1
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Schröder HC, Neufurth M, Zhou H, Wang S, Wang X, Müller WEG. Inorganic Polyphosphate: Coacervate Formation and Functional Significance in Nanomedical Applications. Int J Nanomedicine 2022; 17:5825-5850. [DOI: 10.2147/ijn.s389819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/03/2022] [Indexed: 12/02/2022] Open
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2
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Gavira JA, Cámara-Artigas A, Neira JL, Torres de Pinedo JM, Sánchez P, Ortega E, Martinez-Rodríguez S. Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding. Acta Crystallogr D Struct Biol 2022; 78:669-682. [PMID: 35503214 PMCID: PMC9063841 DOI: 10.1107/s2059798322003709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
Abstract
Choline-O-sulfatase (COSe; EC 3.1.6.6) is a member of the alkaline phosphatase (AP) superfamily, and its natural function is to hydrolyze choline-O-sulfate into choline and sulfate. Despite its natural function, the major interest in this enzyme resides in the landmark catalytic/substrate promiscuity of sulfatases, which has led to attention in the biotechnological field due to their potential in protein engineering. In this work, an in-depth structural analysis of wild-type Sinorhizobium (Ensifer) meliloti COSe (SmeCOSe) and its C54S active-site mutant is reported. The binding mode of this AP superfamily member to both products of the reaction (sulfate and choline) and to a substrate-like compound are shown for the first time. The structures further confirm the importance of the C-terminal extension of the enzyme in becoming part of the active site and participating in enzyme activity through dynamic intra-subunit and inter-subunit hydrogen bonds (Asn146A-Asp500B-Asn498B). These residues act as the `gatekeeper' responsible for the open/closed conformations of the enzyme, in addition to assisting in ligand binding through the rearrangement of Leu499 (with a movement of approximately 5 Å). Trp129 and His145 clamp the quaternary ammonium moiety of choline and also connect the catalytic cleft to the C-terminus of an adjacent protomer. The structural information reported here contrasts with the proposed role of conformational dynamics in promoting the enzymatic catalytic proficiency of an enzyme.
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Affiliation(s)
- Jose Antonio Gavira
- Laboratorio de Estudios Cristalográficos, CSIC, Armilla, 18100 Granada, Spain
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Research Centre for Agricultural and Food Biotechnology (BITAL), Carretera de Sacramento s/n, Almería, 04120, Spain
| | - Jose Luis Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR–CSIC–BIFI and GBsC–CSIC–BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Jesús M. Torres de Pinedo
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18071 Granada, Spain
| | - Pilar Sánchez
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18071 Granada, Spain
| | - Esperanza Ortega
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18071 Granada, Spain
| | - Sergio Martinez-Rodríguez
- Laboratorio de Estudios Cristalográficos, CSIC, Armilla, 18100 Granada, Spain
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18071 Granada, Spain
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3
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Yang Z, Twidale RM, Gervasoni S, Suardíaz R, Colenso CK, Lang EJM, Spencer J, Mulholland AJ. Multiscale Workflow for Modeling Ligand Complexes of Zinc Metalloproteins. J Chem Inf Model 2021; 61:5658-5672. [PMID: 34748329 DOI: 10.1021/acs.jcim.1c01109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zinc metalloproteins are ubiquitous, with protein zinc centers of structural and functional importance, involved in interactions with ligands and substrates and often of pharmacological interest. Biomolecular simulations are increasingly prominent in investigations of protein structure, dynamics, ligand interactions, and catalysis, but zinc poses a particular challenge, in part because of its versatile, flexible coordination. A computational workflow generating reliable models of ligand complexes of biological zinc centers would find broad application. Here, we evaluate the ability of alternative treatments, using (nonbonded) molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) at semiempirical (DFTB3) and density functional theory (DFT) levels of theory, to describe the zinc centers of ligand complexes of six metalloenzyme systems differing in coordination geometries, zinc stoichiometries (mono- and dinuclear), and the nature of interacting groups (specifically the presence of zinc-sulfur interactions). MM molecular dynamics (MD) simulations can overfavor octahedral geometries, introducing additional water molecules to the zinc coordination shell, but this can be rectified by subsequent semiempirical (DFTB3) QM/MM MD simulations. B3LYP/MM geometry optimization further improved the accuracy of the description of coordination distances, with the overall effectiveness of the approach depending upon factors, including the presence of zinc-sulfur interactions that are less well described by semiempirical methods. We describe a workflow comprising QM/MM MD using DFTB3 followed by QM/MM geometry optimization using DFT (e.g., B3LYP) that well describes our set of zinc metalloenzyme complexes and is likely to be suitable for creating accurate models of zinc protein complexes when structural information is more limited.
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Affiliation(s)
- Zongfan Yang
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.,School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
| | - Silvia Gervasoni
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.,Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli, 25, I-20133 Milano, Italy
| | - Reynier Suardíaz
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
| | - Charlotte K Colenso
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.,School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K
| | - Eric J M Lang
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K
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4
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Tserendavga B, Ohshima N, Fujita C, Yuzawa K, Ohshima M, Yanaka N, Minamishima YA, Izumi T. Characterization of recombinant murine GDE4 and GDE7, enzymes producing lysophosphatidic acid and/or cyclic phosphatidic acid. J Biochem 2021; 170:713-727. [PMID: 34523685 DOI: 10.1093/jb/mvab091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
GDE4 and GDE7 are membrane-bound enzymes that exhibit lysophospholipase D (lysoPLD) activities. We found that GDE7 produced not only lysophosphatidic acid (LPA) but also cyclic phosphatidic acid (cPA) from lysophospholipids by a transphosphatidylation reaction. In contrast, GDE4 produced only LPA. The analysis of substrate specificity showed that 1-alkyl-lysophosphospholipids were preferred substrates for both enzymes rather than 1-alkyl-lysophospholipids and 1-alkenyl-lysophospholipids. Among the various lysophospholipids with different polar head groups that were tested, lysophosphatidylglycerol and lysophosphatidylserine were preferred substrates for GDE4 and GDE7, respectively. The detailed analysis of the dependency of the enzyme activities of GDE4 and GDE7 on divalent cations suggested multiple divalent cations were bound in the active sites of both enzymes. Taken together, these results suggest the possibility that GDE7 functions as a cPA-producing enzyme in the body.
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Affiliation(s)
- Binderiya Tserendavga
- Department of Biochemistry, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Noriyasu Ohshima
- Department of Biochemistry, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Chiaki Fujita
- Department of Biochemistry, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Koji Yuzawa
- Group of Pharmaceutical Analysis, ENVIRONMENTAL TECHNICAL CO., LTD, Takasaki, Gunma 370-3511, Japan
| | - Mari Ohshima
- Department of Biochemistry, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan.,Group of Pharmaceutical Analysis, ENVIRONMENTAL TECHNICAL CO., LTD, Takasaki, Gunma 370-3511, Japan
| | - Noriyuki Yanaka
- Department of Molecular and Applied Bioscience, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Yoji Andrew Minamishima
- Department of Biochemistry, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Takashi Izumi
- Department of Biochemistry, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan.,Faculty of Health Care, Teikyo Heisei University, Tokyo, 170-8445, Japan
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5
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Costa PFA, de Abreu R, Fontana AB, Fiedler HD, Kirby AJ, Quina FH, Nome F, Gerola AP. The role of hydrophobicity in supramolecular polymer/surfactant catalysts: An understandable model for enzymatic catalysis. J Colloid Interface Sci 2020; 588:456-468. [PMID: 33429342 DOI: 10.1016/j.jcis.2020.12.081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/24/2022]
Abstract
Enzymes are highly significant catalysts, essential to biological systems, and a source of inspiration for the design of artificial enzymes. Although many models have been developed describing enzymatic catalysis, a deeper understanding of these biocatalysts remains a major challenge. Herein we detail the formation, characterization, performance, and catalytic mechanisms of a series of bio-inspired supramolecular polymer/surfactant complexes acting as artificial enzymes. The supramolecular complexes were characterized and exhibited exceptional catalytic efficiency for the dephosphorylation of an activated phosphate diester, the reaction rate being highly responsive to: (a) pH, (b) surfactant concentration, and (c) the length of the hydrophobic chain of the surfactant. Under optimal conditions (at pH > 8 for the more hydrophobic systems and at pre-micellar concentrations), enzyme-like rate enhancements of up to 6.0 × 109-fold over the rate of the spontaneous hydrolysis reaction in water were verified. The catalytic performance is a consequence of synergy between the hydrophobicity of the aggregates and the catalytic functionalities of the polymer and the catalytic mechanism is modulated by the nature of the hydrophobic pockets of these catalysts, changing from a general base mechanism to a nucleophilic mechanism as the hydrophobicity increases. Taken as a whole, the present results provide fundamental insights, through an understandable model, which are highly relevant to the design of novel bioinspired enzyme surrogates with multifunctional potentialities for future practical applications.
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Affiliation(s)
- Paulo F A Costa
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Rafael de Abreu
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Andressa B Fontana
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Haidi D Fiedler
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Anthony J Kirby
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Frank H Quina
- Institute of Chemistry, University of São Paulo, CEP 05508-000 São Paulo, Brazil
| | - Faruk Nome
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Adriana P Gerola
- Department of Chemistry, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil.
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6
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Borosky GL. Alkaline Phosphatases: in Silico Study on the Catalytic Effect of Conserved Active Site Residues Using Human Placental Alkaline Phosphatase (PLAP) As a Model Protein. J Chem Inf Model 2020; 60:6228-6241. [PMID: 33306371 DOI: 10.1021/acs.jcim.0c00860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The metalloenzymes from the alkaline phosphatase (AP) superfamily catalyze the hydrolysis and transphosphorylation of phosphate monoesters. The role of several amino acids highly conserved in the active site of this family of enzymes was examined, using human placental AP (PLAP) as a model protein. By employing an active-site model based on the X-ray crystal structure of PLAP, mutations of several key residues were modeled by quantum mechanical methods in order to determine their impact on the catalytic activity. Kinetic and thermodynamic estimations were achieved for each reaction step of the catalytic mechanism by characterization of the intermediates and transition states on the reaction pathway, and the effects of mutations on the activation barriers were analyzed. A good accordance was observed between the present computational results and experimental measurements reported in the literature.
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Affiliation(s)
- Gabriela L Borosky
- INFIQC, CONICET and Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina
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7
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Gupta MN, Alam A, Hasnain SE. Protein promiscuity in drug discovery, drug-repurposing and antibiotic resistance. Biochimie 2020; 175:50-57. [PMID: 32416199 DOI: 10.1016/j.biochi.2020.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/01/2022]
Abstract
Proteins are supposed to bind to their substrates/ligands in a specific manner via their pre-formed binding sites, according to classical biochemistry. In recent years, several types of deviations from this norm have been observed and called promiscuous behavior. Enzymatic promiscuities allow several biochemical functions to be carried out by the same enzyme. The promiscuous activity can also be the origin of "new proteins" via gene duplication. In more recent years, proteins from prokaryotes, eukaryotes and viruses have been found to have intrinsic disorder and lack a preformed binding site. Intrinsic disorder is exploited in regulatory proteins such as those that are involved in transcription and signal transduction. Such proteins function by folding locally while binding to their ligands or interacting with other proteins. These phenomena have also been classified as examples of protein promiscuity and encompass diverse kinds of ligands that can bind to a protein. Given the significant extent of structural homology in many protein families, it is not surprising that ligands also have been found to display promiscuity. Promiscuous behavior of proteins offers both challenges and opportunities to the drug discovery programs such as drug repurposing. Pathogens when exposed to antibiotics exploit protein promiscuity in several ways to develop resistance to the drug. There is increasing evidence now to support that the disorder in proteins is a major tool used by pathogens for virulence and evade drug action by exploiting protein promiscuity. This review provides a holistic view of this multi-faceted phenomenon called protein promiscuity.
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Affiliation(s)
- Munishwar N Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Anwar Alam
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Seyed E Hasnain
- JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Professor CR Rao Road, Hyderabad, 500046, India.
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8
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Singla P, Bhardwaj RD. Enzyme promiscuity – A light on the “darker” side of enzyme specificity. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1696779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Prabhjot Singla
- Department of Biochemistry, Punjab Agricultural University, Ludhiana, India
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9
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Salar U, Mohammed Khan K, Ejaz SA, Hameed A, al-Rashida M, Perveen S, Tahir MN, Iqbal J, Taha M. Coumarinyl Aryl/Alkyl Sulfonates with Dual Potential: Alkaline Phosphatase and ROS Inhibitory Activities: In-Silico Molecular Modeling and ADME Evaluation. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180327125738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background: Alkaline Phosphatase (AP) is a physiologically important metalloenzyme
that belongs to a large family of ectonucleotidase enzymes. Over-expression of tissue non-specific
alkaline phosphatase has been linked with ectopic calcification including vascular and aortic calcification.
