101
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Boehr DD, D'Amico RN, O'Rourke KF. Engineered control of enzyme structural dynamics and function. Protein Sci 2018; 27:825-838. [PMID: 29380452 DOI: 10.1002/pro.3379] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 12/20/2022]
Abstract
Enzymes undergo a range of internal motions from local, active site fluctuations to large-scale, global conformational changes. These motions are often important for enzyme function, including in ligand binding and dissociation and even preparing the active site for chemical catalysis. Protein engineering efforts have been directed towards manipulating enzyme structural dynamics and conformational changes, including targeting specific amino acid interactions and creation of chimeric enzymes with new regulatory functions. Post-translational covalent modification can provide an additional level of enzyme control. These studies have not only provided insights into the functional role of protein motions, but they offer opportunities to create stimulus-responsive enzymes. These enzymes can be engineered to respond to a number of external stimuli, including light, pH, and the presence of novel allosteric modulators. Altogether, the ability to engineer and control enzyme structural dynamics can provide new tools for biotechnology and medicine.
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Affiliation(s)
- David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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102
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Cooperativity and flexibility in enzyme evolution. Curr Opin Struct Biol 2018; 48:83-92. [DOI: 10.1016/j.sbi.2017.10.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 11/23/2022]
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103
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Mehaffey MR, Cammarata MB, Brodbelt JS. Tracking the Catalytic Cycle of Adenylate Kinase by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2018; 90:839-846. [PMID: 29188992 PMCID: PMC5750083 DOI: 10.1021/acs.analchem.7b03591] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The complex interplay of dynamic protein plasticity and specific side-chain interactions with substrate molecules that allows enzymes to catalyze reactions has yet to be fully unraveled. Top-down ultraviolet photodissociation (UVPD) mass spectrometry is used to track snapshots of conformational fluctuations in the phosphotransferase adenylate kinase (AK) throughout its active reaction cycle by characterization of complexes containing AK and each of four different adenosine phosphate ligands. Variations in efficiencies of UVPD backbone cleavages were consistently observed for three α-helices and the adenosine binding regions for AK complexes representing different steps of the catalytic cycle, implying that these stretches of the protein sample various structural microstates as the enzyme undergoes global open-to-closed transitions. Focusing on the conformational impact of recruiting or releasing the Mg2+ cofactor highlights two loop regions for which fragmentation increases upon UVPD, signaling an increase in loop flexibility as the metal cation disrupts the loop interactions with the substrate ligands. Additionally, the observation of holo ions and variations in UVPD backbone cleavage efficiency at R138 implicate this conserved active site residue in stabilizing the donor phosphoryl group during catalysis. This study showcases the utility of UVPD-MS to provide insight into conformational fluctuations of single residues for active enzymes.
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Affiliation(s)
- M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
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104
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Roca M, Moliner V, Tuñón I. Origin of Enzymatic Kinetic Isotope Effects in Human Purine Nucleoside Phosphorylase. ACS Catal 2017. [DOI: 10.1021/acscatal.7b04199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Roca
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - V. Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - I. Tuñón
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
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105
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Klinman JP, Offenbacher AR, Hu S. Origins of Enzyme Catalysis: Experimental Findings for C-H Activation, New Models, and Their Relevance to Prevailing Theoretical Constructs. J Am Chem Soc 2017; 139:18409-18427. [PMID: 29244501 PMCID: PMC5812730 DOI: 10.1021/jacs.7b08418] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The physical basis for enzymatic rate accelerations is a subject of great fundamental interest and of direct relevance to areas that include the de novo design of green catalysts and the pursuit of new drug regimens. Extensive investigations of C-H activating systems have provided considerable insight into the relationship between an enzyme's overall structure and the catalytic chemistry at its active site. This Perspective highlights recent experimental data for two members of distinct, yet iconic C-H activation enzyme classes, lipoxygenases and prokaryotic alcohol dehydrogenases. The data necessitate a reformulation of the dominant textbook definition of biological catalysis. A multidimensional model emerges that incorporates a range of protein motions that can be parsed into a combination of global stochastic conformational thermal fluctuations and local donor-acceptor distance sampling. These motions are needed to achieve a high degree of precision with regard to internuclear distances, geometries, and charges within the active site. The available model also suggests a physical framework for understanding the empirical enthalpic barrier in enzyme-catalyzed processes. We conclude by addressing the often conflicting interface between computational and experimental chemists, emphasizing the need for computation to predict experimental results in advance of their measurement.
