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Bihani SC, Nagar V, Kumar M. Mechanistic and evolutionary insights into alkaline phosphatase superfamily through structure-function studies on Sphingomonas alkaline phosphatase. Arch Biochem Biophys 2023; 736:109524. [PMID: 36716801 DOI: 10.1016/j.abb.2023.109524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/20/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Alkaline phosphatases (APs), represented by E. coli AP (ECAP), employ an arginine residue to stabilize the phosphoryl group in the active site; whereas, AP from Sphingomonas (SPAP) shows a unique combination of substrate-binding residues; Thr89, Asn110, Lys171, and Arg173. Although such combination has been observed only in SPAP, these residues are present separately in different members of the AP superfamily. Here, we establish the presence of two distinct classes of APs; ECAP-type and SPAP-type. Bioinformatic analyses show that SPAP-type of APs are widely distributed in the bacterial kingdom. The role of active site residues in the catalytic mechanism has been delineated through a set of crystal structures reported here. These structures, representing different stages of the reaction pathway provide wealth of information for the catalytic mechanism. Despite critical differences in the substrate binding residues, SPAP follows a mechanism similar to that of ECAP-type of APs. Structure-based phylogenetic analysis suggests that SPAP and ECAP may have diverged very early during the evolution from a common ancestor. Moreover, it is proposed that the SPAP-type of APs are fundamental members of the AP superfamily and are more closely related to other members of the superfamily as compared to the ECAP-type of APs.
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Affiliation(s)
- Subhash C Bihani
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
| | - Vandan Nagar
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India; Food Microbiology Group, Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Mukesh Kumar
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
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2
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Shen R, Crean RM, Olsen KJ, Corbella M, Calixto AR, Richan T, Brandão TAS, Berry RD, Tolman A, Loria JP, Johnson SJ, Kamerlin SCL, Hengge AC. Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases. Chem Sci 2022; 13:13524-13540. [PMID: 36507179 PMCID: PMC9682893 DOI: 10.1039/d2sc04135a] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) possess a conserved mobile catalytic loop, the WPD-loop, which brings an aspartic acid into the active site where it acts as an acid/base catalyst. Prior experimental and computational studies, focused on the human enzyme PTP1B and the PTP from Yersinia pestis, YopH, suggested that loop conformational dynamics are important in regulating both catalysis and evolvability. We have generated a chimeric protein in which the WPD-loop of YopH is transposed into PTP1B, and eight chimeras that systematically restored the loop sequence back to native PTP1B. Of these, four chimeras were soluble and were subjected to detailed biochemical and structural characterization, and a computational analysis of their WPD-loop dynamics. The chimeras maintain backbone structural integrity, with somewhat slower rates than either wild-type parent, and show differences in the pH dependency of catalysis, and changes in the effect of Mg2+. The chimeric proteins' WPD-loops differ significantly in their relative stability and rigidity. The time required for interconversion, coupled with electrostatic effects revealed by simulations, likely accounts for the activity differences between chimeras, and relative to the native enzymes. Our results further the understanding of connections between enzyme activity and the dynamics of catalytically important groups, particularly the effects of non-catalytic residues on key conformational equilibria.
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Affiliation(s)
- Ruidan Shen
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Rory M. Crean
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden
| | - Keith J. Olsen
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Marina Corbella
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden
| | - Ana R. Calixto
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden
| | - Teisha Richan
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Tiago A. S. Brandão
- Departamento de Química, ICEX, Universidade Federal de Minas GeraisBelo HorizonteMinas Gerais31270-901Brazil
| | - Ryan D. Berry
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Alex Tolman
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - J. Patrick Loria
- Department of Chemistry, Yale University225 Prospect StreetNew HavenCT 06520USA,Department of Molecular Biophysics and Biochemistry, Yale University266 Whitney AvenueNew HavenCT 06520USA
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Shina C. L. Kamerlin
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden,School of Chemistry and Biochemistry, Georgia Institute of Technology901 Atlantic Drive NWAtlanta, GA 30332-0400USA
| | - Alvan C. Hengge
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
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3
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Recent advances in enzyme inhibition based-electrochemical biosensors for pharmaceutical and environmental analysis. Talanta 2022. [DOI: 10.1016/j.talanta.2022.124092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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4
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Markússon S, Hjörleifsson JG, Kursula P, Ásgeirsson B. Structural Characterization of Functionally Important Chloride Binding Sites in the Marine Vibrio Alkaline Phosphatase. Biochemistry 2022; 61:2248-2260. [PMID: 36194497 DOI: 10.1021/acs.biochem.2c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzyme stability and function can be affected by various environmental factors, such as temperature, pH, and ionic strength. Enzymes that are located outside the relatively unchanging environment of the cytosol, such as those residing in the periplasmic space of bacteria or extracellularly secreted, are challenged by more fluctuations in the aqueous medium. Bacterial alkaline phosphatases (APs) are generally affected by ionic strength of the medium, but this varies substantially between species. An AP from the marine bacterium Vibrio splendidus (VAP) shows complex pH-dependent activation and stabilization in the 0-1.0 M range of halogen salts and has been hypothesized to specifically bind chloride anions. Here, using X-ray crystallography and anomalous scattering, we have located two chloride binding sites in the structure of VAP, one in the active site and another one at a peripheral site. Further characterization of the binding sites using site-directed mutagenesis and small-angle X-ray scattering showed that upon binding of chloride to the peripheral site, structural dynamics decreased locally, resulting in thermal stabilization of the VAP active conformation. Binding of the chloride ion in the active site did not displace the bound inorganic phosphate product, but it may promote product release by facilitating rotational stabilization of the substrate-binding Arg129. Overall, these results reveal the complex nature and dynamics of chloride binding to enzymes through long-range modulation of electronic potential in the vicinity of the active site, resulting in increased catalytic efficiency and stability.
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Affiliation(s)
- Sigurbjörn Markússon
- Science Institute, University of Iceland, 107 Reykjavik, Iceland.,Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90570 Oulu, Finland.,Biocenter Oulu, University of Oulu, 90570 Oulu, Finland
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5
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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 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]
Abstract
The first structures of a choline-O-sulfatase bound to different ligands are reported. 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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6
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Wu B, Zhao S, Yang X, Zhou L, Ma Y, Zhang H, Li W, Wang H. Biomimetic Heterodimerization of Tetrapeptides to Generate Liquid Crystalline Hydrogel in A Two-Component System. ACS NANO 2022; 16:4126-4138. [PMID: 35230089 DOI: 10.1021/acsnano.1c09860] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Anisotropic structures made by hierarchical self-assembly and crystallization play an essential role in the living system. However, the spontaneous formation of liquid crystalline hydrogel of low molecular weight organic molecules with controlled properties remains challenging. This work describes a rational design of tetrapeptide without N-terminal modification and chemical conjugation that utilizes intermolecular interactions to drive the formation of nanofiber bundles in a two-component system, which could not be accessed by a single component. The diameter of nanofibers can be simply controlled by varying the enantiomer of electrostatic pairs. Mutation of lysine (K) to arginine (R) results in an over 30-fold increase of mechanical property. Mechanistic studies using different techniques unravel the mechanism of self-assembly and formation of anisotropic liquid crystalline domains. All-atom molecular dynamics simulations reveal that the mixture of heterochiral peptides self-assembles into a nanofiber with a larger width compared to the homochiral assemblies due to the different stacking pattern and intermolecular interactions. The intermolecular interactions show an obvious increase by substituting the K with R, facilitating a more stable assembly and further altering the assembly mechanics and bulk material properties. Moreover, we also demonstrated that the hydrogel properties can be easily controlled by incorporating a light-responsive group. This work provides a method to generate the liquid crystalline hydrogel from isotropic monomers.
