Title: The relationship between experimentally validated intracellular human protein stability and the features of its solvent accessible surface

Authors: Xiaofeng Song; Yan Jing; Ping Han

Addresses: Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China ' Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China ' Department of Gynecology and Obstetrics, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China

Abstract: Protein degradation is critical for most cellular processes, and investigating the degradation signals in the sequence and structure is beneficial for analysing the protein stability. In this paper, we investigated in depth the intrinsic factors affecting the protein degradation based on the sequence and structure features. The results indicated that there are more hydrophobic residues on the surface of short-lived protein than the long-lived protein. The secondary structure such as coil tends to be on the surface of short-lived protein. There are more serine phosphorylation sites on the short-lived protein surface, and there is higher possibility for the short-lived proteins to start the degradation by signal of PEST motif than long-lived proteins. We also found that almost all of N terminal residues are exposed to be on the surface; therefore, the specific features of the solvent accessible surface residues are the key factors affecting intracellular protein stability.

Keywords: intracellular protein stability; solvent accessible surfaces; protein sequence features; protein structure features; protein degradation; hydrophobic residues; coil; serine phosphorylation sites; PEST motif; bioinformatics.

DOI: 10.1504/IJDMB.2015.066338

International Journal of Data Mining and Bioinformatics, 2015 Vol.11 No.1, pp.84 - 101

Received: 20 Aug 2012
Accepted: 06 Mar 2013
Published online: 17 Dec 2014 *

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