In Vascular Smooth Muscles Cells (VSMCs), the high level of Reactive Oxygen Species
(ROS) resulted in the up-regulation of TNAP. Accordingly, there is a need to identify highly potent
and selective inhibitors of APs for treatment of disorders related to hyper activity of APs.
</P><P>
Methods: Herein, a series of coumarinyl alkyl/aryl sulfonates (1-40) with known Reactive Oxygen
Species (ROS) inhibition activity, was evaluated for alkaline phosphatase inhibition against human
Tissue Non-specific Alkaline Phosphatase (hTNAP) and Intestinal Alkaline Phosphatase (hIAP).
</P><P>
Results: With the exception of only two compounds, all other compounds in the series exhibited
excellent AP inhibition. For hIAP and hTNAP inhibition, IC50 values were observed in the range
0.62-23.5 µM, and 0.51-21.5 µM, respectively. Levamisole (IC50 = 20.21 ± 1.9 µM) and Lphenylalanine
(IC50 = 100.1 ± 3.15 µM) were used as standards for hIAP and hTNAP inhibitory
activities, respectively. 4-Substituted coumarinyl sulfonate derivative 23 (IC50 = 0.62 ± 0.02 µM)
was found to be the most potent hIAP inhibitor. Another 4-substituted coumarinyl sulfonate derivative
16 (IC50 = 0.51 ± 0.03 µM) was found to be the most active hTNAP inhibitor. Some of the
compounds were also found to be highly selective inhibitors of APs. Detailed Structure-Activity
Relationship (SAR) and Structure-Selectivity Relationship (SSR) analysis were carried out to identify
structural elements necessary for efficient and selective AP inhibition. Molecular modeling and
docking studies were carried out to rationalize the most probable binding site interactions of the
inhibitors with the AP enzymes. In order to evaluate drug-likeness of compounds, in silico ADMETox
evaluation was carried out, most of the compounds were found to have favorable ADME profiles
with good predicted oral bioavailability. X-ray crystal structures of compounds 38 and 39 were
also determined.
</P><P>
Conclusion: Compounds from this series may serve as lead candidates for future research in order
to design even more potent, and selective inhibitors of APs.
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Affiliation(s)
- Uzma Salar
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Syeda Abida Ejaz
- Centre for Advanced Drug Research, COMSATS Institute of Information Technology, Abbottabad 22060, Pakistan
| | - Abdul Hameed
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Mariya al-Rashida
- Department of Chemistry, Forman Christian College (A Chartered University), Ferozepur Road, Lahore-54600, Pakistan
| | - Shahnaz Perveen
- PCSIR Laboratories Complex, Shahrah-e-Dr. Salimuzzaman Siddiqui, Karachi- 75280, Pakistan
| | | | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS Institute of Information Technology, Abbottabad 22060, Pakistan
| | - Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam- 31441, Saudi Arabia
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10
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Molecular modeling of conformational dynamics and its role in enzyme evolution. Curr Opin Struct Biol 2018; 52:50-57. [PMID: 30205262 DOI: 10.1016/j.sbi.2018.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
Abstract
With increasing computational power, biomolecular simulations have become an invaluable tool for understanding enzyme mechanisms and the origins of enzyme catalysis. More recently, computational studies have started to focus on understanding how enzyme activity itself evolves, both in terms of enhancing the native or new activities on existing enzyme scaffolds, or completely de novo on previously non-catalytic scaffolds. In this context, both experiment and molecular modeling provided strong evidence for an important role of conformational dynamics in the evolution of enzyme functions. This contribution will present a brief overview of the current state of the art for computationally exploring enzyme conformational dynamics in enzyme evolution, and, using several showcase studies, illustrate the ways molecular modeling can be used to shed light on how enzyme function evolves, at the most fundamental molecular level.
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11
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Roston D, Lu X, Fang D, Demapan D, Cui Q. Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations. Methods Enzymol 2018; 607:53-90. [PMID: 30149869 DOI: 10.1016/bs.mie.2018.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We discuss the application of quantum mechanics/molecular mechanics (QM/MM) free energy simulations to the analysis of phosphoryl transfers catalyzed by two enzymes: alkaline phosphatase and myosin. We focus on the nature of the transition state and the issue of mechanochemical coupling, respectively, in the two enzymes. The results illustrate unique insights that emerged from the QM/MM simulations, especially concerning the interpretation of experimental data regarding the nature of enzymatic transition states and coupling between global structural transition and catalysis in the active site. We also highlight a number of technical issues worthy of attention when applying QM/MM free energy simulations, and comment on a number of technical and mechanistic issues that require further studies.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Dong Fang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Darren Demapan
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States.
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12
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Petrović D, Risso VA, Kamerlin SCL, Sanchez-Ruiz JM. Conformational dynamics and enzyme evolution. J R Soc Interface 2018; 15:20180330. [PMID: 30021929 PMCID: PMC6073641 DOI: 10.1098/rsif.2018.0330] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/27/2018] [Indexed: 12/21/2022] Open
Abstract
Enzymes are dynamic entities, and their dynamic properties are clearly linked to their biological function. It follows that dynamics ought to play an essential role in enzyme evolution. Indeed, a link between conformational diversity and the emergence of new enzyme functionalities has been recognized for many years. However, it is only recently that state-of-the-art computational and experimental approaches are revealing the crucial molecular details of this link. Specifically, evolutionary trajectories leading to functional optimization for a given host environment or to the emergence of a new function typically involve enriching catalytically competent conformations and/or the freezing out of non-competent conformations of an enzyme. In some cases, these evolutionary changes are achieved through distant mutations that shift the protein ensemble towards productive conformations. Multifunctional intermediates in evolutionary trajectories are probably multi-conformational, i.e. able to switch between different overall conformations, each competent for a given function. Conformational diversity can assist the emergence of a completely new active site through a single mutation by facilitating transition-state binding. We propose that this mechanism may have played a role in the emergence of enzymes at the primordial, progenote stage, where it was plausibly promoted by high environmental temperatures and the possibility of additional phenotypic mutations.
