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Murillo-Lopez JA, Villegas-Escobar N, Vogt-Geisse S, Vöhringer-Martinez E. Molecular Environment Modulates CO 2 Liberation from Carboxy-Biotin. J Phys Chem B 2024; 128:5327-5335. [PMID: 38771940 DOI: 10.1021/acs.jpcb.4c00910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Carboxy-biotin serves as a coenzyme in certain carboxylases, exhibiting the remarkable capability to transfer a carboxy group to specific substrates. This process is made possible by the presence of biotin, a unique molecule that consists of a sulfur-containing tetrahydrothiophene ring fused to a ureido group. It is covalently attached to the enzyme via a flexible linker, allowing for its functionality. Biotin-dependent carboxylases consist of two distinct domains. The first domain (BC) facilitates biotin carboxylation by utilizing ATP, while the second domain (CT) transfers CO2 to the substrate. The process of ATP-dependent carboxylation using bicarbonate in the biotin carboxylase domain (BC) is well-known. However, the precise mechanism by which CO2 is released in the carboxyltransferase domain (CT) is still not fully understood. We employed advanced computational chemistry methods to investigate the decarboxylation process of carboxy-biotin in various molecular environments and different protonation states. Regardless of the polarity of the molecular surroundings, decarboxylation only occurs spontaneously in the protonated form. To determine the protonation state of biotin in different environments, we established an accurate computational chemistry method for calculating the pKa value of carboxy-biotin, reaching sub-kcal/mol accuracy. Based on our findings, nonpolar environments, such as the active site of the carboxyltransferase domain, have the ability to cause the spontaneous release of CO2 from carboxy-biotin. The CO2 release takes place spontaneously from protonated carboxy-biotin, promoting the carboxylation of substrates.
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Affiliation(s)
- Juliana A Murillo-Lopez
- Departamento de Físico-Química Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4070139, Chile
| | - Nery Villegas-Escobar
- Departamento de Físico-Química Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4070139, Chile
| | - Stefan Vogt-Geisse
- Departamento de Físico-Química Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4070139, Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4070139, Chile
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Demapan D, Kussmann J, Ochsenfeld C, Cui Q. Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition. J Chem Theory Comput 2022; 18:2530-2542. [PMID: 35226489 PMCID: PMC9652774 DOI: 10.1021/acs.jctc.1c00714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To analyze the impact of various technical details on the results of quantum mechanical (QM)/molecular mechanical (MM) enzyme simulations, including the QM region size, catechol-O-methyltransferase (COMT) is studied as a model system using an approximate QM/MM method (DFTB3/CHARMM). The results show that key equilibrium and kinetic properties for methyl transfer in COMT exhibit limited variations with respect to the size of the QM region, which ranges from ∼100 to ∼500 atoms in this study. With extensive sampling, local and global structural characteristics of the enzyme are largely conserved across the studied QM regions, while the nature of the transition state (e.g., secondary kinetic isotope effect) and reaction exergonicity are largely maintained. Deviations in the free energy profile with different QM region sizes are similar in magnitude to those observed with changes in other simulation protocols, such as different initial enzyme conformations and boundary conditions. Electronic structural properties, such as the covariance matrix of residual charge fluctuations, appear to exhibit rather long-range correlations, especially when the peptide backbone is included in the QM region; this observation holds when a range-separated DFT approach is used as the QM region, suggesting that delocalization error is unlikely the origin. Overall, the analyses suggest that multiple simulation details determine the results of QM/MM enzyme simulations with comparable contributions.
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Affiliation(s)
- Darren Demapan
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany.,Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jörg Kussmann
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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Li R, Du T, Liu J, Aquino AJA, Zhang J. Theoretical Study of O-CH 3 Bond Dissociation Enthalpy in Anisole Systems. ACS OMEGA 2021; 6:21952-21959. [PMID: 34497890 PMCID: PMC8412933 DOI: 10.1021/acsomega.1c02310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Understanding ubiquitous methyl transfer reactions requires a systematic study of thermodynamical parameters that could reveal valuable information about the nature of the chemical bond and the feasibility of those processes. In the present study, the O-CH3 bond dissociation enthalpies (BDEs) of 67 compounds belonging to phenol/anisole systems were calculated employing the Gaussian-4 (G4) method. Those compounds contain different substituents including alkyl groups, electron-donating groups (EDGs), and electron-withdrawing groups (EWGs). The results show that the bigger branched alkyl groups and EDGs will destabilize the O-CH3 bond, while EWGs have the opposite effect. A combination of different effects including steric effects, hydrogen bonds, and substituents and their position can achieve around 20 kcal/mol difference compared to the basic phenyl frame. Also, the linear correlation between σp + and O-CH3 BDE can provide a reference for the O-CH3 BDE prediction. The present study represents a step forward to establish a comprehensive O-CH3 BDE database to understand the substituent effect and make its contribution to the rational design of inhibitors and drugs.
