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Juretić D, Bonačić Lošić Ž. Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation. ENTROPY (BASEL, SWITZERLAND) 2024; 26:151. [PMID: 38392406 PMCID: PMC10888251 DOI: 10.3390/e26020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni-uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production-the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics.
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Affiliation(s)
- Davor Juretić
- Mediterranean Institute for Life Sciences, Šetalište Ivana Meštrovića 45, 21000 Split, Croatia
- Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
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Abstract
Computational methods for modeling biochemical processes implemented in GAMESS package are reviewed; in particular, quantum mechanics combined with molecular mechanics (QM/MM), semi-empirical, and fragmentation approaches. A detailed summary of capabilities is provided for the QM/MM implementation in QuanPol program and the fragment molecular orbital (FMO) method. Molecular modeling and visualization packages useful for biochemical simulations with GAMESS are described. GAMESS capabilities with corresponding references are tabulated for reader's convenience.
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Öberg H, Brinck T. Fragment molecular orbital study of the cAMP-dependent protein kinase catalyzed phosphoryl transfer: a comparison with the differential transition state stabilization method. Phys Chem Chem Phys 2018; 18:15153-61. [PMID: 27197750 DOI: 10.1039/c6cp02623k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The importance of key residues to the activity of the cAMP-dependent protein kinase catalyzed phosphoryl transfer and to the stabilization of the transition state of the reaction has been investigated by means of the fragment molecular orbital (FMO) method. To evaluate the accuracy of the method and its capability of fragmenting covalent bonds, we have compared stabilization energies due to the interactions between individual residues and the reaction center to results obtained with the differential transition state stabilization method (Szarek, et al., J. Phys. Chem. B, 2008, 112, 11819-11826) and observe, despite a size difference in the fragment describing the reaction center, near-quantitative agreement. We have also computed deletion energies to investigate the effect of virtual deletion of key residues on the activation energy. These results are consistent with the stabilization energies and yield additional information as they clearly capture the effect of secondary interactions, i.e. interactions in the second coordination layer of the reaction center. We find that using FMO to calculate deletion energies is a powerful and time efficient approach to analyze the importance of key residues to the activity of an enzyme catalyzed reaction.
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Affiliation(s)
- H Öberg
- Applied Physical Chemistry, KTH Royal Institute of Technology, Teknikringen 30, SE-100 44 Stockholm, Sweden.
| | - T Brinck
- Applied Physical Chemistry, KTH Royal Institute of Technology, Teknikringen 30, SE-100 44 Stockholm, Sweden.
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4
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Abstract
In recent years, there has been much discussion regarding the origin of enzymatic catalysis and whether including protein dynamics is necessary for understanding catalytic enhancement. An important contribution in this debate was made with the application of the vibrational Stark effect spectroscopy to measure electric fields in the active site. This provided a window on electric fields at the transition state in enzymatic reactions. We performed computational studies on two enzymes where we have shown that fast dynamics is part of the reaction mechanism and calculated the electric field near the bond-breaking event. We found that the fast motions that we had identified lead to an increase of the electric field, thus preparing an enzymatic configuration that is electrostatically favorable for the catalytic chemical step. We also studied the enzyme that has been the subject of Stark spectroscopy, ketosteroid isomerase, and found electric fields of a similar magnitude to the two previous examples.
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Fedorov DG. The fragment molecular orbital method: theoretical development, implementation in
GAMESS
, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1322] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD‐FMat)National Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
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Pruitt SR, Steinmann C. Mapping Interaction Energies in Chorismate Mutase with the Fragment Molecular Orbital Method. J Phys Chem A 2017; 121:1797-1807. [DOI: 10.1021/acs.jpca.6b12830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Spencer R. Pruitt
- Academic & Research Computing, Worcester Polytechnic Institute, Worcester, Massachusetts 01602, United States
| | - Casper Steinmann
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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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.
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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
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Ishikawa T. [Applications of the Fragment Molecular Orbital Method in Drug Discovery]. YAKUGAKU ZASSHI 2016; 136:121-30. [PMID: 26725679 DOI: 10.1248/yakushi.15-00230-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recently, ab initio quantum mechanical calculations have been applied to large molecules, including biomolecular systems. The fragment molecular orbital (FMO) method is one of the most efficient approaches for the quantum mechanical investigation of such molecules. In the FMO method, dividing a target molecule into small fragments reduces computational effort. The clear definition of inter-fragment interaction energy (IFIE) as an expression of total energy is another valuable feature of the FMO method because it provides the ability to analyze interactions in biomolecules. Thus, the FMO method is expected to be useful for drug discovery. This study demonstrates applications of the FMO method related to drug discovery. First, IFIE, according to FMO calculations, was used in the optimization of drug candidates for the development of anti-prion compounds. The second example involved interaction analysis of the human immunodeficiency virus type 1 (HIV-1) protease and a drug compound that used a novel analytical method for dispersion interaction, i.e., fragment interaction analysis based on LMP2 (FILM).
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Affiliation(s)
- Takeshi Ishikawa
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University
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Nakata H, Fedorov DG, Nagata T, Kitaura K, Nakamura S. Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method. J Chem Theory Comput 2015; 11:3053-64. [DOI: 10.1021/acs.jctc.5b00277] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Research
Cluster for Innovation, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Dmitri G. Fedorov
- Nanosystem
Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Takeshi Nagata
- Nanosystem
Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Shinichiro Nakamura
- Research
Cluster for Innovation, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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