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Affiliation(s)
- Dušan Petrović
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Valeria A Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071 Granada, Spain
| | | | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071 Granada, Spain
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13
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Petrović D, Szeler K, Kamerlin SCL. Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chem Commun (Camb) 2018; 54:3077-3089. [PMID: 29412205 DOI: 10.1039/c7cc09504j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.
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Affiliation(s)
- Dušan Petrović
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
| | - Klaudia Szeler
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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14
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Yoon H, Warshel A. Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis. Proteins 2017; 85:1446-1453. [PMID: 28383109 DOI: 10.1002/prot.25305] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/20/2017] [Accepted: 03/27/2017] [Indexed: 11/06/2022]
Abstract
Pol η belongs to the important Y family of DNA polymerases that can catalyze translesion synthesis across sites of damaged DNA. This activity involves the reduced fidelity of Pol η for 8-oxo-7,8-dhyedro-2'-deoxoguanosin(8-oxoG). The fundamental interest in Pol η has grown recently with the demonstration of the importance of a 3rd Mg2+ ion. The current work explores both the fidelity of Pol η and the role of the 3rd metal ion, by using empirical valence bond (EVB) simulations. The simulations reproduce the observed trend in fidelity and shed a new light on the role of the 3rd metal ion. It is found that this ion does not lead to a major catalytic effect, but most probably plays an important role in reducing the product release barrier. Furthermore, it is concluded, in contrast to some implications, that the effect of this metal does not violate transition state theory, and the evaluation of the catalytic effect must conserve the molecular composition upon moving from the reactant to the transition state. Proteins 2017; 85:1446-1453. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Hanwool Yoon
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California, 90089-1062
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California, 90089-1062
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15
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Salar U, Khan KM, Iqbal J, Ejaz SA, Hameed A, al-Rashida M, Perveen S, Tahir MN. Coumarin sulfonates: New alkaline phosphatase inhibitors; in vitro and in silico studies. Eur J Med Chem 2017; 131:29-47. [DOI: 10.1016/j.ejmech.2017.03.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 12/17/2022]
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16
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Tong KJ, Duchêne S, Lo N, Ho SYW. The impacts of drift and selection on genomic evolution in insects. PeerJ 2017; 5:e3241. [PMID: 28462044 PMCID: PMC5410144 DOI: 10.7717/peerj.3241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/28/2017] [Indexed: 11/20/2022] Open
Abstract
Genomes evolve through a combination of mutation, drift, and selection, all of which act heterogeneously across genes and lineages. This leads to differences in branch-length patterns among gene trees. Genes that yield trees with the same branch-length patterns can be grouped together into clusters. Here, we propose a novel phylogenetic approach to explain the factors that influence the number and distribution of these gene-tree clusters. We apply our method to a genomic dataset from insects, an ancient and diverse group of organisms. We find some evidence that when drift is the dominant evolutionary process, each cluster tends to contain a large number of fast-evolving genes. In contrast, strong negative selection leads to many distinct clusters, each of which contains only a few slow-evolving genes. Our work, although preliminary in nature, illustrates the use of phylogenetic methods to shed light on the factors driving rate variation in genomic evolution.
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Affiliation(s)
- K Jun Tong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Sebastián Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.,Centre for Systems Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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17
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Borosky GL. Quantum-Mechanical Study on the Catalytic Mechanism of Alkaline Phosphatases. J Chem Inf Model 2017; 57:540-549. [DOI: 10.1021/acs.jcim.6b00755] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriela L. Borosky
- INFIQC, CONICET and Departamento
de Química Teórica y Computacional, Facultad de Ciencias
Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina
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18
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Hinchliffe P, Yang QE, Portal E, Young T, Li H, Tooke CL, Carvalho MJ, Paterson NG, Brem J, Niumsup PR, Tansawai U, Lei L, Li M, Shen Z, Wang Y, Schofield CJ, Mulholland AJ, Shen J, Fey N, Walsh TR, Spencer J. Insights into the Mechanistic Basis of Plasmid-Mediated Colistin Resistance from Crystal Structures of the Catalytic Domain of MCR-1. Sci Rep 2017; 7:39392. [PMID: 28059088 PMCID: PMC5216409 DOI: 10.1038/srep39392] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/22/2016] [Indexed: 11/09/2022] Open
Abstract
The polymixin colistin is a "last line" antibiotic against extensively-resistant Gram-negative bacteria. Recently, the mcr-1 gene was identified as a plasmid-mediated resistance mechanism in human and animal Enterobacteriaceae, with a wide geographical distribution and many producer strains resistant to multiple other antibiotics. mcr-1 encodes a membrane-bound enzyme catalysing phosphoethanolamine transfer onto bacterial lipid A. Here we present crystal structures revealing the MCR-1 periplasmic, catalytic domain to be a zinc metalloprotein with an alkaline phosphatase/sulphatase fold containing three disulphide bonds. One structure captures a phosphorylated form representing the first intermediate in the transfer reaction. Mutation of residues implicated in zinc or phosphoethanolamine binding, or catalytic activity, restores colistin susceptibility of recombinant E. coli. Zinc deprivation reduces colistin MICs in MCR-1-producing laboratory, environmental, animal and human E. coli. Conversely, over-expression of the disulphide isomerase DsbA increases the colistin MIC of laboratory E. coli. Preliminary density functional theory calculations on cluster models suggest a single zinc ion may be sufficient to support phosphoethanolamine transfer. These data demonstrate the importance of zinc and disulphide bonds to MCR-1 activity, suggest that assays under zinc-limiting conditions represent a route to phenotypic identification of MCR-1 producing E. coli, and identify key features of the likely catalytic mechanism.
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Affiliation(s)
- Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Qiu E Yang
- Institute of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Edward Portal
- Institute of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Tom Young
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Hui Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Maria J Carvalho
- Institute of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Neil G Paterson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Pannika R Niumsup
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Uttapoln Tansawai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Lei Lei
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Mei Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | | | | | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Natalie Fey
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Timothy R Walsh
- Institute of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
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19
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Romero-Rivera A, Garcia-Borràs M, Osuna S. Computational tools for the evaluation of laboratory-engineered biocatalysts. Chem Commun (Camb) 2016; 53:284-297. [PMID: 27812570 PMCID: PMC5310519 DOI: 10.1039/c6cc06055b] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022]
Abstract
Biocatalysis is based on the application of natural catalysts for new purposes, for which enzymes were not designed. Although the first examples of biocatalysis were reported more than a century ago, biocatalysis was revolutionized after the discovery of an in vitro version of Darwinian evolution called Directed Evolution (DE). Despite the recent advances in the field, major challenges remain to be addressed. Currently, the best experimental approach consists of creating multiple mutations simultaneously while limiting the choices using statistical methods. Still, tens of thousands of variants need to be tested experimentally, and little information is available on how these mutations lead to enhanced enzyme proficiency. This review aims to provide a brief description of the available computational techniques to unveil the molecular basis of improved catalysis achieved by DE. An overview of the strengths and weaknesses of current computational strategies is explored with some recent representative examples. The understanding of how this powerful technique is able to obtain highly active variants is important for the future development of more robust computational methods to predict amino-acid changes needed for activity.
