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Romero PR, Kobayashi N, Wedell JR, Baskaran K, Iwata T, Yokochi M, Maziuk D, Yao H, Fujiwara T, Kurusu G, Ulrich EL, Hoch JC, Markley JL. BioMagResBank (BMRB) as a Resource for Structural Biology. Methods Mol Biol 2020; 2112:187-218. [PMID: 32006287 DOI: 10.1007/978-1-0716-0270-6_14] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB), founded in 1988, serves as the archive for data generated by nuclear magnetic resonance (NMR) spectroscopy of biological systems. NMR spectroscopy is unique among biophysical approaches in its ability to provide a broad range of atomic and higher-level information relevant to the structural, dynamic, and chemical properties of biological macromolecules, as well as report on metabolite and natural product concentrations in complex mixtures and their chemical structures. BMRB became a core member of the Worldwide Protein Data Bank (wwPDB) in 2007, and the BMRB archive is now a core archive of the wwPDB. Currently, about 10% of the structures deposited into the PDB archive are based on NMR spectroscopy. BMRB stores experimental and derived data from biomolecular NMR studies. Newer BMRB biopolymer depositions are divided about evenly between those associated with structure determinations (atomic coordinates and supporting information archived in the PDB) and those reporting experimental information on molecular dynamics, conformational transitions, ligand binding, assigned chemical shifts, or other results from NMR spectroscopy. BMRB also provides resources for NMR studies of metabolites and other small molecules that are often macromolecular ligands and/or nonstandard residues. This chapter is directed to the structural biology community rather than the metabolomics and natural products community. Our goal is to describe various BMRB services offered to structural biology researchers and how they can be accessed and utilized. These services can be classified into four main groups: (1) data deposition, (2) data retrieval, (3) data analysis, and (4) services for NMR spectroscopists and software developers. The chapter also describes the NMR-STAR data format used by BMRB and the tools provided to facilitate its use. For programmers, BMRB offers an application programming interface (API) and libraries in the Python and R languages that enable users to develop their own BMRB-based tools for data analysis, visualization, and manipulation of NMR-STAR formatted files. BMRB also provides users with direct access tools through the NMRbox platform.
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Affiliation(s)
- Pedro R Romero
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Naohiro Kobayashi
- PDBj-BMRB, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Jonathan R Wedell
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Kumaran Baskaran
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Takeshi Iwata
- PDBj-BMRB, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Masashi Yokochi
- PDBj-BMRB, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Dimitri Maziuk
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Hongyang Yao
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Toshimichi Fujiwara
- PDBj-BMRB, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Genji Kurusu
- PDBj-BMRB, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Eldon L Ulrich
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Jeffrey C Hoch
- BMRB, Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| | - John L Markley
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA.
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Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Crystallogr D Struct Biol 2019; 75:451-454. [PMID: 30988261 PMCID: PMC6465986 DOI: 10.1107/s2059798319004522] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/03/2019] [Indexed: 11/10/2022] Open
Abstract
This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).
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Affiliation(s)
- Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kumaran Baskaran
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gerard Bricogne
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - David G. Brown
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Minyu Chen
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Claus Flensburg
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jeffrey C. Hoch
- BioMagResBank (BMRB), UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Yasuyo Ikegawa
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yumiko Kengaku
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Eugene Krissinel
- CCP4, Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
| | - Genji Kurisu
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yuhe Liang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - John L. Markley
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Martin Noble
- Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Irina Persikova
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eldon L. Ulrich
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Clemens Vonrhein
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - John Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Marcin Wojdyr
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
- CCP4, Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
| | - Masashi Yokochi
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Ulrich EL, Baskaran K, Dashti H, Ioannidis YE, Livny M, Romero PR, Maziuk D, Wedell JR, Yao H, Eghbalnia HR, Hoch JC, Markley JL. NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments. J Biomol NMR 2019; 73:5-9. [PMID: 30580387 PMCID: PMC6441402 DOI: 10.1007/s10858-018-0220-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/14/2018] [Indexed: 05/16/2023]
Abstract
The growth of the biological nuclear magnetic resonance (NMR) field and the development of new experimental technology have mandated the revision and enlargement of the NMR-STAR ontology used to represent experiments, spectral and derived data, and supporting metadata. We present here a brief description of the NMR-STAR ontology and software tools for manipulating NMR-STAR data files, editing the files, extracting selected data, and creating data visualizations. Detailed information on these is accessible from the links provided.
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Affiliation(s)
- Eldon L Ulrich
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kumaran Baskaran
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Hesam Dashti
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Miron Livny
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Pedro R Romero
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dimitri Maziuk
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jonathan R Wedell
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Hongyang Yao
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Hamid R Eghbalnia
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - John L Markley
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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4
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Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Costanzo LD, Christie C, Duarte JM, Dutta S, Feng Z, Ghosh S, Goodsell DS, Green RK, Guranovic V, Guzenko D, Hudson BP, Liang Y, Lowe R, Peisach E, Periskova I, Randle C, Rose A, Sekharan M, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook J, Young J, Zardecki C, Zhuravleva M, Kurisu G, Nakamura H, Kengaku Y, Cho H, Sato J, Kim JY, Ikegawa Y, Nakagawa A, Yamashita R, Kudou T, Bekker GJ, Suzuki H, Iwata T, Yokochi M, Kobayashi N, Fujiwara T, Velankar S, Kleywegt GJ, Anyango S, Armstrong DR, Berrisford JM, Conroy MJ, Dana JM, Deshpande M, Gane P, Gáborová R, Gupta D, Gutmanas A, Koča J, Mak L, Mir S, Mukhopadhyay A, Nadzirin N, Nair S, Patwardhan A, Paysan-Lafosse T, Pravda L, Salih O, Sehnal D, Varadi M, Vařeková R, Markley JL, Hoch JC, Romero PR, Baskaran K, Maziuk D, Ulrich EL, Wedell JR, Yao H, Livny M, Ioannidis YE. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res 2019; 47:D520-D528. [PMID: 30357364 PMCID: PMC6324056 DOI: 10.1093/nar/gky949] [Citation(s) in RCA: 505] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 09/28/2018] [Accepted: 10/05/2018] [Indexed: 01/10/2023] Open
Abstract
The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.
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5
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Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ. Validation of Structures in the Protein Data Bank. Structure 2017; 25:1916-1927. [PMID: 29174494 PMCID: PMC5718880 DOI: 10.1016/j.str.2017.10.009] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/08/2017] [Accepted: 10/27/2017] [Indexed: 11/01/2022]
Abstract
The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade.
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Affiliation(s)
- Swanand Gore
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eduardo Sanz García
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pieter M S Hendrickx
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - John D Westbrook
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Huanwang Yang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zukang Feng
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kumaran Baskaran
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John M Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brian P Hudson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yasuyo Ikegawa
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Naohiro Kobayashi
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Catherine L Lawson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Steve Mading
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas J Oldfield
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ardan Patwardhan
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ezra Peisach
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gaurav Sahni
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Monica R Sekharan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sanchayita Sen
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Chenghua Shao
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Oliver S Smart
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eldon L Ulrich
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Reiko Yamashita
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Martha Quesada
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jasmine Y Young
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Haruki Nakamura
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - John L Markley
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Helen M Berman
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gerard J Kleywegt
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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6
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Maciejewski MW, Schuyler AD, Gryk MR, Moraru II, Romero PR, Ulrich EL, Eghbalnia HR, Livny M, Delaglio F, Hoch JC. NMRbox: A Resource for Biomolecular NMR Computation. Biophys J 2017; 112:1529-1534. [PMID: 28445744 DOI: 10.1016/j.bpj.2017.03.011] [Citation(s) in RCA: 274] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/06/2017] [Accepted: 03/13/2017] [Indexed: 10/19/2022] Open
Abstract
Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users.
