Mechanical Model of DNA Allostery

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F14%3A10287355" target="_blank" >RIV/00216208:11310/14:10287355 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/14:00437506 RIV/61388963:_____/14:00437506 RIV/00216224:14740/14:00077973 RIV/61989592:15310/14:33152185

Výsledek na webu

<a href="http://dx.doi.org/10.1021/jz501826q" target="_blank" >http://dx.doi.org/10.1021/jz501826q</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/jz501826q" target="_blank" >10.1021/jz501826q</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Mechanical Model of DNA Allostery

Popis výsledku v původním jazyce

The importance of allosteric effects in DNA is becoming increasingly appreciated, but the underlying mechanisms remain poorly understood. In this work, we propose a general modeling framework to study DNA allostery. We describe DNA in a coarse-grained manner by intra-base pair and base pair step coordinates, complemented by groove widths. Quadratic deformation energy is assumed, yielding linear relations between the constraints and their effect. Model parameters are inferred from standard unrestrained,explicit-solvent molecular dynamics simulations of naked DNA. We applied the approach to study minor groove binding of diamidines and pyrrole-imidazole polyamides. The predicted DNA bending is in quantitative agreement with experiment and suggests that diamidine binding to the alternating TA sequence brings the DNA closer to the A-tract conformation, with potentially important functional consequences. The approach can be readily applied to other allosteric effects in DNA and generalized

Název v anglickém jazyce

Mechanical Model of DNA Allostery

Popis výsledku anglicky

The importance of allosteric effects in DNA is becoming increasingly appreciated, but the underlying mechanisms remain poorly understood. In this work, we propose a general modeling framework to study DNA allostery. We describe DNA in a coarse-grained manner by intra-base pair and base pair step coordinates, complemented by groove widths. Quadratic deformation energy is assumed, yielding linear relations between the constraints and their effect. Model parameters are inferred from standard unrestrained,explicit-solvent molecular dynamics simulations of naked DNA. We applied the approach to study minor groove binding of diamidines and pyrrole-imidazole polyamides. The predicted DNA bending is in quantitative agreement with experiment and suggests that diamidine binding to the alternating TA sequence brings the DNA closer to the A-tract conformation, with potentially important functional consequences. The approach can be readily applied to other allosteric effects in DNA and generalized

Druh

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

CEP obor

BO - Biofyzika

OECD FORD obor

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Projekt

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

Návaznosti

S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2014

Kód důvěrnosti údajů

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

Název periodika

Journal of Physical Chemistry Letters

ISSN

1948-7185

e-ISSN

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Svazek periodika

5

Číslo periodika v rámci svazku

21

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

5

Strana od-do

3831-3835

Kód UT WoS článku

000344579500022

EID výsledku v databázi Scopus

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