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Rossi P, Shi L, Liu G, Barbieri CM, Lee HW, Grant TD, Luft JR, Xiao R, Acton TB, Snell EH, Montelione GT, Baker D, Lange OF, Sgourakis NG. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta. Proteins 2015; 83:309-17. [PMID: 25388768 PMCID: PMC5061451 DOI: 10.1002/prot.24719] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 07/23/2014] [Revised: 10/10/2014] [Accepted: 10/29/2014] [Indexed: 01/26/2023]
Abstract
Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology-based methods, protein-protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet-V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1. Unlike conventional methods relying on a dense network of experimental restraints, the sparse data are used to limit conformational search during optimization of a physically realistic energy function. This work highlights a new approach for studying minor conformational changes due to structural plasticity within a single dimeric interface in solution.
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Affiliation(s)
- Paolo Rossi
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
| | - Lei Shi
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Gaohua Liu
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
| | - Christopher M. Barbieri
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
| | - Hsiau-Wei Lee
- Department of Chemistry, Complex Carbohydrate Research Center, and Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia 30602
- Department of Biochemistry & Molecular Biology, Complex Carbohydrate Research Center, and Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia 30602
| | - Thomas D. Grant
- Hauptman–Woodward Medical Research Institute, and Northeast Structural Genomics Consortium, Buffalo, New York 14203
- SUNY Buffalo Department of Structural Biology, Buffalo, New York 14203
| | - Joseph R. Luft
- Hauptman–Woodward Medical Research Institute, and Northeast Structural Genomics Consortium, Buffalo, New York 14203
- SUNY Buffalo Department of Structural Biology, Buffalo, New York 14203
| | - Rong Xiao
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
| | - Thomas B. Acton
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, and Northeast Structural Genomics Consortium, Buffalo, New York 14203
- SUNY Buffalo Department of Structural Biology, Buffalo, New York 14203
| | - Gaetano T. Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854
- Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195
| | - Oliver F. Lange
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Nikolaos G. Sgourakis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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Mohanty B, Serrano P, Geralt M, Wüthrich K. NMR structure determination of the protein NP_344798.1 as the first representative of Pfam PF06042. J Biomol NMR 2015; 61:83-7. [PMID: 25430057 PMCID: PMC4304887 DOI: 10.1007/s10858-014-9878-3] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/17/2014] [Indexed: 05/13/2023]
Abstract
We present the NMR structure determination of the protein NP_344798.1, which forms a CCA-adding enzyme head-domain architecture and is the first structural representative of the Pfam protein family PF06042. Its structure can now serve as a template for homology modeling of the other 785 members of this protein family. With 191 residues, NP_344798.1 is the largest single-domain protein structure determined so far with the J-UNIO protocol for automated NMR structure determination. The present work thus also shows that J-UNIO based exclusively on automated projection spectroscopy (APSY) and 3D heteronuclear-resolved [1H,1H]-NOESY experiments, can successfully be used to obtain high-quality NMR structures of protein domains with up to 200 residues.
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Affiliation(s)
- Biswaranjan Mohanty
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics, (http://www.jcsg.org), La Jolla, CA 92037, USA. Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics, (http://www.jcsg.org), La Jolla, CA 92037, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics, (http://www.jcsg.org), La Jolla, CA 92037, USA
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Jaudzems K, Pedrini B, Geralt M, Serrano P, Wüthrich K. J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4. J Biomol NMR 2015; 61:65-72. [PMID: 25428766 PMCID: PMC4304919 DOI: 10.1007/s10858-014-9886-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 09/23/2014] [Accepted: 11/21/2014] [Indexed: 05/13/2023]
Abstract
The NMR structure of the 206-residue protein NP_346487.1 was determined with the J-UNIO protocol, which includes extensive automation of the structure determination. With input from three APSY-NMR experiments, UNIO-MATCH automatically yielded 77 % of the backbone assignments, which were interactively validated and extended to 97 %. With an input of the near-complete backbone assignments and three 3D heteronuclear-resolved [(1)H,(1)H]-NOESY spectra, automated side chain assignment with UNIO-ATNOS/ASCAN resulted in 77 % of the expected assignments, which was extended interactively to about 90 %. Automated NOE assignment and structure calculation with UNIO-ATNOS/CANDID in combination with CYANA was used for the structure determination of this two-domain protein. The individual domains in the NMR structure coincide closely with the crystal structure, and the NMR studies further imply that the two domains undergo restricted hinge motions relative to each other in solution. NP_346487.1 is so far the largest polypeptide chain to which the J-UNIO structure determination protocol has successfully been applied.
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Affiliation(s)
- Kristaps Jaudzems
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Bill Pedrini
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA. Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
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