamayo
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Eli M. Espinoza
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - John A. Clark
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
| | - Valentine I. Vullev
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
- Department of Chemistry, University of California, Riverside, CA 92521, USA
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
- Materials Science and Engineering Program, University of California, Riverside, CA 92521, USA
| |
Collapse
|
6
|
Abstract
What happens inside an enzyme's active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists' attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme's active site. These experiments have provided compelling evidence supporting a major electrostatic contribution to enzymatic catalysis. Here, we review these results and develop a simple model for electrostatic catalysis that enables us to incorporate disparate concepts introduced by many investigators to describe how enzymes work into a more unified framework stressing the importance of electric fields at the active site.
Collapse
Affiliation(s)
- Stephen D Fried
- Proteins and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305;
| |
Collapse
|
7
|
Bhowmick A, Sharma SC, Head-Gordon T. The Importance of the Scaffold for de Novo Enzymes: A Case Study with Kemp Eliminase. J Am Chem Soc 2017; 139:5793-5800. [DOI: 10.1021/jacs.6b12265] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Teresa Head-Gordon
- Chemical
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
| |
Collapse
|
8
|
Lu X, Ovchinnikov V, Demapan D, Roston D, Cui Q. Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin. Biochemistry 2017; 56:1482-1497. [PMID: 28225609 DOI: 10.1021/acs.biochem.7b00016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanism of ATP hydrolysis in the myosin motor domain is analyzed using a combination of DFTB3/CHARMM simulations and enhanced sampling techniques. The motor domain is modeled in the pre-powerstroke state, in the post-rigor state, and as a hybrid based on the post-rigor state with a closed nucleotide-binding pocket. The ATP hydrolysis activity is found to depend on the positioning of nearby water molecules, and a network of polar residues facilitates proton transfer and charge redistribution during hydrolysis. Comparison of the observed hydrolysis pathways and the corresponding free energy profiles leads to detailed models for the mechanism of ATP hydrolysis in the pre-powerstroke state and proposes factors that regulate the hydrolysis activity in different conformational states. In the pre-powerstroke state, the scissile Pγ-O3β bond breaks early in the reaction. Proton transfer from the lytic water to the γ-phosphate through active site residues is an important part of the kinetic bottleneck; several hydrolysis pathways that feature distinct proton transfer routes are found to have similar free energy barriers, suggesting a significant degree of plasticity in the hydrolysis mechanism. Comparison of hydrolysis in the pre-powerstroke state and the closed post-rigor model suggests that optimization of residues beyond the active site for electrostatic stabilization and preorganization is likely important to enzyme design.
Collapse
Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Boston, Massachusetts 02138, United States
| | - Darren Demapan
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
9
|
Beker W, van der Kamp MW, Mulholland AJ, Sokalski WA. Rapid Estimation of Catalytic Efficiency by Cumulative Atomic Multipole Moments: Application to Ketosteroid Isomerase Mutants. J Chem Theory Comput 2017; 13:945-955. [PMID: 28103023 DOI: 10.1021/acs.jctc.6b01131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a simple atomic multipole electrostatic model to rapidly evaluate the effects of mutation on enzyme activity and test its performance on wild-type and mutant ketosteroid isomerase. The predictions of our atomic multipole model are similar to those obtained with symmetry-adapted perturbation theory at a fraction of the computational cost. We further show that this approach is relatively insensitive to the precise amino acid side chain conformation in mutants and may thus be useful in computational enzyme (re)design.
Collapse
Affiliation(s)
- Wiktor Beker
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wrocław University of Science and Technology , Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Marc W van der Kamp
- School of Biochemistry, Biomedical Sciences Building, University Walk , Bristol BS8 1TD, United Kingdom.,BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, Tyndall Avenue, University of Bristol , Bristol BS8 1TQ, United Kingdom.,Centre of Computational Chemistry, School of Chemistry, Cantock's Close, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - Adrian J Mulholland
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, Tyndall Avenue, University of Bristol , Bristol BS8 1TQ, United Kingdom.,Centre of Computational Chemistry, School of Chemistry, Cantock's Close, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - W Andrzej Sokalski
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wrocław University of Science and Technology , Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| |
Collapse
|
10
|
Schneider SH, Boxer SG. Vibrational Stark Effects of Carbonyl Probes Applied to Reinterpret IR and Raman Data for Enzyme Inhibitors in Terms of Electric Fields at the Active Site. J Phys Chem B 2016; 120:9672-84. [PMID: 27541577 DOI: 10.1021/acs.jpcb.6b08133] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases. These results demonstrate that the vibrational Stark effect provides a general framework for estimating the electrostatic contribution to the catalytic rate and may provide a metric for the design or modification of enzymes. Opportunities and limitations of the approach are also described.
Collapse
Affiliation(s)
- Samuel H Schneider
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| |
Collapse
|