Effect of DNA on the conformational dynamics of the endonucleases I-DmoI as provided by molecular dynamics simulations

Alessandro Grottesi; Simone Cecconi; Rafael Molina; Marco D'abramo

doi:10.1002/bip.22933

Effect of DNA on the conformational dynamics of the endonucleases I-DmoI as provided by molecular dynamics simulations

Alessandro Grottesi, Simone Cecconi, Rafael Molina, Marco D'abramo

Protein Structure and Function Program

1 Citation (Scopus)

Abstract

The conformational behavior of the wild-type endonucleases I-DmoI and two of its mutants has been studied in the presence and in the absence of DNA target sequences by means of extended molecular dynamics simulations. Our results show that in the absence of DNA, the three protein forms explore a similar essential conformational space, whereas when bound to the same DNA target sequence of 25 base pairs, they diversify and restrain the subspace explored. In addition, the differences in the essential subspaces explored by the residues near the catalytic site for both the bound and unbound forms are discussed in background of the experimental protein activity.

Original language	English
Journal	Biopolymers
Volume	105
Issue number	12
Pages (from-to)	898-904
Number of pages	7
ISSN	0006-3525
DOIs	https://doi.org/10.1002/bip.22933
Publication status	Published - 1 Dec 2016

Keywords

DNA/chemistry
Deoxyribonucleases, Type I Site-Specific/chemistry
Molecular Dynamics Simulation

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10.1002/bip.22933

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title = "Effect of DNA on the conformational dynamics of the endonucleases I-DmoI as provided by molecular dynamics simulations",

abstract = "The conformational behavior of the wild-type endonucleases I-DmoI and two of its mutants has been studied in the presence and in the absence of DNA target sequences by means of extended molecular dynamics simulations. Our results show that in the absence of DNA, the three protein forms explore a similar essential conformational space, whereas when bound to the same DNA target sequence of 25 base pairs, they diversify and restrain the subspace explored. In addition, the differences in the essential subspaces explored by the residues near the catalytic site for both the bound and unbound forms are discussed in background of the experimental protein activity. ",

keywords = "DNA/chemistry, Deoxyribonucleases, Type I Site-Specific/chemistry, Molecular Dynamics Simulation",

author = "Alessandro Grottesi and Simone Cecconi and Rafael Molina and Marco D'abramo",

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T1 - Effect of DNA on the conformational dynamics of the endonucleases I-DmoI as provided by molecular dynamics simulations

AU - Grottesi, Alessandro

AU - Cecconi, Simone

AU - Molina, Rafael

AU - D'abramo, Marco

PY - 2016/12/1

Y1 - 2016/12/1

N2 - The conformational behavior of the wild-type endonucleases I-DmoI and two of its mutants has been studied in the presence and in the absence of DNA target sequences by means of extended molecular dynamics simulations. Our results show that in the absence of DNA, the three protein forms explore a similar essential conformational space, whereas when bound to the same DNA target sequence of 25 base pairs, they diversify and restrain the subspace explored. In addition, the differences in the essential subspaces explored by the residues near the catalytic site for both the bound and unbound forms are discussed in background of the experimental protein activity.

AB - The conformational behavior of the wild-type endonucleases I-DmoI and two of its mutants has been studied in the presence and in the absence of DNA target sequences by means of extended molecular dynamics simulations. Our results show that in the absence of DNA, the three protein forms explore a similar essential conformational space, whereas when bound to the same DNA target sequence of 25 base pairs, they diversify and restrain the subspace explored. In addition, the differences in the essential subspaces explored by the residues near the catalytic site for both the bound and unbound forms are discussed in background of the experimental protein activity.

KW - DNA/chemistry

KW - Deoxyribonucleases, Type I Site-Specific/chemistry

KW - Molecular Dynamics Simulation

U2 - 10.1002/bip.22933

DO - 10.1002/bip.22933

M3 - Journal article

C2 - 27506595

SN - 0006-3525

VL - 105

SP - 898

EP - 904

JO - Biopolymers

JF - Biopolymers

IS - 12

ER -

Effect of DNA on the conformational dynamics of the endonucleases I-DmoI as provided by molecular dynamics simulations

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Keywords

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