1
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Wang Y, Liu L, Gao Y, Zhao J, Liu C, Gong L, Yang Z. Development of a QM/MM(ABEEM) method for the deprotonation of neutral and cation radicals in the G-tetrad and GGX(8-oxo-G) tetrad. Phys Chem Chem Phys 2023; 26:504-516. [PMID: 38084041 DOI: 10.1039/d3cp04357f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The rapid deprotonation of G˙+ in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G˙+ in the G-tetrad makes it a more suitable carrier for hole conduction. The QM/MM(ABEEM) combined method, which involves the integration of QM and the ABEEM polarizable force field (ABEEM PFF), was developed to investigate the deprotonation of neutral and cation free radicals in the G-tetrad and GGX(8-oxo-G) tetrad (xanthine and 8-oxoguanine dual substituted G-tetrad). By incorporating valence-state electronegativity piecewise functions χ*(r) and implementing charge local conservation conditions, QM/MM(ABEEM) possesses the advantage of accurately simulating charge transfer and polarization effect during deprotonation. The activation energy calculated by the QM method of X˙ is the lowest among other bases in the GGX(8-oxo-G) tetrad, which is supported by the computation of the average electronegativity calculated by ABEEM PFF. By utilizing QM/MM(ABEEM) with a two-way free energy perturbation method, the deprotonation activation energy of X˙ in the GGX(8-oxo-G) tetrad is determined to be 33.0 ± 2.1 kJ mol-1, while that of G˙+ in the G-tetrad is 20.7 ± 0.6 kJ mol-1, consistent with the experimental measurement of 20 ± 1.0 kJ mol-1. These results manifest that X˙ in the GGX(8-oxo-G) tetrad exhibits a slower deprotonation rate than G˙+ in the G-tetrad, suggesting that the GGX(8-oxo-G) tetrad may serve as a more favorable hole transport carrier. Furthermore, the unequal average electronegativities of bases in the GGX(8-oxo-G) tetrad impede the deprotonation rate. This study provides a potential foundation for investigating the microscopic mechanism of DNA electronic devices.
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Affiliation(s)
- Yue Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Linlin Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Yue Gao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Jiayue Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Lidong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Zhongzhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
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2
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Tomar V, Rikkerink EHA, Song J, Sofkova-Bobcheva S, Bus VGM. Structure-Function Characterisation of Eop1 Effectors from the Erwinia-Pantoea Clade Reveals They May Acetylate Their Defence Target through a Catalytic Dyad. Int J Mol Sci 2023; 24:14664. [PMID: 37834112 PMCID: PMC10572645 DOI: 10.3390/ijms241914664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The YopJ group of acetylating effectors from phytopathogens of the genera Pseudomonas and Ralstonia have been widely studied to understand how they modify and suppress their host defence targets. In contrast, studies on a related group of effectors, the Eop1 group, lag far behind. Members of the Eop1 group are widely present in the Erwinia-Pantoea clade of Gram-negative bacteria, which contains phytopathogens, non-pathogens and potential biocontrol agents, implying that they may play an important role in agroecological or pathological adaptations. The lack of research in this group of YopJ effectors has left a significant knowledge gap in their functioning and role. For the first time, we perform a comparative analysis combining AlphaFold modelling, in planta transient expressions and targeted mutational analyses of the Eop1 group effectors from the Erwinia-Pantoea clade, to help elucidate their likely activity and mechanism(s). This integrated study revealed several new findings, including putative binding sites for inositol hexakisphosphate and acetyl coenzyme A and newly postulated target-binding domains, and raises questions about whether these effectors function through a catalytic triad mechanism. The results imply that some Eop1s may use a catalytic dyad acetylation mechanism that we found could be promoted by the electronegative environment around the active site.
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Affiliation(s)
- Vishant Tomar
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand;
| | - Erik H. A. Rikkerink
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
| | - Janghoon Song
- Pear Research Institute, National Institute of Horticultural & Herbal Science, Rural Development Administration, Naju 58216, Republic of Korea
| | - Svetla Sofkova-Bobcheva
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand;
| | - Vincent G. M. Bus
- Hawkes Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North 4130, New Zealand;
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3
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Pick LM, Wenzlaff J, Yousefi M, Davari MD, Ansorge-Schumacher MB. Lipase-Mediated Conversion of Protecting Group Silyl Ethers: An Unspecific Side Reaction. Chembiochem 2023; 24:e202300384. [PMID: 37224395 DOI: 10.1002/cbic.202300384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 05/26/2023]
Abstract
Silyl ether protecting groups are important tools in organic synthesis, ensuring selective reactions of hydroxyl functional groups. Enantiospecific formation or cleavage could simultaneously enable the resolution of racemic mixtures and thus significantly increase the efficiency of complex synthetic pathways. Based on reports that lipases, which today are already particularly important tools in chemical synthesis, can catalyze the enantiospecific turnover of trimethylsilanol (TMS)-protected alcohols, the goal of this study was to determine the conditions under which such a catalysis occurs. Through detailed experimental and mechanistic investigation, we demonstrated that although lipases mediate the turnover of TMS-protected alcohols, this occurs independently of the known catalytic triad, as this is unable to stabilize a tetrahedral intermediate. The reaction is essentially non-specific and therefore most likely completely independent of the active site. This rules out lipases as catalysts for the resolution of racemic mixtures of alcohols through protection or deprotection with silyl groups.
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Affiliation(s)
- Lisa M Pick
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Jessica Wenzlaff
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Mohammad Yousefi
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
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4
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Díaz-Cervantes E, Robles J, Solà M, Swart M. The peptide bond rupture mechanism in the serine proteases: an in silico study based on sequential scale models. Phys Chem Chem Phys 2023; 25:8043-8049. [PMID: 36876585 DOI: 10.1039/d2cp04872h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Given the importance of serine proteases for biochemical processes, we have studied the peptide bond rupture mechanism using three sequential scale models as representations of the KLK5 enzyme (a protein overexpressed in ovarian cancer). The first model contains the basic functional groups of the residues that conform to the catalytic triad present in serine proteases; the second model contains some additional residues and, finally, the last representation includes all atoms of the KLK5 protein together with 10.000 explicit water molecules. This separation into three scale models allows us to separate the intrinsic reactivity of the catalytic triad from the process taking place in the enzyme. The methodologies employed in this work include full DFT calculations with a dielectric continuum in the first two models and a multi-level setup with a Quantum Mechanics/Molecular Mechanics (QM/MM) partition in the whole protein system. Our results show that the peptide-bond rupture mechanism is a stepwise process involving two proton transfer reactions. The rate-determining step is the second proton transfer from the imidazole group to the amidic nitrogen of the substrate. In addition, we find that the simplest model does not provide accurate results compared to the full protein system. This can be attributed to the electronic stabilization conferred by the residues around the reaction site. Interestingly, the energy profile obtained with the second scale model with additional residues shows the same trends as the full system and could therefore be considered an appropriate model system. It could be used for studying the peptide bond rupture mechanism in case full QM/MM calculations cannot be performed, or as a rapid tool for screening purposes.
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Affiliation(s)
- Erik Díaz-Cervantes
- Departamento de Alimentos, Centro Interdisciplinario del Noreste, Universidad de Guanajuato, 37975 Tierra Blanca, Guanajuato, Mexico.,Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, 17003 Girona, Spain.
| | - Juvencio Robles
- Departamento de Farmacia, Universidad de Guanajuato, Noria Alta S/N, Gto. 36050, Guanajuato, Mexico
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, 17003 Girona, Spain.
