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Like-charge guanidinium pairing from molecular dynamics and ab initio calculations

Tutkimustuotosvertaisarvioitu

Standard

Like-charge guanidinium pairing from molecular dynamics and ab initio calculations. / Vazdar, Mario; Vymětal, Jiři; Heyda, Jan; Vondrášek, Jiři; Jungwirth, Pavel.

julkaisussa: Journal of Physical Chemistry A, Vuosikerta 115, Nro 41, 20.10.2011, s. 11193-11201.

Tutkimustuotosvertaisarvioitu

Harvard

Vazdar, M, Vymětal, J, Heyda, J, Vondrášek, J & Jungwirth, P 2011, 'Like-charge guanidinium pairing from molecular dynamics and ab initio calculations', Journal of Physical Chemistry A, Vuosikerta. 115, Nro 41, Sivut 11193-11201. https://doi.org/10.1021/jp203519p

APA

Vazdar, M., Vymětal, J., Heyda, J., Vondrášek, J., & Jungwirth, P. (2011). Like-charge guanidinium pairing from molecular dynamics and ab initio calculations. Journal of Physical Chemistry A, 115(41), 11193-11201. https://doi.org/10.1021/jp203519p

Vancouver

Vazdar M, Vymětal J, Heyda J, Vondrášek J, Jungwirth P. Like-charge guanidinium pairing from molecular dynamics and ab initio calculations. Journal of Physical Chemistry A. 2011 loka 20;115(41):11193-11201. https://doi.org/10.1021/jp203519p

Author

Vazdar, Mario ; Vymětal, Jiři ; Heyda, Jan ; Vondrášek, Jiři ; Jungwirth, Pavel. / Like-charge guanidinium pairing from molecular dynamics and ab initio calculations. Julkaisussa: Journal of Physical Chemistry A. 2011 ; Vuosikerta 115, Nro 41. Sivut 11193-11201.

Bibtex - Lataa

@article{a7853287c23c42d3b46ce0c7a4e237c7,
title = "Like-charge guanidinium pairing from molecular dynamics and ab initio calculations",
abstract = "Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.",
author = "Mario Vazdar and Jiři Vymětal and Jan Heyda and Jiři Vondr{\'a}šek and Pavel Jungwirth",
year = "2011",
month = "10",
day = "20",
doi = "10.1021/jp203519p",
language = "English",
volume = "115",
pages = "11193--11201",
journal = "Journal of Physical Chemistry A",
issn = "1089-5639",
publisher = "American Chemical Society",
number = "41",

}

RIS (suitable for import to EndNote) - Lataa

TY - JOUR

T1 - Like-charge guanidinium pairing from molecular dynamics and ab initio calculations

AU - Vazdar, Mario

AU - Vymětal, Jiři

AU - Heyda, Jan

AU - Vondrášek, Jiři

AU - Jungwirth, Pavel

PY - 2011/10/20

Y1 - 2011/10/20

N2 - Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.

AB - Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.

UR - http://www.scopus.com/inward/record.url?scp=80054686180&partnerID=8YFLogxK

U2 - 10.1021/jp203519p

DO - 10.1021/jp203519p

M3 - Article

VL - 115

SP - 11193

EP - 11201

JO - Journal of Physical Chemistry A

JF - Journal of Physical Chemistry A

SN - 1089-5639

IS - 41

ER -