Molecular simulations on the thermal stabilization of DNA by hyperthermophilic chromatin protein Sac7d, and associated conformational transitions

U. Deva Priyakumar, G. Harika, Suresh Gorle

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of DNA at higher growth temperatures. It is capable of binding DNA nonspecifically, and is responsible for the increase in the melting temperature of DNA in the bound form up to 85 °C. Molecular dynamics (MD) simulations were performed at different temperatures on two protein-DNA complexes of Sac7d. Various structural and energetic parameters were calculated to examine the DNA stability and to investigate the conformational changes in DNA and the protein-DNA interactions. Room temperature simulations indicated very good agreement with the experimental structures. The protein structure is nearly unchanged at both 300 and 360 K, and only up to five base pairs of the DNA are stabilized by Sac7d at 360 K. However, the MD simulations on DNA alone systems show that they lose their helical structures at 360 K further supporting the role of Sac7d in stabilizing the oligomers. At higher temperatures (420 and 480 K), DNA undergoes denaturation in the presence and the absence of the protein. The DNA molecules were found to undergo B- to A-form transitions consistent with experimental studies, and the extent of these transitions are examined in detail. The extent of sampling B- and A-form regions was found to show temperature and sequence dependence. Multiple MD simulations yielded similar results validating the proposed model. Interaction energy calculations corresponding to protein-DNA binding indicates major contribution due to DNA backbone, explaining the nonspecific interactions of Sac7d.

Original languageEnglish (US)
Pages (from-to)16548-16557
Number of pages10
JournalJournal of Physical Chemistry B
Volume114
Issue number49
DOIs
StatePublished - Dec 16 2010
Externally publishedYes

Fingerprint

chromatin
Chromatin
DNA
deoxyribonucleic acid
Stabilization
Hot Temperature
stabilization
proteins
Proteins
simulation
Temperature
Molecular Dynamics Simulation
Nucleic Acid Denaturation
Molecular dynamics
molecular dynamics
Computer simulation
DNA-Binding Proteins
Denaturation
Base Pairing
Growth temperature

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

Molecular simulations on the thermal stabilization of DNA by hyperthermophilic chromatin protein Sac7d, and associated conformational transitions. / Priyakumar, U. Deva; Harika, G.; Gorle, Suresh.

In: Journal of Physical Chemistry B, Vol. 114, No. 49, 16.12.2010, p. 16548-16557.

Research output: Contribution to journalArticle

@article{8a277ce6519b48779b0fd9a1dc2aa47f,
title = "Molecular simulations on the thermal stabilization of DNA by hyperthermophilic chromatin protein Sac7d, and associated conformational transitions",
abstract = "Sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of DNA at higher growth temperatures. It is capable of binding DNA nonspecifically, and is responsible for the increase in the melting temperature of DNA in the bound form up to 85 °C. Molecular dynamics (MD) simulations were performed at different temperatures on two protein-DNA complexes of Sac7d. Various structural and energetic parameters were calculated to examine the DNA stability and to investigate the conformational changes in DNA and the protein-DNA interactions. Room temperature simulations indicated very good agreement with the experimental structures. The protein structure is nearly unchanged at both 300 and 360 K, and only up to five base pairs of the DNA are stabilized by Sac7d at 360 K. However, the MD simulations on DNA alone systems show that they lose their helical structures at 360 K further supporting the role of Sac7d in stabilizing the oligomers. At higher temperatures (420 and 480 K), DNA undergoes denaturation in the presence and the absence of the protein. The DNA molecules were found to undergo B- to A-form transitions consistent with experimental studies, and the extent of these transitions are examined in detail. The extent of sampling B- and A-form regions was found to show temperature and sequence dependence. Multiple MD simulations yielded similar results validating the proposed model. Interaction energy calculations corresponding to protein-DNA binding indicates major contribution due to DNA backbone, explaining the nonspecific interactions of Sac7d.",
author = "Priyakumar, {U. Deva} and G. Harika and Suresh Gorle",
year = "2010",
month = "12",
day = "16",
doi = "10.1021/jp101583d",
language = "English (US)",
volume = "114",
pages = "16548--16557",
journal = "Journal of Physical Chemistry B Materials",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "49",

}

TY - JOUR

T1 - Molecular simulations on the thermal stabilization of DNA by hyperthermophilic chromatin protein Sac7d, and associated conformational transitions

AU - Priyakumar, U. Deva

AU - Harika, G.

AU - Gorle, Suresh

PY - 2010/12/16

Y1 - 2010/12/16

N2 - Sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of DNA at higher growth temperatures. It is capable of binding DNA nonspecifically, and is responsible for the increase in the melting temperature of DNA in the bound form up to 85 °C. Molecular dynamics (MD) simulations were performed at different temperatures on two protein-DNA complexes of Sac7d. Various structural and energetic parameters were calculated to examine the DNA stability and to investigate the conformational changes in DNA and the protein-DNA interactions. Room temperature simulations indicated very good agreement with the experimental structures. The protein structure is nearly unchanged at both 300 and 360 K, and only up to five base pairs of the DNA are stabilized by Sac7d at 360 K. However, the MD simulations on DNA alone systems show that they lose their helical structures at 360 K further supporting the role of Sac7d in stabilizing the oligomers. At higher temperatures (420 and 480 K), DNA undergoes denaturation in the presence and the absence of the protein. The DNA molecules were found to undergo B- to A-form transitions consistent with experimental studies, and the extent of these transitions are examined in detail. The extent of sampling B- and A-form regions was found to show temperature and sequence dependence. Multiple MD simulations yielded similar results validating the proposed model. Interaction energy calculations corresponding to protein-DNA binding indicates major contribution due to DNA backbone, explaining the nonspecific interactions of Sac7d.

AB - Sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of DNA at higher growth temperatures. It is capable of binding DNA nonspecifically, and is responsible for the increase in the melting temperature of DNA in the bound form up to 85 °C. Molecular dynamics (MD) simulations were performed at different temperatures on two protein-DNA complexes of Sac7d. Various structural and energetic parameters were calculated to examine the DNA stability and to investigate the conformational changes in DNA and the protein-DNA interactions. Room temperature simulations indicated very good agreement with the experimental structures. The protein structure is nearly unchanged at both 300 and 360 K, and only up to five base pairs of the DNA are stabilized by Sac7d at 360 K. However, the MD simulations on DNA alone systems show that they lose their helical structures at 360 K further supporting the role of Sac7d in stabilizing the oligomers. At higher temperatures (420 and 480 K), DNA undergoes denaturation in the presence and the absence of the protein. The DNA molecules were found to undergo B- to A-form transitions consistent with experimental studies, and the extent of these transitions are examined in detail. The extent of sampling B- and A-form regions was found to show temperature and sequence dependence. Multiple MD simulations yielded similar results validating the proposed model. Interaction energy calculations corresponding to protein-DNA binding indicates major contribution due to DNA backbone, explaining the nonspecific interactions of Sac7d.

UR - http://www.scopus.com/inward/record.url?scp=78650098369&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78650098369&partnerID=8YFLogxK

U2 - 10.1021/jp101583d

DO - 10.1021/jp101583d

M3 - Article

C2 - 21086967

AN - SCOPUS:78650098369

VL - 114

SP - 16548

EP - 16557

JO - Journal of Physical Chemistry B Materials

JF - Journal of Physical Chemistry B Materials

SN - 1520-6106

IS - 49

ER -