engleski

Quanitification of complexity of integral membrane protein secondary structure

Structures of integral membrane proteins are characterized by the existence of one or more transmembrane segment(s) in the protein sequence. Depending on whether these segments are of alpha (~20 residues in length) or beta (~11 residues) secondary structure, integral membrane proteins are classified as those of alpha or beta type. Sequences of membrane proteins range in lengths from 20-30 till more than 1000 amino acid residues. Intuitively, structure of an alpha membrane having 200 amino acids and five transmembrane segments (each having 20 amino acids) is more complex than the structure of membrane protein having 200 amino acids and one transmembrane segment. We proposed a biophysical procedure for quantification of structure complexity by counting the number of possible realizations of membrane protein structure. It is applied to analysis of complexity of representative data sets [1-4] of alpha membrane proteins used in development of modeling methods for prediction of structure of membrane proteins. [1] Rath, Emma M et al., BMC bioinformatics 14(1): 111, 2013. [2] Reeb, Jonas et al., Proteins 83(3):473-484, 2015. [3] Bernhofer M et al., Proteins 84:1706–1716, 2016. [4] Batista J., Vikić-Topić D., & Lučić B., Croat. Chem. Acta, 89(4):527-534, 2016.

integral membrane protein ; secondary structure ; structure prediction ; quantifying complexity ; number of structure realizations

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