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, 17003 Girona, Spain. .,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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5
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Honeder SE, Tomin T, Schinagl M, Pfleger R, Hoehlschen J, Darnhofer B, Schittmayer M, Birner‐Gruenberger R. Research Advances Through Activity‐Based Lipid Hydrolase Profiling. Isr J Chem 2023. [DOI: 10.1002/ijch.202200078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sophie Elisabeth Honeder
- Research and Diagnostic Institute of Pathology Medical University of Graz Stiftingtalstraße 6 8036 Graz Austria
| | - Tamara Tomin
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Maximilian Schinagl
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Raphael Pfleger
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Julia Hoehlschen
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Barbara Darnhofer
- Core Facility Mass Spectrometry Center for Medical Research Medical University of Graz Neue Stiftingtalstraße 24 8036 Graz Austria
| | - Matthias Schittmayer
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Ruth Birner‐Gruenberger
- Research and Diagnostic Institute of Pathology Medical University of Graz Stiftingtalstraße 6 8036 Graz Austria
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
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6
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Liu C, Jiang H, Li Y, Xue B, Yao YY, Yang ZZ. Development of a QM/MM(ABEEM) method combined with a polarizable force field to investigate the excision reaction mechanism of damaged thymine. Phys Chem Chem Phys 2023; 25:3432-3448. [PMID: 36637033 DOI: 10.1039/d2cp05873a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This paper focuses on the development of a quantum mechanics/molecular mechanics method using the ABEEM polarizable force field (QM/MM(ABEEM) method) to investigate the excision reaction mechanism of damaged thymine. This method does not simply combine the QM method with the polarizable force field. A valence electronegativity piecewise function with the distance between atoms as a variable is introduced to describe the atomic partial charges, and changes greatly during the reaction process. At the same time, the charge transfer effect is treated using the condition of local charge conservation. Compared with the traditional QM/MM method, the QM/MM(ABEEM) method can more accurately simulate the polarization effect and charge transfer effect in the reaction process. Focusing on the controversial problems of the excision of damaged bases, six reaction pathways were designed for monofunctional and difunctional deglycosylation of neutral bases and protonated bases. The results show that the QM/MM(ABEEM) method accurately simulates the polarization effect, charge transfer effect, activation energy and other properties of the reaction process. The process in which the active residue Asp activates the nucleophile H2O to attack the protonated base is the preferred path. The average activation energy and free activation energy of the protonated base are 7.00-14.00 kcal mol-1 lower than that of the neutral base. The study in this paper is helpful to understand the mechanism of repair enzymes in repairing bases.
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Affiliation(s)
- Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - He Jiang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Yue Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Bing Xue
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Yu-Ying Yao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
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7
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Zlobin A, Belyaeva J, Golovin A. Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms. J Chem Inf Model 2023; 63:546-560. [PMID: 36633836 DOI: 10.1021/acs.jcim.2c01071] [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: 01/13/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) simulations fuel discoveries in many fields of science including computational biochemistry and enzymology. Development of more convenient tools leads to an increase in the number of works in which mechanical insights into enzymes' mode of operation are obtained. Most commonly, these tools feature hydrogen-capping (link atom) approach to provide coupling between QM and MM subsystems across a covalent bond. Extensive studies were conducted to provide a solid foundation for the correctness of such an approach when a bond to a nonpolar MM atom is considered. However, not every task may be accomplished this way. Certain scenarios of using QM/MM in computational enzymology encourage or even necessitate the incorporation of backbone atoms into the QM region. Two out of three backbone atoms are polar, and in QM/MM with electrostatic embedding, a neighboring link atom will be hyperpolarized. Several schemes to mitigate this effect were previously proposed alongside a rigorous assessment of quantitative effects on model systems. However, it was not clear whether they may translate into qualitatively different results and how link atom hyperpolarization may manifest itself in a real-life enzymological scenario. Here, we show that the consequences of such an artifact may be severe and may completely overturn the conclusions drawn from the simulations. Our case advocates for the use of charge redistribution schemes whenever intra-backbone QM/MM boundaries are considered. Moreover, we addressed how different boundary types and charge redistribution schemes influence backbone dynamics. We showed that the results are heavily dependent on which boundary MM terms are retained, with charge alteration being of secondary importance. In the worst case, only three intra-backbone boundaries may be used with relative confidence in the adequacy of resulting simulations, irrespective of the hyperpolarization mitigation scheme. Thus, advances in the field are certainly needed to fuel new discoveries. As of now, we believe that issues raised in this work might encourage authors in the field to report what boundaries, boundary MM terms, and charge redistribution schemes they are using, so their results may be correctly interpreted.
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Affiliation(s)
- Alexander Zlobin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Julia Belyaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Andrey Golovin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
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8
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Liu C, Ren Y, Gao XQ, Du X, Yang ZZ. Development of QM/MM (ABEEM polarizable force field) method to simulate the excision reaction mechanism of damaged cytosine. J Comput Chem 2022; 43:2139-2153. [PMID: 36151878 DOI: 10.1002/jcc.27008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/25/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022]
Abstract
DNA damages are regarded as having harmful effects on cell. The base excision repair mechanism combats these effects by removing damaged bases. The deglycosylation mechanism of excising damaged bases by DNA glycosylase and the state of the leaving base have been controversial. The enzymatic reaction of DNA glycosylase to remove the damaged bases involves not only the formation and breaking of chemical bonds, but also complex polarization effect and charge transfer, which cannot be accurately simulated by the QM/MM method combined with the fixed charge force field. This work has developed the ABEEM fluctuating polarizable force field combining with the QM method, that is (QM/MM[ABEEM]), to accurately simulate the proton transfer, charge transfer and the charge distribution. The piecewise function is used as the valence-state electronegativity in the QM/MM (ABEEM) to realize the accurate fitting of the charge distribution in reaction. And the charge transfer is accurately simulated by the local charge conservation conditions. Four deglycosylation mechanisms including the monofunctional and difunctional mechanisms of four neutral and protonated cytosine derivatives are explored. It is confirmed that the monofunctional mechanism of Asp-activated nucleophile water is a better deglycosylation mechanism and the base is protonated before the reaction occurs. Protonization of the base reduced the activation energy by 10.00-17.00 kcal/mol. Asp provides the necessary charge for the reaction, and DNA glycosylase preferentially cleaves ɛC. This work provides a theoretical basis for the research of excising damaged bases by DNA glycosylase.
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Affiliation(s)
- Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Yang Ren
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Xiao-Qin Gao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Xue Du
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
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9
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Gisdon FJ, Bombarda E, Ullmann GM. Serine and Cysteine Peptidases: So Similar, Yet Different. How the Active-Site Electrostatics Facilitates Different Reaction Mechanisms. J Phys Chem B 2022; 126:4035-4048. [PMID: 35609250 DOI: 10.1021/acs.jpcb.2c01484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The catalytic mechanisms of serine and cysteine peptidases are similar: the proton of the nucleophile (serine or cysteine) is transferred to the catalytic histidine, and the nucleophile attacks the substrate for cleavage. However, they differ in an important aspect: cysteine peptidases form a stable ion-pair intermediate in a stepwise mechanism, while serine peptidases follow a concerted mechanism. While it is known that a positive electrostatic potential at the active site of cysteine peptidases stabilizes the cysteine anion in the ion-pair state, the physical basis of the concerted mechanism of serine peptidases is poorly understood. In this work, we use continuum electrostatic analysis and quantum mechanical/molecular mechanical (QM/MM) simulations to demonstrate that a destabilization of an anionic serine by a negative electrostatic potential in combination with a compact active site geometry facilitates a concerted mechanism in serine peptidases. Moreover, we show that an anionic serine would destabilize the protein significantly compared to an anionic cysteine in cysteine peptidases, which underlines the necessity of a concerted mechanism for serine peptidases. On the basis of our calculations on an inactive serine mutant of a natural cysteine peptidase, we show that the energy barrier for the catalytic mechanism can be substantially decreased by introducing a negative electrostatic potential and by reducing the relevant distances indicating that these parameters are essential for the activity of serine peptidases. Our work demonstrates that the concerted mechanism of serine peptidases represents an evolutionary innovative way to perform catalysis without the energetically expensive need to stabilize the anionic serine. In contrast in cysteine peptidases, the anionic cysteine is energetically easily accessible and it is a very efficient nucleophile, making these peptidases mechanistically simple. However, a cysteine is highly oxygen sensitive, which is problematic in an aerobic environment. On the basis of the analysis in this work, we suggest that serine peptidases represent an oxygen-insensitive alternative to cysteine peptidases.