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Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive, Los Angeles, California 90095, USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
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20
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Lu X, Fang D, Ito S, Okamoto Y, Ovchinnikov V, Cui Q. QM/MM free energy simulations: recent progress and challenges. MOLECULAR SIMULATION 2016; 42:1056-1078. [PMID: 27563170 DOI: 10.1080/08927022.2015.1132317] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Dong Fang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Shingo Ito
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Boston, MA 02138
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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21
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Pabis A, Duarte F, Kamerlin SCL. Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer. Biochemistry 2016; 55:3061-81. [PMID: 27187273 PMCID: PMC4899807 DOI: 10.1021/acs.biochem.6b00297] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The
enzymes that facilitate phosphate and sulfate hydrolysis are
among the most proficient natural catalysts known to date. Interestingly,
a large number of these enzymes are promiscuous catalysts that exhibit
both phosphatase and sulfatase activities in the same active site
and, on top of that, have also been demonstrated to efficiently catalyze
the hydrolysis of other additional substrates with varying degrees
of efficiency. Understanding the factors that underlie such multifunctionality
is crucial both for understanding functional evolution in enzyme superfamilies
and for the development of artificial enzymes. In this Current Topic,
we have primarily focused on the structural and mechanistic basis
for catalytic promiscuity among enzymes that facilitate both phosphoryl
and sulfuryl transfer in the same active site, while comparing this
to how catalytic promiscuity manifests in other promiscuous phosphatases.
We have also drawn on the large number of experimental and computational
studies of selected model systems in the literature to explore the
different features driving the catalytic promiscuity of such enzymes.
Finally, on the basis of this comparative analysis, we probe the plausible
origins and determinants of catalytic promiscuity in enzymes that
catalyze phosphoryl and sulfuryl transfer.
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Affiliation(s)
- Anna Pabis
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K.,Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
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22
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Catechol oxidase and phenoxazinone synthase: Biomimetic functional models and mechanistic studies. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.11.002] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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23
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Lin B, Su H, Ma G, Liu Y, Hou Q. Theoretical study of the hydrolysis mechanism of dihydrocoumarin catalyzed by serum paraoxonase 1 (PON1): different roles of Glu53 and His115 for catalysis. RSC Adv 2016. [DOI: 10.1039/c6ra09735a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the PON1-catalyzed hydrolysis of dihydrocoumarin, Glu53 is necessary whereas His115 is not essential but can promote the activity.
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Affiliation(s)
- Beibei Lin
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Hao Su
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Guangcai Ma
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Qianqian Hou
- Shandong Non-metallic Materials Institute
- Jinan
- China
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24
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Pabis A, Kamerlin SCL. Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily. Curr Opin Struct Biol 2015; 37:14-21. [PMID: 26716576 DOI: 10.1016/j.sbi.2015.11.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/09/2015] [Accepted: 11/17/2015] [Indexed: 12/17/2022]
Abstract
Catalytic promiscuity, that is, the ability of single enzymes to facilitate the turnover of multiple, chemically distinct substrates, is a widespread phenomenon that plays an important role in the evolution of enzyme function. Additionally, such pre-existing multifunctionality can be harnessed in artificial enzyme design. The members of the alkaline phosphatase superfamily have served extensively as both experimental and computational model systems for enhancing our understanding of catalytic promiscuity. In this Opinion, we present key recent computational studies into the catalytic activity of these highly promiscuous enzymes, highlighting the valuable insight they have provided into both the molecular basis for catalytic promiscuity in general, and its implications for the evolution of phosphatase activity.
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Affiliation(s)
- Anna Pabis
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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25
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Kumar A, Glembo TJ, Ozkan SB. The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin. Biophys J 2015; 109:1273-81. [PMID: 26255589 PMCID: PMC4576160 DOI: 10.1016/j.bpj.2015.06.060] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/18/2015] [Accepted: 06/30/2015] [Indexed: 12/26/2022] Open
Abstract
Determining the three-dimensional structure of myoglobin, the first solved structure of a protein, fundamentally changed the way protein function was understood. Even more revolutionary was the information that came afterward: protein dynamics play a critical role in biological functions. Therefore, understanding conformational dynamics is crucial to obtaining a more complete picture of protein evolution. We recently analyzed the evolution of different protein families including green fluorescent proteins (GFPs), β-lactamase inhibitors, and nuclear receptors, and we observed that the alteration of conformational dynamics through allosteric regulation leads to functional changes. Moreover, proteome-wide conformational dynamics analysis of more than 100 human proteins showed that mutations occurring at rigid residue positions are more susceptible to disease than flexible residue positions. These studies suggest that disease-associated mutations may impair dynamic allosteric regulations, leading to loss of function. Thus, in this study, we analyzed the conformational dynamics of the wild-type light chain subunit of human ferritin protein along with the neutral and disease forms. We first performed replica exchange molecular dynamics simulations of wild-type and mutants to obtain equilibrated dynamics and then used perturbation response scanning (PRS), where we introduced a random Brownian kick to a position and computed the fluctuation response of the chain using linear response theory. Using this approach, we computed the dynamic flexibility index (DFI) for each position in the chain for the wild-type and the mutants. DFI quantifies the resilience of a position to a perturbation and provides a flexibility/rigidity measurement for a given position in the chain. The DFI analysis reveals that neutral variants and the wild-type exhibit similar flexibility profiles in which experimentally determined functionally critical sites act as hinges in controlling the overall motion. However, disease mutations alter the conformational dynamic profile, making hinges more loose (i.e., softening the hinges), thus impairing the allosterically regulated dynamics.
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Affiliation(s)
- Avishek Kumar
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - Tyler J Glembo
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona.
