Helix kinks are equally prevalent in soluble and membrane proteins

• Published in: Proteins, structure, function, and bioinformatics Vol. 82; no. 9; pp. 1960 - 1970
• Main Authors: Wilman, Henry R., Shi, Jiye, Deane, Charlotte M.
• Format: Journal Article
• Language: English
• Published: United States Blackwell Publishing Ltd 01.09.2014; Wiley Subscription Services, Inc; BlackWell Publishing Ltd
• Subjects: Amino Acid Sequence; Amino acids; helix bend; helix distortion; helix kink; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; membrane protein; Membrane Proteins - chemistry; Membrane Proteins - metabolism; Models, Molecular; Proline - chemistry; Protein Folding; protein helix; protein structure; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins; soluble protein; helix kink; protein structure; helix bend; membrane protein; protein helix; soluble protein; helix distortion
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.24550

ABSTRACT Helix kinks are a common feature of α‐helical membrane proteins, but are thought to be rare in soluble proteins. In this study we find that kinks are a feature of long α‐helices in both soluble and membrane proteins, rather than just transmembrane α‐helices. The apparent rarity of kinks in soluble proteins is due to the relative infrequency of long helices (≥20 residues) in these proteins. We compare length‐matched sets of soluble and membrane helices, and find that the frequency of kinks, the role of Proline, the patterns of other amino acid around kinks (allowing for the expected differences in amino acid distributions between the two types of protein), and the effects of hydrogen bonds are the same for the two types of helices. In both types of protein, helices that contain Proline in the second and subsequent turns are very frequently kinked. However, there are a sizeable proportion of kinked helices that do not contain a Proline in either their sequence or sequence homolog. Moreover, we observe that in soluble proteins, kinked helices have a structural preference in that they typically point into the solvent. Proteins 2014; 82:1960–1970. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.