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| Paper IPM / Computer Science / 10937 |
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In the present work, we address the question of whether different amino acids have different �-sheet initiating and terminating characteristics. Using a large scale analysis of parallel and antiparallel �-sheets in a non-redundant dataset of proteins, we observed that most of the amino acids show significant under- or over-representation in at least one of the positions at the two ends of �-sheets, which are denoted as N-cap and C-cap. In addition, based on statistical data and structural comparison, we found that certain amino acids, especially Asp, Asn, Gly and Pro have strong tendencies to block �-sheet continuation. Hence, we can consider these residues as �-sheet terminators. It was also proposed that the dipole moments in parallel �-sheets, whose direction is from C-terminal (partially negative) to N-terminal (partially positive), are much stronger than has previously been suggested. In fact, enhancement of dipole moments in parallel �-sheets is a result of the positioning of positively charged residues at N-cap and negatively charged residues at C-cap. This enhancement in dipole moment magnitude leads to strengthened dipolar interactions between parallel �-sheets dipoles and other partners especially a-helices dipoles. The results provide an explanation for the antiparallel alignment of parallel �-sheets with a-helices.
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