1
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Wu HN, Fujisawa Y, Tozuka Z, Fomenkov A, Nakura Y, Kajiyama SI, Fujiwara S, Yasukawa K, Roberts RJ, Yanagihara I. Identification of an endonuclease and N 6-adenine methyltransferase from Ureaplasma parvum SV3F4 strain. Enzyme Microb Technol 2024; 180:110471. [PMID: 38959818 DOI: 10.1016/j.enzmictec.2024.110471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/12/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024]
Abstract
Here, we report a novel endonuclease and N6-adenine DNA methyltransferase (m6A methyltransferase) in the Ureaplasma parvum SV3F4 strain. Our previous study found that the SV3F4 strain carries 17 unique genes, which are not encoded in the two previously reported U. parvum serovar 3 strain, OMC-P162 and ATCC 700970. Of these 17 unique genes, UP3_c0261 and UP3_c0262, were originally annotated as encoding hypothetical proteins. Comparative genomics analyses more recently indicated they encode a Type II restriction endonuclease and an m6A methyltransferase, respectively. The UP3_c0261 and UP3_c0262 genes were individually expressed and purified in Escherichia coli. The UP3_c0261 recombinant protein showed endonuclease activity on the pT7Blue vector, recognizing and cleaving a GTNAC motif, resulting in a 5 base 5' extension. The UP3_c0261 protein digested a polymerase chain reaction (PCR) product harboring the GTNAC motif. The endonuclease UP3_c0261 was designated as UpaF4I. Treatment of the PCR product with the recombinant protein UP3_c0262 completely blocked the restriction enzyme activity of UpaF4I. Analysis of the treated PCR product harboring a modified nucleotide by UP3_c0262 with HPLC-MS/MS and MS/MS showed that UP3_c0262 was an m6A methyltransferase containing a methylated A residue in both DNA strands of the GTNAC motif. Whole genome methylation analysis of SV3F4 showed that 99.9 % of the GTNAC motif was m6A modified. These results suggest the UP3_c0261 and UP3_c0262 genes may act as a novel Type II restriction-modification system in the Ureaplasma SV3F4 strain.
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Affiliation(s)
- Heng Ning Wu
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Yuya Fujisawa
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan; Division of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa City, Wakayama 649-6493, Japan
| | - Zenzaburo Tozuka
- Center for Supporting Drug Discovery and Life Science Research, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita City, Osaka 565-0871, Japan
| | - Alexey Fomenkov
- New England Biolabs Inc., 240 County Rd., Ipswich, MA 01938, USA
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan
| | - Shin-Ichiro Kajiyama
- Division of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa City, Wakayama 649-6493, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 1 Gakuen-Uegahara, Sanda City, Hyogo 669-1330, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto City 606-8502, Japan
| | | | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi City, Osaka 594-1101, Japan.
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2
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Prešern U, Goličnik M. Enzyme Databases in the Era of Omics and Artificial Intelligence. Int J Mol Sci 2023; 24:16918. [PMID: 38069254 PMCID: PMC10707154 DOI: 10.3390/ijms242316918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Enzyme research is important for the development of various scientific fields such as medicine and biotechnology. Enzyme databases facilitate this research by providing a wide range of information relevant to research planning and data analysis. Over the years, various databases that cover different aspects of enzyme biology (e.g., kinetic parameters, enzyme occurrence, and reaction mechanisms) have been developed. Most of the databases are curated manually, which improves reliability of the information; however, such curation cannot keep pace with the exponential growth in published data. Lack of data standardization is another obstacle for data extraction and analysis. Improving machine readability of databases is especially important in the light of recent advances in deep learning algorithms that require big training datasets. This review provides information regarding the current state of enzyme databases, especially in relation to the ever-increasing amount of generated research data and recent advancements in artificial intelligence algorithms. Furthermore, it describes several enzyme databases, providing the reader with necessary information for their use.
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Affiliation(s)
| | - Marko Goličnik
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia;
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3
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Huang J, Xie X, Zheng Z, Ye L, Wang P, Xu L, Wu Y, Yan J, Yang M, Yan Y. De Novo Computational Design of a Lipase with Hydrolysis Activity towards Middle-Chained Fatty Acid Esters. Int J Mol Sci 2023; 24:ijms24108581. [PMID: 37239928 DOI: 10.3390/ijms24108581] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Innovations in biocatalysts provide great prospects for intolerant environments or novel reactions. Due to the limited catalytic capacity and the long-term and labor-intensive characteristics of mining enzymes with the desired functions, de novo enzyme design was developed to obtain industrial application candidates in a rapid and convenient way. Here, based on the catalytic mechanisms and the known structures of proteins, we proposed a computational protein design strategy combining de novo enzyme design and laboratory-directed evolution. Starting with the theozyme constructed using a quantum-mechanical approach, the theoretical enzyme-skeleton combinations were assembled and optimized via the Rosetta "inside-out" protocol. A small number of designed sequences were experimentally screened using SDS-PAGE, mass spectrometry and a qualitative activity assay in which the designed enzyme 1a8uD1 exhibited a measurable hydrolysis activity of 24.25 ± 0.57 U/g towards p-nitrophenyl octanoate. To improve the activity of the designed enzyme, molecular dynamics simulations and the RosettaDesign application were utilized to further optimize the substrate binding mode and amino acid sequence, thus keeping the residues of theozyme intact. The redesigned lipase 1a8uD1-M8 displayed enhanced hydrolysis activity towards p-nitrophenyl octanoate-3.34 times higher than that of 1a8uD1. Meanwhile, the natural skeleton protein (PDB entry 1a8u) did not display any hydrolysis activity, confirming that the hydrolysis abilities of the designed 1a8uD1 and the redesigned 1a8uD1-M8 were devised from scratch. More importantly, the designed 1a8uD1-M8 was also able to hydrolyze the natural middle-chained substrate (glycerol trioctanoate), for which the activity was 27.67 ± 0.69 U/g. This study indicates that the strategy employed here has great potential to generate novel enzymes exhibiting the desired reactions.
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Affiliation(s)
- Jinsha Huang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaoman Xie
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhen Zheng
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Luona Ye
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Pengbo Wang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Li Xu
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ying Wu
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jinyong Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Min Yang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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4
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Jiang Y, Neti SS, Sitarik I, Pradhan P, To P, Xia Y, Fried SD, Booker SJ, O'Brien EP. How synonymous mutations alter enzyme structure and function over long timescales. Nat Chem 2023; 15:308-318. [PMID: 36471044 PMCID: PMC11267483 DOI: 10.1038/s41557-022-01091-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/17/2022] [Indexed: 12/12/2022]
Abstract
The specific activity of enzymes can be altered over long timescales in cells by synonymous mutations that alter a messenger RNA molecule's sequence but not the encoded protein's primary structure. How this happens at the molecular level is unknown. Here, we use multiscale modelling of three Escherichia coli enzymes (type III chloramphenicol acetyltransferase, D-alanine-D-alanine ligase B and dihydrofolate reductase) to understand experimentally measured changes in specific activity due to synonymous mutations. The modelling involves coarse-grained simulations of protein synthesis and post-translational behaviour, all-atom simulations to test robustness and quantum mechanics/molecular mechanics calculations to characterize enzymatic function. We show that changes in codon translation rates induced by synonymous mutations cause shifts in co-translational and post-translational folding pathways that kinetically partition molecules into subpopulations that very slowly interconvert to the native, functional state. Structurally, these states resemble the native state, with localized misfolding near the active sites of the enzymes. These long-lived states exhibit reduced catalytic activity, as shown by their increased activation energies for the reactions they catalyse.
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Affiliation(s)
- Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Syam Sundar Neti
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Priya Pradhan
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Philip To
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Yingzi Xia
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Squire J Booker
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Howard Hughes Medical Institute, Pennsylvania State University, University Park, PA, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA.
