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Ding Y, Huang J. DP/MM: A Hybrid Model for Zinc-Protein Interactions in Molecular Dynamics. J Phys Chem Lett 2024; 15:616-627. [PMID: 38198685 DOI: 10.1021/acs.jpclett.3c03158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Zinc-containing proteins are vital for many biological processes, yet accurately modeling them using classical force fields is hindered by complicated polarization and charge transfer effects. This study introduces DP/MM, a hybrid force field scheme that utilizes a deep potential model to correct the atomic forces of zinc ions and their coordinated atoms, elevating them from MM to QM levels of accuracy. Trained on the difference between MM and QM atomic forces across diverse zinc coordination groups, the DP/MM model faithfully reproduces structural characteristics of zinc coordination during simulations, such as the tetrahedral coordination of Cys4 and Cys3His1 groups. Furthermore, DP/MM allows water exchange in the zinc coordination environment. With its unique blend of accuracy, efficiency, flexibility, and transferability, DP/MM serves as a valuable tool for studying structures and dynamics of zinc-containing proteins and also represents a pioneering approach in the evolving landscape of machine learning potentials for molecular modeling.
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Affiliation(s)
- Ye Ding
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Jing Huang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
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Why Monoamine Oxidase B Preferably Metabolizes N-Methylhistamine over Histamine: Evidence from the Multiscale Simulation of the Rate-Limiting Step. Int J Mol Sci 2022; 23:ijms23031910. [PMID: 35163835 PMCID: PMC8836602 DOI: 10.3390/ijms23031910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 11/18/2022] Open
Abstract
Histamine levels in the human brain are controlled by rather peculiar metabolic pathways. In the first step, histamine is enzymatically methylated at its imidazole Nτ atom, and the produced N-methylhistamine undergoes an oxidative deamination catalyzed by monoamine oxidase B (MAO-B), as is common with other monoaminergic neurotransmitters and neuromodulators of the central nervous system. The fact that histamine requires such a conversion prior to oxidative deamination is intriguing since MAO-B is known to be relatively promiscuous towards monoaminergic substrates; its in-vitro oxidation of N-methylhistamine is about 10 times faster than that for histamine, yet this rather subtle difference appears to be governing the decomposition pathway. This work clarifies the MAO-B selectivity toward histamine and N-methylhistamine by multiscale simulations of the rate-limiting hydride abstraction step for both compounds in the gas phase, in aqueous solution, and in the enzyme, using the established empirical valence bond methodology, assisted by gas-phase density functional theory (DFT) calculations. The computed barriers are in very good agreement with experimental kinetic data, especially for relative trends among systems, thereby reproducing the observed MAO-B selectivity. Simulations clearly demonstrate that solvation effects govern the reactivity, both in aqueous solution as well as in the enzyme although with an opposing effect on the free energy barrier. In the aqueous solution, the transition-state structure involving histamine is better solvated than its methylated analog, leading to a lower barrier for histamine oxidation. In the enzyme, the higher hydrophobicity of N-methylhistamine results in a decreased number of water molecules at the active side, leading to decreased dielectric shielding of the preorganized catalytic electrostatic environment provided by the enzyme. This renders the catalytic environment more efficient for N-methylhistamine, giving rise to a lower barrier relative to histamine. In addition, the transition state involving N-methylhistamine appears to be stabilized by the surrounding nonpolar residues to a larger extent than with unsubstituted histamine, contributing to a lower barrier with the former.
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Sanchez-Andrada P, Vidal-Vidal A, Prieto T, Elguero J, Alkorta I, Marin-Luna M. Alkylammonium Cation Affinities of Nitrogenated Organobases: The Roles of Hydrogen Bonding and Proton Transfer. Chempluschem 2021; 86:1097-1105. [PMID: 34251758 DOI: 10.1002/cplu.202100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/29/2021] [Indexed: 11/06/2022]
Abstract
Alkylammonium cation affinities of 64 nitrogen-containing organobases, as well as the respective proton transfer processes from the alkylammonium cations to the base, have been computed in the gas phase by using DFT methods. The guanidine bases show the highest proton transfer values (191.9-233 kJ mol-1 ) whereas the cis-2,2'-biimidazole presents the largest affinity towards the alkylammonium cations (>200 kJ mol-1 ) values. The resulting data have been compared with the experimentally reported proton affinities of the studied nitrogen-containing organobases revealing that the propensity of an organobase for the proton transfer process increases linearly with its proton affinity. This work can provide a tool for designing senors for bioactive compounds containing amino groups that are protonated at physiological pH.
