Dynamic charge interactions create surprising rigidity in the ER/K α-helical protein motif

Sivaraj Sivaramakrishnan, Benjamin J. Spink, Adelene Y.L. Sim, Sebastian Doniach, James A. Spudich

Research output: Contribution to journalArticlepeer-review

69 Scopus citations

Abstract

Protein α-helices are ubiquitous secondary structural elements, seldom considered to be stable without tertiary contacts. However, amino acid sequences in proteins that are based on alternating repeats of four glutamic acid (E) residues and four positively charged residues, a combination of arginine (R) and lysine (K), have been shown to form stable α-helices in a few proteins, in the absence of tertiary interactions. Here, we find that this ER/K motif is more prevalent than previously reported, being represented in proteins of diverse function from archaea to humans. By using molecular dynamics (MD) simulations, we characterize a dynamic pattern of side-chain interactions that extends along the backbone of ER/K α-helices. A simplified model predicts that side-chain interactions alone contribute substantial bending rigidity (0.5 pN/ nm) to ER/K α-helices. Results of small-angle x-ray scattering (SAXS) and single-molecule optical-trap analyses are consistent with the high bending rigidity predicted by our model. Thus, the ER/K α-helix is an isolated secondary structural element that can efficiently span long distances in proteins, making it a promising tool in designing synthetic proteins. We propose that the significant rigidity of the ER/K α-helix can help regulate protein function, as a force transducer between protein subdomains.

Original languageEnglish (US)
Pages (from-to)13356-13361
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume105
Issue number36
DOIs
StatePublished - Sep 9 2008

Keywords

  • Md simulations
  • Protein structure
  • Single-molecule analysis
  • Small-angle x-ray scattering

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