Mechanical Model of DNA Allostery

J 2014

Mechanical Model of DNA Allostery

DRŠATA, Tomáš, Marie ZGARBOVÁ, Naděžda ŠPAČKOVÁ, Petr JUREČKA, Jiří ŠPONER et. al.

Basic information

Original name

Mechanical Model of DNA Allostery

Authors

DRŠATA, Tomáš (203 Czech Republic), Marie ZGARBOVÁ (203 Czech Republic), Naděžda ŠPAČKOVÁ (203 Czech Republic, belonging to the institution), Petr JUREČKA (203 Czech Republic), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution) and Filip LANKAŠ (203 Czech Republic)

Edition

Journal of Physical Chemistry Letters, Washington, American Chemical Society, 2014, 1948-7185

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 7.458

RIV identification code

RIV/00216224:14740/14:00077973

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/jz501826q

UT WoS

000344579500022

Keywords in English

MOLECULAR-DYNAMICS SIMULATIONS; MINOR-GROOVE BINDERS; PYRROLE-IMIDAZOLE POLYAMIDE; BASE-PAIR LEVEL; B-DNA; A-TRACTS; BINDING; DEFORMABILITY; PROTEIN; COMPLEXES

Abstract

V originále

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 to model allostery in various molecular systems. [GRAPHICS]

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Citovat

DRŠATA, Tomáš, Marie ZGARBOVÁ, Naděžda ŠPAČKOVÁ, Petr JUREČKA, Jiří ŠPONER and Filip LANKAŠ. Mechanical Model of DNA Allostery. Journal of Physical Chemistry Letters. Washington: American Chemical Society, 2014, vol. 5, No 21, p. 3831-3835. ISSN 1948-7185. Available from: https://dx.doi.org/10.1021/jz501826q.

@article{1214799,
   author = {Dršata, Tomáš and Zgarbová, Marie and Špačková, Naděžda and Jurečka, Petr and Šponer, Jiří and Lankaš, Filip},
   article_location = {Washington},
   article_number = {21},
   doi = {http://dx.doi.org/10.1021/jz501826q},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; MINOR-GROOVE BINDERS; PYRROLE-IMIDAZOLE POLYAMIDE; BASE-PAIR LEVEL; B-DNA; A-TRACTS; BINDING; DEFORMABILITY; PROTEIN; COMPLEXES},
   language = {eng},
   issn = {1948-7185},
   journal = {Journal of Physical Chemistry Letters},
   title = {Mechanical Model of DNA Allostery},
   url = {http://pubs.acs.org/doi/abs/10.1021/jz501826q},
   volume = {5},
   year = {2014}
}

TY  - JOUR
ID  - 1214799
AU  - Dršata, Tomáš - Zgarbová, Marie - Špačková, Naděžda - Jurečka, Petr - Šponer, Jiří - Lankaš, Filip
PY  - 2014
TI  - Mechanical Model of DNA Allostery
JF  - Journal of Physical Chemistry Letters
VL  - 5
IS  - 21
SP  - 3831-3835
EP  - 3831-3835
PB  - American Chemical Society
SN  - 19487185
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - MINOR-GROOVE BINDERS
KW  - PYRROLE-IMIDAZOLE POLYAMIDE
KW  - BASE-PAIR LEVEL
KW  - B-DNA
KW  - A-TRACTS
KW  - BINDING
KW  - DEFORMABILITY
KW  - PROTEIN
KW  - COMPLEXES
UR  - http://pubs.acs.org/doi/abs/10.1021/jz501826q
L2  - http://pubs.acs.org/doi/abs/10.1021/jz501826q
N2  - 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 to model allostery in various molecular systems. [GRAPHICS]
ER  -

DRŠATA, Tomáš, Marie ZGARBOVÁ, Naděžda ŠPAČKOVÁ, Petr JUREČKA, Jiří ŠPONER and Filip LANKAŠ. Mechanical Model of DNA Allostery. \textit{Journal of Physical Chemistry Letters}. Washington: American Chemical Society, 2014, vol.~5, No~21, p.~3831-3835. ISSN~1948-7185. Available from: https://dx.doi.org/10.1021/jz501826q.

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