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5
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Czapinska H, Bochtler M. The Nϵ-Rule for Serine, but Not Cysteine Catalytic Triads. Angew Chem Int Ed Engl 2022; 61:e202206945. [PMID: 35983934 PMCID: PMC9825947 DOI: 10.1002/anie.202206945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Indexed: 01/11/2023]
Abstract
Catalytic triads, composed of a serine or cysteine nucleophile, a histidine, and a third triad residue (typically Asp/Glu/Asn), are common in enzyme active sites and catalyze a wide variety of chemical reactions. Two types of triads can be distinguished: We refer to them as Nδ- or Nϵ-configured, depending on whether the histidine imidazole Nδ or Nϵ atom is close to the nucleophile Oγ/Sγ. In this study, we have analyzed triad configuration. In structural triads, the more stable Nδ-configuration predominates. For catalytic triads, the configuration depends on the nucleophile. When it is a cysteine residue, both configuration types occur, depending on the family. However, when the nucleophile is a serine residue, the less stable Nϵ-configuration is almost exclusively found. We posit that the energetically less favored conformation is selected for in serine triads to facilitate the otherwise difficult proton transfer from the nucleophile to the histidine residue.
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Affiliation(s)
- Honorata Czapinska
- International Institute of Molecular and Cell BiologyTrojdena 402-109WarsawPoland
| | - Matthias Bochtler
- International Institute of Molecular and Cell BiologyTrojdena 402-109WarsawPoland,Institute of Biochemistry and Biophysics of the Polish Academy of SciencesPawinskiego 5a02-106WarsawPoland
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6
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The Nε‐Rule for Serine, but Not Cysteine Catalytic Triads. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Frenkel-Pinter M, Rajaei V, Glass JB, Hud NV, Williams LD. Water and Life: The Medium is the Message. J Mol Evol 2021; 89:2-11. [PMID: 33427903 PMCID: PMC7884305 DOI: 10.1007/s00239-020-09978-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Abstract
Water, the most abundant compound on the surface of the Earth and probably in the universe, is the medium of biology, but is much more than that. Water is the most frequent actor in the chemistry of metabolism. Our quantitation here reveals that water accounts for 99.4% of metabolites in Escherichia coli by molar concentration. Between a third and a half of known biochemical reactions involve consumption or production of water. We calculated the chemical flux of water and observed that in the life of a cell, a given water molecule frequently and repeatedly serves as a reaction substrate, intermediate, cofactor, and product. Our results show that as an E. coli cell replicates in the presence of molecular oxygen, an average in vivo water molecule is chemically transformed or is mechanistically involved in catalysis ~ 3.7 times. We conclude that, for biological water, there is no distinction between medium and chemical participant. Chemical transformations of water provide a basis for understanding not only extant biochemistry, but the origins of life. Because the chemistry of water dominates metabolism and also drives biological synthesis and degradation, it seems likely that metabolism co-evolved with biopolymers, which helps to reconcile polymer-first versus metabolism-first theories for the origins of life.
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Affiliation(s)
- Moran Frenkel-Pinter
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Vahab Rajaei
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Jennifer B Glass
- NASA Center for the Origins of Life, Atlanta, GA, USA
- School of Earth and Atmospheric Science, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332-0340, USA
| | - Nicholas V Hud
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Loren Dean Williams
- NASA Center for the Origins of Life, Atlanta, GA, USA.
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA.
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA.
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8
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Ueno Y, Muraoka S, Sato T. Skeletal animation for visualizing dynamic shapes of macromolecules. J Integr Bioinform 2020. [DOI: 10.1515/jib-2018-0098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractWe apply a skeletal animation technique developed for general computer graphics animation to display the dynamic shape of protein molecules. Polygon-based models for macromolecules such as atomic representations, surface models, and protein ribbon models are deformed by the motion of skeletal bones that provide coarse-grained descriptions of detailed computer graphics models. Using the animation software Blender, we developed methods to generate the skeletal bones for molecules. Our example of the superposition of normal modes demonstrates the thermal fluctuating motion obtained from normal mode analysis. The method is also applied to display the motions of protein molecules using trajectory coordinates of a molecular dynamics simulation. We found that a standard motion capture file was practical and useful for describing the motion of the molecule using available computer graphics tools.
