Examining the Conservation of Kinks in Alpha Helices

PLoS One. 2016 Jun 17;11(6):e0157553. doi: 10.1371/journal.pone.0157553. eCollection 2016.

Abstract

Kinks are a structural feature of alpha-helices and many are known to have functional roles. Kinks have previously tended to be defined in a binary fashion. In this paper we have deliberately moved towards defining them on a continuum, which given the unimodal distribution of kink angles is a better description. From this perspective, we examine the conservation of kinks in proteins. We find that kink angles are not generally a conserved property of homologs, pointing either to their not being functionally critical or to their function being related to conformational flexibility. In the latter case, the different structures of homologs are providing snapshots of different conformations. Sequence identity between homologous helices is informative in terms of kink conservation, but almost equally so is the sequence identity of residues in spatial proximity to the kink. In the specific case of proline, which is known to be prevalent in kinked helices, loss of a proline from a kinked helix often also results in the loss of a kink or reduction in its kink angle. We carried out a study of the seven transmembrane helices in the GPCR family and found that changes in kinks could be related both to subfamilies of GPCRs and also, in a particular subfamily, to the binding of agonists or antagonists. These results suggest conformational change upon receptor activation within the GPCR family. We also found correlation between kink angles in different helices, and the possibility of concerted motion could be investigated further by applying our method to molecular dynamics simulations. These observations reinforce the belief that helix kinks are key, functional, flexible points in structures.

MeSH terms

  • Confidence Intervals
  • Crystallography, X-Ray
  • Databases, Protein
  • Membrane Proteins / chemistry*
  • Proline / chemistry*
  • Protein Conformation
  • Protein Conformation, alpha-Helical*
  • Receptors, G-Protein-Coupled / chemistry*
  • Sequence Alignment

Substances

  • Membrane Proteins
  • Receptors, G-Protein-Coupled
  • Proline

Grants and funding

This work was supported by Engineering and Physical Sciences Research Council (https://www.epsrc.ac.uk/) grant EP/G037280/1 to ECL, and UCB Pharma (http://www.ucbpharma.co.uk/home) funding to ECL and HRW. SK and JS of UCB provided ideas for the design of the study and contributed to the editing of the manuscript. The funder provided support in the form of salaries for authors SK and JS, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the “author contributions” section.