Bioinformatics Studies on Transmembrane Strand Proteins

Abstract

Outer membrane proteins perform a variety of functions, such as mediating non-specific, passive transport of ions and small molecules, selectively passing the molecules like maltose and sucrose and are involved in voltage dependent anion channels. These proteins contain β-strands as their membrane spanning segments and are found in the outer membranes of bacteria, mitochondria and chloroplast. The assembly of transmembrane strand (TMS) proteins is somewhat more complex when compared to the assembly of transmembrane helical proteins having α-helices as transmembrane parts. This is probably due to the difference of amino acid sequences of the transmembrane part strands and helices. Because of this feature, most predictive schemes, which are successful in predicting transmembrane helical segments, fail to predict the transmembrane strand segments. Further, discriminating TMS and all-β globular (βG) proteins, and fishing TMS proteins from genomic sequences are other related important tasks in genome research. We have analyzed the three dimensional structures of TMS and βG proteins and derived several important parameters for the 20 amino acid residues. We have also delineated the cation-π interactions in TMS protein structures and estimated the inter-residue contacts in these structures. Further, we have developed a neural network based algorithm for predicting the membrane spanning β-strand segments in TMS proteins. A web interface has been setup and made it available for the users, which can be used for predicting the transmembrane β-strand segments in any outer membrane protein.