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Affiliation(s)
- Yutaka Ueno
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Shinya Muraoka
- Graduate School of Information Science, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Tetsuo Sato
- Department of Radiological Technology, Gunma Prefectural College of Health Sciences, 323-1 Kamioki, Maebashi, Gunma 371-0052, Japan
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9
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A De Novo Designed Esterase with p-Nitrophenyl Acetate Hydrolysis Activity. Molecules 2020; 25:molecules25204658. [PMID: 33066055 PMCID: PMC7587395 DOI: 10.3390/molecules25204658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/04/2020] [Accepted: 10/10/2020] [Indexed: 11/18/2022] Open
Abstract
Esterases are a large family of enzymes with wide applications in the industry. However, all esterases originated from natural sources, limiting their use in harsh environments or newly- emerged reactions. In this study, we designed a new esterase to develop a new protocol to satisfy the needs for better biocatalysts. The ideal spatial conformation of the serine catalytic triad and the oxygen anion hole at the substrate-binding site was constructed by quantum mechanical calculation. The catalytic triad and oxygen anion holes were then embedded in the protein scaffold using the new enzyme protocol in Rosetta 3. The design results were subsequently evaluated, and optimized designs were used for expression and purification. The designed esterase had significant lytic activities towards p-nitrophenyl acetate, which was confirmed by point mutations. Thus, this study developed a new protocol to obtain novel enzymes that may be useful in unforgiving environments or novel reactions.
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10
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Sun D, Cheng X, Tian Y, Ding S, Zhang D, Cai P, Hu QN. EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature. Database (Oxford) 2020; 2023:baaa065. [PMID: 33002112 PMCID: PMC10755256 DOI: 10.1093/database/baaa065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 07/19/2020] [Accepted: 07/24/2020] [Indexed: 11/14/2022]
Abstract
Addition of chemical structural information in enzymatic reactions has proven to be significant for accurate enzyme function prediction. However, such chemical data lack systematic feature mining and hardly exist in enzyme-related databases. Therefore, global mining of enzymatic reactions will offer a unique landscape for researchers to understand the basic functional mechanisms of natural bioprocesses and facilitate enzyme function annotation. Here, we established a new knowledge base called EnzyMine, through which we propose to elucidate enzymatic reaction features and then link them with sequence and structural annotations. EnzyMine represents an advanced database that extends enzyme knowledge by incorporating reaction chemical feature strategies, strengthening the connectivity between enzyme and metabolic reactions. Therefore, it has the potential to reveal many new metabolic pathways involved with given enzymes, as well as expand enzyme function annotation. Database URL: http://www.rxnfinder.org/enzymine/.
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Affiliation(s)
- Dandan Sun
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200333, P. R. China
| | - Xingxiang Cheng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200333, P. R. China
| | - Yu Tian
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, Hubei 430023, China and
| | - Shaozhen Ding
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200333, P. R. China
| | - Dachuan Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200333, P. R. China
| | - Pengli Cai
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200333, P. R. China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Qian-nan Hu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200333, P. R. China
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11
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Affiliation(s)
- Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Centre for Clinical Research, St. Ann’s Hospital, 602 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Centre for Clinical Research, St. Ann’s Hospital, 602 00 Brno, Czech Republic
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12
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Ribeiro AJM, Tyzack JD, Borkakoti N, Holliday GL, Thornton JM. A global analysis of function and conservation of catalytic residues in enzymes. J Biol Chem 2019; 295:314-324. [PMID: 31796628 DOI: 10.1074/jbc.rev119.006289] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The catalytic residues of an enzyme comprise the amino acids located in the active center responsible for accelerating the enzyme-catalyzed reaction. These residues lower the activation energy of reactions by performing several catalytic functions. Decades of enzymology research has established general themes regarding the roles of specific residues in these catalytic reactions, but it has been more difficult to explore these roles in a more systematic way. Here, we review the data on the catalytic residues of 648 enzymes, as annotated in the Mechanism and Catalytic Site Atlas (M-CSA), and compare our results with those in previous studies. We structured this analysis around three key properties of the catalytic residues: amino acid type, catalytic function, and sequence conservation in homologous proteins. As expected, we observed that catalysis is mostly accomplished by a small set of residues performing a limited number of catalytic functions. Catalytic residues are typically highly conserved, but to a smaller degree in homologues that perform different reactions or are nonenzymes (pseudoenzymes). Cross-analysis yielded further insights revealing which residues perform particular functions and how often. We obtained more detailed specificity rules for certain functions by identifying the chemical group upon which the residue acts. Finally, we show the mutation tolerance of the catalytic residues based on their roles. The characterization of the catalytic residues, their functions, and conservation, as presented here, is key to understanding the impact of mutations in evolution, disease, and enzyme design. The tools developed for this analysis are available at the M-CSA website and allow for user specific analysis of the same data.