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Affiliation(s)
- Bihan Wu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province China
| | - Shuang Zhao
- Key Laboratory of 3D Micro/Nano Fabrication and Characterization of Zhejiang Province, School of Engineering, Institute of Advanced Technology, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province China
| | - Xuejiao Yang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province China
| | - Laicheng Zhou
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province China
| | - Yang Ma
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province China
| | - Hongyue Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province China
| | - Wenbin Li
- Key Laboratory of 3D Micro/Nano Fabrication and Characterization of Zhejiang Province, School of Engineering, Institute of Advanced Technology, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province China
| | - Huaimin Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province China
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7
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Gade M, Tan LL, Damry AM, Sandhu M, Brock JS, Delaney A, Villar-Briones A, Jackson CJ, Laurino P. Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. JACS AU 2021; 1:2349-2360. [PMID: 34977903 PMCID: PMC8715544 DOI: 10.1021/jacsau.1c00464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 05/14/2023]
Abstract
Protein conformational changes can facilitate the binding of noncognate substrates and underlying promiscuous activities. However, the contribution of substrate conformational dynamics to this process is comparatively poorly understood. Here, we analyze human (hMAT2A) and Escherichia coli (eMAT) methionine adenosyltransferases that have identical active sites but different substrate specificity. In the promiscuous hMAT2A, noncognate substrates bind in a stable conformation to allow catalysis. In contrast, noncognate substrates sample stable productive binding modes less frequently in eMAT owing to altered mobility in the enzyme active site. Different cellular concentrations of substrates likely drove the evolutionary divergence of substrate specificity in these orthologues. The observation of catalytic promiscuity in hMAT2A led to the detection of a new human metabolite, methyl thioguanosine, that is produced at elevated levels in a cancer cell line. This work establishes that identical active sites can result in different substrate specificity owing to the effects of substrate and enzyme dynamics.
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Affiliation(s)
- Madhuri Gade
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
| | - Li Lynn Tan
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Adam M. Damry
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Mahakaran Sandhu
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Joseph S. Brock
- Research
School of Biology, Australian National University, Canberra 2601, Australia
| | - Andie Delaney
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Alejandro Villar-Briones
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
| | - Colin J. Jackson
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, ACT, Australia
- Australian
Research Council Centre of Excellence in Synthetic Biology, Research
School of Chemistry, Australian National
University, Canberra 2601, ACT, Australia
| | - Paola Laurino
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
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8
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Crean RM, Biler M, van der Kamp MW, Hengge AC, Kamerlin SCL. Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases. J Am Chem Soc 2021; 143:3830-3845. [PMID: 33661624 PMCID: PMC8031367 DOI: 10.1021/jacs.0c11806] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatases (PTPs) play an important role in cellular signaling and have been implicated in human cancers, diabetes, and obesity. Despite shared catalytic mechanisms and transition states for the chemical steps of catalysis, catalytic rates within the PTP family vary over several orders of magnitude. These rate differences have been implied to arise from differing conformational dynamics of the closure of a protein loop, the WPD-loop, which carries a catalytically critical residue. The present work reports computational studies of the human protein tyrosine phosphatase 1B (PTP1B) and YopH from Yersinia pestis, for which NMR has demonstrated a link between their respective rates of WPD-loop motion and catalysis rates, which differ by an order of magnitude. We have performed detailed structural analysis, both conventional and enhanced sampling simulations of their loop dynamics, as well as empirical valence bond simulations of the chemical step of catalysis. These analyses revealed the key residues and structural features responsible for these differences, as well as the residues and pathways that facilitate allosteric communication in these enzymes. Curiously, our wild-type YopH simulations also identify a catalytically incompetent hyper-open conformation of its WPD-loop, sampled as a rare event, previously only experimentally observed in YopH-based chimeras. The effect of differences within the WPD-loop and its neighboring loops on the modulation of loop dynamics, as revealed in this work, may provide a facile means for the family of PTP enzymes to respond to environmental changes and regulate their catalytic activities.
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Affiliation(s)
- Rory M. Crean
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| | - Michal Biler
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| | - Marc W. van der Kamp
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, University
Walk, Bristol BS8 1TD, United Kingdom
| | - Alvan C. Hengge
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322-0300, United States
| | - Shina C. L. Kamerlin
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
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9
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Jones BJ, Evans RL, Mylrea NJ, Chaudhury D, Luo C, Guan B, Pierce CT, Gordon WR, Wilmot CM, Kazlauskas RJ. Larger active site in an ancestral hydroxynitrile lyase increases catalytically promiscuous esterase activity. PLoS One 2020; 15:e0235341. [PMID: 32603354 PMCID: PMC7326234 DOI: 10.1371/journal.pone.0235341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/14/2020] [Indexed: 12/02/2022] Open
Abstract
Hydroxynitrile lyases (HNL's) belonging to the α/β-hydrolase-fold superfamily evolved from esterases approximately 100 million years ago. Reconstruction of an ancestral hydroxynitrile lyase in the α/β-hydrolase fold superfamily yielded a catalytically active hydroxynitrile lyase, HNL1. Several properties of HNL1 differ from the modern HNL from rubber tree (HbHNL). HNL1 favors larger substrates as compared to HbHNL, is two-fold more catalytically promiscuous for ester hydrolysis (p-nitrophenyl acetate) as compared to mandelonitrile cleavage, and resists irreversible heat inactivation to 35 °C higher than for HbHNL. We hypothesized that the x-ray crystal structure of HNL1 may reveal the molecular basis for the differences in these properties. The x-ray crystal structure solved to 1.96-Å resolution shows the expected α/β-hydrolase fold, but a 60% larger active site as compared to HbHNL. This larger active site echoes its evolution from esterases since related esterase SABP2 from tobacco also has a 38% larger active site than HbHNL. The larger active site in HNL1 likely accounts for its ability to accept larger hydroxynitrile substrates. Site-directed mutagenesis of HbHNL to expand the active site increased its promiscuous esterase activity 50-fold, consistent with the larger active site in HNL1 being the primary cause of its promiscuous esterase activity. Urea-induced unfolding of HNL1 indicates that it unfolds less completely than HbHNL (m-value = 0.63 for HNL1 vs 0.93 kcal/mol·M for HbHNL), which may account for the ability of HNL1 to better resist irreversible inactivation upon heating. The structure of HNL1 shows changes in hydrogen bond networks that may stabilize regions of the folded structure.