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Affiliation(s)
- Judith P Klinman
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
| | - Adam R Offenbacher
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
| | - Shenshen Hu
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
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106
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Paul I, Goswami A, Mittal N, Schmittel M. Catalytic Three-Component Machinery: Control of Catalytic Activity by Machine Speed. Angew Chem Int Ed Engl 2017; 57:354-358. [DOI: 10.1002/anie.201709644] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/30/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Indrajit Paul
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I; University of Siegen; Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Abir Goswami
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I; University of Siegen; Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Nikita Mittal
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I; University of Siegen; Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Michael Schmittel
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I; University of Siegen; Adolf-Reichwein-Str. 2 57068 Siegen Germany
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107
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Paul I, Goswami A, Mittal N, Schmittel M. Katalytische Drei-Komponenten-Maschinen: Steuerung der katalytischen Aktivität mittels Maschinengeschwindigkeit. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Indrajit Paul
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I; Universität Siegen; Adolf-Reichwein-Straße 2 57068 Siegen Deutschland
| | - Abir Goswami
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I; Universität Siegen; Adolf-Reichwein-Straße 2 57068 Siegen Deutschland
| | - Nikita Mittal
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I; Universität Siegen; Adolf-Reichwein-Straße 2 57068 Siegen Deutschland
| | - Michael Schmittel
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I; Universität Siegen; Adolf-Reichwein-Straße 2 57068 Siegen Deutschland
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108
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Ranasinghe C, Guo Q, Sapienza PJ, Lee AL, Quinn DM, Cheatum CM, Kohen A. Protein Mass Effects on Formate Dehydrogenase. J Am Chem Soc 2017; 139:17405-17413. [PMID: 29083897 PMCID: PMC5800309 DOI: 10.1021/jacs.7b08359] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isotopically labeled enzymes (denoted as "heavy" or "Born-Oppenheimer" enzymes) have been used to test the role of protein dynamics in catalysis. The original idea was that the protein's higher mass would reduce the frequency of its normal-modes without altering its electrostatics. Heavy enzymes have been used to test if the vibrations in the native enzyme are coupled to the chemistry it catalyzes, and different studies have resulted in ambiguous findings. Here the temperature-dependence of intrinsic kinetic isotope effects of the enzyme formate dehydrogenase is used to examine the distribution of H-donor to H-acceptor distance as a function of the protein's mass. The protein dynamics are altered in the heavy enzyme to diminish motions that determine the transition state sampling in the native enzyme, in accordance with a Born-Oppenheimer-like effect on bond activation. Findings of this work suggest components related to fast frequencies that can be explained by Born-Oppenheimer enzyme hypothesis (vibrational) and also slower time scale events that are non-Born-Oppenheimer in nature (electrostatic), based on evaluations of protein mass dependence of donor-acceptor distance and forward commitment to catalysis along with steady state and single turnover measurements. Together, the findings suggest that the mass modulation affected both local, fast, protein vibrations associated with the catalyzed chemistry and the protein's macromolecular electrostatics at slower time scales; that is, both Born-Oppenheimer and non-Born-Oppenheimer effects are observed. Comparison to previous studies leads to the conclusion that isotopic labeling of the protein may have different effects on different systems, however, making heavy enzyme studies a very exciting technique for exploring the dynamics link to catalysis in proteins.
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Affiliation(s)
- Chethya Ranasinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | - Qi Guo
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | - Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel M. Quinn
- 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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109
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Zinovjev K, Tuñón I. Quantifying the limits of transition state theory in enzymatic catalysis. Proc Natl Acad Sci U S A 2017; 114:12390-12395. [PMID: 29101125 PMCID: PMC5703300 DOI: 10.1073/pnas.1710820114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While being one of the most popular reaction rate theories, the applicability of transition state theory to the study of enzymatic reactions has been often challenged. The complex dynamic nature of the protein environment raised the question about the validity of the nonrecrossing hypothesis, a cornerstone in this theory. We present a computational strategy to quantify the error associated to transition state theory from the number of recrossings observed at the equicommittor, which is the best possible dividing surface. Application of a direct multidimensional transition state optimization to the hydride transfer step in human dihydrofolate reductase shows that both the participation of the protein degrees of freedom in the reaction coordinate and the error associated to the nonrecrossing hypothesis are small. Thus, the use of transition state theory, even with simplified reaction coordinates, provides a good theoretical framework for the study of enzymatic catalysis.
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Affiliation(s)
- Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
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110
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Gurinov AA, Denisov GS, Borissova AO, Goloveshkin AS, Greindl J, Limbach HH, Shenderovich IG. NMR Study of Solvation Effect on the Geometry of Proton-Bound Homodimers of Increasing Size. J Phys Chem A 2017; 121:8697-8705. [PMID: 29064692 DOI: 10.1021/acs.jpca.7b09285] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bond geometries in the proton-bound homodimers of quinoline and acridine derivatives in an aprotic polar solution have been experimentally studied using 1H NMR at 120 K. The reported results show that an increase of the dielectric permittivity of the medium results in contraction of the N···N distance. The degree of contraction depends on the homodimer's size and its substituent-specific solvation features. Neither of these effects can be reproduced using conventional implicit solvent models employed in computational studies. In general, the N···N distance in the homodimers of pyridine, quinoline, and acridine derivatives decreases in the sequence gas phase > solid state > polar solvent.