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Affiliation(s)
- António J M Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
| | - Jonathan D Tyzack
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Neera Borkakoti
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Gemma L Holliday
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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13
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Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM. Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic Acids Res 2019; 46:D618-D623. [PMID: 29106569 PMCID: PMC5753290 DOI: 10.1093/nar/gkx1012] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/13/2017] [Indexed: 12/28/2022] Open
Abstract
M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at www.ebi.ac.uk/thornton-srv/m-csa. Our objectives with M-CSA are to provide an open data resource for the community to browse known enzyme reaction mechanisms and catalytic sites, and to use the dataset to understand enzyme function and evolution. M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic sites of enzymes. We are releasing M-CSA as a new website and underlying database architecture. At the moment, M-CSA contains 961 entries, 423 of these with detailed mechanism information, and 538 with information on the catalytic site residues only. In total, these cover 81% (195/241) of third level EC numbers with a PDB structure, and 30% (840/2793) of fourth level EC numbers with a PDB structure, out of 6028 in total. By searching for close homologues, we are able to extend M-CSA coverage of PDB and UniProtKB to 51 993 structures and to over five million sequences, respectively, of which about 40% and 30% have a conserved active site.
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Affiliation(s)
- António J M Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gemma L Holliday
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 1HT, UK
| | - Jonathan D Tyzack
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Katherine Ferris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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14
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Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SCH, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3074783. [PMID: 28365730 PMCID: PMC5467563 DOI: 10.1093/database/bax006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/23/2017] [Indexed: 12/11/2022]
Abstract
With ever-increasing amounts of sequence data available in both the primary literature and sequence repositories, there is a bottleneck in annotating molecular function to a sequence. This article describes the biocuration process and methods used in the structure-function linkage database (SFLD) to help address some of the challenges. We discuss how the hierarchy within the SFLD allows us to infer detailed functional properties for functionally diverse enzyme superfamilies in which all members are homologous, conserve an aspect of their chemical function and have associated conserved structural features that enable the chemistry. Also presented is the Enzyme Structure-Function Ontology (ESFO), which has been designed to capture the relationships between enzyme sequence, structure and function that underlie the SFLD and is used to guide the biocuration processes within the SFLD. Database URL:http://sfld.rbvi.ucsf.edu/
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - David Mischel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Michael A Hicks
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.,Human Longevity, Inc, San Diego, CA 92121, USA
| | - John H Morris
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Conrad C Huang
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Elaine C Meng
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | | | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.,Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
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15
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Schomburg I, Jeske L, Ulbrich M, Placzek S, Chang A, Schomburg D. The BRENDA enzyme information system–From a database to an expert system. J Biotechnol 2017; 261:194-206. [DOI: 10.1016/j.jbiotec.2017.04.020] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/11/2017] [Accepted: 04/18/2017] [Indexed: 02/06/2023]
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16
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Ramezani S, Asoodeh A. Biochemical characterization and gene cloning of a novel alkaline endo -1-4-glucanase from Bacillus subtilis DR8806. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Nagano N, Umemura M, Izumikawa M, Kawano J, Ishii T, Kikuchi M, Tomii K, Kumagai T, Yoshimi A, Machida M, Abe K, Shin-ya K, Asai K. Class of cyclic ribosomal peptide synthetic genes in filamentous fungi. Fungal Genet Biol 2016; 86:58-70. [DOI: 10.1016/j.fgb.2015.12.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 11/10/2015] [Accepted: 12/14/2015] [Indexed: 01/24/2023]
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18
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Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav063. [PMID: 26284514 PMCID: PMC4499208 DOI: 10.1093/database/bav063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/14/2015] [Accepted: 05/18/2015] [Indexed: 11/14/2022]
Abstract
During 11–12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.