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Affiliation(s)
- Mark W Maciejewski
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut
| | - Adam D Schuyler
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut
| | - Michael R Gryk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut
| | - Ion I Moraru
- Department of Cell Biology, UConn Health, Farmington, Connecticut
| | - Pedro R Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Eldon L Ulrich
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Hamid R Eghbalnia
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Miron Livny
- Computer Sciences Department, University of Wisconsin-Madison, Madison, Wisconsin
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland
| | - Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut.
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7
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Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. Structure 2017; 25:536-545. [PMID: 28190782 DOI: 10.1016/j.str.2017.01.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/08/2016] [Accepted: 01/10/2017] [Indexed: 10/20/2022]
Abstract
OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.
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Affiliation(s)
- Jasmine Y Young
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - John D Westbrook
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zukang Feng
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Raul Sala
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ezra Peisach
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Thomas J Oldfield
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Sanchayita Sen
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - David R Armstrong
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - John M Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Li Chen
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Minyu Chen
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Luigi Di Costanzo
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dimitris Dimitropoulos
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Guanghua Gao
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sutapa Ghosh
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Swanand Gore
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Vladimir Guranovic
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Pieter M S Hendrickx
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Brian P Hudson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Reiko Igarashi
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yasuyo Ikegawa
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Naohiro Kobayashi
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Catherine L Lawson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yuhe Liang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Steve Mading
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - M Saqib Mir
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Ardan Patwardhan
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Irina Persikova
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Luana Rinaldi
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Eduardo Sanz-Garcia
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Monica R Sekharan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chenghua Shao
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - G Jawahar Swaminathan
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Lihua Tan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Eldon L Ulrich
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Glen van Ginkel
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Reiko Yamashita
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Huanwang Yang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Marina A Zhuravleva
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Martha Quesada
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gerard J Kleywegt
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Helen M Berman
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John L Markley
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Haruki Nakamura
- PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Stephen K Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
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8
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Eghbalnia HR, Romero PR, Westler WM, Baskaran K, Ulrich EL, Markley JL. Increasing rigor in NMR-based metabolomics through validated and open source tools. Curr Opin Biotechnol 2016; 43:56-61. [PMID: 27643760 DOI: 10.1016/j.copbio.2016.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/15/2016] [Accepted: 08/30/2016] [Indexed: 01/18/2023]
Abstract
The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker discovery, and the broader characterization of small molecules in mixtures. Owing to their close proximity to the functional endpoints that govern an organism's phenotype, metabolites are highly informative about functional states. The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. Information acquired from nuclear magnetic spectroscopy (NMR), mass spectrometry (MS), and the published literature, as processed by statistical approaches, are driving increasingly wider applications of metabolomics. This review focuses on the role of databases and software tools in advancing the rigor, robustness, reproducibility, and validation of metabolomics studies.
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Affiliation(s)
- Hamid R Eghbalnia
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
| | - Pedro R Romero
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - William M Westler
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Kumaran Baskaran
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Eldon L Ulrich
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - John L Markley
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
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9
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Yokochi M, Kobayashi N, Ulrich EL, Kinjo AR, Iwata T, Ioannidis YE, Livny M, Markley JL, Nakamura H, Kojima C, Fujiwara T. Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. J Biomed Semantics 2016; 7:16. [PMID: 27927232 PMCID: PMC5143449 DOI: 10.1186/s13326-016-0057-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 03/18/2016] [Indexed: 11/20/2022] Open
Abstract
Background The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. Findings To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. Conclusions We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources. Electronic supplementary material The online version of this article (doi:10.1186/s13326-016-0057-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Masashi Yokochi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eldon L Ulrich
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Akira R Kinjo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeshi Iwata
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yannis E Ioannidis
- Department of Informatics & Telecommunications, University of Athens, Athens, Greece
| | - Miron Livny
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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10
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Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL. Probabilistic validation of protein NMR chemical shift assignments. J Biomol NMR 2016; 64:17-25. [PMID: 26724815 PMCID: PMC4744101 DOI: 10.1007/s10858-015-0007-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/20/2015] [Indexed: 05/05/2023]
Abstract
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data . ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/.
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Affiliation(s)
- Hesam Dashti
- Graduate Program in Biophysics, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Marco Tonelli
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Woonghee Lee
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - William M Westler
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Gabriel Cornilescu
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Eldon L Ulrich
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - John L Markley
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA.
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA.
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11
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Abstract
MolProbity is a powerful software program for validating structures of proteins and nucleic acids. Although MolProbity includes scripts for batch analysis of structures, because these scripts analyze structures one at a time, they are not well suited for the validation of a large dataset of structures. We have created a version of MolProbity (MolProbity-HTC) that circumvents these limitations and takes advantage of a high-throughput computing cluster by using the HTCondor software. MolProbity-HTC enables the longitudinal analysis of large sets of structures, such as those deposited in the PDB or generated through theoretical computation-tasks that would have been extremely time-consuming using previous versions of MolProbity. We have used MolProbity-HTC to validate the entire PDB, and have developed a new visual chart for the BioMagResBank website that enables users to easily ascertain the quality of each model in an NMR ensemble and to compare the quality of those models to the rest of the PDB.
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Affiliation(s)
- Vincent B Chen
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Jonathan R Wedell
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - R Kent Wenger
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Eldon L Ulrich
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA.
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12
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Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PMS, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW. NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol 2015; 22:433-4. [PMID: 26036565 PMCID: PMC4546829 DOI: 10.1038/nsmb.3041] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aleksandras Gutmanas
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Paul D Adams
- Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, California, USA
| | - Benjamin Bardiaux
- 1] Département de Biologie Structurale et Chimie, Unité de Bioinformatique Structurale, Institut Pasteur, Paris, France. [2] Unité Mixte de Recherche 3528, Centre National de la Recherche Scientifique, Paris, France
| | - Helen M Berman
- Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | - Rasmus H Fogh
- Department of Biochemistry, University of Leicester, Leicester, UK
| | - Peter Güntert
- 1] Institute of Biophysical Chemistry, Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main, Frankfurt am Main, Germany. [2] Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan. [3] Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Pieter M S Hendrickx
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Torsten Herrmann
- 1] Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, Ecole Normale Supérieure de Lyon, Villeurbanne, France. [2] Institut des Sciences Analytiques, Unité Mixte de Recherche 5280, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Oliver F Lange
- Biomolecular NMR, Munich Center for Integrated Protein Science, Department Chemie, Technische Universität München, Garching, Germany
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gaetano T Montelione
- 1] Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA. [2] Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | - Michael Nilges
- 1] Département de Biologie Structurale et Chimie, Unité de Bioinformatique Structurale, Institut Pasteur, Paris, France. [2] Unité Mixte de Recherche 3528, Centre National de la Recherche Scientifique, Paris, France
| | - Timothy J Ragan
- Department of Biochemistry, University of Leicester, Leicester, UK
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, USA
| | - Roberto Tejero
- Departamento de Quίmica Fίsica, Universidad de Valencia, Valencia, Spain
| | - Eldon L Ulrich
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Wim F Vranken
- 1] Structural Biology Research Centre, Vlaams Instituut voor Biotechnologie, Brussels, Belgium. [2] Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium. [3] Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
| | - Jonathan R Wedell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John Westbrook
- Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | - David S Wishart
- 1] Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada. [2] Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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13
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Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AMJJ, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CAM, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 2015; 23:1156-67. [PMID: 26095030 PMCID: PMC4933300 DOI: 10.1016/j.str.2015.05.013] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 05/11/2015] [Accepted: 05/18/2015] [Indexed: 01/20/2023]
Abstract
Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, on October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models?