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Affiliation(s)
- Florian J Gisdon
- Biochemistry, University of Bayreuth, Universitätsstraße 30, BGI, 95447 Bayreuth, Germany.,Computational Biochemistry, University of Bayreuth, Universitätsstraße 30, BGI, 95447 Bayreuth, Germany
| | - Elisa Bombarda
- Computational Biochemistry, University of Bayreuth, Universitätsstraße 30, BGI, 95447 Bayreuth, Germany
| | - G Matthias Ullmann
- Computational Biochemistry, University of Bayreuth, Universitätsstraße 30, BGI, 95447 Bayreuth, Germany
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10
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Teixeira LC, Coimbra JT, Ramos MJ, Fernandes PA. Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic. J Chem Inf Model 2022; 62:2510-2521. [PMID: 35549216 PMCID: PMC9113003 DOI: 10.1021/acs.jcim.1c01561] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Despite the development of vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, there is an urgent need for efficient drugs to treat infected patients. An attractive drug target is the human transmembrane protease serine 2 (TMPRSS2) because of its vital role in the viral infection mechanism of SARS-CoV-2 by activation of the virus spike protein (S protein). Having in mind that the information derived from quantum mechanics/molecular mechanics (QM/MM) studies could be an important tool in the design of transition-state (TS) analogue inhibitors, we resorted to adiabatic QM/MM calculations to determine the mechanism of the first step (acylation) of proteolytic cleavage of the S protein with atomistic details. Acylation occurred in two stages: (i) proton transfer from Ser441 to His296 concerted with the nucleophilic attack of Ser441 to the substrate's P1-Arg and (ii) proton transfer from His296 to the P1'-Ser residue concerted with the cleavage of the ArgP1-SerP1' peptide bond, with a Gibbs activation energy of 17.1 and 15.8 kcal mol-1, relative to the reactant. An oxyanion hole composed of two hydrogen bonds stabilized the rate-limiting TS by 8 kcal mol-1. An analysis of the TMPRSS2 interactions with the high-energy, short-lived tetrahedral intermediate highlighted the limitations of current clinical inhibitors and pointed out specific ways to develop higher-affinity TS analogue inhibitors. The results support the development of more efficient drugs against SARS-CoV-2 using a human target, free from resistance development.
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11
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Zheng C, Schneider M, Marion A, Antes I. The Q41R mutation in the HCV-protease enhances the reactivity towards MAVS by suppressing non-reactive pathways. Phys Chem Chem Phys 2022; 24:2126-2138. [PMID: 35029245 DOI: 10.1039/d1cp05002h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent experimental findings pointed out a new mutation in the HCV protease, Q41R, responsible for a significant enhancement of the enzyme's reactivity towards the mitochondrial antiviral-signaling protein (MAVS). The Q41R mutation is located rather far from the active site, and its involvement in the overall reaction mechanism is thus unclear. We used classical molecular dynamics and QM/MM to study the acylation reaction of HCV NS3/4A protease variants bound to MAVS and the NS4A/4B substrate and uncovered the indirect mechanism by which the Q41R mutation plays a critical role in the efficient cleavage of the substrate. Our simulations reveal that there are two major conformations of the MAVS H1'(p) residue for the wild type protease and only one conformation for the Q41R mutant. The conformational space of H1'(p) is restricted by the Q41R mutation due to a π-π stacking between H1'(p) and R41 as well as a strong hydrogen bond between the backbone of H57 and the side chain of R41. Further QM/MM calculations indicate that the complex with the conformation ruled out by the Q41R substitution is a non-reactive species due to its higher free energy barrier for the acylation reaction. Based on our calculations, we propose a kinetic mechanism that explains experimental data showing an increase of apparent rate constants for MAVS cleavage in Q41R mutants. Our model predicts that the non-reactive conformation of the enzyme-substrate complex modulates reaction kinetics like an uncompetitive inhibitor.
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Affiliation(s)
- Chen Zheng
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
| | - Markus Schneider
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
| | - Antoine Marion
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Middle East Technical University, Department of Chemistry, Ankara 06800, Turkey.
| | - Iris Antes
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
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12
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Chen Y, Wei W, Zhou Y, Xie D. The role of hydrogen bond in catalytic triad of serine proteases. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2110194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Yani Chen
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wanqing Wei
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yanzi Zhou
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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13
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Pinto AV, Ferreira P, Neves RPP, Fernandes PA, Ramos MJ, Magalhães AL. Reaction Mechanism of MHETase, a PET Degrading Enzyme. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02444] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Alexandre V. Pinto
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Rui P. P. Neves
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Alexandre L. Magalhães
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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14
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Sgrignani J, Cavalli A. Computational Identification of a Putative Allosteric Binding Pocket in TMPRSS2. Front Mol Biosci 2021; 8:666626. [PMID: 33996911 PMCID: PMC8119889 DOI: 10.3389/fmolb.2021.666626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/01/2021] [Indexed: 12/23/2022] Open
Abstract
Camostat, nafamostat, and bromhexine are inhibitors of the transmembrane serine protease TMPRSS2. The inhibition of TMPRSS2 has been shown to prevent the viral infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses. However, while camostat and nafamostat inhibit TMPRSS2 by forming a covalent adduct, the mode of action of bromhexine remains unclear. TMPRSS2 is autocatalytically activated from its inactive form, zymogen, through a proteolytic cleavage that promotes the binding of Ile256 to a putative allosteric pocket (A-pocket). Computer simulations, reported here, indicate that Ile256 binding induces a conformational change in the catalytic site, thus providing the atomistic rationale to the activation process of the enzyme. Furthermore, computational docking and molecular dynamics simulations indicate that bromhexine competes with the N-terminal Ile256 for the same binding site, making it a potential allosteric inhibitor. Taken together, these findings provide the atomistic basis for the development of more selective and potent TMPRSS2 inhibitors.
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Affiliation(s)
- Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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15
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Elsässer B, Goettig P. Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies. Int J Mol Sci 2021; 22:3232. [PMID: 33810118 PMCID: PMC8004986 DOI: 10.3390/ijms22063232] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/11/2022] Open
Abstract
Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.
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Affiliation(s)
| | - Peter Goettig
- Structural Biology Group, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria;
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16
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Silveira RL, Knott BC, Pereira CS, Crowley MF, Skaf MS, Beckham GT. Transition Path Sampling Study of the Feruloyl Esterase Mechanism. J Phys Chem B 2021; 125:2018-2030. [PMID: 33616402 DOI: 10.1021/acs.jpcb.0c09725] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Serine hydrolases cleave peptide and ester bonds and are ubiquitous in nature, with applications in biotechnology, in materials, and as drug targets. The serine hydrolase two-step mechanism employs a serine-histidine-aspartate/glutamate catalytic triad, where the histidine residue acts as a base to activate poor nucleophiles (a serine residue or a water molecule) and as an acid to allow the dissociation of poor leaving groups. This mechanism has been the subject of debate regarding how histidine shuttles the proton from the nucleophile to the leaving group. To elucidate the reaction mechanism of serine hydrolases, we employ quantum mechanics/molecular mechanics-based transition path sampling to obtain the reaction coordinate using the Aspergillus niger feruloyl esterase A (AnFaeA) as a model enzyme. The optimal reaction coordinates include terms involving nucleophilic attack on the carbonyl carbon and proton transfer to, and dissociation of, the leaving group. During the reaction, the histidine residue undergoes a reorientation on the time scale of hundreds of femtoseconds that supports the "moving histidine" mechanism, thus calling into question the "ring flip" mechanism. We find a concerted mechanism, where the transition state coincides with the tetrahedral intermediate with the histidine residue pointed between the nucleophile and the leaving group. Moreover, motions of the catalytic aspartate toward the histidine occur concertedly with proton abstraction by the catalytic histidine and help stabilize the transition state, thus partially explaining how serine hydrolases enable poor nucleophiles to attack the substrate carbonyl carbon. Rate calculations indicate that the second step (deacylation) is rate-determining, with a calculated rate constant of 66 s-1. Overall, these results reveal the pivotal role of active-site dynamics in the catalytic mechanism of AnFaeA, which is likely similar in other serine hydrolases.