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Affiliation(s)
- Bryan J. Jones
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Robert L. Evans
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Nathan J. Mylrea
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Debayan Chaudhury
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Christine Luo
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Bo Guan
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Colin T. Pierce
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Wendy R. Gordon
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Carrie M. Wilmot
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Romas J. Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
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10
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Jones BJ, Evans RL, Mylrea NJ, Chaudhury D, Luo C, Guan B, Pierce CT, Gordon WR, Wilmot CM, Kazlauskas RJ. Larger active site in an ancestral hydroxynitrile lyase increases catalytically promiscuous esterase activity.. [DOI: 10.1101/2020.04.06.027797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
AbstractHydroxynitrile lyases (HNL’s) belonging to the α/β-hydrolase-fold superfamily evolved from esterases approximately 100 million years ago. Reconstruction of an ancestral hydroxynitrile lyase in the α/β-hydrolase fold superfamily yielded a catalytically active hydroxynitrile lyase, HNL1. Several properties of HNL1 differ from the modern HNL from rubber tree (HbHNL). HNL1 favors larger substrates as compared to HbHNL, is two-fold more catalytically promiscuous for ester hydrolysis (p-nitrophenyl acetate) as compared to mandelonitrile cleavage, and resists irreversible heat inactivation to 35 °C higher than for HbHNL. We hypothesized that the x-ray crystal structure of HNL1 may reveal the molecular basis for the differences in these properties. The x-ray crystal structure solved to 1.96-Å resolution shows the expected α/β-hydrolase fold, but a 60% larger active site as compared to HbHNL. This larger active site echoes its evolution from esterases since related esterase SABP2 from tobacco also has a 38% larger active site than HbHNL. The larger active site in HNL1 likely accounts for its ability to accept larger hydroxynitrile substrates. Site-directed mutagenesis of HbHNL to expand the active site increased its promiscuous esterase activity 50-fold, consistent with the larger active site in HNL1 being the primary cause of its promiscuous esterase activity. Urea-induced unfolding of HNL1 indicates that it unfolds less completely than HbHNL (m-value = 0.63 for HNL1 vs 0.93 kcal/ mol·M for HbHNL), which may account for the ability of HNL1 to better resist irreversible inactivation upon heating. The structure of HNL1 shows changes in hydrogen bond networks that may stabilize regions of the folded structure.
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11
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Copley SD. The physical basis and practical consequences of biological promiscuity. Phys Biol 2020; 17:10.1088/1478-3975/ab8697. [PMID: 32244231 PMCID: PMC9291633 DOI: 10.1088/1478-3975/ab8697] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteins interact with metabolites, nucleic acids, and other proteins to orchestrate the myriad catalytic, structural and regulatory functions that support life from the simplest microbes to the most complex multicellular organisms. These molecular interactions are often exquisitely specific, but never perfectly so. Adventitious "promiscuous" interactions are ubiquitous due to the thousands of macromolecules and small molecules crowded together in cells. Such interactions may perturb protein function at the molecular level, but as long as they do not compromise organismal fitness, they will not be removed by natural selection. Although promiscuous interactions are physiologically irrelevant, they are important because they can provide a vast reservoir of potential functions that can provide the starting point for evolution of new functions, both in nature and in the laboratory.
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Affiliation(s)
- Shelley D Copley
- Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado, UNITED STATES
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12
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Gardner JM, Biler M, Risso VA, Sanchez-Ruiz JM, Kamerlin SCL. Manipulating Conformational Dynamics To Repurpose Ancient Proteins for Modern Catalytic Functions. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00722] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jasmine M. Gardner
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Michal Biler
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Valeria A. Risso
- Departamento de Quı́mica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quı́mica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quı́mica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quı́mica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Shina C. L. Kamerlin
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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13
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van Loo B, Berry R, Boonyuen U, Mohamed MF, Golicnik M, Hengge AC, Hollfelder F. Transition-State Interactions in a Promiscuous Enzyme: Sulfate and Phosphate Monoester Hydrolysis by Pseudomonas aeruginosa Arylsulfatase. Biochemistry 2019; 58:1363-1378. [PMID: 30810299 PMCID: PMC11098524 DOI: 10.1021/acs.biochem.8b00996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudomonas aeruginosa arylsulfatase (PAS) hydrolyzes sulfate and, promiscuously, phosphate monoesters. Enzyme-catalyzed sulfate transfer is crucial to a wide variety of biological processes, but detailed studies of the mechanistic contributions to its catalysis are lacking. We present linear free energy relationships (LFERs) and kinetic isotope effects (KIEs) of PAS and analyses of active site mutants that suggest a key role for leaving group (LG) stabilization. In LFERs PASWT has a much less negative Brønsted coefficient (βleaving groupobs-Enz = -0.33) than the uncatalyzed reaction (βleaving groupobs = -1.81). This situation is diminished when cationic active site groups are exchanged for alanine. The considerable degree of bond breaking during the transition state (TS) is evidenced by an 18Obridge KIE of 1.0088. LFER and KIE data for several active site mutants point to leaving group stabilization by active site K375, in cooperation with H211. 15N KIEs and the increased sensitivity to leaving group ability of the sulfatase activity in neat D2O (Δβleaving groupH-D = +0.06) suggest that the mechanism for S-Obridge bond fission shifts, with decreasing leaving group ability, from charge compensation via Lewis acid interactions toward direct proton donation. 18Ononbridge KIEs indicate that the TS for PAS-catalyzed sulfate monoester hydrolysis has a significantly more associative character compared to the uncatalyzed reaction, while PAS-catalyzed phosphate monoester hydrolysis does not show this shift. This difference in enzyme-catalyzed TSs appears to be the major factor favoring specificity toward sulfate over phosphate esters by this promiscuous hydrolase, since other features are either too similar (uncatalyzed TS) or inherently favor phosphate (charge).
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Affiliation(s)
- Bert van Loo
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ryan Berry
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Usa Boonyuen
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mark F. Mohamed
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Marko Golicnik
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alvan C. Hengge
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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14
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Baier F, Hong N, Yang G, Pabis A, Miton CM, Barrozo A, Carr PD, Kamerlin SC, Jackson CJ, Tokuriki N. Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes. eLife 2019; 8:40789. [PMID: 30719972 PMCID: PMC6372284 DOI: 10.7554/elife.40789] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
Genetic variation among orthologous proteins can cause cryptic phenotypic properties that only manifest in changing environments. Such variation may impact the evolvability of proteins, but the underlying molecular basis remains unclear. Here, we performed comparative directed evolution of four orthologous metallo-β-lactamases toward a new function and found that different starting genotypes evolved to distinct evolutionary outcomes. Despite a low initial fitness, one ortholog reached a significantly higher fitness plateau than its counterparts, via increasing catalytic activity. By contrast, the ortholog with the highest initial activity evolved to a less-optimal and phenotypically distinct outcome through changes in expression, oligomerization and activity. We show how cryptic molecular properties and conformational variation of active site residues in the initial genotypes cause epistasis, that could lead to distinct evolutionary outcomes. Our work highlights the importance of understanding the molecular details that connect genetic variation to protein function to improve the prediction of protein evolution.
