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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/8236000
- author
- Bywater, Robert P
and Veryazov, Valera
LU
- organization
- publishing date
- 2015
- type
- Contribution to journal
- publication status
- published
- subject
- in
- SpringerPlus
- volume
- 4
- article number
- 668
- publisher
- Springer Science and Business Media B.V.
- external identifiers
-
- pmid:26558171
- wos:000368704000002
- scopus:84946121362
- pmid:26558171
- ISSN
- 2193-1801
- DOI
- 10.1186/s40064-015-1430-8
- language
- English
- LU publication?
- yes
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)
- id
- 34e348c9-0756-4614-a6ad-0e77d2447157 (old id 8236000)
- date added to LUP
- 2016-04-01 13:14:48
- date last changed
- 2025-01-03 07:02:24
@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.}},
author = {{Bywater, Robert P and Veryazov, Valera}},
issn = {{2193-1801}},
language = {{eng}},
publisher = {{Springer Science and Business Media B.V.}},
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}},
doi = {{10.1186/s40064-015-1430-8}},
volume = {{4}},
year = {{2015}},
}