-
1
-
-
0033573827
-
Structural features of protein-nucleic acid recognition sites
-
Nadassy,K.,Wodak,S.J.,andJanin,J.(1999)Structuralfeaturesofprotein- nucleicacidrecognitionsites,Biochemistry38,1999-2017.(Pubitemid129506282)
-
(1999)
Biochemistry
, vol.38
, Issue.7
, pp. 1999-2017
-
-
Nadassy, K.1
Wodak, S.J.2
Janin, J.3
-
2
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B., and Nicholls, A. (1995) Classical electrostatics in biology and chemistry. Science 268, 1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
3
-
-
0035800599
-
Structure-based analysis of protein-RNA interactions using the program ENTANGLE
-
DOI 10.1006/jmbi.2001.4857
-
3. Allers, J., and Shamoo, Y. (2001) Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J. Biol. Biol. 311, 75-86. (Pubitemid 32735315)
-
(2001)
Journal of Molecular Biology
, vol.311
, Issue.1
, pp. 75-86
-
-
Allers, J.1
Shamoo, Y.2
-
4
-
-
0025264701
-
Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids
-
Mascotti, D. P., and Lohman, T. M. (1990) Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids. Proc. Natl. Acad. Sci. U.S.A. 87, 3146.
-
(1990)
Proc. Natl. Acad. Sci. U.S.A.
, vol.87
, pp. 3146
-
-
Mascotti, D.P.1
Lohman, T.M.2
-
5
-
-
0027379588
-
Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition
-
Mascotti, D. P., and Lohman, T. M. (1993) Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition, Biochemistry 32, 10568-10579.
-
(1993)
Biochemistry
, vol.32
, pp. 10568-10579
-
-
Mascotti, D.P.1
Lohman, T.M.2
-
6
-
-
0026730188
-
Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan
-
Mascotti, D. P., and Lohman, T. M. (1992) Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan. Biochemistry 31, 8932-8946.
-
(1992)
Biochemistry
, vol.31
, pp. 8932-8946
-
-
Mascotti, D.P.1
Lohman, T.M.2
-
7
-
-
0019330787
-
Pentalysine-deoxyribonucleic acid interactions: A model for the general effects of ion concentrations on the interactions of proteins with nucleic acids
-
Lohman, T. M., deHaseth, P. L., and Record, M. T., Jr. (1980) Pentalysine-deoxyribonucleic acid interactions: a model for the general effects of ion concentrations on the interactions of proteins with nucleic acids, Biochemistry 19, 3522-3530.
-
(1980)
Biochemistry
, vol.19
, pp. 3522-3530
-
-
Lohman, T.M.1
Dehaseth, P.L.2
Record Jr., M.T.3
-
8
-
-
0017146579
-
Ion. effects on ligand-nucleic acid, interactions.
-
Record, M. T., Jr., Lohman, T. M., and deHaseth, P. (1976) Ion. effects on ligand-nucleic acid, interactions. .J. Mol. Biol. 107, 145-158.
-
(1976)
J.Mol. Biol.
, vol.107
, pp. 145-158
-
-
Record Jr., M.T.1
Lohman, T.M.2
Dehaseth, P.3
-
9
-
-
0014144576
-
Protein-nucleic acid interactions. II. Oligopeptide-polyribonucleotide binding studies
-
Latt, S. A., and Sober, H. A. (1967) Protein-nucleic acid interactions. II. Oligopeptide-polyribonucleotide binding studies, Biochemistry 6, 3293-3306.
-
(1967)
Biochemistry
, vol.6
, pp. 3293-3306
-
-
Latt, S.A.1
Sober, H.A.2
-
10
-
-
0014144513
-
Protein-nucleic acid interactions. III. Cation effect on. binding strength and specificity
-
Latt, S. A., and Sober, H. A. (1967) Protein-nucleic acid interactions. III. Cation effect on. binding strength and specificity, Biochemistry 6, 3307-3314.
-
(1967)
Biochemistry
, vol.6
, pp. 3307-3314
-
-
Latt, S.A.1
Sober, H.A.2
-
11
-
-
0019399694
-
Interactions of oligopeptides with nucleic acids
-
Helene, C., and Maurizot, J. C. (1981) Interactions of oligopeptides with nucleic acids. CRC Crit. Rev. Biochem. 10, 213-258.
-
(1981)
CRC Crit. Rev. Biochem.