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Affiliation(s)
- Florian Baier
- Michael Smith Laboratory, University of British Columbia, Vancouver, Canada
| | - Nansook Hong
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Gloria Yang
- Michael Smith Laboratory, University of British Columbia, Vancouver, Canada
| | - Anna Pabis
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Charlotte M Miton
- Michael Smith Laboratory, University of British Columbia, Vancouver, Canada
| | - Alexandre Barrozo
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Paul D Carr
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Shina Cl Kamerlin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Nobuhiko Tokuriki
- Michael Smith Laboratory, University of British Columbia, Vancouver, Canada
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15
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Abstract
Recent years have seen an explosion of interest in both sequence- and structure-based approaches toward in silico-directed evolution. We recently developed a novel computational toolkit, CADEE, which facilitates the computer-aided directed evolution of enzymes. Our initial work (Amrein et al., IUCrJ 4:50-64, 2017) presented a pedagogical example of the application of CADEE to triosephosphate isomerase, to illustrate the CADEE workflow. In this contribution, we describe this workflow in detail, including code input/output snippets, in order to allow users to set up and execute CADEE simulations on any system of interest.
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16
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Kulkarni Y, Kamerlin SCL. Computational physical organic chemistry using the empirical valence bond approach. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2019. [DOI: 10.1016/bs.apoc.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Liao Q, Kulkarni Y, Sengupta U, Petrović D, Mulholland AJ, van der Kamp MW, Strodel B, Kamerlin SCL. Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case. J Am Chem Soc 2018; 140:15889-15903. [PMID: 30362343 DOI: 10.1021/jacs.8b09378] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Conformational changes are crucial for the catalytic action of many enzymes. A prototypical and well-studied example is loop opening and closure in triosephosphate isomerase (TIM), which is thought to determine the rate of catalytic turnover in many circumstances. Specifically, TIM loop 6 "grips" the phosphodianion of the substrate and, together with a change in loop 7, sets up the TIM active site for efficient catalysis. Crystal structures of TIM typically show an open or a closed conformation of loop 6, with the tip of the loop moving ∼7 Å between conformations. Many studies have interpreted this motion as a two-state, rigid-body transition. Here, we use extensive molecular dynamics simulations, with both conventional and enhanced sampling techniques, to analyze loop motion in apo and substrate-bound TIM in detail, using five crystal structures of the dimeric TIM from Saccharomyces cerevisiae. We find that loop 6 is highly flexible and samples multiple conformational states. Empirical valence bond simulations of the first reaction step show that slight displacements away from the fully closed-loop conformation can be sufficient to abolish most of the catalytic activity; full closure is required for efficient reaction. The conformational change of the loops in TIM is thus not a simple "open and shut" case and is crucial for its catalytic action. Our detailed analysis of loop motion in a highly efficient enzyme highlights the complexity of loop conformational changes and their role in biological catalysis.
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Affiliation(s)
- Qinghua Liao
- Department of Chemistry - BMC , Uppsala University , BMC Box 576, 751 23 Uppsala , Sweden
| | - Yashraj Kulkarni
- Department of Chemistry - BMC , Uppsala University , BMC Box 576, 751 23 Uppsala , Sweden
| | - Ushnish Sengupta
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich , 52425 Jülich , Germany.,German Research School for Simulation Sciences , RWTH Aachen University , 52062 Aachen , Germany
| | - Dušan Petrović
- Department of Chemistry - BMC , Uppsala University , BMC Box 576, 751 23 Uppsala , Sweden.,Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Cantock's Close , BS8 1TS Bristol , United Kingdom
| | - Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Cantock's Close , BS8 1TS Bristol , United Kingdom.,School of Biochemistry , University of Bristol , University Walk , BS8 1TD Bristol , United Kingdom
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , 40225 Düsseldorf , Germany
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18
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Uduwela DR, Pabis A, Stevenson BJ, Kamerlin SCL, McLeod MD. Enhancing the Steroid Sulfatase Activity of the Arylsulfatase from Pseudomonas aeruginosa. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dimanthi R. Uduwela
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Anna Pabis
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Bradley J. Stevenson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Shina C. L. Kamerlin
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Malcolm D. McLeod
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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19
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Maurer D, Enugala TR, Hamnevik E, Bauer P, Lüking M, Petrović D, Hillier H, Kamerlin SCL, Dobritzsch D, Widersten M. Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01762] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Dirk Maurer
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Thilak Reddy Enugala
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Emil Hamnevik
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Paul Bauer
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
- Biophysics, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| | - Malin Lüking
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Dušan Petrović
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Heidi Hillier
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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20
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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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21
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Alphey MS, Fisher G, Ge Y, Gould ER, Machado TFG, Liu H, Florence GJ, Naismith JH, da Silva RG. Catalytic and Anticatalytic Snapshots of a Short-Form ATP Phosphoribosyltransferase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00867] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | | | | | - James H. Naismith
- Division of Structural Biology, University of Oxford, Oxford OX3 7BN, U.K
- Research Complex at Harwell, Didcot, Oxon OX11 0FA, U.K
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22
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Janfalk Carlsson Å, Bauer P, Dobritzsch D, Kamerlin SCL, Widersten M. Epoxide hydrolysis as a model system for understanding flux through a branched reaction scheme. IUCRJ 2018; 5:269-282. [PMID: 29755743 PMCID: PMC5929373 DOI: 10.1107/s2052252518003573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
The epoxide hydrolase StEH1 catalyzes the hydrolysis of trans-methylstyrene oxide to 1-phenyl-propane-1,2-diol. The (S,S)-epoxide is exclusively transformed into the (1R,2S)-diol, while hydrolysis of the (R,R)-epoxide results in a mixture of product enantiomers. In order to understand the differences in the stereoconfigurations of the products, the reactions were studied kinetically during both the pre-steady-state and steady-state phases. A number of closely related StEH1 variants were analyzed in parallel, and the results were rationalized by structure-activity analysis using the available crystal structures of all tested enzyme variants. Finally, empirical valence-bond simulations were performed in order to provide additional insight into the observed kinetic behaviour and ratios of the diol product enantiomers. These combined data allow us to present a model for the flux through the catalyzed reactions. With the (R,R)-epoxide, ring opening may occur at either C atom and with similar energy barriers for hydrolysis, resulting in a mixture of diol enantiomer products. However, with the (S,S)-epoxide, although either epoxide C atom may react to form the covalent enzyme intermediate, only the pro-(R,S) alkylenzyme is amenable to subsequent hydrolysis. Previously contradictory observations from kinetics experiments as well as product ratios can therefore now be explained for this biocatalytically relevant enzyme.
