Article

Beta-sheet capping: signals that initiate and terminate beta-sheet formation.

Department of Biotechnology, College of Science, University of Tehran, Enghelab Avenue, Tehran, Iran.
Journal of Structural Biology (impact factor: 3.41). 02/2008; 161(1):101-10. DOI:10.1016/j.jsb.2007.09.024 pp.101-10
Source: PubMed

ABSTRACT In the present work, we address the question of whether different amino acids have different beta-sheet initiating and terminating characteristics. Using a large scale analysis of parallel and antiparallel beta-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 beta-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 beta-sheet continuation. Hence, we can consider these residues as beta-sheet terminators. It was also proposed that the dipole moments in parallel beta-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 beta-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 beta-sheets dipoles and other partners especially alpha-helices dipoles. The results provide an explanation for the antiparallel alignment of parallel beta-sheets with alpha-helices.

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Keywords

alpha-helices
 
amino acids
 
antiparallel alignment
 
antiparallel beta-sheets
 
certain amino acids
 
different amino acids
 
dipolar interactions
 
dipole moment magnitude
 
dipole moments
 
large scale analysis
 
non-redundant dataset
 
parallel beta-sheets
 
parallel beta-sheets dipoles
 
present work
 
Pro
 
proteins
 
residues
 
statistical data
 
structural comparison
 
terminating characteristics