GeNMR: a Web Server for Rapid NMR-based Protein Structure Determination

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2009 May 2

PMID 19406927

Citations 20

Authors

Mark Berjanskii

Peter Tang

Jack Liang

Joseph A Cruz

Jianjun Zhou

You Zhou

Edward Bassett

Cam MacDonell

Paul Lu

Guohui Lin

David S Wishart

Affiliations

Soon will be listed here.

Abstract

GeNMR (GEnerate NMR structures) is a web server for rapidly generating accurate 3D protein structures using sequence data, NOE-based distance restraints and/or NMR chemical shifts as input. GeNMR accepts distance restraints in XPLOR or CYANA format as well as chemical shift files in either SHIFTY or BMRB formats. The web server produces an ensemble of PDB coordinates for the protein within 15-25 min, depending on model complexity and completeness of experimental restraints. GeNMR uses a pipeline of several pre-existing programs and servers to calculate the actual protein structure. In particular, GeNMR combines genetic algorithms for structure optimization along with homology modeling, chemical shift threading, torsion angle and distance predictions from chemical shifts/NOEs as well as ROSETTA-based structure generation and simulated annealing with XPLOR-NIH to generate and/or refine protein coordinates. GeNMR greatly simplifies the task of protein structure determination as users do not have to install or become familiar with complex stand-alone programs or obscure format conversion utilities. Tests conducted on a sample of 90 proteins from the BioMagResBank indicate that GeNMR produces high-quality models for all protein queries, regardless of the type of NMR input data. GeNMR was developed to facilitate rapid, user-friendly structure determination of protein structures via NMR spectroscopy. GeNMR is accessible at http://www.genmr.ca.

Citing Articles

Recent Advances in NMR Protein Structure Prediction with ROSETTA.

Leman J, Kunze G Int J Mol Sci. 2023; 24(9).

PMID: 37175539 PMC: 10178863. DOI: 10.3390/ijms24097835.

Insights to Human γD-Crystallin Unfolding by NMR Spectroscopy and Molecular Dynamics Simulations.

Hsueh S, Wang S, Chen S, Wang C, Wu W, Lin T Int J Mol Sci. 2022; 23(3).

PMID: 35163513 PMC: 8836049. DOI: 10.3390/ijms23031591.

Rapid and reliable protein structure determination via chemical shift threading.

Hafsa N, Berjanskii M, Arndt D, Wishart D J Biomol NMR. 2017; 70(1):33-51.

PMID: 29196969 DOI: 10.1007/s10858-017-0154-1.

NMR Structure of the C-Terminal Transmembrane Domain of the HDL Receptor, SR-BI, and a Functionally Relevant Leucine Zipper Motif.

Chadwick A, Jensen D, Hanson P, Lange P, Proudfoot S, Peterson F Structure. 2017; 25(3):446-457.

PMID: 28162952 PMC: 5575897. DOI: 10.1016/j.str.2017.01.001.

A robust algorithm for optimizing protein structures with NMR chemical shifts.

Berjanskii M, Arndt D, Liang Y, Wishart D J Biomol NMR. 2015; 63(3):255-64.

PMID: 26345175 DOI: 10.1007/s10858-015-9982-z.

References

Cavalli A, Salvatella X, Dobson C, Vendruscolo M . Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci U S A. 2007; 104(23):9615-20. PMC: 1887584. DOI: 10.1073/pnas.0610313104. View

Wishart D, Arndt D, Berjanskii M, Guo A, Shi Y, Shrivastava S . PPT-DB: the protein property prediction and testing database. Nucleic Acids Res. 2007; 36(Database issue):D222-9. PMC: 2238980. DOI: 10.1093/nar/gkm800. View

Prestegard J, Bougault C, Kishore A . Residual dipolar couplings in structure determination of biomolecules. Chem Rev. 2004; 104(8):3519-40. DOI: 10.1021/cr030419i. View

Ulrich E, Akutsu H, Doreleijers J, Harano Y, Ioannidis Y, Lin J . BioMagResBank. Nucleic Acids Res. 2007; 36(Database issue):D402-8. PMC: 2238925. DOI: 10.1093/nar/gkm957. View

BRYANT S, Lawrence C . An empirical energy function for threading protein sequence through the folding motif. Proteins. 1993; 16(1):92-112. DOI: 10.1002/prot.340160110. View

Guntert P, Mumenthaler C, Wuthrich K . Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol. 1997; 273(1):283-98. DOI: 10.1006/jmbi.1997.1284. View

Wishart D, Case D . Use of chemical shifts in macromolecular structure determination. Methods Enzymol. 2001; 338:3-34. DOI: 10.1016/s0076-6879(02)38214-4. View

Wuthrich K . NMR - this other method for protein and nucleic acid structure determination. Acta Crystallogr D Biol Crystallogr. 1995; 51(Pt 3):249-70. DOI: 10.1107/S0907444994010188. View

Levitt M . Growth of novel protein structural data. Proc Natl Acad Sci U S A. 2007; 104(9):3183-8. PMC: 1802002. DOI: 10.1073/pnas.0611678104. View

10.

Guntert P . Automated NMR structure calculation with CYANA. Methods Mol Biol. 2004; 278:353-78. DOI: 10.1385/1-59259-809-9:353. View

11.

Wishart D, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G . CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res. 2008; 36(Web Server issue):W496-502. PMC: 2447725. DOI: 10.1093/nar/gkn305. View

12.

Neal S, Nip A, Zhang H, Wishart D . Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR. 2003; 26(3):215-40. DOI: 10.1023/a:1023812930288. View

13.

Walther D . WebMol--a Java-based PDB viewer. Trends Biochem Sci. 1997; 22(7):274-5. DOI: 10.1016/s0968-0004(97)89047-0. View

14.

Berman H, Henrick K, Nakamura H, Markley J . The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 2006; 35(Database issue):D301-3. PMC: 1669775. DOI: 10.1093/nar/gkl971. View

15.

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

16.

Wishart D, Sykes B . The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR. 1994; 4(2):171-80. DOI: 10.1007/BF00175245. View

17.

Schwieters C, Kuszewski J, Tjandra N, Clore G . The Xplor-NIH NMR molecular structure determination package. J Magn Reson. 2003; 160(1):65-73. DOI: 10.1016/s1090-7807(02)00014-9. View

18.

Nilges M, Macias M, ODonoghue S, Oschkinat H . Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol. 1997; 269(3):408-22. DOI: 10.1006/jmbi.1997.1044. View

19.

Zhang H, Neal S, Wishart D . RefDB: a database of uniformly referenced protein chemical shifts. J Biomol NMR. 2003; 25(3):173-95. DOI: 10.1023/a:1022836027055. View

20.

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View