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26
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Barrozo A, Duarte F, Bauer P, Carvalho ATP, Kamerlin SCL. Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily. J Am Chem Soc 2015; 137:9061-76. [PMID: 26091851 PMCID: PMC4513756 DOI: 10.1021/jacs.5b03945] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is becoming widely accepted that catalytic promiscuity, i.e., the ability of a single enzyme to catalyze the turnover of multiple, chemically distinct substrates, plays a key role in the evolution of new enzyme functions. In this context, the members of the alkaline phosphatase superfamily have been extensively studied as model systems in order to understand the phenomenon of enzyme multifunctionality. In the present work, we model the selectivity of two multiply promiscuous members of this superfamily, namely the phosphonate monoester hydrolases from Burkholderia caryophylli and Rhizobium leguminosarum. We have performed extensive simulations of the enzymatic reaction of both wild-type enzymes and several experimentally characterized mutants. Our computational models are in agreement with key experimental observables, such as the observed activities of the wild-type enzymes, qualitative interpretations of experimental pH-rate profiles, and activity trends among several active site mutants. In all cases the substrates of interest bind to the enzyme in similar conformations, with largely unperturbed transition states from their corresponding analogues in aqueous solution. Examination of transition-state geometries and the contribution of individual residues to the calculated activation barriers suggest that the broad promiscuity of these enzymes arises from cooperative electrostatic interactions in the active site, allowing each enzyme to adapt to the electrostatic needs of different substrates. By comparing the structural and electrostatic features of several alkaline phosphatases, we suggest that this phenomenon is a generalized feature driving selectivity and promiscuity within this superfamily and can be in turn used for artificial enzyme design.
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Affiliation(s)
- Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Fernanda Duarte
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Paul Bauer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
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27
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Martínez Cuesta S, Rahman SA, Furnham N, Thornton JM. The Classification and Evolution of Enzyme Function. Biophys J 2015; 109:1082-6. [PMID: 25986631 DOI: 10.1016/j.bpj.2015.04.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 11/30/2022] Open
Abstract
Enzymes are the proteins responsible for the catalysis of life. Enzymes sharing a common ancestor as defined by sequence and structure similarity are grouped into families and superfamilies. The molecular function of enzymes is defined as their ability to catalyze biochemical reactions; it is manually classified by the Enzyme Commission and robust approaches to quantitatively compare catalytic reactions are just beginning to appear. Here, we present an overview of studies at the interface of the evolution and function of enzymes.
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Affiliation(s)
- Sergio Martínez Cuesta
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Syed Asad Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
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28
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Sánchez-Lombardo I, Alvarez S, McLauchlan CC, Crans DC. Evaluating transition state structures of vanadium-phosphatase protein complexes using shape analysis. J Inorg Biochem 2015; 147:153-64. [PMID: 25953100 DOI: 10.1016/j.jinorgbio.2015.04.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 04/08/2015] [Accepted: 04/08/2015] [Indexed: 12/19/2022]
Abstract
Shape analysis of coordination complexes is well-suited to evaluate the subtle distortions in the trigonal bipyramidal (TBPY-5) geometry of vanadium coordinated in the active site of phosphatases and characterized by X-ray crystallography. Recent studies using the tau (τ) analysis support the assertion that vanadium is best described as a trigonal bipyramid, because this geometry is the ideal transition state geometry of the phosphate ester substrate hydrolysis (C.C. McLauchlan, B.J. Peters, G.R. Willsky, D.C. Crans, Coord. Chem. Rev. http://dx.doi.org/10.1016/j.ccr.2014.12.012 ; D.C. Crans, M.L. Tarlton, C.C. McLauchlan, Eur. J. Inorg. Chem. 2014, 4450-4468). Here we use continuous shape measures (CShM) analysis to investigate the structural space of the five-coordinate vanadium-phosphatase complexes associated with mechanistic transformations between the tetrahedral geometry and the five-coordinate high energy TBPY-5 geometry was discussed focusing on the protein tyrosine phosphatase 1B (PTP1B) enzyme. No evidence for square pyramidal geometries was observed in any vanadium-protein complexes. The shape analysis positioned the metal ion and the ligands in the active site reflecting the mechanism of the cleavage of the organic phosphate in a phosphatase. We identified the umbrella distortions to be directly on the reaction path between tetrahedral phosphate and the TBPY-5-types of high-energy species. The umbrella distortions of the trigonal bipyramid are therefore identified as being the most relevant types of transition state structures for the phosphoryl group transfer reactions for phosphatases and this may be related to the possibility that vanadium is an inhibitor for enzymes that support both exploded and five-coordinate transition states.
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Affiliation(s)
| | - Santiago Alvarez
- Departament de Química Inorganica, Institut de Química Teorica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franques, 1-11, 08028 Barcelona, Spain.
| | - Craig C McLauchlan
- Department of Chemistry, Illinois State University, Campus Box 4160, Normal, IL 61790, USA
| | - Debbie C Crans
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.
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29
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Theoretical studies of the hydrolysis of antibiotics catalyzed by a metallo-β-lactamase. Arch Biochem Biophys 2015; 582:116-26. [PMID: 25622886 DOI: 10.1016/j.abb.2015.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 12/27/2022]
Abstract
In this paper, hybrid QM/MM molecular dynamics (MD) simulations have been performed to explore the mechanisms of hydrolysis of two antibiotics, Imipenen (IMI), an antibiotic belonging to the subgroup of carbapenems, and the Cefotaxime (CEF), a third-generation cephalosporin antibiotic, in the active site of a mono-nuclear β-lactamase, CphA from Aeromonas hydrophila. Significant different transition state structures are obtained for the hydrolysis of both antibiotics: while the TS of the CEF is an ionic species with negative charge on nitrogen, the IMI TS presents a tetrahedral-like character with negative charge on oxygen atom of the carbonyl group of the lactam ring. Thus, dramatic conformational changes can take place in the cavity of CphA to accommodate different substrates, which would be the origin of its substrate promiscuity. Since CphA shows only activity against carbapenem antibiotic, this study sheds some light into the origin of the selectivity of the different MbL and, as a consequence, into the discovery of specific and potent MβL inhibitors against a broad spectrum of bacterial pathogens. We have finally probed that a re-parametrization of semiempirical methods should be done to properly describe the behavior the metal cation in active site, Zn(2+), when used in QM/MM calculations.