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Affiliation(s)
- Pilar Sanchez-Andrada
- Departamento de Química Orgánica Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia Facultad de Química, Campus de Espinardo, E-30100, Murcia, Spain
| | - Angel Vidal-Vidal
- Departamento de Química Orgánica, Universidade de Vigo Campus Lagoas-Marcosende, Vigo, Spain
| | - Tania Prieto
- Departamento de Química Orgánica, Universidade de Vigo Campus Lagoas-Marcosende, Vigo, Spain
| | - José Elguero
- Instituto de Química Médica, Centro Superior de Investigaciones Científicas (CSIC), Juan de la Cierva, 3, E-28006, Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, Centro Superior de Investigaciones Científicas (CSIC), Juan de la Cierva, 3, E-28006, Madrid, Spain
| | - Marta Marin-Luna
- Departamento de Química Orgánica Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia Facultad de Química, Campus de Espinardo, E-30100, Murcia, Spain
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Comas-Basté O, Sánchez-Pérez S, Veciana-Nogués MT, Latorre-Moratalla M, Vidal-Carou MDC. Histamine Intolerance: The Current State of the Art. Biomolecules 2020; 10:E1181. [PMID: 32824107 PMCID: PMC7463562 DOI: 10.3390/biom10081181] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/18/2022] Open
Abstract
Histamine intolerance, also referred to as enteral histaminosis or sensitivity to dietary histamine, is a disorder associated with an impaired ability to metabolize ingested histamine that was described at the beginning of the 21st century. Although interest in histamine intolerance has considerably grown in recent years, more scientific evidence is still required to help define, diagnose and clinically manage this condition. This article will provide an updated review on histamine intolerance, mainly focusing on its etiology and the existing diagnostic and treatment strategies. In this work, a glance on histamine intoxication will also be provided, as well as the analysis of some uncertainties historically associated to histamine intoxication outbreaks that may be better explained by the existence of interindividual susceptibility to ingested histamine.
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Affiliation(s)
- Oriol Comas-Basté
- Departament de Nutrició, Ciències de l’Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l’Alimentació, Campus de l’Alimentació de Torribera, Universitat de Barcelona, Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain; (O.C.-B.); (S.S.-P.); (M.T.V.-N.); (M.L.-M.)
- Institut de Recerca en Nutrició i Seguretat Alimentària (INSA·UB), Universitat de Barcelona, Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
- Xarxa de Referència en Tecnologia dels Aliments de la Generalitat de Catalunya (XaRTA), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Sònia Sánchez-Pérez
- Departament de Nutrició, Ciències de l’Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l’Alimentació, Campus de l’Alimentació de Torribera, Universitat de Barcelona, Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain; (O.C.-B.); (S.S.-P.); (M.T.V.-N.); (M.L.-M.)
- Institut de Recerca en Nutrició i Seguretat Alimentària (INSA·UB), Universitat de Barcelona, Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
- Xarxa de Referència en Tecnologia dels Aliments de la Generalitat de Catalunya (XaRTA), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Maria Teresa Veciana-Nogués
- Departament de Nutrició, Ciències de l’Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l’Alimentació, Campus de l’Alimentació de Torribera, Universitat de Barcelona, Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain; (O.C.-B.); (S.S.-P.); (M.T.V.-N.); (M.L.-M.)
- Institut de Recerca en Nutrició i Seguretat Alimentària (INSA·UB), Universitat de Barcelona, Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
- Xarxa de Referència en Tecnologia dels Aliments de la Generalitat de Catalunya (XaRTA), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Mariluz Latorre-Moratalla
- Departament de Nutrició, Ciències de l’Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l’Alimentació, Campus de l’Alimentació de Torribera, Universitat de Barcelona, Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain; (O.C.-B.); (S.S.-P.); (M.T.V.-N.); (M.L.-M.)
