On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22310%2F16%3A43902850" target="_blank" >RIV/60461373:22310/16:43902850 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/16:00458973 RIV/61388963:_____/16:00458973 RIV/00216224:14740/16:00090498 RIV/61989592:15310/16:33161265

Výsledek na webu

<a href="http://dx.doi.org/10.1016/j.bpj.2015.12.039" target="_blank" >http://dx.doi.org/10.1016/j.bpj.2015.12.039</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.bpj.2015.12.039" target="_blank" >10.1016/j.bpj.2015.12.039</a>

Jazyk výsledku

angličtina

Název v původním jazyce

On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA

Popis výsledku v původním jazyce

A recent study described an allosteric effect in which the binding of a protein to DNA is influenced by another protein bound nearby. The effect shows a periodicity of ?10 basepairs and decays with increasing protein-protein distance. As a mechanistic explanation, the authors reported a similar periodic, decaying pattern of the correlation coefficient between major groove widths inferred from a shorter molecular dynamics simulation. Here we show that in a state-of-the-art, microsecond-long simulation of the same DNA sequence, the periodicity of the correlation coefficient is not observed. To study the problem further, we extend an earlier mechanical model of DNA allostery based on constrained minimization of effective quadratic deformation energy of the DNA. We demonstrate that, if the constraints mimicking the bound proteins are properly applied, the periodicity in the binding energy is indeed recovered. ? 2016 Biophysical Society.

Název v anglickém jazyce

On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA

Popis výsledku anglicky

A recent study described an allosteric effect in which the binding of a protein to DNA is influenced by another protein bound nearby. The effect shows a periodicity of ?10 basepairs and decays with increasing protein-protein distance. As a mechanistic explanation, the authors reported a similar periodic, decaying pattern of the correlation coefficient between major groove widths inferred from a shorter molecular dynamics simulation. Here we show that in a state-of-the-art, microsecond-long simulation of the same DNA sequence, the periodicity of the correlation coefficient is not observed. To study the problem further, we extend an earlier mechanical model of DNA allostery based on constrained minimization of effective quadratic deformation energy of the DNA. We demonstrate that, if the constraints mimicking the bound proteins are properly applied, the periodicity in the binding energy is indeed recovered. ? 2016 Biophysical Society.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2016

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

BIOPHYSICAL JOURNAL

ISSN

0006-3495

e-ISSN

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Svazek periodika

110

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

3

Strana od-do

874-876

Kód UT WoS článku

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EID výsledku v databázi Scopus

2-s2.0-84959458120