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Affiliation(s)
- Åsa Janfalk Carlsson
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Paul Bauer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, 751 24 Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, 751 24 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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23
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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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24
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Cooperativity and flexibility in enzyme evolution. Curr Opin Struct Biol 2018; 48:83-92. [DOI: 10.1016/j.sbi.2017.10.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 11/23/2022]
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25
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Martínez-Martínez M, Coscolín C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernández J, Bollinger A, Thies S, Méndez-García C, Popovic A, Brown G, Chernikova TN, García-Moyano A, Bjerga GEK, Pérez-García P, Hai T, Del Pozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V, Peláez AI, Sánchez J, Buchholz PCF, Pleiss J, Fernández-Guerra A, Glöckner FO, Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, Guallar V, Ferrer M, The INMARE Consortium. Determinants and Prediction of Esterase Substrate Promiscuity Patterns. ACS Chem Biol 2018; 13:225-234. [PMID: 29182315 DOI: 10.1021/acschembio.7b00996] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Esterases receive special attention because of their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases' substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here, we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps rank (classify) the promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence data sets.
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Affiliation(s)
| | - Cristina Coscolín
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Gerard Santiago
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Jennifer Chow
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Christoph Gertler
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - José Navarro-Fernández
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Alexander Bollinger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
| | - Stephan Thies
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
| | - Celia Méndez-García
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ana Popovic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | | | | | - Gro E. K. Bjerga
- Uni Research AS, Center for Applied Biotechnology, 5006 Bergen, Norway
| | - Pablo Pérez-García
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Tran Hai
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Mercedes V. Del Pozo
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Runar Stokke
- Department of Biology and KG Jebsen Centre for Deep Sea Research, University of Bergen, 5020 Bergen, Norway
| | - Ida H. Steen
- Department of Biology and KG Jebsen Centre for Deep Sea Research, University of Bergen, 5020 Bergen, Norway
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Boguslaw P. Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, 60439 Illinois, United States
| | - María Alcaide
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Marco Distaso
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Victoria Mesa
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ana I. Peláez
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Jesús Sánchez
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Antonio Fernández-Guerra
- Jacobs University Bremen gGmbH, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- University of Oxford, Oxford e-Research Centre, Oxford, United Kingdom
| | - Frank O. Glöckner
- Jacobs University Bremen gGmbH, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Olga V. Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Michail M. Yakimov
- Institute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche, 98122 Messina, Italy
- Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
- Institute for Bio- and Geosciences IBG-1: Biotechnology, Forschunsgzentrum Jülich GmbH, 52425 Jülich, Germany
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Wolfgang R. Streit
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Peter N. Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Víctor Guallar
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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26
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Barrozo A, Liao Q, Esguerra M, Marloie G, Florián J, Williams NH, Kamerlin SCL. Computer simulations of the catalytic mechanism of wild-type and mutant β-phosphoglucomutase. Org Biomol Chem 2018; 16:2060-2073. [DOI: 10.1039/c8ob00312b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
β-Phosphoglucomutase (β-PGM) has served as an important model system for understanding biological phosphoryl transfer.
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Affiliation(s)
- Alexandre Barrozo
- Science for Life Laboratory
- Department of Cell and Molecular Biology
- Uppsala University
- S-75124 Uppsala
- Sweden
| | - Qinghua Liao
- Science for Life Laboratory
- Department of Cell and Molecular Biology
- Uppsala University
- S-75124 Uppsala
- Sweden
| | - Mauricio Esguerra
- Science for Life Laboratory
- Department of Cell and Molecular Biology
- Uppsala University
- S-75124 Uppsala
- Sweden
| | - Gaël Marloie
- Science for Life Laboratory
- Department of Cell and Molecular Biology
- Uppsala University
- S-75124 Uppsala
- Sweden
| | - Jan Florián
- Department of Chemistry and Biochemistry
- Loyola University Chicago
- Chicago
- USA
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27
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Purg M, Kamerlin SCL. Empirical Valence Bond Simulations of Organophosphate Hydrolysis: Theory and Practice. Methods Enzymol 2018; 607:3-51. [DOI: 10.1016/bs.mie.2018.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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Majumdar S, Acharya A, Prakash B. Structural plasticity mediates distinct GAP-dependent GTP hydrolysis mechanisms in Rab33 and Rab5. FEBS J 2017; 284:4358-4375. [PMID: 29095572 DOI: 10.1111/febs.14314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/02/2017] [Accepted: 10/27/2017] [Indexed: 11/27/2022]
Abstract
The classical GTP hydrolysis mechanism, as seen in Ras, employs a catalytic glutamine provided in cis by the GTPase and an arginine supplied in trans by a GTPase activating protein (GAP). The key idea emergent from a large body of research on small GTPases is that GTPases employ a variety of different hydrolysis mechanisms; evidently, these variations permit diverse rates of GTPase inactivation, crucial for temporal regulation of different biological processes. Recently, we unified these variations and argued that a steric clash between active site residues (corresponding to positions 12 and 61 of Ras) governs whether a GTPase utilizes the cis-Gln or the trans-Gln (from the GAP) for catalysis. As the cis-Gln encounters a steric clash, the Rab GTPases employ the so-called dual finger mechanism where the interacting GAP supplies a trans-Gln for catalysis. Using experimental and computational methods, we demonstrate how the cis-Gln of Rab33 overcomes the steric clash when it is stabilized by a residue in the vicinity. In effect, this demonstrates how both cis-Gln- and trans-Gln-mediated mechanisms could operate in the same GTPase in different contexts, i.e. depending on the GAP that regulates its action. Interestingly, in the case of Rab5, which possesses a higher intrinsic GTP hydrolysis rate, a similar stabilization of the cis-Gln appears to overcome the steric clash. Taken together with the mechanisms seen for Rab1, it is evident that the observed variations in Rab and their GAP partners allow structural plasticity, or in other words, the choice of different catalytic mechanisms.
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Affiliation(s)
- Soneya Majumdar
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Abhishek Acharya
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India.,Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Balaji Prakash
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India
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29
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Liao Q, Pabis A, Strodel B, Kamerlin SCL. Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions. J Phys Chem Lett 2017; 8:5408-5414. [PMID: 29022713 PMCID: PMC5672556 DOI: 10.1021/acs.jpclett.7b02358] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/12/2017] [Indexed: 05/28/2023]
Abstract
Modeling metalloproteins often requires classical molecular dynamics (MD) simulations in order to capture their relevant motions, which in turn necessitates reliable descriptions of the metal centers involved. One of the most successful approaches to date is provided by the "cationic dummy model", where the positive charge of the metal ion is transferred toward dummy particles that are bonded to the central metal ion in a predefined coordination geometry. While this approach allows for ligand exchange, and captures the correct electrostatics as demonstrated for different divalent metal ions, current dummy models neglect ion-induced dipole interactions. In the present work, we resolve this weakness by taking advantage of the recently introduced 12-6-4 type Lennard-Jones potential to include ion-induced dipole interactions. We revise our previous dummy model for Mg2+ and demonstrate that the resulting model can simultaneously reproduce the experimental solvation free energy and metal-ligand distances without the need for artificial restraints or bonds. As ion-induced dipole interactions become particularly important for highly charged metal ions, we develop dummy models for the biologically relevant ions Al3+, Fe3+, and Cr3+. Finally, the effectiveness of our new models is demonstrated in MD simulations of several diverse (and highly challenging to simulate) metalloproteins.