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Affiliation(s)
- Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall Room 503B, University of California, San Francisco, 1700 4(th) Street, San Francisco, CA 94158-2330, USA.
| | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Torsten Schwede
- Swiss Institute of Bioinformatics Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Jill Trewhella
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia
| | - Gerard Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - John Markley
- BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Haruki Nakamura
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Paul Adams
- Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, UC Berkeley, Berkeley, CA 94720, USA
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Wah Chiu
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Frank Di Maio
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7370, USA
| | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry and Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, 600 16(th) Street, San Francisco, CA 94158-2517, USA
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre of Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Richard Henderson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Kenji Iwasaki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Graham Johnson
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, 600 16(th) Street, San Francisco, CA 94158-2330, USA
| | - Catherine L Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Marc A Marti-Renom
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG) and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08028 Barcelona, Spain
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Michael Nilges
- Département de Biologie Structurale et Chimie, Unité de Bioinformatique Structurale, Institut Pasteur, F-75015 Paris, France; Unité Mixte de Recherche 3258, Centre National de la Recherche Scientifique, F-75015 Paris, France
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Helen Saibil
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Claus A M Seidel
- Chair for Molecular Physical Chemistry, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Eldon L Ulrich
- BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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14
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Oldfield CJ, Xue B, Van YY, Ulrich EL, Markley JL, Dunker AK, Uversky VN. Utilization of protein intrinsic disorder knowledge in structural proteomics. Biochim Biophys Acta 2012; 1834:487-98. [PMID: 23232152 DOI: 10.1016/j.bbapap.2012.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 12/02/2012] [Accepted: 12/03/2012] [Indexed: 12/01/2022]
Abstract
Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed.
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Affiliation(s)
- Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.
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15
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Abstract
New software and increasingly sophisticated NMR metabolite spectral databases are advancing the unique abilities of NMR spectroscopy to identify and quantify small molecules in solution for studies of metabolite biomarkers and metabolic flux. Public and commercial databases now contain experimental 1D 1H, 13C and 2D 1H-13C spectra and extracted spectral parameters for over a thousand compounds and theoretical data for thousands more. Public databases containing experimental NMR data from complex metabolic studies are emerging. These databases are providing information vital for the construction and testing of new computational algorithms for NMR-based chemometric and quantitative metabolomics studies. In this review we focus on database and software tools that support a quantitative NMR approach to the analysis of 1D and 2D NMR spectra of complex biological mixtures.
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Affiliation(s)
- James J Ellinger
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison WI 53706, USA
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16
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Kobayashi N, Harano Y, Tochio N, Nakatani E, Kigawa T, Yokoyama S, Mading S, Ulrich EL, Markley JL, Akutsu H, Fujiwara T. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database. J Biomol NMR 2012; 53:311-320. [PMID: 22689068 PMCID: PMC4308039 DOI: 10.1007/s10858-012-9641-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 05/23/2012] [Indexed: 05/30/2023]
Abstract
Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including (1)H, (13)C and (15)N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001-2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.
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Affiliation(s)
- Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871 Osaka, Japan.
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17
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Doreleijers JF, Vranken WF, Schulte C, Markley JL, Ulrich EL, Vriend G, Vuister GW. NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res 2011; 40:D519-24. [PMID: 22139937 PMCID: PMC3245154 DOI: 10.1093/nar/gkr1134] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists are available, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. The accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculation using the available experimental data and present-day software. Such efforts, however, generally fail on half of all NMR ensembles due to the syntactic and semantic heterogeneity of the underlying data and the wide variety of formats used for their deposition. We have combined the remediated restraint information from our NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank and the Common Interface for NMR structure Generation (CING) structure validation reports into the weekly updated NRG-CING database (http://nmr.cmbi.ru.nl/NRG-CING). Eleven programs have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available experimental NMR data. The longitudinal validation of these data in a publicly available relational database yields a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The remediated NMR experimental data sets and validation reports are freely available online.
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Affiliation(s)
- Jurgen F Doreleijers
- IMM, Radboud University Nijmegen, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.
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18
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Penkett CJ, van Ginkel G, Velankar S, Swaminathan J, Ulrich EL, Mading S, Stevens TJ, Fogh RH, Gutmanas A, Kleywegt GJ, Henrick K, Vranken WF. Straightforward and complete deposition of NMR data to the PDBe. J Biomol NMR 2010; 48:85-92. [PMID: 20680401 PMCID: PMC2950272 DOI: 10.1007/s10858-010-9439-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Accepted: 07/19/2010] [Indexed: 05/29/2023]
Abstract
We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information and associated datasets through the lifetime of an NMR project. CCPN projects can be created within the CcpNmr Analysis software or by importing existing NMR data files using the CcpNmr FormatConverter. After further data entry and checking with the ECI, the project can then be rapidly deposited to the PDBe using AutoDep, or exported as a complete deposition NMR-STAR file. In full CCPN projects created with ECI, it is straightforward to select chemical shift lists, restraint data sets, structural ensembles and all relevant associated experimental collection details, which all are or will become mandatory when depositing to the PDB. Instructions and download information for the ECI are available from the PDBe web site at http://www.ebi.ac.uk/pdbe/nmr/deposition/eci.html .
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Affiliation(s)
- Christopher J. Penkett
- Protein Data Bank in Europe, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Glen van Ginkel
- Protein Data Bank in Europe, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Jawahar Swaminathan
- Protein Data Bank in Europe, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Eldon L. Ulrich
- BioMagResBank, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Dr., Madison, WI 53706 USA
| | - Steve Mading
- BioMagResBank, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Dr., Madison, WI 53706 USA
| | - Tim J. Stevens
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Rasmus H. Fogh
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Gerard J. Kleywegt
- Protein Data Bank in Europe, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Kim Henrick
- Protein Data Bank in Europe, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Wim F. Vranken
- Protein Data Bank in Europe, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
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19
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Doreleijers JF, Vranken WF, Schulte C, Lin J, Wedell JR, Penkett CJ, Vuister GW, Vriend G, Markley JL, Ulrich EL. The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. J Biomol NMR 2009; 45:389-96. [PMID: 19809795 PMCID: PMC2777234 DOI: 10.1007/s10858-009-9378-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 09/17/2009] [Indexed: 05/19/2023]
Abstract
Several pilot experiments have indicated that improvements in older NMR structures can be expected by applying modern software and new protocols (Nabuurs et al. in Proteins 55:483-186, 2004; Nederveen et al. in Proteins 59:662-672, 2005; Saccenti and Rosato in J Biomol NMR 40:251-261, 2008). A recent large scale X-ray study also has shown that modern software can significantly improve the quality of X-ray structures that were deposited more than a few years ago (Joosten et al. in J. Appl Crystallogr 42:376-384, 2009; Sanderson in Nature 459:1038-1039, 2009). Recalculation of three-dimensional coordinates requires that the original experimental data are available and complete, and are semantically and syntactically correct, or are at least correct enough to be reconstructed. For multiple reasons, including a lack of standards, the heterogeneity of the experimental data and the many NMR experiment types, it has not been practical to parse a large proportion of the originally deposited NMR experimental data files related to protein NMR structures. This has made impractical the automatic recalculation, and thus improvement, of the three dimensional coordinates of these structures. We here describe a large-scale international collaborative effort to make all deposited experimental NMR data semantically and syntactically homogeneous, and thus useful for further research. A total of 4,014 out of 5,266 entries were 'cleaned' in this process. For 1,387 entries, human intervention was needed. Continuous efforts in automating the parsing of both old, and newly deposited files is steadily decreasing this fraction. The cleaned data files are available from the NMR restraints grid at http://restraintsgrid.bmrb.wisc.edu .
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Affiliation(s)
- Jurgen F Doreleijers
- Radboud University Medical Centre Nijmegen, Geert Grooteplein 26-28, HB, Nijmegen, The Netherlands.
