A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy

• DOI: 10.1093/bioinformatics/btr234
• Publication Date: 2011-04-20T04:06:58Z
• Authors: Ali Abdul-Gader; Andrew John Miles; B. A. Wallace
• Keywords: 0301 basic medicine; 03 medical and health sciences; Circular Dichroism; Membrane Proteins; Databases, Protein; Protein Structure, Secondary; Synchrotrons

Empirical analyses of protein secondary structures based on circular dichroism (CD) and synchrotron radiation (SRCD) spectroscopic data rely the availability reference datasets comprised spectra relevant proteins, whose crystal have been determined. Datasets only soluble proteins not proven suitable for analysing membrane proteins.A new dataset, MP180, has created containing 30 encompassing structure fold space covered by all known structures. In addition a mixed SMP180, created, which includes 98 (SP) plus MP180 spectra. Calculations both using SMP180 are significantly improved with respect to those produced, protein-only datasets. The dataset also enables determination percentage transmembrane residues, thus enhancing information previously obtainable from CD spectroscopy.Reference online at DichroWeb analysis server (http://dichroweb.cryst.bbk.ac.uk); individual in Protein Circular Dichroism Data Bank (http://pcddb.cryst.bbk.ac.uk).