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Affiliation(s)
- Andrei A Gurinov
- Institute of Chemistry and Biochemistry, Free University Berlin , Takustrasse 3, 14195 Berlin, Germany.,The Imaging and Characterization Core Lab, King Abdullah University of Science and Technology , Al-Khawarizimi Building 01, Thuwal 23955-6900, Saudi Arabia
| | - Gleb S Denisov
- Institute of Physics, St. Petersburg State University , Ulyanovskaya str. 1, 198504 St. Petersburg, Russian Federation
| | - Alexandra O Borissova
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , 119991, Vavilov Str., 28, Moscow, Russia
| | - Alexander S Goloveshkin
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , 119991, Vavilov Str., 28, Moscow, Russia
| | - Julian Greindl
- Institute of Organic Chemistry, University of Regensburg , Universitaetstrasse 31, 93053 Regensburg, Germany
| | - Hans-Heinrich Limbach
- Institute of Chemistry and Biochemistry, Free University Berlin , Takustrasse 3, 14195 Berlin, Germany
| | - Ilya G Shenderovich
- Institute of Chemistry and Biochemistry, Free University Berlin , Takustrasse 3, 14195 Berlin, Germany.,Institute of Organic Chemistry, University of Regensburg , Universitaetstrasse 31, 93053 Regensburg, Germany
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111
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Multiscale approach to the activation and phosphotransfer mechanism of CpxA histidine kinase reveals a tight coupling between conformational and chemical steps. Biochem Biophys Res Commun 2017; 498:305-312. [PMID: 28911864 DOI: 10.1016/j.bbrc.2017.09.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/23/2017] [Accepted: 09/08/2017] [Indexed: 11/21/2022]
Abstract
Sensor histidine kinases (SHKs) are an integral component of the molecular machinery that permits bacteria to adapt to widely changing environmental conditions. CpxA, an extensively studied SHK, is a multidomain homodimeric protein with each subunit consisting of a periplasmic sensor domain, a transmembrane domain, a signal-transducing HAMP domain, a dimerization and histidine phospho-acceptor sub-domain (DHp) and a catalytic and ATP-binding subdomain (CA). The key activation event involves the rearrangement of the HAMP-DHp helical core and translation of the CA towards the acceptor histidine, which presumably results in an autokinase-competent complex. In the present work we integrate coarse-grained, all-atom, and hybrid QM-MM computer simulations to probe the large-scale conformational reorganization that takes place from the inactive to the autokinase-competent state (conformational step), and evaluate its relation to the autokinase reaction itself (chemical step). Our results highlight a tight coupling between conformational and chemical steps, underscoring the advantage of CA walking along the DHp core, to favor a reactive tautomeric state of the phospho-acceptor histidine. The results not only represent an example of multiscale modelling, but also show how protein dynamics can promote catalysis.
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112
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Lee YV, Choi SB, Wahab HA, Choong YS. Active Site Flexibility of Mycobacterium tuberculosis Isocitrate Lyase in Dimer Form. J Chem Inf Model 2017; 57:2351-2357. [PMID: 28820943 DOI: 10.1021/acs.jcim.7b00265] [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
Tuberculosis (TB) still remains a global threat due to the emergence of a drug-resistant strain. Instead of focusing on the drug target of active stage TB, we are highlighting the isocitrate lyase (ICL) at the dormant stage TB. ICL is one of the persistent factors for Mycobacterium tuberculosis (MTB) to survive during the dormant phase. In addition, the absence of ICL in human has made ICL a potential drug target for TB therapy. However, the dynamic details of ICL which could give insights to the ICL-ligand interaction have yet to be solved. Therefore, a series of ICL dimer dynamics studies through molecular dynamics simulation were performed in this work. The ICL active site entrance gate closure is contributed to by hydrogen bonding and electrostatic interactions with the C-terminal. Analysis suggested that the open-closed behavior of the ICL active site entrance depends on the type of ligand present in the active site. We also observed four residues (Ser91, Asp108, Asp153, and Cys191) which could possibly be the nucleophiles for nucleophilic attack on the cleavage of isocitrate at the C2-C3 bond. We hope that the elucidation of ICL dynamics can benefit future works such as lead identification or antibody design against ICL for TB therapeutics.