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20
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Markley JL, Ulrich EL, Berman HM, Henrick K, Nakamura H, Akutsu H. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR 2008; 40:153-5. [PMID: 18288446 PMCID: PMC2268728 DOI: 10.1007/s10858-008-9221-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Accepted: 01/18/2008] [Indexed: 05/10/2023]
Abstract
We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. All PDB depositions of structures based on NMR data must now be accompanied by experimental restraints. A scheme has been devised that allows depositors to specify a representative structure and to define residues within that structure found experimentally to be largely unstructured. The BMRB now accepts coordinate sets representing three-dimensional structural models based on experimental NMR data of molecules of biological interest that fall outside the guidelines of the Protein Data Bank (i.e., the molecule is a peptide with 23 or fewer residues, a polynucleotide with 3 or fewer residues, a polysaccharide with 3 or fewer sugar residues, or a natural product), provided that the coordinates are accompanied by representation of the covalent structure of the molecule (atom connectivity), assigned NMR chemical shifts, and the structural restraints used in generating model. The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems.
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Affiliation(s)
- John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA.
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21
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Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM. Remediation of the protein data bank archive. Nucleic Acids Res 2008; 36:D426-33. [PMID: 18073189 PMCID: PMC2238854 DOI: 10.1093/nar/gkm937] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 10/08/2007] [Accepted: 10/11/2007] [Indexed: 11/13/2022] Open
Abstract
The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp://ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The members of the wwPDB-RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)-have remediated this archive to address inconsistencies that have been introduced over the years. The scope and methods used in this project are presented.
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Affiliation(s)
- Kim Henrick
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Zukang Feng
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wolfgang F. Bluhm
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Dimitris Dimitropoulos
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jurgen F. Doreleijers
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuchismita Dutta
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Judith L. Flippen-Anderson
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - John Ionides
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chisa Kamada
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eugene Krissinel
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Catherine L. Lawson
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - John L. Markley
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruki Nakamura
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Richard Newman
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yukiko Shimizu
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jawahar Swaminathan
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Sameer Velankar
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jeramia Ory
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eldon L. Ulrich
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wim Vranken
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - John Westbrook
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Reiko Yamashita
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Huanwang Yang
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jasmine Young
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Muhammed Yousufuddin
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Helen M. Berman
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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22
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Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL. BioMagResBank. Nucleic Acids Res 2008; 36:D402-8. [PMID: 17984079 PMCID: PMC2238925 DOI: 10.1093/nar/gkm957] [Citation(s) in RCA: 1215] [Impact Index Per Article: 75.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 10/15/2007] [Accepted: 10/16/2007] [Indexed: 12/15/2022] Open
Abstract
The BioMagResBank (BMRB: www.bmrb.wisc.edu) is a repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies of biological molecules. BMRB is a partner in the Worldwide Protein Data Bank (wwPDB). The BMRB archive consists of four main data depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors (assigned chemical shifts, coupling constants and peak lists) and derived data (relaxation parameters, residual dipolar couplings, hydrogen exchange rates, pK(a) values, etc.), (ii) databases for NMR restraints processed from original author depositions available from the Protein Data Bank, (iii) time-domain (raw) spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules and (iv) a database of one- and two-dimensional (1)H and (13)C one- and two-dimensional NMR spectra for over 250 metabolites. The BMRB website provides free access to all of these data. BMRB has tools for querying the archive and retrieving information and an ftp site (ftp.bmrb.wisc.edu) where data in the archive can be downloaded in bulk. Two BMRB mirror sites exist: one at the PDBj, Protein Research Institute, Osaka University, Osaka, Japan (bmrb.protein.osaka-u.ac.jp) and the other at CERM, University of Florence, Florence, Italy (bmrb.postgenomicnmr.net/). The site at Osaka also accepts and processes data depositions.
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Affiliation(s)
- Eldon L Ulrich
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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23
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Hegeman AD, Schulte CF, Cui Q, Lewis IA, Huttlin EL, Eghbalnia H, Harms AC, Ulrich EL, Markley JL, Sussman MR. Stable isotope assisted assignment of elemental compositions for metabolomics. Anal Chem 2007; 79:6912-21. [PMID: 17708672 DOI: 10.1021/ac070346t] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Assignment of individual compound identities within mixtures of thousands of metabolites in biological extracts is a major challenge for metabolomic technology. Mass spectrometry offers high sensitivity over a large dynamic range of abundances and molecular weights but is limited in its capacity to discriminate isobaric compounds. In this article, we have extended earlier studies using isotopic labeling for elemental composition elucidation (Rodgers, R. P.; Blumer, E. N.; Hendrickson, C. L.; Marshall, A. G. J. Am. Soc. Mass Spectrom. 2000, 11, 835-40) to limit the formulas consistent with any exact mass measurement by comparing observations of metabolites extracted from Arabidopsis thaliana plants grown with (I) (12)C and (14)N (natural abundance), (II) (12)C and (15)N, (III) (13)C and (14)N, or (IV) (13)C and (15)N. Unique elemental compositions were determined over a dramatically enhanced mass range by analyzing exact mass measurement data from the four extracts using two methods. In the first, metabolite masses were matched with a library of 11,000 compounds known to be present in living cells by using values calculated for each of the four isotopic conditions. In the second method, metabolite masses were searched against masses calculated for a constrained subset of possible atomic combinations in all four isotopic regimes. In both methods, the lists of elemental compositions from each labeling regime were compared to find common formulas with similar retention properties by HPLC in at least three of the four regimes. These results demonstrate that metabolic labeling can be used to provide additional constraints for higher confidence formula assignments over an extended mass range.
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Affiliation(s)
- Adrian D Hegeman
- Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, Wisconsin 53706, USA
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24
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Markley JL, Anderson ME, Cui Q, Eghbalnia HR, Lewis IA, Hegeman AD, Li J, Schulte CF, Sussman MR, Westler WM, Ulrich EL, Zolnai Z. New bioinformatics resources for metabolomics. Pac Symp Biocomput 2007:157-168. [PMID: 17990489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We recently developed two databases and a laboratory information system as resources for the metabolomics community. These tools are freely available and are intended to ease data analysis in both MS and NMR based metabolomics studies. The first database is a metabolomics extension to the BioMagResBank (BMRB, http://www.bmrb.wisc.edu), which currently contains experimental spectral data on over 270 pure compounds. Each small molecule entry consists of five or six one- and two-dimensional NMR data sets, along with information about the source of the compound, solution conditions, data collection protocol and the NMR pulse sequences. Users have free access to peak lists, spectra, and original time-domain data. The BMRB database can be queried by name, monoisotopic mass and chemical shift. We are currently developing a deposition tool that will enable people in the community to add their own data to this resource. Our second database, the Madison Metabolomics Consortium Database (MMCD, available from http://mmcd.nmrfam.wisc.edu/), is a hub for information on over 10,000 metabolites. These data were collected from a variety of sites with an emphasis on metabolites found in Arabidopsis. The MMC database supports extensive search functions and allows users to make bulk queries using experimental MS and/or NMR data. In addition to these databases, we have developed a new module for the Sesame laboratory information management system (http://www.sesame.wisc.edu) that captures all of the experimental protocols, background information, and experimental data associated with metabolomics samples. Sesame was designed to help coordinate research efforts in laboratories with high sample throughput and multiple investigators and to track all of the actions that have taken place in a particular study.
