TY - JOUR
T1 - Binding of proteins to the minor groove of DNA: What are the structural and energetic determinants for kinking a basepair step?
AU - Bosch, David
AU - Campillo, Mercedes
AU - Pardo, Leonardo
PY - 2003/4/30
Y1 - 2003/4/30
N2 - The structural and energetic determinants for kinking a basepair step by minor groove-insertion of the protein side chains of PurR, LacI, LEF-1, IHF, Sac7d, and Sso7d, have been calculated by molecular dynamics/potential of mean force simulations. The structural determinants of the kinked structures are: two contiguous furanose rings achieve different conformations, in the region of C3'endo (A-DNA) and C2'endo (B-DNA); the χ torsion angle always takes values characteristic of the C2'endo conformation of B-DNA, independently of sugar puckering; and protein side chain insertion increases slide (from negative to positive values), rise, and roll, and decreases twist. The energetic determinants of DNA kinking are: the conformational transition of the sugar-phosphate backbone is not energetically demanding; the relative importance of the interbase parameters in the free energy penalty is slide, followed by twist and rise, and concluding with shift and roll; and the characteristic increase of roll and decrease of twist, upon side chain insertion, tends to stabilize the process of DNA kinking. © 2003 Wiley Periodicals, Inc.
AB - The structural and energetic determinants for kinking a basepair step by minor groove-insertion of the protein side chains of PurR, LacI, LEF-1, IHF, Sac7d, and Sso7d, have been calculated by molecular dynamics/potential of mean force simulations. The structural determinants of the kinked structures are: two contiguous furanose rings achieve different conformations, in the region of C3'endo (A-DNA) and C2'endo (B-DNA); the χ torsion angle always takes values characteristic of the C2'endo conformation of B-DNA, independently of sugar puckering; and protein side chain insertion increases slide (from negative to positive values), rise, and roll, and decreases twist. The energetic determinants of DNA kinking are: the conformational transition of the sugar-phosphate backbone is not energetically demanding; the relative importance of the interbase parameters in the free energy penalty is slide, followed by twist and rise, and concluding with shift and roll; and the characteristic increase of roll and decrease of twist, upon side chain insertion, tends to stabilize the process of DNA kinking. © 2003 Wiley Periodicals, Inc.
KW - Minor groove-binding proteins
KW - Molecular dynamics
KW - Potential of mean force
KW - Protein-DNA interactions
U2 - https://doi.org/10.1002/jcc.10200
DO - https://doi.org/10.1002/jcc.10200
M3 - Article
VL - 24
SP - 682
EP - 691
JO - Journal of Computational Chemistry
JF - Journal of Computational Chemistry
SN - 0192-8651
ER -