Structural and Functional Characterization of π Bulges and Other Short Intrahelical Deformations

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• 作者：Cartailler ; Jean-Philippe ; Luecke ; Hartmut
• 刊名：Structure
• 出版年：2004
• 出版时间：January, 2004
• 年：2004
• 卷：12
• 期：1
• 页码：133-144
• 全文大小：220 K

文摘

We data-mined the Protein Data Bank for short intrahelical deformations, including π bulges. These are defined as a contiguous stretch of intrahelical residues deviating from the standard α-helical i→i-4 hydrogen bonding pattern, bilaterally flanked by at least one α-helical turn resulting in a helix kink of less than 40°. We find that such motifs exist in 4.7 % of a PDB subset filtered by quality metrics (resolution < 2.5 Å, R-factor < 0.25, sequence identity < 35 % ). These are typically characterized by at least one i→i-5 main chain hydrogen bond, with energetically favorable main chain dihedral angles, followed by a variable number of main chain carbonyl groups that do not accept intrahelical main chain hydrogen bonds. Their stabilization commonly occurs via hydrogen bonding to water molecules or polar groups. Numerous deformations are implicated in basic yet vital functional roles, commonly as ligand binding site contributors.