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Borosky GL. Catalytic Activity of Human Placental Alkaline Phosphatase (PLAP): Insights from a Computational Study. J Phys Chem B 2014; 118:14302-13. [DOI: 10.1021/jp511221c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Gabriela L. Borosky
- INFIQC, CONICET and Departamento
de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina
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Duarte F, Åqvist J, Williams NH, Kamerlin SCL. Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis. J Am Chem Soc 2014; 137:1081-93. [PMID: 25423607 PMCID: PMC4311964 DOI: 10.1021/ja5082712] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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Understanding
phosphoryl and sulfuryl transfer is central to many
biochemical processes. However, despite decades of experimental and
computational studies, a consensus concerning the precise mechanistic
details of these reactions has yet to be reached. In this work we
perform a detailed comparative theoretical study of the hydrolysis
of p-nitrophenyl phosphate, methyl phosphate and p-nitrophenyl sulfate, all of which have served as key model
systems for understanding phosphoryl and sulfuryl transfer reactions,
respectively. We demonstrate the existence of energetically similar
but mechanistically distinct possibilities for phosphate monoester
hydrolysis. The calculated kinetic isotope effects for p-nitrophenyl phosphate provide a means to discriminate between substrate-
and solvent-assisted pathways of phosphate monoester hydrolysis, and
show that the solvent-assisted pathway dominates in solution. This
preferred mechanism for p-nitrophenyl phosphate hydrolysis
is difficult to find computationally due to the limitations of compressing
multiple bonding changes onto a 2-dimensional energy surface. This
problem is compounded by the need to include implicit solvation to
at least microsolvate the system and stabilize the highly charged
species. In contrast, methyl phosphate hydrolysis shows a preference
for a substrate-assisted mechanism. For p-nitrophenyl
sulfate hydrolysis there is only one viable reaction pathway, which
is similar to the solvent-assisted pathway for phosphate hydrolysis,
and the substrate-assisted pathway is not accessible. Overall, our
results provide a unifying mechanistic framework that is consistent
with the experimentally measured kinetic isotope effects and reconciles
the discrepancies between theoretical and experimental models for
these biochemically ubiquitous classes of reaction.
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Affiliation(s)
- Fernanda Duarte
- Department of Cell and Molecular Biology (ICM), Uppsala University , SE-751 24 Uppsala, Sweden
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32
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Zou T, Risso VA, Gavira JA, Sanchez-Ruiz JM, Ozkan SB. Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme. Mol Biol Evol 2014; 32:132-43. [PMID: 25312912 DOI: 10.1093/molbev/msu281] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
β-Lactamases are produced by many modern bacteria as a mechanism of resistance toward β-lactam antibiotics, the most common antibiotics in use. β-Lactamases, however, are ancient enzymes that originated billions of years ago. Recently, proteins corresponding to 2- to 3-Gy-old Precambrian nodes in the evolution of Class A β-lactamases have been prepared and shown to be moderately efficient promiscuous catalysts, able to degrade a variety of antibiotics with catalytic efficiency levels similar to those of an average modern enzyme. Remarkably, there are few structural differences (in particular at the active-site regions) between the resurrected enzymes and a penicillin-specialist modern β-lactamase. Here, we propose that the ancestral promiscuity originates from conformational dynamics. We investigate the differences in conformational dynamics of the ancient and extant β-lactamases through MD simulations and quantify the contribution of each position to functionally related dynamics through Dynamic Flexibility Index. The modern TEM-1 lactamase shows a comparatively rigid active-site region, likely reflecting adaptation for efficient degradation of a specific substrate (penicillin), whereas enhanced deformability at the active-site neighborhood in the ancestral resurrected proteins likely accounts for the binding and subsequent degradation of antibiotic molecules of different size and shape. Clustering of the conformational dynamics on the basis of Principal Component Analysis is in agreement with the functional divergence, as the ancient β-lactamases cluster together, separated from their modern descendant. Finally, our analysis leads to testable predictions, as sites of potential relevance for the evolution of dynamics are identified and mutations at those sites are expected to alter substrate-specificity.
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Affiliation(s)
- Taisong Zou
- Center for Biological Physics, Department of Physics, Arizona State University
| | - Valeria A Risso
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Jose A Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-Universidad de Granada), Granada, Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - S Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University
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Lu X, Gaus M, Elstner M, Cui Q. Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B 2014; 119:1062-82. [PMID: 25178644 PMCID: PMC4306495 DOI: 10.1021/jp506557r] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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We report the parametrization of
the approximate density functional
theory, DFTB3, for magnesium and zinc for chemical and biological
applications. The parametrization strategy follows that established
in previous work that parametrized several key main group elements
(O, N, C, H, P, and S). This 3OB set of parameters can thus be used
to study many chemical and biochemical systems. The parameters are
benchmarked using both gas-phase and condensed-phase systems. The
gas-phase results are compared to DFT (mostly B3LYP), ab initio (MP2 and G3B3), and PM6, as well as to a previous DFTB parametrization
(MIO). The results indicate that DFTB3/3OB is particularly successful
at predicting structures, including rather complex dinuclear metalloenzyme
active sites, while being semiquantitative (with a typical mean absolute
deviation (MAD) of ∼3–5 kcal/mol) for energetics. Single-point
calculations with high-level quantum mechanics (QM) methods generally
lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic
properties. DFTB3/MM simulations for solution and two enzyme systems
also lead to encouraging structural and energetic properties in comparison
to available experimental data. The remaining limitations of DFTB3,
such as the treatment of interaction between metal ions and highly
charged/polarizable ligands, are also discussed.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM. The evolution of enzyme function in the isomerases. Curr Opin Struct Biol 2014; 26:121-30. [PMID: 25000289 PMCID: PMC4139412 DOI: 10.1016/j.sbi.2014.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 06/02/2014] [Accepted: 06/10/2014] [Indexed: 01/14/2023]
Abstract
The advent of computational approaches to measure functional similarity between enzymes adds a new dimension to existing evolutionary studies based on sequence and structure. This paper reviews research efforts aiming to understand the evolution of enzyme function in superfamilies, presenting a novel strategy to provide an overview of the evolution of enzymes belonging to an individual EC class, using the isomerases as an exemplar.