, vol.10
, pp. 213-258
-
-
Helene, C.1
Maurizot, J.C.2
-
12
-
-
0020012345
-
Interactions between functional groups in protein-nucleic acids associations
-
Helene, C., and Lancelot, G. (1982) Interactions between functional groups in protein-nucleic acids associations, Prog. Biophys. Mol. Biol. 39, 1-68.
-
(1982)
Prog. Biophys. Mol. Biol.
, vol.39
, pp. 1-68
-
-
Helene, C.1
Lancelot, G.2
-
13
-
-
0030920231
-
Thermodynamics of oligoarginines binding to RNA and DNA
-
DOI 10.1021/bi970272n
-
Mascotti, D. P., and Lohman, T. M. (1997) Thermodynamics of oligoarginines binding to RNA and DNA. Biochemistry 36, 7272-7279. (Pubitemid 27258144)
-
(1997)
Biochemistry
, vol.36
, Issue.23
, pp. 7272-7279
-
-
Mascotti, D.P.1
Lohman, T.M.2
-
14
-
-
0025914242
-
Crystal structure of a CAP-DNA complex: The DNA is bent by 90°
-
Schultz,S.C.,Shields,G.C.,andSteitz,T.A.(1991)CrystalstructureofaCAP- DNAcomplex-theDNAisbentby90°.Science253,1001-1007.(Pubitemid21917242)
-
(1991)
Science
, vol.253
, Issue.5023
, pp. 1001-1007
-
-
Schultz, S.C.1
Shields, G.C.2
Steitz, T.A.3
-
15
-
-
0030593510
-
Structure of the CAP-DNA complex at 2.5 A resolution: A complete picture of the protein-DNA interface
-
DOI 10.1006/jmbi.1996.0409
-
Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y. W., Ebright, R. E., and Berman, H. M. (1996) Structure of the CAP-DNA complex at 2.5 Å resolution: A complete picture of the protein-DNA interface. J. Biol. Biol. 260, 395-408. (Pubitemid 26254119)
-
(1996)
Journal of Molecular Biology
, vol.260
, Issue.3
, pp. 395-408
-
-
Parkinson, G.1
Wilson, C.2
Gunasekera, A.3
Ebright, Y.W.4
Ebright, R.E.5
Berman, H.M.6
-
16
-
-
0028979476
-
Structure of the NF-/cB p50 homodimer bound to DNA
-
Muller, C. W., Rey, F. A., Sodeoka, M., Verdine, G. L., and Harrison, S. C. (1995) Structure of the NF-/cB p50 homodimer bound to DNA. Naure 373, 311-317.
-
(1995)
Naure
, vol.373
, pp. 311-317
-
-
Muller, C.W.1
Rey, F.A.2
Sodeoka, M.3
Verdine, G.L.4
Harrison, S.C.5
-
17
-
-
0032518398
-
Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution
-
DOI 10.1038/34593
-
Doublie, S., Tabor, S., Long, A. M., Richardson, C. C., and Ellenberger, T. (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Â resolution. Nature 391, 251-258. (Pubitemid 28099004)
-
(1998)
Nature
, vol.391
, Issue.6664
, pp. 251-258
-
-
Doublie, S.1
Tabor, S.2
Long, A.M.3
Richardson, C.C.4
Ellenberger, T.5
-
18
-
-
0025780755
-
Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA
-
Luisi,B.F.,Xu,W.X.,Otwinowski,Z.,Freedman,L.P.,Yamamoto,K.R.,andSigler,P. B.(1991)Crystallographyanalysisoftheinteraction, oftheglucocorticoidreceptorwithDNA.Nature352,497-505.(Pubitemid21912367)
-
(1991)
Nature
, vol.352
, Issue.6335
, pp. 497-505
-
-
Luisi, B.F.1
Xu, W.X.2
Otwinowski, Z.3
Freedman, L.P.4
Yamamoto, K.R.5
Sigler, P.B.6
-
19
-
-
32244436130
-
Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p
-
DOI 10.1038/nsmb1053, PII NSMB1053
-
Aviv, T., Lin, Z., Ben-Ari, G., Smibert, C. A., and Sicheri, F. (2006) Sequence-specific recognition of RNA hairpins by the SAM domain of Vtslp. Nat. Struct. Mol. Biol. 13, 168-176. (Pubitemid 43214721)
-
(2006)
Nature Structural and Molecular Biology
, vol.13
, Issue.2
, pp. 168-176
-
-
Aviv, T.1
Lin, Z.2
Ben-Ari, G.3
Smibert, C.A.4
Sicheri, F.5
-
20
-
-
0028947982
-
Deoxynucleoside triphosphate and pyrophosphate binding-sites in the catalytically competent ternary complex for the polymerase reaction, catalyzed by DNA-Polymerase-I (Kienow fragment)
-
Astatke, M., Grindley, N. D. F., and Joyce, C. M. (1995) Deoxynucleoside triphosphate and pyrophosphate binding-sites in the catalytically competent ternary complex for the polymerase reaction, catalyzed by DNA-Polymerase-I (Kienow fragment). J. Biol. Chem. 270, 1945-1954.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 1945-1954