- Institut de Recerca en Nutrició i Seguretat Alimentària (INSA·UB), Universitat de Barcelona, Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
- Xarxa de Referència en Tecnologia dels Aliments de la Generalitat de Catalunya (XaRTA), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - María del Carmen Vidal-Carou
- Departament de Nutrició, Ciències de l’Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l’Alimentació, Campus de l’Alimentació de Torribera, Universitat de Barcelona, Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain; (O.C.-B.); (S.S.-P.); (M.T.V.-N.); (M.L.-M.)
- Institut de Recerca en Nutrició i Seguretat Alimentària (INSA·UB), Universitat de Barcelona, Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
- Xarxa de Referència en Tecnologia dels Aliments de la Generalitat de Catalunya (XaRTA), C/Baldiri Reixac 4, 08028 Barcelona, Spain
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Berestova TV, Khursan SL, Mustafin AG. Experimental and theoretical substantiation of differences of geometric isomers of copper(II) α-amino acid chelates in ATR-FTIR spectra. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117950. [PMID: 31862653 DOI: 10.1016/j.saa.2019.117950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/20/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
Stereo and structural isomerism of the copper(II) chelate complexes define their biological activity. At the same time, the identification of the geometric isomers of such complexes is a nontrivial task of modern coordination chemistry. In the presented work we have studied the trans- and cis-isomers of chelates bis(S-valinato)copper(II), (R,S-valinato)copper(II) and other mixed ligand copper(II) amino acid complexes with the joint use of experimental by ATR-FTIR spectroscopy and DFT simulations. Using DFT simulations (method M06/6 311+G(d)) the optimum conformers of the geometric isomers of copper(II) a-amino acid chelate complexes were found and their characteristic stretching vibrations were established in the mid-wave region of the IR spectra. The experimental ATR-FTIR bands of the compounds well agree with the theoretical estimates. Such a joint use allows to determine of cis- and trans-isomers of copper(II) N,O-amino acid chelates in the mid-wave region of the ATR-FTIR spectrum.
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Affiliation(s)
| | - Sergey L Khursan
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, Ufa, Russian Federation
| | - Akhat G Mustafin
- Bashkir State University, Department of Chemistry, Ufa, Russian Federation; Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, Ufa, Russian Federation
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Calixto AR, Ramos MJ, Fernandes PA. Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway. Chem Sci 2019; 10:7212-7221. [PMID: 31588289 PMCID: PMC6677113 DOI: 10.1039/c9sc01464k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/10/2019] [Indexed: 02/04/2023] Open
Abstract
The role of conformational diversity in enzyme catalysis has been a matter of analysis in recent studies. Pre-organization of the active site has been pointed out as the major source for enzymes' catalytic power. Following this line of thought, it is becoming clear that specific, instantaneous, non-rare enzyme conformations that make the active site perfectly pre-organized for the reaction lead to the lowest activation barriers that mostly contribute to the macroscopically observed reaction rate. The present work is focused on exploring the relationship between structure and catalysis in HIV-1 protease (PR) with an adiabatic mapping method, starting from different initial structures, collected from a classical MD simulation. The first, rate-limiting step of the HIV-1 PR catalytic mechanism was studied with the ONIOM QM/MM methodology (B3LYP/6-31G(d):ff99SB), with activation and reaction energies calculated at the M06-2X/6-311++G(2d,2p):ff99SB level of theory, in 19 different enzyme:substrate conformations. The results showed that the instantaneous enzyme conformations have two independent consequences on the enzyme's chemistry: they influence the barrier height, something also observed in the past in other enzymes, and they also influence the specific reaction pathway, which is something unusual and unexpected, challenging the "one enzyme-one substrate-one reaction mechanism" paradigm. Two different reaction mechanisms, with similar reactant probabilities and barrier heights, lead to the same gem-diol intermediate. Subtle nanosecond-timescale rearrangements in the active site hydrogen bonding network were shown to determine which reaction the enzyme follows. We named this phenomenon chemical disorder. The results make us realize the unexpected mechanistic consequences of conformational diversity in enzymatic reactivity.
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Affiliation(s)
- Ana Rita Calixto
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
| | - Maria João Ramos
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
| | - Pedro Alexandrino Fernandes
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
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