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Affiliation(s)
- Yie-Vern Lee
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
| | - Sy Bing Choi
- Pharmaceutical Design and Simulation Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
| | - Habibah A Wahab
- Pharmaceutical Design and Simulation Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
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113
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Elementary S N 2 reaction revisited. Effects of solvent and alkyl chain length on kinetics of halogen exchange in haloalkanes elucidated by Empirical Valence Bond simulation. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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114
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Sharma B, Jamdar SN, Ghosh B, Yadav P, Kumar A, Kundu S, Goyal VD, Makde RD. Active site gate of M32 carboxypeptidases illuminated by crystal structure and molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1406-1415. [PMID: 28844748 DOI: 10.1016/j.bbapap.2017.07.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 01/09/2023]
Abstract
Enzyme gates are important dynamic features that regulate function. Study of these features is critical for understanding of enzyme mechanism. In this study, the active-site gate of M32 carboxypeptidases (M32CP) is illuminated. Only a handful of members of this family have been structurally and functionally characterized and various aspects of their activity and mechanism are yet not clarified. Here, crystal structure of putative M32CP from Deinococcus radiodurans (M32dr) was solved to 2.4Å resolution. Enzymatic assays confirmed its identity as a carboxypeptidase. Open and relatively closed conformations observed in the structure provided supporting evidence for previously hypothesized hinge motion in this family of enzymes. Molecular dynamics simulations of 1.5μs displayed distinct open and closed conformations revealing amplitude of the motion to be beyond what was observed in the crystal structure. Hinge region and anchoring region of this shell-type gate were identified. A small displacement of 3Å and a helical tilt of 9° propagated by the hinge region translates into a 10Å motion at the top of the gate. The dynamics of the gate was supported by our mutagenesis experiment involving formation of disulphide bond across helices of the gate. The nearly inactive mutant enzyme showed 65-fold increase in the enzymatic activity in presence of reducing agent. Further, while a previously proposed structural basis would have led to its classification in subfamily II, experimentally observed substrate length restriction places M32dr in subfamily I of M32CPs.
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Affiliation(s)
- Bhaskar Sharma
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Biplab Ghosh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Pooja Yadav
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.
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115
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Abstract
Enzyme isotope effects, or the kinetic effects of "heavy" enzymes, refer to the effect of isotopically labeled protein residues on the enzyme's activity or physical properties. These effects are increasingly employed in the examination of the possible contributions of protein dynamics to enzyme catalysis. One hypothesis assumed that isotopic substitution of all 12C, 14N, and nonexchangeable 1H by 13C, 15N, and 2H, would slow down protein picosecond to femtosecond dynamics without any effect on the system's electrostatics following the Born-Oppenheimer approximation. It was suggested that reduced reaction rates reported for several "heavy" enzymes accords with that hypothesis. However, numerous deviations from the predictions of that hypothesis were also reported. Current studies also attempt to test the role of individual residues by site-specific labeling or by labeling a pattern of residues on activity. It appears that in several systems the protein's fast dynamics are indeed reduced in "heavy" enzymes in a way that reduces the probability of barrier crossing of its chemical step. Other observations, however, indicated that slower protein dynamics are electrostatically altered in isotopically labeled enzymes. Interestingly, these effects appear to be system dependent, thus it might be premature to suggest a general role of "heavy" enzymes' effect on catalysis.
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116
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Filip-Granit N, Goldberg E, Samish I, Ashur I, van der Boom ME, Cohen H, Scherz A. Submolecular Gates Self-Assemble for Hot-Electron Transfer in Proteins. J Phys Chem B 2017; 121:6981-6988. [PMID: 28498662 DOI: 10.1021/acs.jpcb.7b00432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Redox reactions play key roles in fundamental biological processes. The related spatial organization of donors and acceptors is assumed to undergo evolutionary optimization facilitating charge mobilization within the relevant biological context. Experimental information from submolecular functional sites is needed to understand the organization strategies and driving forces involved in the self-development of structure-function relationships. Here we exploit chemically resolved electrical measurements (CREM) to probe the atom-specific electrostatic potentials (ESPs) in artificial arrays of bacteriochlorophyll (BChl) derivatives that provide model systems for photoexcited (hot) electron donation and withdrawal. On the basis of computations we show that native BChl's in the photosynthetic reaction center (RC) self-assemble at their ground-state as aligned gates for functional charge transfer. The combined computational and experimental results further reveal how site-specific polarizability perpendicular to the molecular plane enhances the hot-electron transport. Maximal transport efficiency is predicted for a specific, ∼5 Å, distance above the center of the metalized BChl, which is in remarkably close agreement with the distance and mutual orientation of corresponding native cofactors. These findings provide new metrics and guidelines for analysis of biological redox centers and for designing charge mobilizing machines such as artificial photosynthesis.
