Molecular dynamics of the frame-shifting pseudoknot from beet
western yellows virus: The role of non- Watson-Crick
base-pairing, ordered hydration, cation binding and base
mutations on stability and unfolding

J 2001

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non- Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding

CSASZAR, Kristina; Naděžda ŠPAČKOVÁ; Richard ŠTEFL; Jiří ŠPONER; Neocles B. LEONTIS et. al.

Základní údaje

Originální název

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non- Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding

Autoři

CSASZAR, Kristina; Naděžda ŠPAČKOVÁ (203 Česká republika); Richard ŠTEFL (203 Česká republika); Jiří ŠPONER (203 Česká republika, garant) a Neocles B. LEONTIS

Vydání

Journal of Molecular Biology, London, Academic Press, 2001, 0022-2836

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10610 Biophysics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 5.826

Kód RIV

RIV/00216224:14310/01:00005555

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

molecular dynamics simulation; pseudoknot; non-Watson-Crick; base-pairs; beet western yellows virus

Štítky

BASE-PAIRS, beet western yellows virus, molecular dynamics simulation, non-Watson-Crick, pseudoknot

Změněno: 26. 1. 2007 17:17, prof. Mgr. Richard Štefl, Ph.D.

Anotace

V originále

Molecular dynamics simulations of the frame-shifting pseudoknot from beet western yellows virus (BWYV, NDB file UR0004) were performed with explicit inclusion of solvent and counterions. In all, 33 ns of simulation were carried out, including 10 ns of the native structure with protonation of the crucial cytosine residue, C8(N3+). The native structure exhibited stable trajectories retaining all Watson-Crick and tertiary base-pairs, except for fluctuations or transient disruptions at spec most significant fluctuations involved the change or disruption of hydrogen-bonding between C8(N3+) and bases G12, A25, and C26, as well as disruption of the water bridges linking C8(N3+) with A25 and C26. The simulations revealed several critical, highly ordered hydration sites with close to 100% occupancies and residency times of individual water molecules of up to 5 ns. Sodium cation coordination sites with occupancies above 50% were also observed.

Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

Citovat

CSASZAR, Kristina; Naděžda ŠPAČKOVÁ; Richard ŠTEFL; Jiří ŠPONER a Neocles B. LEONTIS. Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non- Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding. Journal of Molecular Biology. London: Academic Press, 2001, roč. 313, č. 5, s. 1073-1091. ISSN 0022-2836.

@article{399756,
   author = {Csaszar, Kristina and Špačková, Naděžda and Štefl, Richard and Šponer, Jiří and Leontis, Neocles B.},
   article_location = {London},
   article_number = {5},
   keywords = {molecular dynamics simulation; pseudoknot; non-Watson-Crick; base-pairs; beet western yellows virus},
   language = {eng},
   issn = {0022-2836},
   journal = {Journal of Molecular Biology},
   title = {Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non- Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding},
   volume = {313},
   year = {2001}
}

TY  - JOUR
ID  - 399756
AU  - Csaszar, Kristina - Špačková, Naděžda - Štefl, Richard - Šponer, Jiří - Leontis, Neocles B.
PY  - 2001
TI  - Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non- Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding
JF  - Journal of Molecular Biology
VL  - 313
IS  - 5
SP  - 1073
EP  - 1073
PB  - Academic Press
SN  - 00222836
KW  - molecular dynamics simulation
KW  - pseudoknot
KW  - non-Watson-Crick
KW  - base-pairs
KW  - beet western yellows virus
N2  - Molecular dynamics simulations of the frame-shifting pseudoknot from beet western yellows virus (BWYV, NDB file UR0004) were performed with explicit inclusion of solvent and counterions. In all, 33 ns of simulation were carried out, including 10 ns of the native structure with protonation of the crucial cytosine residue, C8(N3+). The native structure exhibited stable trajectories retaining all Watson-Crick and tertiary base-pairs, except for fluctuations or transient disruptions at spec most significant fluctuations involved the change or disruption of hydrogen-bonding between C8(N3+) and bases G12, A25, and C26, as well as disruption of the water bridges linking C8(N3+) with A25 and C26. The simulations revealed several critical, highly ordered hydration sites with close to 100% occupancies and residency times of individual water molecules of up to 5 ns. Sodium cation coordination sites with occupancies above 50% were also observed.
ER  -

CSASZAR, Kristina; Naděžda ŠPAČKOVÁ; Richard ŠTEFL; Jiří ŠPONER a Neocles B. LEONTIS. Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non- Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding. \textit{Journal of Molecular Biology}. London: Academic Press, 2001, roč.~313, č.~5, s.~1073-1091. ISSN~0022-2836.

Přehled o publikaci