RESEARCH ARTICLE


Systematic Comparison of Crystal and NMR Protein Structures Deposited in the Protein Data Bank



Kresimir Sikic1, 2, Sanja Tomic3, Oliviero Carugo*, 1, 4
1 Departement of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna University, Austria
2 Faculty of Electrical Engineering and Computing, University of Zagreb, Croatia
3 Rudjer Boskovic Institute, Zagreb, Croatia
4 Departement of General Chemistry, University of Pavia, Italy


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© Sikic et al.; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License (http: //creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Department for Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria; Tel: +43 1 4277 52208; Fax: +43 1 4277 9522; E-mail: oliviero.carugo@univie.ac.at


Abstract

Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR – X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution.

Keywords: Large scale structure comparison, NMR spectroscopy, Protein Data Bank, structure similarity, X-ray crystallography.