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Affiliation(s)
- Neta Filip-Granit
- Department of Plant and Environmental Sciences, ‡Department of Organic Chemistry, and §Department of Chemical Research Support, Weizmann Institute of Science , Rehovot, 7610001, Israel
| | - Eran Goldberg
- Department of Plant and Environmental Sciences, ‡Department of Organic Chemistry, and §Department of Chemical Research Support, Weizmann Institute of Science , Rehovot, 7610001, Israel
| | - Ilan Samish
- Department of Plant and Environmental Sciences, ‡Department of Organic Chemistry, and §Department of Chemical Research Support, Weizmann Institute of Science , Rehovot, 7610001, Israel
| | - Idan Ashur
- Department of Plant and Environmental Sciences, ‡Department of Organic Chemistry, and §Department of Chemical Research Support, Weizmann Institute of Science , Rehovot, 7610001, Israel
| | - Milko E van der Boom
- Department of Plant and Environmental Sciences, ‡Department of Organic Chemistry, and §Department of Chemical Research Support, Weizmann Institute of Science , Rehovot, 7610001, Israel
| | - Hagai Cohen
- Department of Plant and Environmental Sciences, ‡Department of Organic Chemistry, and §Department of Chemical Research Support, Weizmann Institute of Science , Rehovot, 7610001, Israel
| | - Avigdor Scherz
- Department of Plant and Environmental Sciences, ‡Department of Organic Chemistry, and §Department of Chemical Research Support, Weizmann Institute of Science , Rehovot, 7610001, Israel
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117
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Verma R, Mitchell-Koch K. In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function. Catalysts 2017; 7:212. [PMID: 30464857 PMCID: PMC6241538 DOI: 10.3390/catal7070212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.
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Affiliation(s)
- Rajni Verma
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
| | - Katie Mitchell-Koch
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
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118
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Roy S, Schopf P, Warshel A. Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions. J Phys Chem B 2017; 121:6520-6526. [PMID: 28613876 DOI: 10.1021/acs.jpcb.7b03698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The origin of the non-Arrhenius behavior of the rate constant for hydride transfer enzymatic reactions has been a puzzling problem since its initial observation. This effect has been used originally to support the idea that enzymes work by dynamical effects and more recently to suggest an entropy funnel model. Our analysis, however, has advanced the idea that the reason for the non-Arrhenius trend reflects the temperature dependence of the rearrangements of the protein polar groups in response to the change in the charge distribution of the reacting system during the transition from the ground state (GS) to the transition state (TS). Here we examine the validity of our early proposal by simulating the catalytic reaction of alcohol dehydrogenase (ADH) and determine the microscopic origin of the entropic and enthalpic contributions to the activation barrier. The corresponding analysis establishes the origin of the non-Arrhenius behaviors and quantifies our original suggestion that the classical effect is due to the entropic contributions of the environment. We also find that the quantum effects reflect in part the temperature dependence of the donor-acceptor distance.
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Affiliation(s)
- Subhendu Roy
- Department of Chemistry, University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Patrick Schopf
- Astex Pharmaceuticals , Cambridge CB4 0QA, United Kingdom
| | - Arieh Warshel
- Department of Chemistry, University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
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119
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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.
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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;
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120
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Koldewey P, Horowitz S, Bardwell JCA. Chaperone-client interactions: Non-specificity engenders multifunctionality. J Biol Chem 2017; 292:12010-12017. [PMID: 28620048 DOI: 10.1074/jbc.r117.796862] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here, we provide an overview of the different mechanisms whereby three different chaperones, Spy, Hsp70, and Hsp60, interact with folding proteins, and we discuss how these chaperones may guide the folding process. Available evidence suggests that even a single chaperone can use many mechanisms to aid in protein folding, most likely due to the need for most chaperones to bind clients promiscuously. Chaperone mechanism may be better understood by always considering it in the context of the client's folding pathway and biological function.
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Affiliation(s)
- Philipp Koldewey
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Scott Horowitz
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109.
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121
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Rekik N, Alshammari MF. Electrical anharmonicity and dampings contributions to Cl- H→ stretching band in gaseous (CH 3 ) 2 O…HCl complex: Quantum dynamic study and prediction of the temperature effects. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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122
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Carter CW, Chandrasekaran SN, Weinreb V, Li L, Williams T. Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:032101. [PMID: 28191480 PMCID: PMC5272822 DOI: 10.1063/1.4974218] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
We measured and cross-validated the energetics of networks in Bacillus stearothermophilus Tryptophanyl-tRNA synthetase (TrpRS) using both multi-mutant and modular thermodynamic cycles. Multi-dimensional combinatorial mutagenesis showed that four side chains from this "molecular switch" move coordinately with the active-site Mg2+ ion as the active site preorganizes to stabilize the transition state for amino acid activation. A modular thermodynamic cycle consisting of full-length TrpRS, its Urzyme, and the Urzyme plus each of the two domains deleted in the Urzyme gives similar energetics. These dynamic linkages, although unlikely to stabilize the transition-state directly, consign the active-site preorganization to domain motion, assuring coupled vectorial behavior.