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Affiliation(s)
- Rodrigo L Silveira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, Sao Paulo 13084-862, Brazil.,Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Brandon C Knott
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Caroline S Pereira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, Sao Paulo 13084-862, Brazil
| | - Michael F Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, Sao Paulo 13084-862, Brazil
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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17
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Hu Q, Jayasinghe-Arachchige VM, Prabhakar R. Degradation of a Main Plastic Pollutant Polyethylene Terephthalate by Two Distinct Proteases (Neprilysin and Cutinase-like Enzyme). J Chem Inf Model 2021; 61:764-776. [PMID: 33534993 DOI: 10.1021/acs.jcim.0c00797] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In this DFT study, hydrolysis of polyethylene terephthalate (PET), a major cause of plastic pollution, by two distinct enzymes, neprilysin (NEP, a mononuclear metalloprotease) and cutinase-like enzyme (CLE, a serine protease), has been investigated. These enzymes utilize different mechanisms for the degradation of PET. NEP uses either the metal-bound hydroxide attack (MH) mechanism or reverse protonation (RP) mechanism, while CLE utilizes a general acid/base mechanism that includes acylation and deacylation processes. Additionally, the RP mechanism of NEP can proceed through three pathways, RP0, RP1, and RP2. The DFT calculations predict that, among all these mechanisms, the MH mechanism is the energetically most favorable one for the NEP enzyme. In comparison, CLE catalyzes this reaction with a significantly higher barrier. These results suggest that the Lewis acid and nucleophile activations provided by the Zn metal center of NEP are more effective than the hydrogen bonding interactions afforded by the catalytic Ser85-His180-Asp165 triad of CLE. They have provided intrinsic details regarding PET degradation and will pave the way for the design of efficient metal-based catalysts for this critical reaction.
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Affiliation(s)
- Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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18
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Ishida T, Parks JM, Smith JC. Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure. J Am Chem Soc 2020; 142:17966-17980. [PMID: 32959658 DOI: 10.1021/jacs.0c02148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction mechanism of biomass decomposition by xylanases remains the subject of debate. To clarify the mechanism we investigated the glycosylation step of GH11 xylanase, an enzyme that catalyzes the hydrolysis of lignocellulosic hemicellulose (xylan). Making use of a recent neutron crystal structure, which revealed the protonation states of relevant residues, we used ab initio quantum mechanics/molecular mechanics (QM/MM) calculations to determine the detailed reaction mechanism of the glycosylation step. In particular, our focus is on the controversial question of whether or not an oxocarbenium ion intermediate is formed on the reaction pathway. The calculations support the validity of a basic retaining mechanism within a double-displacement scheme. The estimated free energy barrier of this reaction is ∼18 kcal/mol with QM/MM-CCSD(T)/6-31(+)G**//MP2/6-31+G**/AMBER calculations, and the rate-determining step of the glycosylation is scission of the glycosidic bond after proton transfer from the acidic Glu177. The estimated lifetime of the oxocarbenium ion intermediate (on the order of tens of ps) and the secondary kinetic isotope effect suggest that there is no accumulation of this intermediate on the reaction path, although the intermediate can be transiently formed. In the enzyme-substrate (ES) complex, the carbohydrate structure of the xylose residue at the -1 subsite has a rather distorted (skewed) geometry, and this xylose unit at the active site has an apparent half-chair conformation when the oxocarbenium ion intermediate is formed. The major catalytic role of the protein environment is to orient residues that take part in the initial proton transfer. Because of a fine alignment of catalytic residues, the enzyme can accelerate the glycosylation reaction without paying a reorganization energy penalty.
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Affiliation(s)
- Toyokazu Ishida
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan
| | - Jerry M Parks
- Center for Molecular Biophysics (CMB), Biosciences Division, Oak Ridge National Laboratory (ORNL), 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C Smith
- Center for Molecular Biophysics (CMB), Biosciences Division, Oak Ridge National Laboratory (ORNL), 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
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19
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Comparison of the in vitro protein digestibility of Protaetia brevitarsis larvae and beef loin before and after defatting. Food Chem 2020; 338:128073. [PMID: 32950872 DOI: 10.1016/j.foodchem.2020.128073] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/17/2022]
Abstract
Protein digestibility of Protaetia brevitarsis larvae before and after defatting by hexane was compared with that of beef loin in an in vitro digestion model. Larvae had higher crude protein content and 10% trichloroacetic acid (10% TCA)-soluble α-amino groups than beef. Decreases in the levels of total free sulfhydryl groups and 10% TCA-soluble α-amino groups were detected in larvae and beef after defatting (P < 0.05). Surface hydrophobicity increased after defatting in both larvae and beef, (P < 0.05) and tryptophan fluorescence intensity decreased in defatted larvae but increased in defatted beef. Levels of proteins digested into sizes under 3 and 10 kDa in larvae were higher than those in beef (P < 0.05), and defatting did not induce an effect in larvae. Therefore, in the aspect of high protein content and digestibility, larvae of P. brevitarsis can be a potential substitute of animal proteins.
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20
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Mori T, Saito S. Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase. J Chem Theory Comput 2020; 16:3396-3407. [PMID: 32268066 DOI: 10.1021/acs.jctc.9b01279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Free energy surfaces have played a central role in studying protein conformational changes and enzymatic reactions over decades. Yet, free energy barriers and kinetics are highly dependent on the coordinates chosen to define the surface, and furthermore, the dynamics during the reactions are often overlooked. Our recent study on the Pin1-catalyzed isomerization reaction has indicated that the isomerization transition events remarkably deviate from the free energy path, highlighting the need to understand the reaction dynamics in more detail. To this end, here we investigate the reaction coordinates that describe the transition states of the free energy and transition pathways by minimizing the cross-entropy function. We show that the isomerization transition events can be expressed by the concerted changes in the improper torsion angle ζ and nearby backbone torsional angles of the ligand, whereas the transition state of the free energy surface involves changes in a broad range of coordinates including multiple protein-ligand interactions. The current result supports the previous finding that the isomerization transitions occur quickly from the conformational excited states, which is in sharp contrast to the slow and collective changes suggested from the free energy path. Our results further indicate that the coordinates derived from the transition trajectories are not sufficient for finding the transition states on the free energy surfaces due to the lack of information from conformational excited states.
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Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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21
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Cuesta SA, Mora JR, Zambrano CH, Torres FJ, Rincón L. Comparative study of the nucleophilic attack step in the proteases catalytic activity: A theoretical study. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1705412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sebastián A. Cuesta
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - José R. Mora
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Cesar H. Zambrano
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - F. Javier Torres
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Luis Rincón
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
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22
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Toma M, Božičević L, Lapić J, Djaković S, Šakić D, Tandarić T, Vianello R, Vrček V. Transacylation in Ferrocenoyl-Purines. NMR and Computational Study of the Isomerization Mechanism. J Org Chem 2019; 84:12471-12480. [PMID: 31479271 DOI: 10.1021/acs.joc.9b01944] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the reaction of purines with ferrocenoyl chloride in dimethylformamide (DMF), a regioselective acylation occurred. The two products have been isolated and, according to detailed NMR analysis, identified as N7- and N9-ferrocenoylated isomers. In a more polar solvent, for example, in dimethylsulfoxide (DMSO), the two isomers interconvert to each other. The N7/N9 isomerization was followed by 1H NMR spectroscopy, until dynamic equilibrium was reached. Both kinetics and thermodynamics of the transacylation process are governed by a C6-substituent on the purine ring (R = NH2, Me, NHBz, OBz). The observed rate constant for the N7/N9-isomerization in the adenine system (R = NH2) is kobs = 0.3668 h-1, whereas the corresponding process in the C6-benzyloxypurine is 56 times slower. By use of density functional theory calculations and molecular dynamics simulations, several reaction pathways were considered and explored. Only the reaction mechanism involving DMSO as a nucleophilic reactant is in harmony with the experimental kinetic data. The calculated barrier (ΔG⧧ = 107.9 kJ/mol; at the M06L/6-311+G(d,p)/SDD level of theory) for this SN2-like reaction in the adenine system agrees well with the experimental value of 102.7 kJ/mol. No isomerization was detected in other organic solvents, for example, acetonitrile, N,N-dimethylformamide, or acetone, which indicated the exceptional nucleophilicity of DMSO. Our results raise a warning when treating or dissolving acylated purines in DMSO as they are prone to isomerization. We observed that the N7/N9-group transfer was specific not only for the organometallic moiety only, but for other acyl groups in purines as well. The relevance of this isomerization may be expected for a series of nucleobases and heterocyclic systems in general.