-
-
Astatke, M.1
Grindley, N.D.F.2
Joyce, C.M.3
-
21
-
-
0035942348
-
Contribution of the active site histidine residues of ribonuclease A to nucleic acid binding
-
DOI 10.1021/bi0100182
-
21. Park, C., Schultz, L. W., and Raines, R. T. (2001) Contribution of the active site histidine residues of ribonuclease A to nucleic acid binding. Biochemistry 40, 4949-4956. (Pubitemid 32332540)
-
(2001)
Biochemistry
, vol.40
, Issue.16
, pp. 4949-4956
-
-
Park, C.1
Schultz, L.W.2
Raines, R.T.3
-
22
-
-
33845865515
-
Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction
-
DOI 10.1093/nar/gkl819
-
22. Kim, O. T. P., Yura, K., and Go, N. (2006) Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction, Nucleic Acids Res. 34, 6450-6460. (Pubitemid 46017942)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.22
, pp. 6450-6460
-
-
Kim, O.T.P.1
Yura, K.2
Go, N.3
-
23
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe, N. M., Laskowski, R. A., and Thornton, J. M. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level, Nucleic Acids Res. 29, 2860-2874.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
24
-
-
0032125578
-
Synthesis and hybridization analysis of a small library of peptide-oligonucleotide conjugates
-
Harrison, J. G., and Balasubramanian, S. (1998) Synthesis and hybridization analysis of a small library of peptide-oligonucleotide conjugates, Nucleic Acids Res. 26, 3136-3145.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 3136-3145
-
-
Harrison, J.G.1
Balasubramanian, S.2
-
25
-
-
0034254242
-
Sequence-specific DNA binding by the glucocorticoid receptor DNA-binding domain is linked to a salt-dependent histidine protonation
-
DOI 10.1021/bi000231i
-
25. Lundback, T., van den. Berg, S., and Hard, T. (2000) Sequence-specific DNA binding by the glucocorticoid receptor DNA-binding domain is linked to a salt-dependent histidine protonation. Biochemistry 39, 8909-8916. (Pubitemid 30602801)
-
(2000)
Biochemistry
, vol.39
, Issue.30
, pp. 8909-8916
-
-
Lundback, T.1
Van Den Berg, S.2
Hard, T.3
-
26
-
-
0017701075
-
Nonspecific interaction of lac repressor with DNA: An association reaction driven by counterion release
-
deHaseth, P. L., Lohman, T. M., and Record, M. T., Jr. (1977) Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release, Biochemistry 16, 4783-4790.
-
(1977)
Biochemistry
, vol.16
, pp. 4783-4790
-
-
Dehaseth, P.L.1
Lohman, T.M.2
Record Jr., M.T.3
-
27
-
-
2642580884
-
T antigen origin-binding domain of simian virus 40: Determinants of specific DNA binding
-
DOI 10.1021/bi030228+
-
27. Bradshaw, E. M., Sanford, D. G., Luo, X., Sudmeier, J. L., GurardLevin, Z. A., Bullock, P. A., and Bachovchin, W. W. (2004) T antigen origin-binding domain of Simian Virus 40: determinants of specific DNA binding, BIochemistry 43, 6928-6936. (Pubitemid 38720511)
-
(2004)
Biochemistry
, vol.43
, Issue.22
, pp. 6928-6936
-
-
Bradshaw, E.M.1
Sanford, D.G.2
Luo, X.3
Sudmeier, J.L.4
Gurard-Levin, Z.A.5
Bullock, P.A.6
Bachovchin, W.W.7
-
28
-
-
64049119694
-
Indirect DNA readout on the protein side: Coupling between histidine protonation, global structural cooperativity, dynamics, and DNA binding of the human papillomavirus type 16 E2C domain
-
Eliseo, T., Sánchez, I. E., Ňadra, A., D., Dellarole, M., Paci, M., de Prat Gay, G., and Cicero, D. O. (2009) Indirect DNA readout on the protein side: coupling between histidine protonation, global structural cooperativity, dynamics, and DNA binding of the human papillomavirus type 16 E2C domain. J. Biol. Biol. 388, 327-344.