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Affiliation(s)
- Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA
| | - Srinivas Niranj Chandrasekaran
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA
| | - Violetta Weinreb
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA
| | - Li Li
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA
| | - Tishan Williams
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7260, USA
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123
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Medvedev MG, Panova MV, Chilov GG, Bushmarinov IS, Novikov FN, Stroganov OV, Zeifman AA, Svitanko IV. Exhaustive conformational search for transition states: the case of catechol O -methyltransferase active site. MENDELEEV COMMUNICATIONS 2017. [DOI: 10.1016/j.mencom.2017.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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124
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Aquilanti V, Coutinho ND, Carvalho-Silva VH. Kinetics of low-temperature transitions and a reaction rate theory from non-equilibrium distributions. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0201. [PMID: 28320904 PMCID: PMC5360900 DOI: 10.1098/rsta.2016.0201] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/14/2016] [Indexed: 05/14/2023]
Abstract
This article surveys the empirical information which originated both by laboratory experiments and by computational simulations, and expands previous understanding of the rates of chemical processes in the low-temperature range, where deviations from linearity of Arrhenius plots were revealed. The phenomenological two-parameter Arrhenius equation requires improvement for applications where interpolation or extrapolations are demanded in various areas of modern science. Based on Tolman's theorem, the dependence of the reciprocal of the apparent activation energy as a function of reciprocal absolute temperature permits the introduction of a deviation parameter d covering uniformly a variety of rate processes, from those where quantum mechanical tunnelling is significant and d < 0, to those where d > 0, corresponding to the Pareto-Tsallis statistical weights: these generalize the Boltzmann-Gibbs weight, which is recovered for d = 0. It is shown here how the weights arise, relaxing the thermodynamic equilibrium limit, either for a binomial distribution if d > 0 or for a negative binomial distribution if d < 0, formally corresponding to Fermion-like or Boson-like statistics, respectively. The current status of the phenomenology is illustrated emphasizing case studies; specifically (i) the super-Arrhenius kinetics, where transport phenomena accelerate processes as the temperature increases; (ii) the sub-Arrhenius kinetics, where quantum mechanical tunnelling propitiates low-temperature reactivity; (iii) the anti-Arrhenius kinetics, where processes with no energetic obstacles are rate-limited by molecular reorientation requirements. Particular attention is given for case (i) to the treatment of diffusion and viscosity, for case (ii) to formulation of a transition rate theory for chemical kinetics including quantum mechanical tunnelling, and for case (iii) to the stereodirectional specificity of the dynamics of reactions strongly hindered by the increase of temperature.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Vincenzo Aquilanti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Instituto de Física, Universidade Federal da Bahia, 40210 Salvador, Brazil
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, 00016 Rome, Italy
| | - Nayara Dantas Coutinho
- Instituto de Química, Universidade de Brasília, Caixa Postal 4478, 70904-970 Brasília, Brazil
| | - Valter Henrique Carvalho-Silva
- Grupo de Química Teórica e Estrutural de Anápolis, Campus de Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, CP 459, 75001-970 Anápolis, GO, Brazil
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125
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Quapp W, Bofill JM, Ribas-Ariño J. Analysis of the Acting Forces in a Theory of Catalysis and Mechanochemistry. J Phys Chem A 2017; 121:2820-2838. [PMID: 28338327 DOI: 10.1021/acs.jpca.7b00022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The theoretical description of a chemical process resulting from the application of mechanical or catalytical stress to a molecule is performed by the generation of an effective potential energy surface (PES). Changes for minima and saddle points by the stress are described by Newton trajectories (NTs) on the original PES. From the analysis of the acting forces we postulate the existence of pulling corridors built by families of NTs that connect the same stationary points. For different exit saddles of different height we discuss the corresponding pulling corridors; mainly by simple two-dimensional surface models. If there are different exit saddles then there can exist saddles of index two, at least, between. Then the case that a full pulling corridor crosses a saddle of index two is the normal case. It leads to an intrinsic hysteresis of such pullings for the forward or the backward reaction. Assuming such relations we can explain some results in the literature. A new finding is the existence of roundabout corridors that can switch between different saddle points by a reversion of the direction. The findings concern the mechanochemistry of molecular systems under a mechanical load as well as the electrostatic force and can be extended to catalytic and enzymatic accelerated reactions. The basic and ground ansatz includes both kinds of forces in a natural way without an extra modification.
