Srinivasan N, Anuradha V S, Ramakrishnan C, Sowdhamini R, Balaram P
Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
Int J Pept Protein Res. 1994 Aug;44(2):112-22. doi: 10.1111/j.1399-3011.1994.tb00565.x.
Backbone conformations at 1064 asparaginyl residues in 123 non-homologous, high-resolution X-ray structures of proteins were analysed. Asn adopts conformations in left-handed alpha-helical region and other partially allowed regions in the Ramachandran map more readily than any other non-glycyl residue. Asn conformational clusters in the (phi, psi) regions of left-handed alpha-helix right-handed alpha-helix and extended (beta) strands were investigated in detail for their occurrence in various secondary structures, especially in beta-turn regions. Preferences were observed for Asn conformations in different positions in various beta-turn types, including the first and fourth positions of the turn. Asparaginyl residues with extended conformations are found to occur frequently in irregular regions, although they are expected to occur predominantly in extended strands or in the third position of type II beta-turns. Asn conformations at the N-cap positions of helices strongly prefer extended conformation than alpha L, which seems to be characteristic of non-glycyl residues at that position. In the liners connecting two extended strands and those connecting an alpha-helix and an extended strand, Asn with alpha L or alpha R conformation is more favoured than Asn with the beta-conformation. Analysis of Asn-Asn doublets and Asn-X-Asn triplets permitted identification of conformational families in such sequences. Results of this investigation provide useful hints in modelling Asn-rich regions in proteins such as malaria parasite coat protein.
分析了123个非同源高分辨率蛋白质X射线结构中1064个天冬酰胺残基的主链构象。与任何其他非甘氨酰残基相比，天冬酰胺在拉氏图中的左手α螺旋区域和其他部分允许区域更容易采用构象。详细研究了左手α螺旋、右手α螺旋和延伸（β）链的（φ，ψ）区域中的天冬酰胺构象簇在各种二级结构中的出现情况，特别是在β转角区域。观察到在各种β转角类型的不同位置，包括转角的第一个和第四个位置，天冬酰胺构象存在偏好。发现具有延伸构象的天冬酰胺残基在不规则区域频繁出现，尽管它们预计主要出现在延伸链或II型β转角的第三个位置。螺旋N端帽位置的天冬酰胺构象比αL构象更强烈地偏好延伸构象，这似乎是该位置非甘氨酰残基的特征。在连接两条延伸链的连接段以及连接α螺旋和延伸链的连接段中，具有αL或αR构象的天冬酰胺比具有β构象的天冬酰胺更受青睐。对天冬酰胺-天冬酰胺双峰和天冬酰胺-X-天冬酰胺三联体的分析允许识别此类序列中的构象家族。这项研究的结果为模拟蛋白质中富含天冬酰胺的区域（如疟原虫表面蛋白）提供了有用的线索。