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Affiliation(s)
- Mateja Toma
- Faculty of Pharmacy and Biochemistry , University of Zagreb , Ante Kovačića 1 , 10000 Zagreb , Croatia
| | - Lucija Božičević
- Faculty of Pharmacy and Biochemistry , University of Zagreb , Ante Kovačića 1 , 10000 Zagreb , Croatia
| | - Jasmina Lapić
- Faculty of Food Technology and Biotechnology , University of Zagreb , Pierottijeva 6 , 10000 Zagreb , Croatia
| | - Senka Djaković
- Faculty of Food Technology and Biotechnology , University of Zagreb , Pierottijeva 6 , 10000 Zagreb , Croatia
| | - Davor Šakić
- Faculty of Pharmacy and Biochemistry , University of Zagreb , Ante Kovačića 1 , 10000 Zagreb , Croatia
| | - Tana Tandarić
- Computational Organic Chemistry and Biochemistry Group, Division of Organic Chemistry and Biochemistry , Rud̵er Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
| | - Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Division of Organic Chemistry and Biochemistry , Rud̵er Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
| | - Valerije Vrček
- Faculty of Pharmacy and Biochemistry , University of Zagreb , Ante Kovačića 1 , 10000 Zagreb , Croatia
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23
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Artificial cysteine-lipases with high activity and altered catalytic mechanism created by laboratory evolution. Nat Commun 2019; 10:3198. [PMID: 31324776 PMCID: PMC6642262 DOI: 10.1038/s41467-019-11155-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/24/2019] [Indexed: 11/13/2022] Open
Abstract
Engineering artificial enzymes with high activity and catalytic mechanism different from naturally occurring enzymes is a challenge in protein design. For example, many attempts have been made to obtain active hydrolases by introducing a Ser → Cys exchange at the respective catalytic triads, but this generally induced a breakdown of activity. We now report that this long-standing dogma no longer pertains, provided additional mutations are introduced by directed evolution. By employing Candida antarctica lipase B (CALB) as the model enzyme with the Ser-His-Asp catalytic triad, a highly active cysteine-lipase having a Cys-His-Asp catalytic triad and additional mutations W104V/A281Y/A282Y/V149G can be evolved, showing a 40-fold higher catalytic efficiency than wild-type CALB in the hydrolysis of 4-nitrophenyl benzoate, and tolerating bulky substrates. Crystal structures, kinetics, MD simulations and QM/MM calculations reveal dynamic features and explain all results, including the preference of a two-step mechanism involving the zwitterionic pair Cys105−/His224+ rather than a concerted process. Candida antarctica lipase B (CALB) is a serine lipase. Here, the authors use directed evolution to exchange serine with cysteine in the catalytic triad of the enzyme, thereby obtaining a highly active CALB variant that — unlike the wild type — accommodates bulky substrates.
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24
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Panche AN, Chandra S, Diwan AD. Multi-Target β-Protease Inhibitors from Andrographis paniculata: In Silico and In Vitro Studies. PLANTS 2019; 8:plants8070231. [PMID: 31319560 PMCID: PMC6681301 DOI: 10.3390/plants8070231] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/15/2019] [Accepted: 06/20/2019] [Indexed: 12/29/2022]
Abstract
Natural products derived from plants play a vital role in the discovery of new drug candidates, and these are used for novel therapeutic drug development. Andrographis paniculata and Spilanthes paniculata are used extensively as medicinal herbs for the treatment of various ailments, and are reported to have neuroprotective properties. β-amyloid is a microscopic brain protein whose significant aggregation is detected in mild cognitive impairment and Alzheimer’s disease (AD) brains. The accumulation of β-amyloid disrupts cell communication and triggers inflammation by activating immune cells, leading to neuronal cell death and cognitive disabilities. The proteases acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and beta secretase-1 (BACE-1) have been reported to be correlated with the synthesis and growth of β-amyloid plaques in the brains of AD patients. In the present study, the phenolic compounds from A. paniculata and S. paniculata that have been reported in the literature were selected for the current investigation. Furthermore, we employed molecular docking and molecular dynamics studies of the phenolic compounds with the proteins AChE, BChE, and BACE-1 in order to evaluate the binding characteristics and identify potent anti-amyloid agents against the neurodegenerative diseases such as AD. In this investigation, we predicted three compounds from A. paniculata with maximum binding affinities with cholinesterases and BACE-1. The computational investigations predicted that these compounds follow the rule of five. We further evaluated these molecules for in vitro inhibition activity against all the enzymes. In the in vitro investigations, 3,4-di-o-caffeoylquinic acid (5281780), apigenin (5280443), and 7-o-methylwogonin (188316) were found to be strong inhibitors of AChE, BChE, and BACE-1. These findings suggest that these compounds can be potent multi-target inhibitors of the proteases that might cumulatively work and inhibit the initiation and formation of β-amyloid plaques, which is a prime cause of neurotoxicity and dementia. According to our knowledge, these findings are the first report on natural compounds isolated from A. paniculata as multi-target potent inhibitors and anti-amyloid agents.
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Affiliation(s)
- Archana N Panche
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, India
- MGM's Institute of Biosciences & Technology, Mahatma Gandhi Mission, N-6, CIDCO, Aurangabad 431003, India
| | - Sheela Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, India.
| | - A D Diwan
- MGM's Institute of Biosciences & Technology, Mahatma Gandhi Mission, N-6, CIDCO, Aurangabad 431003, India
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25
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Nutho B, Mulholland AJ, Rungrotmongkol T. The reaction mechanism of Zika virus NS2B/NS3 serine protease inhibition by dipeptidyl aldehyde: a QM/MM study. Phys Chem Chem Phys 2019; 21:14945-14956. [PMID: 31236554 DOI: 10.1039/c9cp02377a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zika virus (ZIKV) infection has become a global public health problem, associated with microcephaly in newborns and Guillain-Barré syndrome in adults. Currently, there are no commercially available anti-ZIKV drugs. The viral protease NS2B/NS3, which is involved in viral replication and maturation, is a potential drug target. Peptidomimetic aldehyde inhibitors bind covalently to the catalytic S135 of the NS3 protease. Here, we apply hybrid quantum mechanics/molecular mechanics (QM/MM) free-energy simulations at the PDDG-PM3/ff14SB level to investigate the inhibition mechanism of the ZIKV protease by a dipeptidyl aldehyde inhibitor (acyl-KR-aldehyde). The results show that proton transfer from the catalytic S135 to H51 occurs in concert with nucleophilic addition on the aldehyde warhead by S135. The anionic covalent complex between the dipeptidyl aldehyde and the ZIKV protease is analogous to the tetrahedral intermediate for substrate hydrolysis. Spontaneous protonation by H51 forms the hemiacetal. In addition, we use correlated ab initio QM/MM potential energy path calculations at levels up to LCCSD(T)/(aug)-cc-pVTZ to obtain accurate potential energy profiles of the reaction, which also support a concerted mechanism. These results provide detailed insight into the mechanism of ZIKV protease inhibition by a peptidyl aldehyde inhibitor, which will guide in the design of inhibitors.