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Affiliation(s)
- John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
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25
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Smith DW, Johnson KA, Bingman CA, Aceti DJ, Blommel PG, Wrobel RL, Frederick RO, Zhao Q, Sreenath H, Fox BG, Volkman BF, Jeon WB, Newman CS, Ulrich EL, Hegeman AD, Kimball T, Thao S, Sussman MR, Markley JL, Phillips GN. Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thaliana. Proteins 2006; 57:854-7. [PMID: 15317023 DOI: 10.1002/prot.20258] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- David W Smith
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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26
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Tyler RC, Aceti DJ, Bingman CA, Cornilescu CC, Fox BG, Frederick RO, Jeon WB, Lee MS, Newman CS, Peterson FC, Phillips GN, Shahan MN, Singh S, Song J, Sreenath HK, Tyler EM, Ulrich EL, Vinarov DA, Vojtik FC, Volkman BF, Wrobel RL, Zhao Q, Markley JL. Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies. Proteins 2006; 59:633-43. [PMID: 15789406 DOI: 10.1002/prot.20436] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a comparative study of protein production from 96 Arabidopsis thaliana open reading frames (ORFs) by cell-based and cell-free protocols. Each target was carried through four pipeline protocols used by the Center for Eukaryotic Structural Genomics (CESG), one for the production of unlabeled protein to be used in crystallization trials and three for the production of 15N-labeled proteins to be analyzed by 1H-15N NMR correlation spectroscopy. Two of the protocols involved Escherichia coli cell-based and two involved wheat germ cell-free technology. The progress of each target through each of the protocols was followed with all failures and successes noted. Failures were of the following types: ORF not cloned, protein not expressed, low protein yield, no cleavage of fusion protein, insoluble protein, protein not purified, NMR sample too dilute. Those targets that reached the goal of analysis by 1H-15N NMR correlation spectroscopy were scored as HSQC+ (protein folded and suitable for NMR structural analysis), HSQC+/- (protein partially disordered or not in a single stable conformational state), HSQC- (protein unfolded, misfolded, or aggregated and thus unsuitable for NMR structural analysis). Targets were also scored as X- for failing to crystallize and X+ for successful crystallization. The results constitute a rich database for understanding differences between targets and protocols. In general, the wheat germ cell-free platform offers the advantage of greater genome coverage for NMR-based structural proteomics whereas the E. coli platform when successful yields more protein, as currently needed for crystallization trials for X-ray structure determination.
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Affiliation(s)
- Robert C Tyler
- Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Wisconsin 53706, USA
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27
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Abstract
The Center for Eukaryotic Structural Genomics (CESG), as part of the Protein Structure Initiative (PSI), has established a high-throughput structure determination pipeline focused on eukaryotic proteins. NMR spectroscopy is an integral part of this pipeline, both as a method for structure determinations and as a means for screening proteins for stable structure. Because computational approaches have estimated that many eukaryotic proteins are highly disordered, about 1 year into the project, CESG began to use an algorithm (the Predictor of Naturally Disordered Regions, PONDR to avoid proteins that were likely to be disordered. We report a retrospective analysis of the effect of this filtering on the yield of viable structure determination candidates. In addition, we have used our current database of results on 70 protein targets from Arabidopsis thaliana and 1 from Caenorhabditis elegans, which were labeled uniformly with nitrogen-15 and screened for disorder by NMR spectroscopy, to compare the original algorithm with 13 other approaches for predicting disorder from sequence. Our study indicates that the efficiency of structural proteomics of eukaryotes can be improved significantly by removing targets predicted to be disordered by an algorithm chosen to provide optimal performance.
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Affiliation(s)
- Christopher J Oldfield
- Center for Eukaryotic Structural Genomics, Biochemistry Department, University of Wisconsin, Madison, Wisconsin 53706, USA
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28
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Doreleijers JF, Nederveen AJ, Vranken W, Lin J, Bonvin AMJJ, Kaptein R, Markley JL, Ulrich EL. BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J Biomol NMR 2005; 32:1-12. [PMID: 16041478 DOI: 10.1007/s10858-005-2195-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Accepted: 01/06/2005] [Indexed: 05/03/2023]
Abstract
We present two new databases of NMR-derived distance and dihedral angle restraints: the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED). These databases currently correspond to 545 proteins with NMR structures deposited in the Protein Databank (PDB). The criteria for inclusion were that these should be unique, monomeric proteins with author-provided experimental NMR data and coordinates available from the PDB capable of being parsed and prepared in a consistent manner. The Wattos program was used to parse the files, and the CcpNmr FormatConverter program was used to prepare them semi-automatically. New modules, including a new implementation of Aqua in the BioMagResBank (BMRB) software Wattos were used to analyze the sets of distance restraints (DRs) for inconsistencies, redundancies, NOE completeness, classification and violations with respect to the original coordinates. Restraints that could not be associated with a known nomenclature were flagged. The coordinates of hydrogen atoms were recalculated from the positions of heavy atoms to allow for a full restraint analysis. The DOCR database contains restraint and coordinate data that is made consistent with each other and with IUPAC conventions. The FRED database is based on the DOCR data but is filtered for use by test calculation protocols and longitudinal analyses and validations. These two databases are available from websites of the BMRB and the Macromolecular Structure Database (MSD) in various formats: NMR-STAR, CCPN XML, and in formats suitable for direct use in the software packages CNS and CYANA.
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Affiliation(s)
- Jurgen F Doreleijers
- BioMagResBank, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Dr., Madison, WI 53706, USA
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29
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Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CAEM, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AMJJ. RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 2005; 59:662-72. [PMID: 15822098 DOI: 10.1002/prot.20408] [Citation(s) in RCA: 293] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
State-of-the-art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500+ proteins for which coordinates and NMR restraints are available from the Protein Data Bank. Curated restraints were obtained from the BioMagResBank FRED database. Although the original NMR structures were determined by various methods, they all were recalculated by CNS and CYANA and refined subsequently by restrained molecular dynamics (CNS) in a hydrated environment. We present an extensive analysis of the results, in terms of various quality indicators generated by PROCHECK and WHAT_CHECK. On average, the quality indicators for packing and Ramachandran appearance moved one standard deviation closer to the mean of the reference database. The structural quality of the recalculated structures is discussed in relation to various parameters, including number of restraints per residue, NOE completeness and positional root mean square deviation (RMSD). Correlations between pairs of these quality indicators were generally low; for example, there is a weak correlation between the number of restraints per residue and the Ramachandran appearance according to WHAT_CHECK (r = 0.31). The set of recalculated coordinates constitutes a unified database of protein structures in which potential user- and software-dependent biases have been kept as small as possible. The database can be used by the structural biology community for further development of calculation protocols, validation tools, structure-based statistical approaches and modeling. The RECOORD database of recalculated structures is publicly available from http://www.ebi.ac.uk/msd/recoord.
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Affiliation(s)
- Aart J Nederveen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
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30
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Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED. The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins 2005; 59:687-96. [PMID: 15815974 DOI: 10.1002/prot.20449] [Citation(s) in RCA: 2506] [Impact Index Per Article: 131.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To address data management and data exchange problems in the nuclear magnetic resonance (NMR) community, the Collaborative Computing Project for the NMR community (CCPN) created a "Data Model" that describes all the different types of information needed in an NMR structural study, from molecular structure and NMR parameters to coordinates. This paper describes the development of a set of software applications that use the Data Model and its associated libraries, thus validating the approach. These applications are freely available and provide a pipeline for high-throughput analysis of NMR data. Three programs work directly with the Data Model: CcpNmr Analysis, an entirely new analysis and interactive display program, the CcpNmr FormatConverter, which allows transfer of data from programs commonly used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment (Carnegie Mellon University), which was rewritten to interact directly with the Data Model. The ARIA 2.0 software for structure calculation (Institut Pasteur) and the QUEEN program for validation of restraints (University of Nijmegen) were extended to provide conversion of their data to the Data Model. During these developments the Data Model has been thoroughly tested and used, demonstrating that applications can successfully exchange data via the Data Model. The software architecture developed by CCPN is now ready for new developments, such as integration with additional software applications and extensions of the Data Model into other areas of research.