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Affiliation(s)
- Rui Li
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
| | - Tianshu Du
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
| | - Jingxing Liu
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
| | - Adelia J. A. Aquino
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
- Department
of Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
- Institute
for Soil Research, University of Natural
Resources and Life Sciences, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Jianyu Zhang
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
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Levina EO, Khrenova MG, Astakhov AA, Tsirelson VG. Revealing electronic features governing hydrolysis of cephalosporins in the active site of the L1 metallo-β-lactamase. RSC Adv 2020; 10:8664-8676. [PMID: 35496524 PMCID: PMC9050041 DOI: 10.1039/c9ra10649a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/14/2020] [Indexed: 11/21/2022] Open
Abstract
The QM/MM simulations followed by electron density feature analysis are carried out to deepen the understanding of the reaction mechanism of cephalosporin hydrolysis in the active site of the L1 metallo-β-lactamase. The differences in reactivity of ten similar cephalosporin compounds are explained by using an extended set of bonding descriptors. The limiting step of the reaction is characterized by the proton transfer to the nitrogen atom of the cephalosporin thiazine ring accompanied with formation of the C4
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C3 double bond in its N–C4–C3 fragment. The temporary N⋯H–Ow hydrogen bond, which is formed in the transition state of the limiting step of the reaction was recognized as a key atomic interaction governing the reactivity of various cephalosporins. Non-local real-space bonding descriptors show that different extent of localization of electron lone pair at N atom in the transition state affect the reactivity of compounds: smaller electron localization is typical for the less reactive species. In particular, the Fermi hole analysis shows how exchange electron correlation in the N⋯H–Ow fragment control electron lone pair localization. Delocalization tensor, linear response kernel and source function indicate that features of electron delocalization in the N–C4–C3 fragment of cephalosporins in the transition state complexes determine the differences in C4–C3 bond for substrates with high and low rate constants. The C4–C3 bond of the N–C4–C3 fragment at the transition state is similar to that of the preceding intermediate for the less reactive species and resembles the features of the enzyme–product complex for more reactive compounds. The power and limitations of the descriptors applied for solving the problem are discussed and the generality of approach is stressed. Combination of QM/MM and modern bonding descriptors explains different reactivity of cephalosporins in the active site of the L1 metallo-β-lactamase.![]()
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Affiliation(s)
- Elena O. Levina
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences
- Moscow
- Russia
- Moscow Institute of Physics and Technology
- Dolgoprudny
| | - Maria G. Khrenova
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences
- Moscow
- Russia
- Lomonosov Moscow State University
- Moscow
| | - Andrey A. Astakhov
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences
- Moscow
- Russia
- Joint Institute for Nuclear Research
- Dubna
| | - Vladimir G. Tsirelson
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences
- Moscow
- Russia
- Mendeleev University of Chemical Technology of Russia
- Moscow
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Gomez A, Vöhringer-Martinez E. Conformational sampling and polarization of Asp26 in pK a calculations of thioredoxin. Proteins 2019; 87:467-477. [PMID: 30714651 DOI: 10.1002/prot.25668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 01/21/2019] [Accepted: 01/31/2019] [Indexed: 12/28/2022]
Abstract
Thioredoxin is a protein that has been used as model system by various computational methods to predict the pKa of aspartate residue Asp26 which is 3.5 units higher than a solvent exposed one (eg, Asp20). Here, we use extensive atomistic molecular dynamics simulations of two different protonation states of Asp26 in combination with conformational analysis based on RMSD clustering and principle component analysis to identify representative conformations of the protein in solution. For each conformation, the Gibbs free energy of proton transfer between Asp26 and Asp20, which is fully solvated in a loop region of the protein, is calculated with the Amber99sb force field in alchemical transformations. The varying polarization of the two residues in different molecular environments and protonation states is described by Hirshfeld-I (HI) atomic charges obtained from the averaged polarized electron density. Our results show that the Gibbs free energy of proton transfer is dependent on the protein conformation, the proper sampling of the neighboring Lys57 residue orientations and on water molecules entering the hydrophobic cavity upon deprotonating Asp26. The inclusion of the polarization of both aspartate residues in the free energy cycle by HI atomic charges corrects the results from the non-polarizable force field and reproduces the experimental ΔpKa value of Asp26.
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Affiliation(s)
- Aharon Gomez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
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Saez DA, Zinovjev K, Tuñón I, Vöhringer-Martinez E. Catalytic Reaction Mechanism in Native and Mutant Catechol-O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis. J Phys Chem B 2018; 122:8861-8871. [DOI: 10.1021/acs.jpcb.8b07339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- David Adrian Saez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
| | - Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
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Lara A, Riquelme M, Vöhringer-Martinez E. Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges. J Comput Chem 2018; 39:1728-1737. [PMID: 29752734 DOI: 10.1002/jcc.25347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/15/2018] [Accepted: 04/08/2018] [Indexed: 01/25/2023]
Abstract
Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- A Lara
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Chile
| | - M Riquelme
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Chile
| | - E Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Chile
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