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Affiliation(s)
- Bodee Nutho
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. and Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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26
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Wei W, Ma J, Xie D, Zhou Y. Linking inhibitor motions to proteolytic stability of sunflower trypsin inhibitor-1. RSC Adv 2019; 9:13776-13786. [PMID: 35519558 PMCID: PMC9063939 DOI: 10.1039/c9ra02114k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/25/2019] [Indexed: 12/20/2022] Open
Abstract
The remarkable capability of an enzyme isn't only determined by its active site but also controlled by the environment. To unravel the environment role in catalysis, the dynamic motions as well as the static mechanism need to be studied. In this work, QM/MM MD simulations were employed to study the proteolysis process of SFTI-1 and BiKF, which revealed that a combination of static non-bonded interactions and dynamic motions along the reaction coordinate can account for the different hydrolysis rates between them. A comparison among SFTI-1 and three analogs with similar non-bonded interactions further revealed a positive correlation between the mobility of inhibitors and the hydrolysis rates. Apart from the cyclic backbone and disulfide bond, intramolecular hydrogen bonds also increase the rigidity of the backbone of inhibitors, and therefore hinder inhibitor motions to resist proteolysis. These new detailed mechanistic insights suggest the need to consider inhibitor motions in the rational design of peptide inhibitors. Besides the non-bonded interactions, inhibitor motions especially rotation of the scissile bond also influence proteolytic stability.![]()
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Affiliation(s)
- Wanqing Wei
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Yanzi Zhou
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
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27
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Li H, Wang D, Zhao X, Lu LN, Liu C, Gong LD, Zhao DX, Yang ZZ. Reaction mechanism of NO with hydrolysates of NAMI-A: an MD simulation by combining the QM/MM(ABEEM) with the MD-FEP method. J Comput Chem 2019; 40:1141-1150. [PMID: 30375671 DOI: 10.1002/jcc.25734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 09/27/2018] [Accepted: 09/28/2018] [Indexed: 11/06/2022]
Abstract
Nitrosylation reaction mechanisms of the hydrolysates of NAMI-A and hydrolysis reactions of ruthenium nitrosyl complexes were investigated in the triplet state and the singlet state. Activation free energies were calculated by combining the QM/MM(ABEEM) method with free energy perturbation theory, and the explicit solvent environment was simulated by an ABEEMσπ polarizable force field. Our results demonstrate that nitrosylation reactions of the hydrolysates of NAMI-A occur in both the triplet and the singlet states. The Ru-N-O angle of the triplet ruthenium nitrosyl complexes is in the range of 132.0°-138.2°. However, all the ruthenium nitrosyl complexes at the singlet state show an almost linear Ru-N-O angle. The nitrosylation reaction happens prior to the hydrolysis reaction for the first-step hydrolysates. The activation free energies of the nitrosylation reactions show that the H2 O-NO exchange reaction of [RuCl4 (Im)(H2 O)] in the singlet spin sate is the most likely one. Comparing with the activation free energies of the hydrolysis reactions of the ruthenium nitrosyl complexes, the results indicate that the rate of the DMSO-H2 O exchange reaction of [RuCl3 (NO)(Im)(DMSO)] is faster than that of [RuCl3 (H2 O)(Im)(DMSO)] in both the triplet spin state and the singlet spin state. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Hui Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China.,Department of Chemistry, Bohai University, Jinzhou 121013, China
| | - Di Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Xin Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Li-Nan Lu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Li-Dong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
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28
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Nutho B, Mulholland AJ, Rungrotmongkol T. Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate. J Phys Chem B 2019; 123:2889-2903. [PMID: 30845796 DOI: 10.1021/acs.jpcb.9b02157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zika virus (ZIKV) is mainly transmitted to humans by Aedes species mosquitoes and is associated with serious pathological disorders including microcephaly in newborns and Guillain-Barré syndrome in adults. Currently, there is no vaccine or anti-ZIKV drug available for preventing or controlling ZIKV infection. An attractive drug target for ZIKV treatment is a two-compartment (NS2B/NS3) serine protease that processes viral polyprotein during infection. Here, conventional molecular dynamics simulations of the ZIKV protease in complex with peptide substrate (TGKRS) sequence at the C-terminus of NS2B show that the substrate is in the active conformation for the cleavage reaction by ZIKV protease. Hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling simulations (PM6/ff14SB) of acylation results reveal that proton transfer from S135 to H51 and nucleophilic attack on the substrate by S135 are concerted. The rate-limiting step involves the formation of a tetrahedral intermediate. In addition, the single-point energy QM/MM calculations, precisely at the level of coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), were performed to correct the potential energy profiles for the first step of the acylation process. The average computed activation barrier at this level of theory is 16.3 kcal mol-1. Therefore, the computational approaches presented here are helpful for further designing of NS2B/NS3 inhibitors based on transition-state analogues.
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Affiliation(s)
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
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29
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Ishida T. Computational analysis of carbohydrate recognition based on hybrid QM/MM modeling: a case study of norovirus capsid protein in complex with Lewis antigen. Phys Chem Chem Phys 2018; 20:4652-4665. [PMID: 29372731 DOI: 10.1039/c7cp07701g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Norovirus is a major pathogen of nonbacterial acute gastroenteritis in humans and animals. Carbohydrate recognition between norovirus capsid proteins and Lewis antigens is considered to play a critical role in initiating infection of eukaryotic cells. In this article, we first report a detailed atomistic simulation study of the norovirus capsid protein in complex with the Lewis antigen based on ab initio QM/MM combined with MD-FEP simulations. To understand the mechanistic details of ligand binding, we analyzed and compared the carbohydrate recognition mechanism of the wild-type P domain protein with a mutant protein. Small structural differences between two capsid proteins are observed on the weak interaction site of residue 389, which is located on the solvent exposed surface of the P domain. To further clarify affinity differences in ligand binding, we directly evaluated free energy changes of the ligand binding process. Although the mutant protein loses its interaction energy with the Lewis antigen, this small amount of energy penalty is compensated for by an increase in the solvation stability, which is induced by structural reorganization at the ligand binding site on the protein surface. As a sum of these opposite energy components, the mutant P domain obtains a slightly enhanced binding affinity for the Lewis antigen. The present computational study clearly demonstrated that a detailed free energy balance of the interaction energy between the capsid protein and the surrounding aqueous solvent is the mechanistic basis of carbohydrate recognition in the norovirus capsid protein.
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Affiliation(s)
- Toyokazu Ishida
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, 305-8568, Japan.
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30
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Wang X, Shang X, Liu P, Xie F, Xiao T, Song S, Gong Z. Kinetic Modeling of Palmitamidopropyl Betaine Synthesis. J SURFACTANTS DETERG 2018. [DOI: 10.1002/jsde.12156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xinrui Wang
- Department of Chemistry and Chemical Engineering; Guangzhou University; Guangzhou 510006 People's Republic of China
| | - Xiaoqin Shang
- Department of Chemistry and Chemical Engineering; Guangzhou University; Guangzhou 510006 People's Republic of China
| | - Peng Liu
- Department of Chemistry and Chemical Engineering; Guangzhou University; Guangzhou 510006 People's Republic of China
| | - Fengwei Xie
- School of Chemical Engineering; The University of Queensland; Brisbane QLD 4072 Australia
| | - Tingyu Xiao
- Department of Chemistry and Chemical Engineering; Guangzhou University; Guangzhou 510006 People's Republic of China
| | - Shanshan Song
- Department of Chemistry and Chemical Engineering; Guangzhou University; Guangzhou 510006 People's Republic of China
| | - Zhe Gong
- Department of Chemistry and Chemical Engineering; Guangzhou University; Guangzhou 510006 People's Republic of China
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31
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Lima MCP, Seabra GM. Reaction mechanism of the dengue virus serine protease: a QM/MM study. Phys Chem Chem Phys 2018; 18:30288-30296. [PMID: 27341353 DOI: 10.1039/c6cp03209e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dengue virus (DENV) is the causative agent of the viral infection dengue fever. In spite of all the efforts made to prevent the spread of the disease, once it is contracted, there is no specific treatment for dengue and the WHO guidelines are limited to rest and symptomatic treatment. In its reproductive cycle, DENV utilizes the NS2B-NS3pro, a serine protease, to cleave the viral polyprotein into its constituents. This enzyme is essential for the virus lifecycle, and presents an attractive target for the development of specific dengue treatments. Here we used a hybrid Quantum Mechanics and Molecular Mechanics (QM/MM) Molecular Dynamics approach and Umbrella Sampling to study the first step (acylation) of the reaction catalyzed by NS2B-NS3pro, using the Pairwise Distance Directed Gaussian PM3 (PDDG/PM3) semi-empirical Hamiltonian for the QM subsystem, and Amber ff99SB for the MM subsystem. Our results indicate that the nucleophilic attack on the substrate by Ser135 occurs in a stepwise manner, in which a proton transfer to His51 first activates Ser135, which only later attacks the substrate. The rate-determining step is the Ser135 activation, with a barrier of 24.1 kcal mol-1. Water molecules completing the oxyanion hole stabilize the negative charge formed on the carbonyl oxygen of the substrate. The final step in the process is a proton transfer from His51 to the substrate's nitrogen, which happens with a lower barrier of 5.1 kcal mol-1, and leads directly to the breakage of the peptide bond.
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Affiliation(s)
- M C P Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Av. Jornalista Anibal Fernandes, s/no, Cidade Universitária - Recife, PE - CEP 50.740-560, Brazil.
| | - G M Seabra
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Av. Jornalista Anibal Fernandes, s/no, Cidade Universitária - Recife, PE - CEP 50.740-560, Brazil.