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Affiliation(s)
- Wim F Vranken
- Macromolecular Structure Database, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
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Stolc V, Samanta MP, Tongprasit W, Sethi H, Liang S, Nelson DC, Hegeman A, Nelson C, Rancour D, Bednarek S, Ulrich EL, Zhao Q, Wrobel RL, Newman CS, Fox BG, Phillips GN, Markley JL, Sussman MR. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci U S A 2005; 102:4453-8. [PMID: 15755812 PMCID: PMC555476 DOI: 10.1073/pnas.0408203102] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Indexed: 11/18/2022] Open
Abstract
Using a maskless photolithography method, we produced DNA oligonucleotide microarrays with probe sequences tiled throughout the genome of the plant Arabidopsis thaliana. RNA expression was determined for the complete nuclear, mitochondrial, and chloroplast genomes by tiling 5 million 36-mer probes. These probes were hybridized to labeled mRNA isolated from liquid grown T87 cells, an undifferentiated Arabidopsis cell culture line. Transcripts were detected from at least 60% of the nearly 26,330 annotated genes, which included 151 predicted genes that were not identified previously by a similar genome-wide hybridization study on four different cell lines. In comparison with previously published results with 25-mer tiling arrays produced by chromium masking-based photolithography technique, 36-mer oligonucleotide probes were found to be more useful in identifying intron-exon boundaries. Using two-dimensional HPLC tandem mass spectrometry, a small-scale proteomic analysis was performed with the same cells. A large amount of strongly hybridizing RNA was found in regions "antisense" to known genes. Similarity of antisense activities between the 25-mer and 36-mer data sets suggests that it is a reproducible and inherent property of the experiments. Transcription activities were also detected for many of the intergenic regions and the small RNAs, including tRNA, small nuclear RNA, small nucleolar RNA, and microRNA. Expression of tRNAs correlates with genome-wide amino acid usage.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/isolation & purification
- Base Sequence
- Chromatography, High Pressure Liquid
- DNA, Complementary/genetics
- DNA, Plant/genetics
- Exons
- Gene Expression Profiling
- Genome, Plant
- Introns
- Oligonucleotide Array Sequence Analysis/methods
- Optics and Photonics
- Photography/methods
- Proteomics/methods
- RNA, Antisense/analysis
- RNA, Antisense/genetics
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Plant/analysis
- RNA, Plant/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Spectrometry, Mass, Electrospray Ionization
- Transcription, Genetic
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Affiliation(s)
- Viktor Stolc
- Genome Research Facility, National Aeronautics and Space Administration Ames Research Center, Moffett Field, CA 94035, USA
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Bingman CA, Johnson KA, Peterson FC, Frederick RO, Zhao Q, Thao S, Fox BG, Volkman BF, Jeon WB, Smith DW, Newman CS, Ulrich EL, Hegeman A, Sussman MR, Markley JL, Phillips GN. Crystal structure of the protein from gene At3g17210 of Arabidopsis thaliana. Proteins 2004; 57:218-20. [PMID: 15326607 DOI: 10.1002/prot.20215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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33
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Zolnai Z, Lee PT, Li J, Chapman MR, Newman CS, Phillips GN, Rayment I, Ulrich EL, Volkman BF, Markley JL. Project management system for structural and functional proteomics: Sesame. J Struct Funct Genomics 2004; 4:11-23. [PMID: 12943363 DOI: 10.1023/a:1024684404761] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A computing infrastructure (Sesame) has been designed to manage and link individual steps in complex projects. Sesame is being developed to support a large-scale structural proteomics pilot project. When complete, the system is expected to manage all steps from target selection to data-bank deposition and report writing. We report here on the design criteria of the Sesame system and on results demonstrating successful achievement of the basic goals of its architecture. The Sesame software package, which follows the client/server paradigm, consists of a framework, which supports secure interactions among the three tiers of the system (the client, server, and database tiers), and application modules that carry out specific tasks. The framework utilizes industry standards. The client tier is written in Java2 and can be accessed anywhere through the Internet. All the development on the server tier is also carried out in Java2 so as to accommodate a wide variety of computer platforms. The database tier employs a commercial database management system. Each Sesame application module consists of a simple user interface in the client tier, corresponding objects in the server tier, and relevant data stored in the centralized database. For security, access to stored data is controlled by access privileges. The system facilitates both local and remote collaborations. Because users interact with the system using Java Web Start or through a web browser, access is limited only by the availability of an Internet connection. We describe several Sesame modules that have been developed to the point where they are being utilized routinely to support steps involved in structural and functional proteomics. This software is available to parties interested in using it and assisting to guide its further development.
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Affiliation(s)
- Zsolt Zolnai
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison Wisconsin 53706, USA.
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Doreleijers JF, Mading S, Maziuk D, Sojourner K, Yin L, Zhu J, Markley JL, Ulrich EL. BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. J Biomol NMR 2003; 26:139-46. [PMID: 12766409 DOI: 10.1023/a:1023514106644] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Experimental constraints associated with NMR structures are available from the Protein Data Bank (PDB) in the form of "Magnetic Resonance" (MR) files. These files contain multiple types of data concatenated without boundary markers and are difficult to use for further research. Reported here are the results of a project initiated to annotate, archive, and disseminate these data to the research community from a searchable resource in a uniform format. The MR files from a set of 1410 NMR structures were analyzed and their original constituent data blocks annotated as to data type using a semi-automated protocol. A new software program called Wattos was then used to parse and archive the data in a relational database. From the total number of MR file blocks annotated as constraints, it proved possible to parse 84% (3337/3975). The constraint lists that were parsed correspond to three data types (2511 distance, 788 dihedral angle, and 38 residual dipolar couplings lists) from the three most popular software packages used in NMR structure determination: XPLOR/CNS (2520 lists), DISCOVER (412 lists), and DYANA/DIANA (405 lists). These constraints were then mapped to a developmental version of the BioMagResBank (BMRB) data model. A total of 31 data types originating from 16 programs have been classified, with the NOE distance constraint being the most commonly observed. The results serve as a model for the development of standards for NMR constraint deposition in computer-readable form. The constraints are updated regularly and are available from the BMRB web site (http://www.bmrb.wisc.edu).
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Affiliation(s)
- Jurgen F Doreleijers
- BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, U.S.A
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Markley JL, Ulrich EL, Westler WM, Volkman BF. Macromolecular structure determination by NMR spectroscopy. Methods Biochem Anal 2003; 44:89-113. [PMID: 12647383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Affiliation(s)
- John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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36
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Chan TM, Hermodson MA, Ulrich EL, Markley JL. Nuclear magnetic resonance studies of two-iron-two-sulfur ferredoxins. 2. Determination of the sequence of Anabaena variabilis ferredoxin II, assignment of aromatic resonances in proton spectra, and effects of chemical modifications. Biochemistry 2002. [DOI: 10.1021/bi00294a045] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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Chan TM, Ulrich EL, Markley JL. Nuclear magnetic resonance studies of two-iron-two-sulfur ferredoxins. 4. Interactions with redox partners. Biochemistry 2002. [DOI: 10.1021/bi00294a047] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pinkerton TC, Howe WJ, Ulrich EL, Comiskey JP, Haginaka J, Murashima T, Walkenhorst WF, Westler WM, Markley JL. Protein binding chiral discrimination of HPLC stationary phases made with whole, fragmented, and third domain turkey ovomucoid. Anal Chem 1995; 67:2354-67. [PMID: 8686875 DOI: 10.1021/ac00110a006] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Individual protein domains and two domains in combination were prepared by enzymatic and chemical cleavage of turkey ovomucoid followed by isolation and purification by size-exclusion and ion-exchange chromatography. Silica bonded-phase HPLC columns were made from either whole or isolated domains of turkey ovomucoid. The protein columns were tested for chiral recognition by their abilities to resolve enantiomers among a wide range of racemates. The columns made from whole turkey ovomucoid displayed chiral activity toward many racemates, where as a combination of the first and second domain resolved only a selected number of aromatic weak bases. The first and second domains independently gave no appreciable chiral activity. The turkey ovomucoid third domain exhibited enantioselective protein binding for fused-ring aromatic weak acids. Glycosylation of the third domain did not affect chiral recognition. Titration of the third domain with model compounds in conjunction with NMR measurements enabled the identification of the amino acids responsible for binding. Molecular modeling of the ligand-protein complexation provided insights into the ability of a protein surface to discriminate enantiomers on the basis of multiple intermolecular interactions.
