Literature DB >> 24464770

Local sequence of protein β-strands influences twist and bend angles.

Kazuo Fujiwara1, Shinichi Ebisawa, Yuka Watanabe, Hiromi Toda, Masamichi Ikeguchi.   

Abstract

β-Sheet twisting is thought to be mainly determined by interstrand hydrogen bonds with little contribution from side chains, but some proteins have large, flat β-sheets, suggesting that side chains influence β-structures. We therefore investigated the relationship between amino acid composition and twists or bends of β-strands. We calculated and statistically analyzed the twist and bend angles of short frames of β-strands in known protein structures. The most frequent twist angles were strongly negatively correlated with the proportion of hydrophilic amino acid residues. The majority of hydrophilic residues (except serine and threonine) were found in the edge regions of β-strands, suggesting that the side chains of these residues likely do not affect β-strand structure. In contrast, the majority of serine, threonine, and asparagine side-chains in β-strands made contacts with a nitrogen atom of the main chain, suggesting that these residues suppress β-strand twisting.
© 2014 Wiley Periodicals, Inc.

Entities:  

Keywords:  effect of side chain to the β-sheet; interstrand hydrogen bond; large flat β-sheet; protein design; statistical analysis

Mesh:

Substances:

Year:  2014        PMID: 24464770     DOI: 10.1002/prot.24518

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  5 in total

1.  De novo design of transmembrane β barrels.

Authors:  Paul White; Binyong Liang; Anastassia A Vorobieva; Jim E Horne; Asim K Bera; Cameron M Chow; Stacey Gerben; Sinduja Marx; Alex Kang; Alyssa Q Stiving; Sophie R Harvey; Dagan C Marx; G Nasir Khan; Karen G Fleming; Vicki H Wysocki; David J Brockwell; Lukas K Tamm; Sheena E Radford; David Baker
Journal:  Science       Date:  2021-02-19       Impact factor: 47.728

2.  An S/T motif controls reversible oligomerization of the Hsp40 chaperone DNAJB6b through subtle reorganization of a β sheet backbone.

Authors:  Theodoros K Karamanos; Vitali Tugarinov; G Marius Clore
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-16       Impact factor: 12.779

3.  Microsecond Backbone Motions Modulate the Oligomerization of the DNAJB6 Chaperone.

Authors:  Emma E Cawood; G Marius Clore; Theodoros K Karamanos
Journal:  Angew Chem Int Ed Engl       Date:  2022-03-19       Impact factor: 16.823

4.  The origin of β-strand bending in globular proteins.

Authors:  Kazuo Fujiwara; Shinichi Ebisawa; Yuka Watanabe; Hiromi Fujiwara; Masamichi Ikeguchi
Journal:  BMC Struct Biol       Date:  2015-10-22

5.  De novo design of a fluorescence-activating β-barrel.

Authors:  Jiayi Dou; Anastassia A Vorobieva; William Sheffler; Lindsey A Doyle; Hahnbeom Park; Matthew J Bick; Binchen Mao; Glenna W Foight; Min Yen Lee; Lauren A Gagnon; Lauren Carter; Banumathi Sankaran; Sergey Ovchinnikov; Enrique Marcos; Po-Ssu Huang; Joshua C Vaughan; Barry L Stoddard; David Baker
Journal:  Nature       Date:  2018-09-12       Impact factor: 49.962

  5 in total

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