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32
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Zhao L, Kong X, Zhang C, Hua Y, Chen Y. Soybean P34 Probable Thiol Protease Probably Has Proteolytic Activity on Oleosins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:5741-5750. [PMID: 28656754 DOI: 10.1021/acs.jafc.7b02190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
P34 probable thiol protease (P34) and Gly m Bd 30K (30K) show high relationship with the protease of 24 kDa oleosin of soybean oil bodies. In this study, 9 day germinated soybean was used to separate bioprocessed P34 (P32) from bioprocessed 30K (28K). Interestingly, P32 existed as dimer, whereas 28K existed as monomer; a P32-rich sample had proteolytic activity and high cleavage site specificity (Lys-Thr of 24 kDa oleosin), whereas a 28K-rich sample showed low proteolytic activity; the P32-rich sample contained one thiol protease. After mixing with purified oil bodies, all P32 dimers were dissociated and bound to 24 kDa oleosins to form P32-24 kDa oleosin complexes. By incubation, 24 kDa oleosin was preferentially hydrolyzed, and two hydrolyzed products (HPs; 17 and 7 kDa) were confirmed. After most of 24 kDa oleosin was hydrolyzed, some P32 existed as dimer, and the other as P32-17 kDa HP. It was suggested that P32 was the protease.
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Affiliation(s)
- Luping Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, School of Food Science and Technology, Jiangnan University , 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, P. R. China
| | - Xiangzhen Kong
- State Key Laboratory of Food Science and Technology, Jiangnan University, School of Food Science and Technology, Jiangnan University , 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, P. R. China
| | - Caimeng Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, School of Food Science and Technology, Jiangnan University , 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, P. R. China
| | - Yufei Hua
- State Key Laboratory of Food Science and Technology, Jiangnan University, School of Food Science and Technology, Jiangnan University , 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, P. R. China
| | - Yeming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, School of Food Science and Technology, Jiangnan University , 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, P. R. China
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33
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Duboué-Dijon E, Pluhařová E, Domin D, Sen K, Fogarty AC, Chéron N, Laage D. Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent. J Phys Chem B 2017; 121:7027-7041. [PMID: 28675789 DOI: 10.1021/acs.jpcb.7b03102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.
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Affiliation(s)
- Elise Duboué-Dijon
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Eva Pluhařová
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Dominik Domin
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Kakali Sen
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Aoife C Fogarty
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Nicolas Chéron
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Damien Laage
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
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34
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Abstract
Hepatitis C virus (HCV) currently affects several million people across the globe. One of the major classes of drugs against HCV inhibits the NS3/4A protease of the polyprotein chain. Efficacy of these drugs is severely limited due to the high mutation rate that results in several genetically related quasispecies. The molecular mechanism of drug resistance is frequently deduced from structural studies and binding free energies. However, prediction of new mutations requires the evaluation of both binding free energy of the drug as well as the parameters (kcat and KM) for the natural substrate. The vitality values offer a good approach to investigate and predict mutations that render resistance to the inhibitor. A successful mutation should only affect the binding of the drug and not the catalytic activity and binding of the natural substrate. In this article, we have calculated the vitality values for four known drug inhibitors that are either currently in use or in clinical trials, evaluating binding free energies by the relevant PDLD/S-LRA method and activation barriers by the EVB method. The molecular details pertaining to resistance are also discussed. We show that our calculations are able to reproduce the catalytic effects and binding free energies in a good agreement with the corresponding observed values. Importantly, previous computational approaches have not been able to achieve this task. The trend for the vitality values is in accordance with experimental findings. Finally, we calculate the vitality values for mutations that have either not been studied experimentally or reported for some inhibitors.
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Affiliation(s)
- Garima Jindal
- Department of Chemistry, University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Dibyendu Mondal
- Department of Chemistry, University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
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35
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Studies on hydrolysis mechanism of anticancer ruthenium drug ImH[trans-Ru(Im)2Cl4] via ABEEMσπ polarizable force field combined with QM and MD-FEP. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-6401-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Li H, Sun TT, Zhang C, Liu L, Zhao D, Yang Z. QM/MM(ABEEM) Study on the Ligand Substitution Processes of Ruthenium(III) Complex NAMI-A. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201600605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hui Li
- Chemistry and Chemical Engineering Faculty; Liaoning Normal University; Dalian Liaoning 116029 China
| | - Ting-Ting Sun
- Chemistry and Chemical Engineering Faculty; Liaoning Normal University; Dalian Liaoning 116029 China
| | - Chao Zhang
- Chemistry and Chemical Engineering Faculty; Liaoning Normal University; Dalian Liaoning 116029 China
| | - Linlin Liu
- Chemistry and Chemical Engineering Faculty; Liaoning Normal University; Dalian Liaoning 116029 China
| | - Dongxia Zhao
- Chemistry and Chemical Engineering Faculty; Liaoning Normal University; Dalian Liaoning 116029 China
| | - Zhongzhi Yang
- Chemistry and Chemical Engineering Faculty; Liaoning Normal University; Dalian Liaoning 116029 China
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37
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Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases. Int J Mol Sci 2016; 17:ijms17121969. [PMID: 27898009 PMCID: PMC5187769 DOI: 10.3390/ijms17121969] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 02/06/2023] Open
Abstract
Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications.
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38
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Yao Z, Zhang L, Gao B, Cui D, Wang F, He X, Zhang JZH, Wei D. A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B. J Chem Inf Model 2016; 56:1979-1994. [DOI: 10.1021/acs.jcim.5b00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhiqiang Yao
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Lujia Zhang
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Bei Gao
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Dongbing Cui
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Fengqing Wang
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Xiao He
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z. H. Zhang
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Dongzhi Wei
- State
Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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39
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Zhou Y, Xie D, Zhang Y. Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides. J Phys Chem Lett 2016; 7:1138-42. [PMID: 26958702 PMCID: PMC4824663 DOI: 10.1021/acs.jpclett.6b00373] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cystine-knot peptides have remarkable stability against protease degradation and are attractive scaffolds for peptide-based therapeutic and diagnostic agents. In this work, by studying the hydrolysis reaction of a cystine-knot inhibitor MCTI-A and its variants with ab initio QM/MM molecular dynamics simulations, we have elucidated an amide rotation hindrance mechanism for proteolysis resistance: The proteolysis of MCTI-A is retarded due to the higher free energy cost during the rotation of NH group around scissile peptide bond at the tetrahedral intermediate of acylation, and covalent constraint provided by disulfide bonds is the key factor to hinder this rotation. A nearly linear correlation has been revealed between free energy barriers of the peptide hydrolysis reaction and the amide rotation free energy changes at the protease-peptide Michaelis complex state. This suggests that amide rotation hindrance could be one useful feature to estimate peptide proteolysis stability.
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Affiliation(s)
- Yanzi Zhou
- Laboratory of Mesoscopic Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Corresponding Author: 1) , 2)
| | - Daiqian Xie
- Laboratory of Mesoscopic Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003 USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Corresponding Author: 1) , 2)
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40
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Uritsky N, Shokhen M, Albeck A. Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015; 55:1680-4. [DOI: 10.1002/anie.201507772] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Neta Uritsky
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
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41
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Uritsky N, Shokhen M, Albeck A. Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Neta Uritsky
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
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42
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Kurisaki I, Barberot C, Takayanagi M, Nagaoka M. Dewetting of S1-Pocket via Water Channel upon Thrombin–Substrate Association Reaction. J Phys Chem B 2015; 119:15807-12. [DOI: 10.1021/acs.jpcb.5b09581] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ikuo Kurisaki
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency,
Honmachi, Kawaguchi 332-0012, Japan
| | - Chantal Barberot
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency,
Honmachi, Kawaguchi 332-0012, Japan
| | - Masayoshi Takayanagi
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency,
Honmachi, Kawaguchi 332-0012, Japan
| | - Masataka Nagaoka
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency,
Honmachi, Kawaguchi 332-0012, Japan
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43
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Yao J, Guo H, Chaiprasongsuk M, Zhao N, Chen F, Yang X, Guo H. Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes. Biochemistry 2015; 54:5366-75. [PMID: 26244568 DOI: 10.1021/acs.biochem.5b00638] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although one of an enzyme's hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. It is known that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. Here we report the results of quantum mechanical/molecular mechanical simulations and an experimental study of salicylic acid binding protein 2 (SABP2). SABP2 has promiscuous esterase activity toward a series of substrates but shows a high activity toward its natural substrate, methyl salicylate (MeSA). Our results demonstrate that this enzyme may use substrate-assisted catalysis involving the hydroxyl group from MeSA to enhance the activity and achieve substrate discrimination.
