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Analysis and prediction of inter-strand packing distances between {beta}-sheets of globular proteins
Nagarajaram Hampapathalu A.; Reddy Boojala V.B.; Blundell Tom L. 《Protein engineering, design & selection : PEDS》1999,12(12):1055-1062
Any two ß-strands belonging to two different ß-sheetsin a protein structure are considered to pack interactivelyif each ß-strand has at least one residue that undergoesa loss of one tenth or more of its solvent contact surface areaupon packing. A data set of protein 3-D structures (determinedat 2.5 Å resolution or better), corresponding to 428 proteinchains, contains 1986 non-identical pairs of ß-strandsinvolved in interactive packing. The inter-axial distance betweenthese is significantly correlated to the weighted sum of thevolumes of the interacting residues at the packing interface.This correlation can be used to predict the changes in the inter-sheetdistances in equivalent ß-sheets in homologous proteinsand, therefore, is of value in comparative modelling of proteins. 相似文献
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K Gunasekaran HA Nagarajaram C Ramakrishnan P Balaram 《Canadian Metallurgical Quarterly》1998,275(5):917-932
An analysis on the nature of alpha-helix stop signals has been carried out, using a dataset of 1057 helices identified from 250 high resolution (=2.0 A), non-homologous, protein crystal structures. The backbone dihedral angles (phi, psi) of the terminating residue (T) were found to cluster either in the left-handed helical region (alphaL: phi=20 degrees to 125 degrees and psi=-45 degrees to 90 degrees ; 469 helices (44%)) or in the extended region (E: phi=-180 degrees to -30 degrees and psi=60 degrees to 180 degrees and -180 degrees to -150 degrees ; 459 helices (43%)) of the Ramachandran map. These two broad categories of helix stop signals, alphaL and E-terminated helices, were further examined for sequence preferences. Gly residues were found to have an overwhelming preference to occur as the "alphaL-terminator (T)" resulting in the classical Schellman motif, with a strong preference for hydrophobic residues at position T-4 and T+1. In the case of E-terminated helices His, Asn, Leu and Phe were found to occur with high propensity at position T. Quite remarkably Pro residues, with single exception, were absent at position T, but had the highest propensity at position T+1. Examination of the frequencies of hydrophobic (h) and polar (p) residues at positions flanking Gly/Pro permitted delineation of exclusive patterns and predictive rules for Gly-terminated helices and Pro-terminated helices. The analysis reveals that Pro residues flanked by polar amino acids have a very strong tendency to terminate helices. Examination of a segment ranging from T-4 to T+3 appeared to be necessary to determine whether helix termination or continuation occur at Gly residues. The two types of helix termination (alphaL, E) signals also differed dramatically in their solvent accessibility. Gly and Pro residues at helix termini appeared to be strongly conserved in homologous sequences. 相似文献
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