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Affiliation(s)
- Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, Lamia, 35100, Greece
| | - Amos Bairoch
- SIB-Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Arnaud Chatonnet
- INRA, UMR866 Dynamique Musculaire et Métabolisme, F-34000 Montpellier, France
| | - Mark Jinan Chen
- Razavi Newman Center for Bioinformatics, Salk Institute, 10010 North Torrey Pines Rd., La Jolla, CA 92037, USA, ; Bioinformatics & Computational Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - David J Craik
- Queensland Bioscience Precinct, 306 Carmody Rd, Building 80, The University of Queensland, Australia
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 København Ø, Denmark
| | - Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France, ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
| | - Vignir Isberg
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 København Ø, Denmark, ; CMBI, Raboudumc, Geert Grootplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Quentin Kaas
- Queensland Bioscience Precinct, 306 Carmody Rd, Building 80, The University of Queensland, Australia
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Nicolas Lenfant
- INRA, UMR866 Dynamique Musculaire et Métabolisme, F-34000 Montpellier, France
| | - Gerard Manning
- Razavi Newman Center for Bioinformatics, Salk Institute, 10010 North Torrey Pines Rd., La Jolla, CA 92037, USA, ; Bioinformatics & Computational Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nozomi Nagano
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | | | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore 560 065, India
| | - Neil D Rawlings
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Milton H Saier
- Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Joanna L Sharman
- Centre for Integrative Physiology, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Michael Spedding
- Spedding Research Solutions, 6 Rue Ampere, 78110 Le Vesinet, France and
| | - Konstantinos D Tsirigos
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Swedish E-Science Research Center, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Ake Vastermark
- Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Gerrit Vriend
- CMBI, Raboudumc, Geert Grootplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
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19
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Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O’Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A. Key challenges for the creation and maintenance of specialist protein resources. Proteins 2015; 83:1005-13. [PMID: 25820941 PMCID: PMC4446195 DOI: 10.1002/prot.24803] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/06/2015] [Accepted: 03/20/2015] [Indexed: 11/12/2022]
Abstract
As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long-term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value.
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of CaliforniaSan Francisco, California, 94158
| | - Amos Bairoch
- SIB—Swiss Institute of Bioinformatics, University of GenevaGeneva, Switzerland
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of ThessalyLamia, 35100, Greece
| | - Arnaud Chatonnet
- INRA, Umr866 Dynamique Musculaire Et MétabolismeMontpellier, F-34000, France
- Université MontpellierMontpellier, F-34000, France
| | - David J Craik
- Institute for Molecular Bioscience. The University of QueenslandBrisbane, Queensland, 4072, Australia
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)Wellcome Trust Genome Campus, Hinxton, Cambridge, Cb10 1SD, United Kingdom
| | - Bernard Henrissat
- Architecture Et Fonction Des Macromolécules Biologiques, CNRS, Aix-Marseille UniversitéMarseille, 13288, France
- Department of Biological Sciences, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, Maryland, 20892
| | - Gerard Manning
- Department of Bioinformatics & Computational Biology, Genentech1 DNA Way, South San Francisco, California, 98010
| | - Nozomi Nagano
- Computational Biology Research Center, National Institute of Advanced Industrial Science and TechnologyTokyo, 135-0064, Japan
| | - Claire O’Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)Wellcome Trust Genome Campus, Hinxton, Cambridge, Cb10 1SD, United Kingdom
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, Maryland, 20892
| | - Neil D Rawlings
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)Wellcome Trust Genome Campus, Hinxton, Cambridge, Cb10 1SD, United Kingdom
- Wellcome Trust Sanger InstituteWellcome Trust Genome Campus, Hinxton, Cambridge, Cb10 1SD, United Kingdom
| | - Milton Saier
- Department of Molecular Biology, University of California at San DiegoLa Jolla, California, 92093
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, TIFRGKVK Campus, Bellary Road, Bangalore, 560065, India
| | - Michael Spedding
- Chair NC-IUPHAR, Spedding Research Solutions SARL6 Rue Ampere, Le Vesinet, 78110, France
| | | | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GANijmegen, The Netherlands
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of CaliforniaSan Francisco, California, 94158
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)Wellcome Trust Genome Campus, Hinxton, Cambridge, Cb10 1SD, United Kingdom
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