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Occurrence, conformational features and amino acid propensities for the pi-helix.

Fodje, Michel LU and Al-Karadaghi, Salam LU (2002) In Protein Engineering 15(5). p.353-358
Abstract
The most abundant helix type in proteins is the alpha-helix, accounting for about 31% of amino acid secondary structure states, while the 3(10)-helix accounts for about 4%. The pi-helix appears to be extremely rare and is considered to be unstable. Existing secondary structure definition methods find very few within the Protein Data Bank. Using an improved pi-helix definition algorithm to search a non-redundant subset of high-resolution and well-refined protein structures, we found that almost every tenth protein contained a pi-helix. This enabled us to show for the first time that the pi-helix has structural parameters that are different from the hypothesized model values. It also has distinctive amino acid preferences and it is conserved... (More)
The most abundant helix type in proteins is the alpha-helix, accounting for about 31% of amino acid secondary structure states, while the 3(10)-helix accounts for about 4%. The pi-helix appears to be extremely rare and is considered to be unstable. Existing secondary structure definition methods find very few within the Protein Data Bank. Using an improved pi-helix definition algorithm to search a non-redundant subset of high-resolution and well-refined protein structures, we found that almost every tenth protein contained a pi-helix. This enabled us to show for the first time that the pi-helix has structural parameters that are different from the hypothesized model values. It also has distinctive amino acid preferences and it is conserved within functionally related proteins. Features that may contribute to the stability of the pi-helical structure have also been identified. In addition to hydrogen bonds, several other factors contribute to the stability of pi-helices. The pi-helix may have some functional advantages over other helical structures. Thus, we describe cases where the side chains of functionally important residues at every fourth position within a pi-helix could be aligned and brought close together in a way that would not be allowed by any other helix type. (Less)
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author
organization
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type
Contribution to journal
publication status
published
subject
in
Protein Engineering
volume
15
issue
5
pages
353 - 358
publisher
Oxford University Press
external identifiers
  • wos:000175911000002
  • pmid:12034854
ISSN
1460-213X
language
English
LU publication?
yes
id
753dcad1-b774-4f8c-b50a-528490d07400 (old id 108571)
alternative location
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12034854&dopt=Abstract
date added to LUP
2007-07-09 15:00:42
date last changed
2017-12-04 15:45:55
@article{753dcad1-b774-4f8c-b50a-528490d07400,
  abstract     = {The most abundant helix type in proteins is the alpha-helix, accounting for about 31% of amino acid secondary structure states, while the 3(10)-helix accounts for about 4%. The pi-helix appears to be extremely rare and is considered to be unstable. Existing secondary structure definition methods find very few within the Protein Data Bank. Using an improved pi-helix definition algorithm to search a non-redundant subset of high-resolution and well-refined protein structures, we found that almost every tenth protein contained a pi-helix. This enabled us to show for the first time that the pi-helix has structural parameters that are different from the hypothesized model values. It also has distinctive amino acid preferences and it is conserved within functionally related proteins. Features that may contribute to the stability of the pi-helical structure have also been identified. In addition to hydrogen bonds, several other factors contribute to the stability of pi-helices. The pi-helix may have some functional advantages over other helical structures. Thus, we describe cases where the side chains of functionally important residues at every fourth position within a pi-helix could be aligned and brought close together in a way that would not be allowed by any other helix type.},
  author       = {Fodje, Michel and Al-Karadaghi, Salam},
  issn         = {1460-213X},
  language     = {eng},
  number       = {5},
  pages        = {353--358},
  publisher    = {Oxford University Press},
  series       = {Protein Engineering},
  title        = {Occurrence, conformational features and amino acid propensities for the pi-helix.},
  volume       = {15},
  year         = {2002},
}