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For: Duarte F, Amrein BA, Kamerlin SCL. Modeling catalytic promiscuity in the alkaline phosphatase superfamily. Phys Chem Chem Phys 2013;15:11160-77. [PMID: 23728154 PMCID: PMC3693508 DOI: 10.1039/c3cp51179k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/02/2013] [Indexed: 12/19/2022]
Number Cited by Other Article(s)
1
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
2
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 CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 11/23/2022]
3
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]
4
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
5
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]
6
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]
7
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]
8
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]
9
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]
10
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]
11
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]
12
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
13
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]
14
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]
15
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]
16
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
17
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]
18
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
19
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]
20
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]
21
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]
22
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]
23
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
24
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]
25
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
26
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]
27
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
28
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]
29
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]
30
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]
31
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]
32
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
33
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]
34
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]
35
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]
36
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]
37
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]
38
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]
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