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Affiliation(s)
- T C Pinkerton
- Upjohn Laboratories, Analytical Research & Specification Development and Computer-Aided Drug Discovery, Upjohn Company, Kalamazoo, Michigan 49001, USA
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39
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Stockman BJ, Scahill TA, Roy M, Ulrich EL, Strakalaitis NA, Brunner DP, Yem AW, Deibel MR. Secondary structure and topology of interleukin-1 receptor antagonist protein determined by heteronuclear three-dimensional NMR spectroscopy. Biochemistry 1992; 31:5237-45. [PMID: 1534997 DOI: 10.1021/bi00138a001] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Interleukin-1 (IL-1) proteins, such as IL-1 beta, play a key role in immune and inflammatory responses. Interaction of these cytokines with the IL-1 receptor induces a variety of biological changes in neurologic, metabolic, hematologic, and endocrinologic systems. Interleukin-1 receptor antagonist protein (IRAP) is a naturally occurring inhibitor of the interleukin-1 receptor. The 153-residue protein binds to the receptor with an affinity similar to that of IL-1 beta but does not elicit any physiological responses. As a first step toward understanding IRAP's mode of action, we have used multidimensional, heteronuclear NMR spectroscopy to determine the antagonist's solution secondary structure and global fold. Using a combination of 3D 1H-15N NOESY-HMQC and TOCSY-HMQC and 3D 1H-15N-13C HNCA and HN(CO)CA experiments on uniformly 15N- or doubly 13C/15N-enriched IRAP, we have made resonance assignments for more than 90% of the main-chain atoms. Analysis of short- and long-range NOE's indicates that IRAP is predominantly beta-sheet, with the same overall topology as IL-1 beta but with different regions of the primary sequence comprising the beta-strands. Two short helical segments also were identified. The 14% sequence identity between IL-1 beta and IRAP increases to 25% when differences in the locations of secondary structure elements in the primary sequences are taken into account. Still, numerous differences in side chains, which ultimately play a major role in receptor interaction, exist.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- B J Stockman
- Upjohn Laboratories, Upjohn Company, Kalamazoo, Michigan 49007
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40
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Zehfus MH, Reily MD, Ulrich EL, Westler WM, Markley JL. 1H, 13C, and 15N resonance assignments for a ferrocytochrome c553 heme by multinuclear NMR spectroscopy. Arch Biochem Biophys 1990; 276:369-73. [PMID: 2154947 DOI: 10.1016/0003-9861(90)90734-g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A novel strategy has been used to assign the 1H, 13C, and 15N resonances of the heme in Anabaena 7120 ferrocytochrome c553. 13C[13C] double-quantum coherence spectroscopy was used to delineate the heme carbons, 1H[13C] single-bond correlation spectroscopy was used to define the attached protons, and 1H[15N] multiple-bond correlation spectroscopy was used to assign the nitrogens. 1H[13C] multiple-bond correlation spectroscopy confirmed many of the assignments. Proteins were labeled uniformly with 13C or 15N to obtain the required spectral sensitivity.
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Affiliation(s)
- M H Zehfus
- Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53706
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41
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Alexandrescu AT, Ulrich EL, Markley JL. Hydrogen-1 NMR evidence for three interconverting forms of staphylococcal nuclease: effects of mutations and solution conditions on their distribution [Erratum to document cited in CA110(5):36063b]. Biochemistry 1989. [DOI: 10.1021/bi00434a075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Alexandrescu AT, Ulrich EL, Markley JL. Hydrogen-1 NMR evidence for three interconverting forms of staphylococcal nuclease: effects of mutations and solution conditions on their distribution. Biochemistry 1989; 28:204-11. [PMID: 2706243 DOI: 10.1021/bi00427a028] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
It has been known for several years that 1H NMR spectra of the enzyme staphylococcal nuclease contain resonances due to conformational heterogeneity [Markley, J. L., Williams, M. N., & Jardetzky, O. (1970) Proc. Natl. Acad. Sci. U.S.A. 65, 645-651]. One source of conformational heterogeneity has been attributed recently to cis/trans isomeriation of the Lys116-Pro117 peptide bond [Evans, P. A., Dobson, C. M., Kautz, R. A., Hatfull, G., & Fox, R. O. (1987) Nature (London) 329, 266-268]. In this paper we present evidence for three interconverting folded forms of nuclease. Forms N and N' are monomeric; form N" appears at higher nuclease concentrations and probably corresponds to dimerized enzyme. Saturation transfer was used to demonstrate that exchange occurs between the denatured state and N". The effects of temperature, pH, and Ca2+ and nucleotide binding on NMR spectra of nuclease were examined. When the temperature is increased or the pH is lowered, form N' is favored relative to N. Binding of a competitive inhibitor (thymidine 3',5'-bisphosphate plus calcium ion) strongly favors one form of nuclease. 1H NMR spectra of wild-type nuclease, the single-mutant nucleases L89F and H124L, and the double-mutant nuclease F76V+H124L were compared. In the unligated proteins, the equilibrium constant for the conformational equilibrium N in equilibrium with N' is approximately 0.1 in wild-type nuclease and nuclease H124L; by contrast, this equilibrium constant is about 0.7 in nuclease L89F and 1.2 in nuclease F76V+H124L under similar conditions.
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Affiliation(s)
- A T Alexandrescu
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706
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Stockman BJ, Reily MD, Westler WM, Ulrich EL, Markley JL. Concerted two-dimensional NMR approaches to hydrogen-1, carbon-13, and nitrogen-15 resonance assignments in proteins. Biochemistry 1989; 28:230-6. [PMID: 2539856 DOI: 10.1021/bi00427a032] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
When used in concert, one-bond carbon-carbon correlations, one-bond and multiple-bond proton-carbon correlations, and multiple-bond proton-nitrogen correlations, derived from two-dimensional (2D) NMR spectra of isotopically enriched proteins, provide a reliable method of assigning proton, carbon, and nitrogen resonances. In contrast to procedures that simply extend proton assignments to carbon or nitrogen resonances, this technique assigns proton, carbon, and nitrogen resonances coordinately on the basis of their integrated coupling networks. Redundant spin coupling pathways provide ways of resolving overlaps frequently encountered in homonuclear 1H 2D NMR spectra and facilitate the elucidation of complex proton spin systems. Carbon-carbon and proton-carbon couplings can be used to bridge the aromatic and aliphatic parts of proton spin systems; this avoids possible ambiguities that may result from the use of nuclear Overhauser effects to assign aromatic amino acid signals. The technique is illustrated for Anabaena 7120 flavodoxin and cytochrome c-553, both uniformly enriched with carbon-13 (26%) or nitrogen-15 (98%).
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Affiliation(s)
- B J Stockman
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706
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Alexandrescu AT, Mills DA, Ulrich EL, Chinami M, Markley JL. NMR assignments of the four histidines of staphylococcal nuclease in native and denatured states. Biochemistry 1988; 27:2158-65. [PMID: 3288282 DOI: 10.1021/bi00406a051] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
NMR signals from all four histidine ring C epsilon protons and three of the four histidine C delta protons in the protein staphylococcal nuclease have been assigned by comparing spectra of the wild-type (Foggi strain) protein to spectra of three variants that each lack a different histidine residue. All proteins studied were cloned and overproduced in Escherichia coli. The NMR spectra of the three mutant proteins (H8R, H46Y, and H124L) used to make these assignments were similar to one another and to those of the wild type, except for signals from the mutated residues. The pKa values of those histidines conserved between the wild type and the mutants remained essentially unchanged. Multiple histidine C epsilon proton resonances due to non-native forms of nuclease were observed in both thermally induced and acid-induced unfolding. Residue-specific assignments of H epsilon protons in the thermally denatured forms of the mutant H46Y were obtained from connectivities to the native state by saturation transfer.