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Affiliation(s)
- Sergio Martinez Cuesta
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Syed Asad Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
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Duarte F, Bauer P, Barrozo A, Amrein BA, Purg M, Aqvist J, Kamerlin SCL. Force field independent metal parameters using a nonbonded dummy model. J Phys Chem B 2014; 118:4351-62. [PMID: 24670003 PMCID: PMC4180081 DOI: 10.1021/jp501737x] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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The cationic dummy atom approach
provides a powerful nonbonded
description for a range of alkaline-earth and transition-metal centers,
capturing both structural and electrostatic effects. In this work
we refine existing literature parameters for octahedrally coordinated
Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce
both M2+–O distances and experimental solvation
free energies, which has not been achieved to date for transition
metals using any other model. The parameters have also been tested
using two different water models and show consistent performance.
Therefore, our parameters are easily transferable to any force field
that describes nonbonded interactions using Coulomb and Lennard-Jones
potentials. Finally, we demonstrate the stability of our parameters
in both the human and Escherichia coli variants of
the enzyme glyoxalase I as showcase systems, as both enzymes are active
with a range of transition metals. The parameters presented in this
work provide a valuable resource for the molecular simulation community,
as they extend the range of metal ions that can be studied using classical
approaches, while also providing a starting point for subsequent parametrization
of new metal centers.
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Affiliation(s)
- Fernanda Duarte
- Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
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36
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Gaus M, Lu X, Elstner M, Cui Q. Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications. J Chem Theory Comput 2014; 10:1518-1537. [PMID: 24803865 PMCID: PMC3985940 DOI: 10.1021/ct401002w] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Indexed: 01/06/2023]
Abstract
We report the parametrization of the approximate density functional tight binding method, DFTB3, for sulfur and phosphorus. The parametrization is done in a framework consistent with our previous 3OB set established for O, N, C, and H, thus the resulting parameters can be used to describe a broad set of organic and biologically relevant molecules. The 3d orbitals are included in the parametrization, and the electronic parameters are chosen to minimize errors in the atomization energies. The parameters are tested using a fairly diverse set of molecules of biological relevance, focusing on the geometries, reaction energies, proton affinities, and hydrogen bonding interactions of these molecules; vibrational frequencies are also examined, although less systematically. The results of DFTB3/3OB are compared to those from DFT (B3LYP and PBE), ab initio (MP2, G3B3), and several popular semiempirical methods (PM6 and PDDG), as well as predictions of DFTB3 with the older parametrization (the MIO set). In general, DFTB3/3OB is a major improvement over the previous parametrization (DFTB3/MIO), and for the majority cases tested here, it also outperforms PM6 and PDDG, especially for structural properties, vibrational frequencies, hydrogen bonding interactions, and proton affinities. For reaction energies, DFTB3/3OB exhibits major improvement over DFTB3/MIO, due mainly to significant reduction of errors in atomization energies; compared to PM6 and PDDG, DFTB3/3OB also generally performs better, although the magnitude of improvement is more modest. Compared to high-level calculations, DFTB3/3OB is most successful at predicting geometries; larger errors are found in the energies, although the results can be greatly improved by computing single point energies at a high level with DFTB3 geometries. There are several remaining issues with the DFTB3/3OB approach, most notably its difficulty in describing phosphate hydrolysis reactions involving a change in the coordination number of the phosphorus, for which a specific parametrization (3OB/OPhyd) is developed as a temporary solution; this suggests that the current DFTB3 methodology has limited transferability for complex phosphorus chemistry at the level of accuracy required for detailed mechanistic investigations. Therefore, fundamental improvements in the DFTB3 methodology are needed for a reliable method that describes phosphorus chemistry without ad hoc parameters. Nevertheless, DFTB3/3OB is expected to be a competitive QM method in QM/MM calculations for studying phosphorus/sulfur chemistry in condensed phase systems, especially as a low-level method that drives the sampling in a dual-level QM/MM framework.
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Affiliation(s)
- Michael Gaus
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Xiya Lu
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstr.
12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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37
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Chen SL, Liao RZ. Phosphate monoester hydrolysis by trinuclear alkaline phosphatase; DFT study of transition States and reaction mechanism. Chemphyschem 2014; 15:2321-30. [PMID: 24683174 DOI: 10.1002/cphc.201402016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 02/25/2014] [Indexed: 12/23/2022]
Abstract
Alkaline phosphatase (AP) is a trinuclear metalloenzyme that catalyzes the hydrolysis of a broad range of phosphate monoesters to form inorganic phosphate and alcohol (or phenol). In this paper, by using density functional theory with a model based on a crystal structure, the AP-catalyzed hydrolysis of phosphate monoesters is investigated by calculating two substrates, that is, methyl and p-nitrophenyl phosphates, which represent alkyl and aryl phosphates, respectively. The calculations confirm that the AP reaction employs a "ping-pong" mechanism involving two chemical displacement steps, that is, the displacement of the substrate leaving group by a Ser102 alkoxide and the hydrolysis of the phosphoseryl intermediate by a Zn2-bound hydroxide. Both displacement steps proceed via a concerted associative pathway no matter which substrate is used. Other mechanistic aspects are also studied. Comparison of our calculations with linear free energy relationships experiments shows good agreement.
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Affiliation(s)
- Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic, Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081 (China), Fax: (+86) 01-6891-1354.
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38
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Prakash P, Gorfe AA. Overview of simulation studies on the enzymatic activity and conformational dynamics of the GTPase Ras. MOLECULAR SIMULATION 2014; 40:839-847. [PMID: 26491216 DOI: 10.1080/08927022.2014.895000] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the last 40 years, we have learnt a great deal about the Ras onco-proteins. These intracellular molecular switches are essential for the function of a variety of physiological processes, including signal transduction cascades responsible for cell growth and proliferation. Molecular simulations and free energy calculations have played an essential role in elucidating the conformational dynamics and energetics underlying the GTP hydrolysis reaction catalysed by Ras. Here we present an overview of the main lessons from molecular simulations on the GTPase reaction and conformational dynamics of this important anti-cancer drug target. In the first part, we summarise insights from quantum mechanical and combined quantum mechanical/molecular mechanical simulations as well as other free energy methods and highlight consensus viewpoints as well as remaining controversies. The second part provides a very brief overview of new insights emerging from large-scale molecular dynamics simulations. We conclude with a perspective regarding future studies of Ras where computational approaches will likely play an active role.
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Affiliation(s)
- Priyanka Prakash
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, 6431 Fannin St, Houston, TX 77030, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, 6431 Fannin St, Houston, TX 77030, USA
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