Molecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator

scientific article published in October 2001

Molecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1002/1097-0282(20011005)59:4<205::AID-BIP1019>3.0.CO;2-4
P698PubMed publication ID11473347

P2093author name stringYoung MA
Beveridge DL
McConnell KJ
Kombo DC
P2860cites workCrystal structure of the nucleosome core particle at 2.8 A resolutionQ22122355
Refined 1.8 A crystal structure of the lambda repressor-operator complexQ27642126
Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-GQ27658049
Recognition of a DNA operator by the repressor of phage 434: a view at high resolutionQ27728537
Crystal structure of trp repressor/operator complex at atomic resolutionQ27728594
Crystal structure of a yeast TBP/TATA-box complexQ27732067
Co-crystal structure of TBP recognizing the minor groove of a TATA elementQ27732068
Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turnQ27734267
The interpretation of protein structures: Estimation of static accessibilityQ27860750
Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degreesQ28301788
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanesQ29397708
The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acidsQ29616630
Hydrogen bond stereochemistry in protein structure and functionQ30412768
Nucleic acids: theory and computer simulation, Y2K.Q30589123
DNA twisting and the affinity of bacteriophage 434 operator for bacteriophage 434 repressorQ33584037
A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvationQ33907726
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexesQ34129678
Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetricallyQ34299902
Atomic-level accuracy in simulations of large protein crystalsQ35743367
Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solutionQ36804416
Mechanism of action of the cro protein of bacteriophage lambdaQ37583399
NH2-terminal arm of phage lambda repressor contributes energy and specificity to repressor binding and determines the effects of operator mutationsQ37684293
The DNA binding arm of lambda repressor: critical contacts from a flexible regionQ44143743
Conserved residues make similar contacts in two repressor-operator complexesQ44497319
Analysis of local helix geometry in three B-DNA decamers and eight dodecamersQ46145638
Regulatory functions of the lambda repressor reside in the amino-terminal domain.Q47965220
The interaction of E. coli IHF protein with its specific binding sites.Q52065221
Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn.Q52237592
CRP-binding sites: evidence for two structural classes with 6-bp and 8-bp spacers.Q52391892
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic MoleculesQ55918670
DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 represserQ59027239
P433issue4
P407language of work or nameEnglishQ1860
P304page(s)205-225
P577publication date2001-10-01
P1433published inBiopolymersQ15767528
P1476titleMolecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator
P478volume59

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cites work (P2860)
Q34190132Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences
Q47349119Microscopic understanding of the conformational features of a protein-DNA complex.

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