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Affiliation(s)
- Wolfgang Quapp
- Mathematisches Institut, Universität Leipzig , PF 100920, D-04009 Leipzig, Germany
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126
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Carter CW. High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction. Annu Rev Biophys 2017; 46:433-453. [PMID: 28375734 DOI: 10.1146/annurev-biophys-070816-033811] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding how distinct parts of proteins produce coordinated behavior has driven and continues to drive advances in protein science and enzymology. However, despite consensus about the conceptual basis for allostery, the idiosyncratic nature of allosteric mechanisms resists general approaches. Computational methods can identify conformational transition states from structural changes, revealing common switching mechanisms that impose multistate behavior. Thermodynamic cycles use factorial perturbations to measure coupling energies between side chains in molecular switches that mediate shear during domain motion. Such cycles have now been complemented by modular cycles that measure energetic coupling between separable domains. For one model system, energetic coupling between domains has been shown to be quantitatively equivalent to that between dynamic side chains. Linkages between domain motion, switching residues, and catalysis make nucleoside triphosphate hydrolysis conditional on domain movement, confirming an essential yet neglected aspect of free energy transduction and suggesting the potential generality of these studies.
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Affiliation(s)
- Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514;
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127
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Cui Q. Perspective: Quantum mechanical methods in biochemistry and biophysics. J Chem Phys 2017; 145:140901. [PMID: 27782516 DOI: 10.1063/1.4964410] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies.
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Affiliation(s)
- Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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128
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Chu JW, Yang H. Identifying the structural and kinetic elements in protein large-amplitude conformational motions. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1283885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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129
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130
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Li S, Wu P, Moses JE, Sharpless KB. Multidimensional SuFEx Click Chemistry: Sequential Sulfur(VI) Fluoride Exchange Connections of Diverse Modules Launched From An SOF4
Hub. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611048] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Suhua Li
- Department of Chemistry and The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Peng Wu
- Department of Chemical Physiology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - John E. Moses
- Department of Chemistry and The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
- School of Chemistry; University of Nottingham; Nottingham NG7 2RD UK
| | - K. Barry Sharpless
- Department of Chemistry and The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
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131
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Li S, Wu P, Moses JE, Sharpless KB. Multidimensional SuFEx Click Chemistry: Sequential Sulfur(VI) Fluoride Exchange Connections of Diverse Modules Launched From An SOF 4 Hub. Angew Chem Int Ed Engl 2017; 56:2903-2908. [PMID: 28165188 DOI: 10.1002/anie.201611048] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 01/30/2023]
Abstract
Sulfur(VI) fluoride exchange (SuFEx) is a new family of click chemistry based transformations that enable the synthesis of covalently linked modules via SVI hubs. Here we report thionyl tetrafluoride (SOF4 ) as the first multidimensional SuFEx connector. SOF4 sits between the commercially mass-produced gases SF6 and SO2 F2 , and like them, is readily synthesized on scale. Under SuFEx catalysis conditions, SOF4 reliably seeks out primary amino groups [R-NH2 ] and becomes permanently anchored via a tetrahedral iminosulfur(VI) link: R-N=(O=)S(F)2 . The pendant, prochiral difluoride groups R-N=(O=)SF2 , in turn, offer two further SuFExable handles, which can be sequentially exchanged to create 3-dimensional covalent departure vectors from the tetrahedral sulfur(VI) hub.
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Affiliation(s)
- Suhua Li
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peng Wu
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - John E Moses
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, UK
| | - K Barry Sharpless
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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132
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On the indirect relationship between protein dynamics and enzyme activity. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 125:52-60. [PMID: 28163054 DOI: 10.1016/j.pbiomolbio.2017.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 02/01/2017] [Indexed: 11/22/2022]
Abstract
The behaviors of simple thermal systems have been well studied in physical chemistry and the principles obtained from such studies have been applied to complex thermal systems, such as proteins and enzymes. But the simple application of such principles is questionable and may lead to mistakes under some circumstances. In enzymology, the transition state theory of chemical reactions has been accepted as a fundamental theory, but the role of protein dynamics in enzyme catalysis is controversial in the context of transition state theory. By studying behaviors of complex thermal systems, we have revised the Arrhenius equation and transition state theory and our model is validated in enzymology. Formally speaking, the revised Arrhenius equation is apparently similar to a conventional Arrhenius equation, but the physical meanings of its parameters differ from that of traditional forms in principle. Within this model, the role of protein dynamics in enzyme catalysis is well defined and quantified.
