PubMed

Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

Moroni E, Caselle M, Fogolari F.

BMC Struct Biol. 2007 Sep 27;7:61.PMID: 17900341 [PubMed - indexed for MEDLINE]Related articlesFree article

Anatomy of specific interactions between lambda repressor and operator DNA.

Oobatake M, Kono H, Wang Y, Sarai A.

Proteins. 2003 Oct 1;53(1):33-43.PMID: 12945047 [PubMed - indexed for MEDLINE]Related articles

Free energy calculations for the relative binding affinity between DNA and lambda-repressor.

Saito M, Sarai A.

Proteins. 2003 Aug 1;52(2):129-36.PMID: 12833537 [PubMed - indexed for MEDLINE]Related articles

Empirical free energy calculations of phage 434 repressor- and cro-DNA complexes support the 'indirect readout' hypothesis of specificity.

Brown LM, Bruccoleri RE, Novotny J.

Pac Symp Biocomput. 1998:339-48.PMID: 9697194 [PubMed - indexed for MEDLINE]Related articlesFree article

Structure-based prediction of DNA target sites by regulatory proteins.

Kono H, Sarai A.

Proteins. 1999 Apr 1;35(1):114-31.PMID: 10090291 [PubMed - indexed for MEDLINE]Related articles

Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences.

Dixit SB, Andrews DQ, Beveridge DL.

Biophys J. 2005 May;88(5):3147-57. Epub 2005 Feb 24.PMID: 15731390 [PubMed - indexed for MEDLINE]Related articlesFree article

Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site.

Frank DE, Saecker RM, Bond JP, Capp MW, Tsodikov OV, Melcher SE, Levandoski MM, Record MT Jr.

J Mol Biol. 1997 Apr 18;267(5):1186-206.PMID: 9150406 [PubMed - indexed for MEDLINE]Related articles

Specificity, free energy and information content in protein-DNA interactions.

Stormo GD, Fields DS.

Trends Biochem Sci. 1998 Mar;23(3):109-13. Review.PMID: 9581503 [PubMed - indexed for MEDLINE]Related articles

Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding.

Selvaraj S, Kono H, Sarai A.

J Mol Biol. 2002 Oct 4;322(5):907-15.PMID: 12367517 [PubMed - indexed for MEDLINE]Related articles

Thermodynamic database for protein-nucleic acid interactions (ProNIT).

Prabakaran P, An J, Gromiha MM, Selvaraj S, Uedaira H, Kono H, Sarai A.

Bioinformatics. 2001 Nov;17(11):1027-34.PMID: 11724731 [PubMed - indexed for MEDLINE]Related articlesFree article

DNA sequence dependent and independent conformational changes in multipartite operator recognition by lambda-repressor.

Deb S, Bandyopadhyay S, Roy S.

Biochemistry. 2000 Mar 28;39(12):3377-83.PMID: 10727231 [PubMed - indexed for MEDLINE]Related articles

Spectroscopic studies on lambda cro protein-DNA interactions.

Torigoe C, Kidokoro S, Takimoto M, Kyogoku Y, Wada A.

J Mol Biol. 1991 Jun 20;219(4):733-46.PMID: 2056536 [PubMed - indexed for MEDLINE]Related articles

Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease.

Misra VK, Hecht JL, Sharp KA, Friedman RA, Honig B.

J Mol Biol. 1994 Apr 29;238(2):264-80.PMID: 8158653 [PubMed - indexed for MEDLINE]Related articles

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

Jayaram B, McConnell K, Dixit SB, Das A, Beveridge DL.

J Comput Chem. 2002 Jan 15;23(1):1-14.PMID: 11913374 [PubMed - indexed for MEDLINE]Related articles

Crystal structure of the lambda repressor and a model for pairwise cooperative operator binding.

Stayrook S, Jaru-Ampornpan P, Ni J, Hochschild A, Lewis M.

Nature. 2008 Apr 24;452(7190):1022-5.PMID: 18432246 [PubMed - indexed for MEDLINE]Related articles

Influence of DNA stiffness in protein-DNA recognition.

Gromiha MM.

J Biotechnol. 2005 May 4;117(2):137-45.PMID: 15823403 [PubMed - indexed for MEDLINE]Related articles

Repertoire selection of variant single-chain Cro: toward directed DNA-binding specificity of helix-turn-helix proteins.

Nilsson MT, Widersten M.

Biochemistry. 2004 Sep 28;43(38):12038-47.PMID: 15379544 [PubMed - indexed for MEDLINE]Related articles

Sequestered water and binding energy are coupled in complexes of lambda Cro repressor with non-consensus binding sequences.

Rau DC.

J Mol Biol. 2006 Aug 11;361(2):352-61. Epub 2006 Jun 30.PMID: 16828799 [PubMed - indexed for MEDLINE]Related articles

Molecular dynamics simulation in solvent of the bacteriophage 434 cI repressor protein DNA binding domain amino acids (R1-69) in complex with its cognate operator (OR1) DNA sequence.

Harris LF, Sullivan MR, Popken-Harris PD.

J Biomol Struct Dyn. 1999 Aug;17(1):1-17.PMID: 10496417 [PubMed - indexed for MEDLINE]Related articles

Structure, thermodynamics and cooperativity of the glucocorticoid receptor DNA-binding domain in complex with different response elements. Molecular dynamics simulation and free energy perturbation studies.

Eriksson MA, Nilsson L.

J Mol Biol. 1995 Oct 27;253(3):453-72.PMID: 7473727 [PubMed - indexed for MEDLINE]Related articles