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Affiliation(s)
- Qinghua Liao
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, Uppsala 75124, Sweden
| | - Anna Pabis
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, Uppsala 75124, Sweden
| | - Birgit Strodel
- Institute
of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Shina Caroline Lynn Kamerlin
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, Uppsala 75124, Sweden
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30
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Dos Santos AM, Lima AH, Alves CN, Lameira J. Unraveling the Addition-Elimination Mechanism of EPSP Synthase through Computer Modeling. J Phys Chem B 2017; 121:8626-8637. [PMID: 28829128 DOI: 10.1021/acs.jpcb.7b05063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enolpyruvyl transfer from phosphoenolpyruvate (PEP) to the hydroxyl group of shikimate-5-OH-3-phosphate (S3P) is catalyzed by 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase in a reaction that involves breaking the C-O bond of PEP. Catalysis involves an addition-elimination mechanism with the formation of a tetrahedral intermediate (THI). Experiments have elucidated the mechanism of THI formation and breakdown. However, the catalytic action of EPSP synthase and the individual roles of catalytic residues Asp313 and Glu341 remains unclear. We have used a hybrid quantum mechanical/molecular mechanical (QM/MM) approach to explore the free energy surface in a reaction catalyzed by EPSP synthase. The Glu341 was the most favorable acid/base catalyst. Our results indicate that the protonation of PEP C3 precedes the nucleophilic attack on PEP C2 in the addition mechanism. Also, the breaking of the C-O bond of THI to form an EPSP cation intermediate must occur before proton transfer from PEP C3 to Glu341 in the elimination mechanism. Analysis of the FES supports cationic intermediate formation during the reaction catalyzed by EPSP synthase. Finally, the computational model indicates a proton transfer shift (Hammond shift) from Glu341 to C3 for an enzyme-based reaction with the shifted transition state, earlier than in the reference reaction in water.
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Affiliation(s)
- Alberto M Dos Santos
- Institute of Biological Sciences, Federal University of Pará , Belém, PA 66075-110, Brazil
| | - Anderson H Lima
- Institute of Biological Sciences, Federal University of Pará , Belém, PA 66075-110, Brazil
| | - Cláudio Nahum Alves
- Institute of Exact and Natural Sciences, Federal University of Pará , Belém, PA 66075-110, Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará , Belém, PA 66075-110, Brazil
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31
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Kulkarni Y, Liao Q, Petrović D, Krüger DM, Strodel B, Amyes TL, Richard JP, Kamerlin SCL. Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase. J Am Chem Soc 2017; 139:10514-10525. [PMID: 28683550 PMCID: PMC5543394 DOI: 10.1021/jacs.7b05576] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Indexed: 12/22/2022]
Abstract
Triosephosphate isomerase (TIM) is a proficient catalyst of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to d-glyceraldehyde phosphate (GAP), via general base catalysis by E165. Historically, this enzyme has been an extremely important model system for understanding the fundamentals of biological catalysis. TIM is activated through an energetically demanding conformational change, which helps position the side chains of two key hydrophobic residues (I170 and L230), over the carboxylate side chain of E165. This is critical both for creating a hydrophobic pocket for the catalytic base and for maintaining correct active site architecture. Truncation of these residues to alanine causes significant falloffs in TIM's catalytic activity, but experiments have failed to provide a full description of the action of this clamp in promoting substrate deprotonation. We perform here detailed empirical valence bond calculations of the TIM-catalyzed deprotonation of DHAP and GAP by both wild-type TIM and its I170A, L230A, and I170A/L230A mutants, obtaining exceptional quantitative agreement with experiment. Our calculations provide a linear free energy relationship, with slope 0.8, between the activation barriers and Gibbs free energies for these TIM-catalyzed reactions. We conclude that these clamping side chains minimize the Gibbs free energy for substrate deprotonation, and that the effects on reaction driving force are largely expressed at the transition state for proton transfer. Our combined analysis of previous experimental and current computational results allows us to provide an overview of the breakdown of ground-state and transition state effects in enzyme catalysis in unprecedented detail, providing a molecular description of the operation of a hydrophobic clamp in triosephosphate isomerase.
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Affiliation(s)
- Yashraj
S. Kulkarni
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala S-751 24, Sweden
| | - Qinghua Liao
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala S-751 24, Sweden
| | - Dušan Petrović
- Institute
of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Dennis M. Krüger
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala S-751 24, Sweden
| | - Birgit Strodel
- Institute
of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, Jülich 52425, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Shina C. L. Kamerlin
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala S-751 24, Sweden
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32
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Risso VA, Martinez-Rodriguez S, Candel AM, Krüger DM, Pantoja-Uceda D, Ortega-Muñoz M, Santoyo-Gonzalez F, Gaucher EA, Kamerlin SCL, Bruix M, Gavira JA, Sanchez-Ruiz JM. De novo active sites for resurrected Precambrian enzymes. Nat Commun 2017; 8:16113. [PMID: 28719578 PMCID: PMC5520109 DOI: 10.1038/ncomms16113] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/30/2017] [Indexed: 11/22/2022] Open
Abstract
Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.
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Affiliation(s)
- Valeria A. Risso
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | | | - Adela M. Candel
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | - Dennis M. Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - David Pantoja-Uceda
- Departamento de Quimica Fisica Biologica, Instituto de Quimica Fisica Rocasolano, CSIC, c/Serrano 119, 28006-Madrid, Spain
| | - Mariano Ortega-Muñoz
- Departamento de Quimica Organica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | | | - Eric A. Gaucher
- School of Biology, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30322, USA
| | - Shina C. L. Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Marta Bruix
- Departamento de Quimica Fisica Biologica, Instituto de Quimica Fisica Rocasolano, CSIC, c/Serrano 119, 28006-Madrid, Spain
| | - Jose A. Gavira
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-University of Granada Avenida de la Palmeras 4, Granada, 18100 Armilla, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
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33
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Zhang Q, Zhang C, Yang M, Yu D, Yu C. Pyrophosphate as substrate for alkaline phosphatase activity: A convenient flow‐injection chemiluminescence assay. LUMINESCENCE 2017; 32:1150-1156. [DOI: 10.1002/bio.3302] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 01/17/2023]
Affiliation(s)
- Qingfeng Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun People's Republic of China
- University of Chinese Academy of Sciences Beijing People's Republic of China
| | - Cuiyun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun People's Republic of China
- University of Chinese Academy of Sciences Beijing People's Republic of China
- School of Materials Science and Engineering Tianjin University Tianjin People's Republic of China
| | - Meiding Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun People's Republic of China
- University of Chinese Academy of Sciences Beijing People's Republic of China
| | - Donghong Yu
- Department of Chemistry and Bioscience Aalborg University Aalborg East DK Denmark
- Sino‐Danish Center for Education and Research Aarhus University Aarhus DK Denmark
| | - Cong Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun People's Republic of China
- University of Chinese Academy of Sciences Beijing People's Republic of China
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34
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Warshel A, Bora RP. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis. J Chem Phys 2017; 144:180901. [PMID: 27179464 DOI: 10.1063/1.4947037] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme's conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions.