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Affiliation(s)
- A T Alexandrescu
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53706
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Ulrich EL, Girvin ME, Cramer WA, Markley JL. Location and mobility of ubiquinones of different chain lengths in artificial membrane vesicles. Biochemistry 1985; 24:2501-8. [PMID: 3839413 DOI: 10.1021/bi00331a016] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ubiquinone (UQn with n = 2, 3, or 10 isoprenoid groups) was incorporated into small, sonicated vesicles made of dipalmitoylphosphatidylcholine (DPPC) or dimyristoylphosphatidylcholine (DMPC). (1) The accessibility of oxidized UQ in DPPC or DMPC vesicles to the reductant sodium borohydride (NaBH4), measured by UV spectroscopy, was UQ2 greater than UQ3 greater than UQ10 (DPPC) and UQ2 greater than UQ3 approximately UQ10 (DMPC). (2) Catalysis of the reduction of entrapped ferricyanide by exogenous NaBH4 was more effective with UQ2 than UQ10 but was slower with all quinones than reduction by added dithionite. (3) The methoxy protons of UQ2 and UQ3 in DPPC and DMPC vesicles exhibited a single NMR resonance centered at approximately 3.95 ppm, whereas the methoxy groups of UQ10 gave rise to two separate proton resonances, at 3.93 ppm and a more narrow resonance at 3.78 ppm. The UQ10 population characterized by the 3.78 ppm resonance was present at a higher concentration in DPPC than in DMPC vesicles and was relatively insensitive to reduction by NaBH4. (4) UQ10 perturbed the melting temperature (Tm) of DPPC vesicles to a smaller extent (delta Tm = -1 degrees C) than did UQ2 and UQ3 (delta Tm = -3 to -4 degrees C). The combined UV and NMR data imply the following: The UQ10 pool characterized by the 3.78 ppm peak corresponds to a more mobile UQ10 fraction that is not reduced by NaBH4 in 2-3 min and is thought to be localized close to the center of the DPPC bilayer since it has little effect on the DPPC Tm.(ABSTRACT TRUNCATED AT 250 WORDS)
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Markley JL, Westler WM, Chan TM, Kojiro CL, Ulrich EL. Two-dimensional NMR approaches to the study of protein structure and function. Fed Proc 1984; 43:2648-56. [PMID: 6430721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two-dimensional Fourier transform methods for homonuclear proton NMR spectroscopy have been introduced by Wüthrich and Ernst as a means of extending assignments in spectra of proteins. Multinuclear two-dimensional approaches also appear promising. We are applying current one- and two-dimensional NMR methods to protein family members that differ from one another by one or more amino acid substitutions. The overall goal is to elucidate relationships among the sequences, structures, and functions of these proteins: for example, to delineate primary structural requirements for changes in observable properties such as conformation, amino acid side chain dynamics, hydrogen exchange dynamics, pK'a values, and oxidation-reduction potentials. The ovomucoids from a variety of species of birds, which include a single set of 12 pairs of third-domain proteins (Mr = 6062 for turkey third domain, similar for others) that differ by single amino acid substitutions, provide a favorable system for the study of the structural and dynamic effects of single amino acid replacements. X-ray crystallographic structures of two ovomucoid third domains are available. Other series of proteins being studied by these methods include the photosynthetic electron transport proteins ferredoxin and plastocyanin.
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47
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Markley JL, Ulrich EL. Detailed analysis of protein structure and function by NMR spectroscopy: survey of resonance assignments. Annu Rev Biophys Bioeng 1984; 13:493-521. [PMID: 6331288 DOI: 10.1146/annurev.bb.13.060184.002425] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Techniques are now available for making extensive assignments in NMR spectra of proteins of moderate size (molecular weight 20,000 or less). Such assignments provide the first step for experiments designed to extract the full complement of NMR parameters for each group in a protein. The stage is set for exciting research scenarios in protein chemistry involving, for example, the determination of hydrogen exchange kinetics at all exchangeable positions whose half times are on the order of 100 ms (277) or longer than a few minutes (316, 569, 570); the characterization of intermediates in protein folding pathways (318); measurement of the distribution of internal motions within a protein molecule (573); a detailed description of the biophysical consequences of single amino acid replacements in small proteins (387); elucidation of the mechanisms of conformational transitions in proteins; and multiparametric characterization of the parts of an enzyme that participate in catalytic mechanisms. Small proteins for which extensive 1H NMR assignments have been made include lysozyme, several cytochromes, ferredoxins, myelin basic proteins, PTI and related proteinase inhibitors, proteinase inhibitors from seminal plasma and avian eggs, apamin, and several snake venom neurotoxins. (References are given in Table 1).
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Ulrich EL, John EM, Gough GR, Brunden MJ, Gilham PT, Westler WM, Markley JL. Imino proton assignments in the proton nuclear magnetic resonance spectrum of the lambda phage OR3 deoxyribonucleic acid fragment. Biochemistry 1983; 22:4362-5. [PMID: 6226312 DOI: 10.1021/bi00288a003] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The 17 base pair duplex d(TATCACCGCAAGGGATAp) . d(TATCCCTTGCGGTGATAp) corresponding to the OR3 operator site of lambda phage has been synthesized and studied by 1H nuclear magnetic resonance spectroscopy at 470 MHz. The 13 imino proton resonances observed at 20 degrees C have been assigned to specific base pairs at positions 3-15 on the basis of nuclear Overhauser effect measurements and studies of the temperature dependence of peak intensities. Resonances from the A-T base pairs at positions 1, 2, 16, and 17 are assumed to be absent from the spectrum because of terminal fraying. Resonance from many of the base pairs suggested by Ohlendorf et al. [Ohlendorf, D. H., Anderson, W. F., Fisher, R. G., Takeda, Y., & Matthews, B. W. (1982) Nature (London) 298, 718-723] to be involved in specific binding of the lambda phage cro repressor are well resolved.
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Ulrich EL, Westler WM, Markley JL. Reassignments in the 1H NMR spectrum of flavin adenine dinucleotide by two-dimensional homonuclear chemical shift correlation. Tetrahedron Lett 1983. [DOI: 10.1016/s0040-4039(00)81440-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Blaszak JA, Ulrich EL, Markley JL, McMillin DR. High-resolution proton nuclear magnetic resonance studies of the nickel(II) derivative of azurin. Biochemistry 1982; 21:6253-8. [PMID: 6817786 DOI: 10.1021/bi00267a033] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
High-resolution (360 and 470 MHz) 1H NMR studies of Ni(II) azurin, the nickel(II) derivative of the blue copper protein azurin, are reported. The aliphatic resonances of Ni(II) azurin closely parallel those of apoazurin and Cu(I) azurin and indicate that no major structural changes are associated with the binding of nickel(II). The magnetic moment of Ni(II) azurin (mueff = 3.2 muB) is in keeping with a pseudotetrahedral coordination environment like that of Cu(I) azurin. Resonances of protons from the ligand moieties are shifted as far as 125 ppm downfield from 4,4-dimethyl-4-silapentane-1-sulfonate and as far as 20 ppm upfield by internal fields due to the nickel center. One of these strongly shifted resonances is assigned to the methyl protons of the methionine ligand. From spectra of Ni(II) azurin as a function of pH, the pKa' values of histidine-35 and histidine-83 have been measured to be approximately 6.0 and 7.5, respectively. Histidine-35 titrates in a discontinuous fashion, and, significantly, so do several of the isotropically shifted ligand protons, also within experimental error with the same pHmid. This result reinforces the suggestion that the conformational change coupled to the protonation of histidine-35 plays an important role in regulating electron transfer reactions of native azurin [Silvestrini, M. C., Brunori, M., Wilson, M. T., & Darley-Usmar, V. M. (1981) J. Inorg. Biochem. 14, 327-338].
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