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133
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Kim TH, Mehrabi P, Ren Z, Sljoka A, Ing C, Bezginov A, Ye L, Pomès R, Prosser RS, Pai EF. The role of dimer asymmetry and protomer dynamics in enzyme catalysis. Science 2017; 355:355/6322/eaag2355. [DOI: 10.1126/science.aag2355] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 12/05/2016] [Indexed: 01/19/2023]
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134
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LI Y, HUANG L, WANG X, CHEN Y. A Study of Electrochemical Sensor Based on BHb-imprinted Magnetic Nanoparticles. ANAL SCI 2017; 33:1105-1110. [DOI: 10.2116/analsci.33.1105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yanxia LI
- Department of Chemistry and Chemical Engineering, Minjiang University
| | - Lu HUANG
- Department of Chemistry and Chemical Engineering, Minjiang University
| | - Xiuping WANG
- Department of Chemistry and Chemical Engineering, Minjiang University
| | - Yiting CHEN
- Department of Chemistry and Chemical Engineering, Minjiang University
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135
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Stare J. Complete sampling of an enzyme reaction pathway: a lesson from gas phase simulations. RSC Adv 2017. [DOI: 10.1039/c6ra27894a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
With proper sampling strategy, convergence of free energy profiles of biomolecular reactions in the gas phase can be achieved in microseconds of simulation.
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Affiliation(s)
- Jernej Stare
- Department of Computational Biochemistry and Drug Design
- National Institute of Chemistry
- SI-1000 Ljubljana
- Slovenia
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136
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Zelleke T, Marx D. Free-Energy Landscape and Proton Transfer Pathways in Oxidative Deamination by Methylamine Dehydrogenase. Chemphyschem 2016; 18:208-222. [DOI: 10.1002/cphc.201601113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Theodros Zelleke
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
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137
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Gao K, Jia Y, Yang M. A Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Binary Complex of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase with MgATP. Biochemistry 2016; 55:6931-6939. [PMID: 27951655 DOI: 10.1021/acs.biochem.6b00720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that, in its binary form, even bound by analogues of MgATP, loops 2 and 3 remain rather flexible; this raises questions about the putative large-scale induced-fit conformational change of the HPPK-MgATP binary complex. In this work, long-time all-atomic molecular dynamics simulations were conducted to investigate the loop dynamics in this complex. Our simulations show that, with loop 3 closed, multiple conformations of loop 2, including the open, semiopen, and closed forms, are all accessible to the binary complex. These results provide valuable structural insights into the details of conformational changes upon 6-hydroxymethyl-7,8-dihydropterin (HP) binding and biological activities of HPPK. Conformational network analysis and principal component analysis related to the loops are also discussed.
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Affiliation(s)
- Kaifu Gao
- Institute of Biophysics and Department of Physics, Central China Normal University , Wuhan 430079, P. R. China
| | - Ya Jia
- Institute of Biophysics and Department of Physics, Central China Normal University , Wuhan 430079, P. R. China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
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138
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Giladi M, Shor R, Lisnyansky M, Khananshvili D. Structure-Functional Basis of Ion Transport in Sodium-Calcium Exchanger (NCX) Proteins. Int J Mol Sci 2016; 17:E1949. [PMID: 27879668 PMCID: PMC5133943 DOI: 10.3390/ijms17111949] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/13/2016] [Accepted: 11/14/2016] [Indexed: 01/19/2023] Open
Abstract
The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α₁ and α₂ repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na⁺ or Ca2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca2+/cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 699780, Israel.
- Tel-Aviv Sourasky Medical Center, Tel-Aviv 6423906, Israel.
| | - Reut Shor
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 699780, Israel.
| | - Michal Lisnyansky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 699780, Israel.
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 699780, Israel.
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139
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Abstract
![]()
Although QM/MM calculations
are the primary current tool for modeling enzymatic reactions, the
reliability of such calculations can be limited by the size of the
QM region. Thus, we examine in this work the dependence of QM/MM calculations
on the size of the QM region, using the reaction of catechol-O-methyl transferase (COMT) as a test case. Our study focuses
on the effect of adding residues to the QM region on the activation
free energy, obtained with extensive QM/MM sampling. It is found that
the sensitivity of the activation barrier to the size of the QM is
rather limited, while the dependence of the reaction free energy is
somewhat larger. Of course, the results depend on the inclusion of
the first solvation shell in the QM regions. For example, the inclusion
of the Mg2+ ion can change the activation barrier due to
charge transfer effects. However, such effects can easily be included
in semiempirical approaches by proper parametrization. Overall, we
establish that QM/MM calculations of activation barriers of enzymatic
reactions are not highly sensitive to the size of the QM region, beyond
the immediate region that describes the reacting atoms.
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