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Affiliation(s)
- Arieh Warshel
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
| | - Ram Prasad Bora
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
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35
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Blaha-Nelson D, Krüger DM, Szeler K, Ben-David M, Kamerlin SCL. Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1. J Am Chem Soc 2017; 139:1155-1167. [PMID: 28026940 PMCID: PMC5269640 DOI: 10.1021/jacs.6b10801] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Serum
paraoxonase 1 (PON1) is a native lactonase capable of promiscuously
hydrolyzing a broad range of substrates, including organophosphates,
esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller
with a flexible loop (residues 70–81) covering the active site.
This loop contains a functionally critical Tyr at position 71. We
have performed detailed experimental and computational analyses of
the role of selected Y71 variants in the active site stability and
catalytic activity in order to probe the role of Y71 in PON1’s
lactonase and organophosphatase activities. We demonstrate that the
impact of Y71 substitutions on PON1’s lactonase activity is
minimal, whereas the kcat for the paraoxonase
activity is negatively perturbed by up to 100-fold, suggesting greater
mutational robustness of the native activity. Additionally, while
these substitutions modulate PON1’s active site shape, volume,
and loop flexibility, their largest effect is in altering the solvent
accessibility of the active site by expanding the active site volume,
allowing additional water molecules to enter. This effect is markedly
more pronounced in the organophosphatase activity than the lactonase
activity. Finally, a detailed comparison of PON1 to other organophosphatases
demonstrates that either a similar “gating loop” or
a highly buried solvent-excluding active site is a common feature
of these enzymes. We therefore posit that modulating the active site
hydrophobicity is a key element in facilitating the evolution of organophosphatase
activity. This provides a concrete feature that can be utilized in
the rational design of next-generation organophosphate hydrolases
that are capable of selecting a specific reaction from a pool of viable
substrates.
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Affiliation(s)
- David Blaha-Nelson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , S-751 24 Uppsala, Sweden
| | - Dennis M Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , S-751 24 Uppsala, Sweden
| | - Klaudia Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , S-751 24 Uppsala, Sweden
| | - Moshe Ben-David
- Department of Biological Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , S-751 24 Uppsala, Sweden
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36
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Amrein BA, Steffen-Munsberg F, Szeler I, Purg M, Kulkarni Y, Kamerlin SCL. CADEE: Computer-Aided Directed Evolution of Enzymes. IUCRJ 2017; 4:50-64. [PMID: 28250941 PMCID: PMC5331465 DOI: 10.1107/s2052252516018017] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/09/2016] [Indexed: 05/10/2023]
Abstract
The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyze in silico semi-automated directed evolution of enzymes. A pedagogical example of the application of CADEE to a real biological system is also presented in order to illustrate the CADEE workflow.
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Affiliation(s)
- Beat Anton Amrein
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Fabian Steffen-Munsberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Ireneusz Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Miha Purg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Yashraj Kulkarni
- 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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37
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Stare J. Complete sampling of an enzyme reaction pathway: a lesson from gas phase simulations. RSC Adv 2017. [DOI: 10.1039/c6ra27894a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
With proper sampling strategy, convergence of free energy profiles of biomolecular reactions in the gas phase can be achieved in microseconds of simulation.
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Affiliation(s)
- Jernej Stare
- Department of Computational Biochemistry and Drug Design
- National Institute of Chemistry
- SI-1000 Ljubljana
- Slovenia
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38
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Purg M, Pabis A, Baier F, Tokuriki N, Jackson C, Kamerlin SCL. Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0150. [PMID: 27698033 PMCID: PMC5052733 DOI: 10.1098/rsta.2016.0150] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 05/27/2023]
Abstract
Diverse organophosphate hydrolases have convergently evolved the ability to hydrolyse man-made organophosphates. Thus, these enzymes are attractive model systems for studying the factors shaping enzyme functional evolution. Methyl parathion hydrolase (MPH) is an enzyme from the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphate, aryl ester and lactone substrates. In addition, MPH demonstrates metal-ion-dependent selectivity patterns. The origins of this remain unclear, but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. Here, we present detailed mechanistic studies of the paraoxonase and arylesterase activities of MPH complexed with five different transition metal ions, and demonstrate that the hydrolysis reactions proceed via similar pathways and transition states. However, while it is possible to discern a clear structural origin for the selectivity between different substrates, the selectivity between different metal ions appears to lie instead in the distinct electrostatic properties of the metal ions themselves, which causes subtle changes in transition state geometries and metal-metal distances at the transition state rather than significant structural changes in the active site. While subtle, these differences can be significant for shaping the metal-ion-dependent activity patterns observed for this enzyme.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
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Affiliation(s)
- Miha Purg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
| | - Anna Pabis
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
| | - Florian Baier
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4
| | - Colin Jackson
- Research School of Chemistry, Building 138, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
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39
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A single electrochemical biosensor for detecting the activity and inhibition of both protein kinase and alkaline phosphatase based on phosphate ions induced deposition of redox precipitates. Biosens Bioelectron 2016; 85:220-225. [DOI: 10.1016/j.bios.2016.05.025] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/04/2016] [Accepted: 05/04/2016] [Indexed: 12/18/2022]
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40
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Allen KN, Dunaway-Mariano D. Catalytic scaffolds for phosphoryl group transfer. Curr Opin Struct Biol 2016; 41:172-179. [PMID: 27526404 DOI: 10.1016/j.sbi.2016.07.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022]
Abstract
A single genome encodes a large number of phosphoryl hydrolases for the purposes of phosphate recycling, primary and secondary metabolism, signal transduction and regulation, and protection from xenobiotics. Phosphate monoester hydrolysis faces a high kinetic barrier, yet there are multiple solutions to the problem both in terms of catalytic mechanisms and three-dimensional structure of the hydrolases. Recent structural and mechanistic findings highlight the trigonal-bipyramidal nature of the transition state for enzyme promoted phosphate monoester hydrolysis and the evolution and role of inserted loops/domains in governing substrate specificity and promiscuity. Important questions remain as to how electrostatics modulate water networks and critical proton-transfer events. How substrate targeting and catalysis is achieved by the independently evolved catalytic platforms is compared and contrasted in this article.
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Affiliation(s)
- Karen N Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215-2521, USA.
