TUTCRIS - Tampereen teknillinen yliopisto

TUTCRIS

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

Tutkimustuotosvertaisarvioitu

Yksityiskohdat

AlkuperäiskieliEnglanti
Sivut11193-11201
Sivumäärä9
JulkaisuJournal of Physical Chemistry A
Vuosikerta115
Numero41
DOI - pysyväislinkit
TilaJulkaistu - 20 lokakuuta 2011
OKM-julkaisutyyppiA1 Alkuperäisartikkeli

Tiivistelmä

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.

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