recognition of interaction interface residues in low-resolution structures of protein assemblies solely from the positions of cα atoms识别的交互界面残留在低分辨率的蛋白质结构组件单独从cα原子的位置.pdfVIP

Recognition of Interaction Interface Residues in Low- Resolution Structures of Protein Assemblies Solely from the Positions of Ca Atoms Rupali A. Gadkari*, Deepthi Varughese, N. Srinivasan* Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India Abstract Background: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the Ca atoms which are modeled with modest accuracy. Methodology/Principal Findings: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of Ca atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of Ca. We extend the method further to recognize potential protein-protein interface residues. Conclusion/ Significance: Our approach to identify buried and exposed residues solely from the positions of Ca atoms resulted in an accuracy of 84%, sensitivity of 83–89% and specificity of 67–94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivit