(Q38324155)

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Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis

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Europe PubMed Central

PubMed publication ID

2 September 2017

Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis (English)

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Europe PubMed Central

PubMed publication ID

2 September 2017

author name string

Lin Chen

1

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Europe PubMed Central

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2 September 2017

Qing-Chuan Zheng

2

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Europe PubMed Central

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2 September 2017

Li-Ying Yu

3

1 reference

Europe PubMed Central

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2 September 2017

Wen-Ting Chu

4

1 reference

Europe PubMed Central

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2 September 2017

Ji-Long Zhang

5

1 reference

Europe PubMed Central

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2 September 2017

Qiao Xue

6

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Europe PubMed Central

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2 September 2017

Hong-Xing Zhang

7

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Europe PubMed Central

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2 September 2017

Chia-Chung Sun

8

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Europe PubMed Central

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2 September 2017

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publication date

26 June 2012

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Europe PubMed Central

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2 September 2017

Journal of Biomolecular Structure and Dynamics

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Europe PubMed Central

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2 September 2017

30

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Europe PubMed Central

PubMed publication ID

2 September 2017

6

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

716-727

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

Nucleotide sequence of a gene encoding a histone-like protein in the archaeon Methanococcus voltae

1 reference

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21 January 2018

Generalized born models of macromolecular solvation effects

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

DNA-binding surface of the Sso7d protein from Sulfolobus solfataricus.

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Isolation, characterization and microsequence analysis of a small basic methylated DNA-binding protein from the Archaebacterium, Sulfolobus solfataricus.

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Partial B-to-A DNA transition upon minor groove binding of protein Sac7d monitored by Raman spectroscopy

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Highly stable binding proteins derived from the hyperthermophilic Sso7d scaffold.

1 reference

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21 January 2018

Energetics of Sequence-Specific Protein−DNA Association: Computational Analysis of Integrase Tn916 Binding to Its Target DNA

1 reference

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21 January 2018

Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

1 reference

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21 January 2018

Cooperative binding of DNA and CBFbeta to the Runt domain of the CBFalpha studied via MD simulations.

1 reference

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21 January 2018

Biochemical characterization of DNA-binding proteins from Pyrobaculum aerophilum and Aeropyrum pernix

1 reference

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21 January 2018

Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

VMD: visual molecular dynamics

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level.

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Thermal unfolding of the DNA-binding protein Sso7d from the hyperthermophile Sulfolobus solfataricus.

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Conformational Analysis of Genotoxic Benzo[a]pyrene-7,8-dione-Duplex DNA Adducts Using a Molecular Dynamics Method (II)

1 reference

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21 January 2018

Cooperativity and specificity of Cys2His2 zinc finger protein-DNA interactions: a molecular dynamics simulation study

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

In vitro DNA binding of the archaeal protein Sso7d induces negative supercoiling at temperatures typical for thermophilic growth.

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

An overview of the structures of protein-DNA complexes

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Molecular dynamics simulations of nucleic acid-protein complexes.

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

The 5-methyl group in thymine dynamically influences the structure of A-tracts in DNA at the local and global level

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Gene cloning, expression, and characterization of the Sac7 proteins from the hyperthermophile Sulfolobus acidocaldarius.

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Structural and dynamic effects of alpha-helix deletion in Sso7d: implications for protein thermal stability

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

A theoretical elucidation of glucose interaction with HSA's domains.

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Terminal Base Pairs of Oligodeoxynucleotides: Imino Proton Exchange and Fraying

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Thermodynamics of DNA binding and distortion by the hyperthermophile chromatin protein Sac7d

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Role of hydrophobic core on the thermal stability of proteins - molecular dynamics simulations on a single point mutant of Sso7d abstract

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Molecular Simulations on the Thermal Stabilization of DNA by Hyperthermophilic Chromatin Protein Sac7d, and Associated Conformational Transitions

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

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21 January 2018

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2012.689702

21 January 2018

Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching

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Influence of the Acetylcholinesterase Active Site Protonation on Omega Loop and Active Site Dynamics

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Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding

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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

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21 January 2018

Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus

1 reference

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21 January 2018

Salt Dependence of the Free Energy, Enthalpy, and Entropy of Nonsequence Specific DNA Binding

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21 January 2018

Identifiers

10.1080/07391102.2012.689702

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

2 September 2017

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