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The dipeptide conformations of all twenty amino acid types in the context of biosynthesis.

Bywater, Robert P and Veryazov, Valera LU (2015) In SpringerPlus 4.
Abstract
There have been many studies of dipeptide structure at a high level of accuracy using quantum chemical methods. Such calculations are resource-consuming (in terms of memory, CPU and other computational imperatives) which is the reason why most previous studies were restricted to the two simplest amino-acid residue types, glycine and alanine. We improve on this by extending the scope of residue types to include all 20 naturally occurring residue types. Our results reveal differences in secondary structure preferences for the all residue types. There are in most cases very deep energy troughs corresponding either to the polyproline II (collagen) helix and the α-helix or both. The β-strand was not strongly favoured energetically although the... (More)
There have been many studies of dipeptide structure at a high level of accuracy using quantum chemical methods. Such calculations are resource-consuming (in terms of memory, CPU and other computational imperatives) which is the reason why most previous studies were restricted to the two simplest amino-acid residue types, glycine and alanine. We improve on this by extending the scope of residue types to include all 20 naturally occurring residue types. Our results reveal differences in secondary structure preferences for the all residue types. There are in most cases very deep energy troughs corresponding either to the polyproline II (collagen) helix and the α-helix or both. The β-strand was not strongly favoured energetically although the extent of this depression in the energy surface is, while not "deeper" (energetically), has a wider extent than the other two types of secondary structure. There is currently great interest in the question of cotranslational folding, the extent to which the nascent polypeptide begins to fold prior to emerging from the ribosome exit tunnel. Accordingly, while most previous quantum studies of dipeptides were carried out in the (simulated) gas or aqueous phase, we wished to consider the first step in polypeptide biosynthesis on the ribosome where neither gas nor aqueous conditions apply. We used a dielectric constant that would be compatible with the water-poor macromolecular (ribosome) environment. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
SpringerPlus
volume
4
publisher
Springer
external identifiers
  • pmid:26558171
  • wos:000368704000002
  • scopus:84946121362
ISSN
2193-1801
DOI
10.1186/s40064-015-1430-8
language
English
LU publication?
yes
id
34e348c9-0756-4614-a6ad-0e77d2447157 (old id 8236000)
date added to LUP
2015-12-16 17:29:51
date last changed
2017-10-22 04:03:53
@article{34e348c9-0756-4614-a6ad-0e77d2447157,
  abstract     = {There have been many studies of dipeptide structure at a high level of accuracy using quantum chemical methods. Such calculations are resource-consuming (in terms of memory, CPU and other computational imperatives) which is the reason why most previous studies were restricted to the two simplest amino-acid residue types, glycine and alanine. We improve on this by extending the scope of residue types to include all 20 naturally occurring residue types. Our results reveal differences in secondary structure preferences for the all residue types. There are in most cases very deep energy troughs corresponding either to the polyproline II (collagen) helix and the α-helix or both. The β-strand was not strongly favoured energetically although the extent of this depression in the energy surface is, while not "deeper" (energetically), has a wider extent than the other two types of secondary structure. There is currently great interest in the question of cotranslational folding, the extent to which the nascent polypeptide begins to fold prior to emerging from the ribosome exit tunnel. Accordingly, while most previous quantum studies of dipeptides were carried out in the (simulated) gas or aqueous phase, we wished to consider the first step in polypeptide biosynthesis on the ribosome where neither gas nor aqueous conditions apply. We used a dielectric constant that would be compatible with the water-poor macromolecular (ribosome) environment.},
  articleno    = {668},
  author       = {Bywater, Robert P and Veryazov, Valera},
  issn         = {2193-1801},
  language     = {eng},
  publisher    = {Springer},
  series       = {SpringerPlus},
  title        = {The dipeptide conformations of all twenty amino acid types in the context of biosynthesis.},
  url          = {http://dx.doi.org/10.1186/s40064-015-1430-8},
  volume       = {4},
  year         = {2015},
}