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Affiliation(s)
- Jianzhuang Yao
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Haobo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Minta Chaiprasongsuk
- Department of Plant Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Nan Zhao
- Department of Plant Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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44
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Aguirre C, Condado-Morales I, Olguin LF, Costas M. Isothermal titration calorimetry determination of individual rate constants of trypsin catalytic activity. Anal Biochem 2015; 479:18-27. [PMID: 25823683 DOI: 10.1016/j.ab.2015.03.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/02/2015] [Accepted: 03/11/2015] [Indexed: 11/25/2022]
Abstract
Determination of individual rate constants for enzyme-catalyzed reactions is central to the understanding of their mechanism of action and is commonly obtained by stopped-flow kinetic experiments. However, most natural substrates either do not fluoresce/absorb or lack a significant change in their spectra while reacting and, therefore, are frequently chemically modified to render adequate molecules for their spectroscopic detection. Here, isothermal titration calorimetry (ITC) was used to obtain Michaelis-Menten plots for the trypsin-catalyzed hydrolysis of several substrates at different temperatures (278-318K): four spectrophotometrically blind lysine and arginine N-free esters, one N-substituted arginine ester, and one amide. A global fitting of these data provided the individual rate constants and activation energies for the acylation and deacylation reactions, and the ratio of the formation and dissociation rates of the enzyme-substrate complex, leading also to the corresponding free energies of activation. The results indicate that for lysine and arginine N-free esters deacylation is the rate-limiting step, but for the N-substituted ester and the amide acylation is the slowest step. It is shown that ITC is able to produce quality kinetic data and is particularly well suited for those enzymatic reactions that cannot be measured by absorption or fluorescence spectroscopy.
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Affiliation(s)
- César Aguirre
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Itzel Condado-Morales
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Luis F Olguin
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico.
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico.
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45
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Martínez-González JÁ, Rodríguez A, Puyuelo MP, González M, Martínez R. Further theoretical insight into the reaction mechanism of the hepatitis C NS3/NS4A serine protease. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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46
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Baba T, Boero M, Kamiya K, Ando H, Negoro S, Nakano M, Shigeta Y. Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: from induced-fit to acylation processes. Phys Chem Chem Phys 2015; 17:4492-504. [DOI: 10.1039/c4cp04419c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To unravel the factor that provides the ability to degrade non-biological amide bond with nylon oligomer hydrolase, we investigated the process from induced-fit to acylation by a combination of different theoretical methods.
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Affiliation(s)
- Takeshi Baba
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Mauro Boero
- Institut de Physique et Chimie des Matériaux de Strasbourg
- UMR 7504 CNRS and University of Strasbourg
- 67034 Strasbourg
- France
| | - Katsumasa Kamiya
- Center for Basic Education and Integrated Learning
- Kanagawa Institute of Technology
- Atsugi
- Japan
| | - Hiroyuki Ando
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Seiji Negoro
- Department of Material Science and Chemistry
- Graduate School of Engineering
- University of Hyogo
- Himeji
- Japan
| | - Masayoshi Nakano
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Yasuteru Shigeta
- Department of Physics
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
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47
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Martı́nez-González JÁ, González M, Masgrau L, Martı́nez R. Theoretical Study of the Free Energy Surface and Kinetics of the Hepatitis C Virus NS3/NS4A Serine Protease Reaction with the NS5A/5B Substrate. Does the Generally Accepted Tetrahedral Intermediate Really Exist? ACS Catal 2014. [DOI: 10.1021/cs5011162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Miguel González
- Departament
de Quı́mica Fı́sica i IQTC, Universitat de Barcelona, C/Martı́ i Franquès, 1, 08028 Barcelona, Spain
| | - Laura Masgrau
- Institut
de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Rodrigo Martı́nez
- Departamento
de Quı́mica, Universidad de La Rioja, C/Madre de
Dios, 51, 26006 Logroño, Spain
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48
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Mashima A, Kurahashi M, Sasahara K, Yoshida T, Chuman H. Connecting Classical QSAR and LERE Analyses Using Modern Molecular Calculations, LERE-QSAR (VI): Hydrolysis of Substituted Hippuric Acid Phenyl Esters by Trypsin. Mol Inform 2014; 33:802-14. [PMID: 27485426 DOI: 10.1002/minf.201400099] [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: 07/14/2014] [Accepted: 09/14/2014] [Indexed: 11/08/2022]
Abstract
The reaction mechanism of trypsin was studied by applying DFT and ab initio molecular orbital (MO) calculations to complexes of trypsin with a congeneric series of eight para-substituted hippuric acid phenyl esters, for which a previous quantitative structureactivity relationship (QSAR) study revealed nice linearity of Hammett substitution constant σ(-) with logarithmic values of the MichaelisMenten and catalytic rate constants. Based on the LERE procedure, we performed QSAR analyses on each elementary reaction step during the acylation process. The present calculations showed that the rate-determining step during the acylation process is the transition state (TS) between the enzymesubstrate complex (ES) and tetrahedral intermediate (TET), and that the proton transfer occurs from Ser195 to His57, not between His57 and Asp102. The LERE-QSAR analysis statistically suggested that the variation of overall free-energy changes leading to formation of TS is governed mostly by that of activation energies required to form TS from ES. In spite of a very limited number of congeneric ligands in the current work, it is critically essential to clarify and verify physicochemical meanings of a typical QSAR/Chemoinformatics parameter, Hammett σ(-) based on quantum chemical calculations on the proteinligand kinetics; how Hammett σ(-) behaves in terms of proteinligand interaction energies.
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Affiliation(s)
- Akira Mashima
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Masahiro Kurahashi
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Katsunori Sasahara
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Hiroshi Chuman
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508.
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49
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Fako VE, Zhang JT, Liu JY. Mechanism of Orlistat Hydrolysis by the Thioesterase of Human Fatty Acid Synthase. ACS Catal 2014; 4:3444-3453. [PMID: 25309810 PMCID: PMC4188697 DOI: 10.1021/cs500956m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 08/15/2014] [Indexed: 01/25/2023]
Abstract
Fatty acid synthase (FASN), the sole protein capable of de novo synthesis of free fatty acids, is overexpressed in a wide variety of human cancers and is associated with poor prognosis and aggressiveness of these cancers. Orlistat, an FDA-approved drug for obesity treatment that inhibits pancreatic lipases in the GI tract, also inhibits the thioesterase (TE) of human FASN. The cocrystal structure of TE with orlistat shows a pseudo TE dimer containing two different forms of orlistat in the active site, an intermediate that is covalently bound to a serine residue (Ser2308) and a hydrolyzed and inactivated product. In this study, we attempted to understand the mechanism of TE-catalyzed orlistat hydrolysis by examining the role of the hexyl tail of the covalently bound orlistat in water activation for hydrolysis using molecular dynamics simulations. We found that the hexyl tail of the covalently bound orlistat undergoes a conformational transition, which is accompanied by destabilization of a hydrogen bond between a hydroxyl moiety of orlistat and the catalytic His2481 of TE that in turn leads to an increased hydrogen bonding between water molecules and His2481 and increased chance for water activation to hydrolyze the covalent bond between orlistat and Ser2308. Thus, the conformation of the hexyl tail of orlistat plays an important role in orlistat hydrolysis. Strategies that stabilize the hexyl tail may lead to the design of more potent irreversible inhibitors that target FASN and block TE activity with greater endurance.
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Affiliation(s)
| | | | - Jing-Yuan Liu
- Department
of Computer and Information Science, Indiana University-Purdue University, 635 Barnhill Drive, Indianapolis, Indiana 46202, United States
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50
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Shokhen M, Hirsch M, Khazanov N, Ozeri R, Perlman N, Traube T, Vijayakumar S, Albeck A. From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Serine and Cysteine Hydrolases. Isr J Chem 2014. [DOI: 10.1002/ijch.201300144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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