Literature DB >> 17985889

Beta-strand flipping and slipping triggered by turn replacement reveal the opportunistic nature of beta-strand pairing.

Koki Makabe1, Shude Yan, Valentina Tereshko, Grzegorz Gawlak, Shohei Koide.   

Abstract

We investigated how the register between adjacent beta-strands is specified using a series of mutants of the single-layer beta-sheet (SLB) in Borrelia OspA. The single-layer architecture of this system eliminates structural restraints imposed by a hydrophobic core, enabling us to address this question. A critical turn (turn 9/10) in the SLB was replaced with a segment with an intentional structural mismatch. Its crystal structure revealed a one-residue insertion into the central beta-strand (strand 9) of the SLB. This insertion triggered a surprisingly large-scale structural rearrangement: (i) the central strand (strand 9) was shifted by one residue, causing the strand to flip with respect to the adjacent beta-strands and thus completely disrupting the native side-chain contacts; (ii) the three-residue turn located on the opposite end of the beta-strand (turn 8/9) was pushed into its preceding beta-strand (strand 8); (iii) the register between strands 8 and 9 was shifted by three residues. Replacing the original sequence for turn 8/9 with a stronger turn motif restored the original strand register but still with a flipped beta-strand 9. The stability differences of these distinct structures were surprisingly small, consistent with an energy landscape where multiple low-energy states with different beta-sheet configurations exist. The observed conformations can be rationalized in terms of maximizing the number of backbone H-bonds. These results suggest that adjacent beta-strands "stick" through the use of factors that are not highly sequence specific and that beta-strands could slide back and forth relatively easily in the absence of external elements such as turns and tertiary packing.

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Year:  2007        PMID: 17985889      PMCID: PMC2596595          DOI: 10.1021/ja074252c

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  38 in total

1.  Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange.

Authors:  Shude Yan; Scott D Kennedy; Shohei Koide
Journal:  J Mol Biol       Date:  2002-10-18       Impact factor: 5.469

2.  Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory.

Authors:  Robert E Steward; Janet M Thornton
Journal:  Proteins       Date:  2002-08-01

Review 3.  Protein folding and misfolding.

Authors:  Christopher M Dobson
Journal:  Nature       Date:  2003-12-18       Impact factor: 49.962

4.  Conformational heterogeneity of an equilibrium folding intermediate quantified and mapped by scanning mutagenesis.

Authors:  Shude Yan; Grzegorz Gawlak; Jonathan Smith; Lin Silver; Akiko Koide; Shohei Koide
Journal:  J Mol Biol       Date:  2004-05-07       Impact factor: 5.469

5.  A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins.

Authors:  Gautam Dantas; Brian Kuhlman; David Callender; Michelle Wong; David Baker
Journal:  J Mol Biol       Date:  2003-09-12       Impact factor: 5.469

6.  A revised set of potentials for beta-turn formation in proteins.

Authors:  E G Hutchinson; J M Thornton
Journal:  Protein Sci       Date:  1994-12       Impact factor: 6.725

7.  A thermodynamic scale for the beta-sheet forming tendencies of the amino acids.

Authors:  C K Smith; J M Withka; L Regan
Journal:  Biochemistry       Date:  1994-05-10       Impact factor: 3.162

8.  Measurement of the beta-sheet-forming propensities of amino acids.

Authors:  D L Minor; P S Kim
Journal:  Nature       Date:  1994-02-17       Impact factor: 49.962

9.  Beta-hairpin families in globular proteins.

Authors:  B L Sibanda; J M Thornton
Journal:  Nature       Date:  1985 Jul 11-17       Impact factor: 49.962

10.  Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics.

Authors:  Songpon Deechongkit; Houbi Nguyen; Evan T Powers; Philip E Dawson; Martin Gruebele; Jeffery W Kelly
Journal:  Nature       Date:  2004-07-01       Impact factor: 49.962

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  2 in total

Review 1.  Fibrillar peptide gels in biotechnology and biomedicine.

Authors:  Jangwook P Jung; Joshua Z Gasiorowski; Joel H Collier
Journal:  Biopolymers       Date:  2010       Impact factor: 2.505

2.  Effects of Hydrodynamic Interactions on the Near-Surface Diffusion of Spheroidal Molecules.

Authors:  Paweł Czajka; Jan M Antosiewicz; Maciej Długosz
Journal:  ACS Omega       Date:  2019-10-03
  2 in total

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