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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41
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Ma X, Zhang X, Guo X, Kang Q, Shen D, Zou G. Sensitive and selective determining ascorbic acid and activity of alkaline phosphatase based on electrochemiluminescence of dual-stabilizers-capped CdSe quantum dots in carbon nanotube-nafion composite. Talanta 2016; 154:175-82. [DOI: 10.1016/j.talanta.2016.03.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/10/2016] [Accepted: 03/12/2016] [Indexed: 12/23/2022]
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42
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Hausmann J, Keune WJ, Hipgrave Ederveen AL, van Zeijl L, Joosten RP, Perrakis A. Structural snapshots of the catalytic cycle of the phosphodiesterase Autotaxin. J Struct Biol 2016; 195:199-206. [PMID: 27268273 DOI: 10.1016/j.jsb.2016.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/17/2016] [Accepted: 06/03/2016] [Indexed: 01/01/2023]
Abstract
Autotaxin (ATX) is a secreted phosphodiesterase that produces the signalling lipid lysophosphatidic acid (LPA). The bimetallic active site of ATX is structurally related to the alkaline phosphatase superfamily. Here, we present a new crystal structure of ATX in complex with orthovanadate (ATX-VO5), which binds the Oγ nucleophile of Thr209 and adopts a trigonal bipyramidal conformation, following the nucleophile attack onto the substrate. We have now a portfolio of ATX structures we discuss as intermediates of the catalytic mechanism: the new ATX-VO5 structure; a unique structure where the nucleophile Thr209 is phosphorylated (ATX-pThr). Comparing these to a complex with the LPA product (ATX-LPA) and with a complex with a phosphate ion (ATX-PO4), that represent the Michaelis complex of the reaction, we observe movements of Thr209, changes in the relative displacement of the zinc ions, and a water molecule that likely fulfils the second nucleophilic attack. We propose that ATX follows the associative two-step in-line displacement mechanism.
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Affiliation(s)
- Jens Hausmann
- Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
| | - Willem-Jan Keune
- Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Agnes L Hipgrave Ederveen
- Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Leonie van Zeijl
- Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Robbie P Joosten
- Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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43
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Roston D, Demapan D, Cui Q. Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site. J Am Chem Soc 2016; 138:7386-94. [PMID: 27186960 DOI: 10.1021/jacs.6b03156] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Darren Demapan
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
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44
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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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45
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Oanca G, Purg M, Mavri J, Shih JC, Stare J. Insights into enzyme point mutation effect by molecular simulation: phenylethylamine oxidation catalyzed by monoamine oxidase A. Phys Chem Chem Phys 2016; 18:13346-56. [PMID: 27121693 DOI: 10.1039/c6cp00098c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The I335Y point mutation effect on the kinetics of phenylethylamine decomposition catalyzed by monoamine oxidase A was elucidated by means of molecular simulation. The established empirical valence bond methodology was used in conjunction with the free energy perturbation sampling technique and a classical force field representing the state of reactants and products. The methodology allows for the simulation of chemical reactions, in the present case the breaking of the α-C-H bond in a phenylethylamine substrate and the subsequent hydrogen transfer to the flavin cofactor, resulting in the formation of the N-H bond on flavin. The empirical parameters were calibrated against the experimental data for the simulated reaction in a wild type protein and then used for the calculation of the reaction free energy profile in the I335Y mutant. In very good agreement with the measured kinetic data, mutation increases the free energy barrier for the rate limiting step by slightly more than 1 kcal mol(-1) and consequently decreases the rate constant by about an order of magnitude. The magnitude of the computed effect slightly varies with simulation settings, but always remains in reasonable agreement with the experiment. Analysis of trajectories reveals a major change in the interaction between phenyl rings of the substrate and the neighboring Phe352 residue upon the I335Y mutation due to the increased local polarity, leading to an attenuated quadrupole interaction between the rings and destabilization of the transition state. Additionally, the increased local polarity in the mutant allows for a larger number of water molecules to be present near the active site, effectively shielding the catalytic effect of the enzyme and contributing to the increased barrier.
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Affiliation(s)
- Gabriel Oanca
- Laboratory of Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia.
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46
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Zhao C, Su H, Liu Y. Catalytic mechanism of acetolactate decarboxylase from Brevibacillus brevis towards both enantiomers of α-acetolactate. RSC Adv 2016. [DOI: 10.1039/c6ra18264j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
QM/MM calculations detail the conversion of both enantiomers of α-acetolactate to (R)-acetoin. (S)-α-acetolactate can be directly converted, whereas (R)-α-acetolactate has to firstly rearrange to the natural (S)-enantiomer through a carboxylate migration.
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Affiliation(s)
- Chenxiao Zhao
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Hao Su
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
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47
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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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48
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Ma H, Szeler K, Kamerlin SCL, Widersten M. Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA). Chem Sci 2015; 7:1415-1421. [PMID: 29910900 PMCID: PMC5975929 DOI: 10.1039/c5sc03666f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/17/2015] [Indexed: 12/13/2022] Open
Abstract
Local mutations in the phosphate binding group of DERA alter global conformation dynamics, catalytic activities and reaction entropies.
DERA, 2-deoxyribose-5-phosphate aldolase, catalyzes the retro-aldol cleavage of 2-deoxy-ribose-5-phosphate (dR5P) into glyceraldehyde-3-phosphate (G3P) and acetaldehyde in a branch of the pentose phosphate pathway. In addition to the physiological reaction, DERA also catalyzes the reverse addition reaction and, hence, is an interesting candidate for bio-catalysis of carbo-ligation reactions, which are central to synthetic chemistry. An obstacle to overcome for this enzyme to become a truly useful biocatalyst, however, is to relax the very strict dependency of this enzyme on phosphorylated substrates. We have studied herein the role of the non-canonical phosphate-binding site of this enzyme, consisting of Ser238 and Ser239, by site-directed and site-saturation mutagenesis, coupled to kinetic analysis of mutants. In addition, we have performed molecular dynamics simulations on the wild-type and four mutant enzymes, to analyse how mutations at this phosphate-binding site may affect the protein structure and dynamics. Further examination of the S239P mutant revealed that this variant increases the enthalpy change at the transition state, relative to the wild-type enzyme, but concomitant loss in entropy causes an overall relative loss in the TS free energy change. This entropy loss, as measured by the temperature dependence of catalysed rates, was mirrored in both a drastic loss in dynamics of the enzyme, which contributes to phosphate binding, as well as an overall loss in anti-correlated motions distributed over the entire protein. Our combined data suggests that the degree of anticorrelated motions within the DERA structure is coupled to catalytic efficiency in the DERA-catalyzed retro-aldol cleavage reaction, and can be manipulated for engineering purposes.
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Affiliation(s)
- Huan Ma
- Department of Chemistry - BMC , Uppsala University , Box 576 , SE-751 23 Uppsala , Sweden .
| | - Klaudia Szeler
- Department of Cell and Molecular Biology , Uppsala University , Box 596 , SE-751 24 , Uppsala , Sweden .
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology , Uppsala University , Box 596 , SE-751 24 , Uppsala , Sweden .
| | - Mikael Widersten
- Department of Chemistry - BMC , Uppsala University , Box 576 , SE-751 23 Uppsala , Sweden .
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