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Rationally selected basis proteins: A new approach to selecting proteins for spectroscopic secondary structure analysis

Structural Biology and Bioinformatics Center, Structure and Function of Biological Membranes Laboratory, Free University of Brussels (ULB), B-1050 Brussels, Belgium

Reprint requests to: Erik Goormaghtigh, Structural Biology and Bioinformatics Center, Structure and Function of Biological Membranes Laboratory, CP 206/2, Free University of Brussels (ULB), Bld du triomphe, Acces 2, B-1050 Brussels, Belgium; e-mail: egoor{at}ulb.ac.be; fax: 32-2-650-5382.

Protein basis sets have been extensively used as reference data for the determination of protein structure with optical methods such as circular dichroism and infrared spectroscopies. We have taken a new approach to basis protein selection by utilizing three crystal structure classification databases: CATH, SCOP, and PDB_SELECT. Through the use of the information available in these and other online resources, we identified 115 commercially available proteins as potential basis set candidates. By carefully screening the quality of the crystal structures and commercial protein preparations, we obtained a final set of 50 rationally selected proteins (RaSP50) that has been optimized for use in spectroscopic protein structure determination studies. These proteins span the full range of known protein folds as well as -helix and ß-sheet contents, and they represent a more comprehensive variety of fold types than any previous reference set. This report includes a detailed presentation of the reasoning behind the rational protein selection process, a description of the properties of the RaSP50 set, and a discussion of the types of structural and spectral variations that are represented in the set.

Keywords: Proteins; analysis; methods; circular dichroism; infrared spectroscopy; crystallography; statistical analysis; secondary structure; chemometrics; basis sets, protein; databases, protein; data interpretation

Abbreviations: AU, absorbance unit • CATH, Class Architecture Topology and Homology • CD, circular dichroism spectroscopy • CSA, camphor sulfonic acid • EMBL, European Molecular Biology Laboratory • FC, fractional composition (percentage) of a secondary structure type in a protein • FTIR, Fourier transform infrared spectroscopy • HSSP, homology-derived secondary structure of proteins • IR, infrared spectroscopy • NMR, nuclear magnetic resonance • PDB, Brookhaven Protein Data Bank • RaSP, rationally selected proteins • RMS, root-mean squared • SCOP, Structural Classification of Proteins

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