-
(2009)
J. Biol. Biol.
, vol.388
, pp. 327-344
-
-
Eliseo, T.1
Sánchez, I.E.2
Ňadra, A.D.3
Dellarole, M.4
Paci, M.5
De Prat Gay, G.6
Cicero, D.O.7
-
29
-
-
1042298819
-
Heat Capacity Effects of Water Molecules and Ions at a Protein-DNA Interface
-
DOI 10.1016/j.jmb.2003.12.061
-
29. Bergqvist, S., Williams, M. A., O'Brien, R., and Ladbury, J. E. (2004) Heat capacity effects of water molecules and ions at a protein-DNA interface. J. Biol. Biol. 336, 829-842. (Pubitemid 38201534)
-
(2004)
Journal of Molecular Biology
, vol.336
, Issue.4
, pp. 829-842
-
-
Bergqvist, S.1
Williams, M.A.2
O'Brien, R.3
Ladbury, J.E.4
-
30
-
-
0016175370
-
Theoretical aspects of DNA-protein interactions: Cooperative and non-cooperative binding of large ligands to a one-dimensional homogeneous lattice
-
McGhee J. D., and von Hippel, P. H. (1974) Theoretical aspects of DNA-protein interactions: cooperative and non-cooperative binding of large ligands to a one-dimensional homogeneous lattice. J.Biol. Biol. 86, 469-489.
-
(1974)
J.Biol. Biol.
, vol.86
, pp. 469-489
-
-
McGhee, J.D.1
Von Hippel, P.H.2
-
31
-
-
0023914505
-
Equilibrium dialysis study of binding of hexammine cobalt(III) to DNA
-
31.Plum,G.E.,andBloomfield,V.A.(1988) Equilibriumdialysisstudyofbindingofhexamminecobalt(III)-DNA.BIopolymers27, 1045-1051.(Pubitemid18146606)
-
(1988)
Biopolymers
, vol.27
, Issue.6
, pp. 1045-1051
-
-
Plum, G.E.1
Bloomfield, V.A.2
-
32
-
-
0019942441
-
Equilibrium dialysis studies of polyamine binding to DNA
-
Braunlin, W. H., Strick, T. J., and Record, M. T., Jr. (1982) Equilibrium dialysis studies of polyamine binding to DNA. Biopolymers 21, 1301-1314.
-
(1982)
Biopolymers
, vol.21
, pp. 1301-1314
-
-
Braunlin, W.H.1
Strick, T.J.2
Record Jr., M.T.3
-
33
-
-
0024403429
-
Negative co-operativity in Escherichia coli single strand binding protein-oligonucleotide interactions. I. Evidence and a quantitative model
-
DOI 10.1016/0022-2836(89)90454-3
-
33. Bujalowski, W., and Lohman, T. M. (1989) Negative cooperativity in Escherichia coli single strand binding protein-oli.gonucleoti.de interactions: I. Evidence and a quantitative model. J. Biol. Biol. 207, 249-268. (Pubitemid 19141255)
-
(1989)
Journal of Molecular Biology
, vol.207
, Issue.1
, pp. 249-268
-
-
Bujalowski, W.1
Lohman, T.M.2
-
34
-
-
0030917624
-
Binding of cationic (+4) alanine- And glycine-containing oligopeptides to double-stranded DNA: Thermodynamic analysis of effects of Coulombic interactions and a-helix induction
-
Padmanabhan, S., Zhang, W., Capp, M. W., Anderson, C. F., and Record, M. T., Jr. (1997) Binding of cationic (+4) alanine- and glycine-containing oligopeptides to double-stranded DNA: thermodynamic analysis of effects of Coulombic interactions and a-helix induction, Biochemistry 36, 5193-5206.
-
(1997)
Biochemistry
, vol.36
, pp. 5193-5206
-
-
Padmanabhan, S.1
Zhang, W.2
Capp, M.W.3
Anderson, C.F.4
Record Jr., M.T.5
-
35
-
-
0029864013
-
Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA
-
Zhang, W., Bond, J. P., Anderson, C. F., Lohman, T. M., and Record, M. T., Jr. (1996) Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA. Proe. Natl. Acad. Sci. U.S.A. 93, 2511-2516.
-
(1996)
Proe. Natl. Acad. Sci. U.S.A.
, vol.93
, pp. 2511-2516
-
-
Zhang, W.1
Bond, J.P.2
Anderson, C.F.3
Lohman, T.M.4
Record Jr., M.T.5
-
36
-
-
0031776135
-
Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilbiria and processes: A practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts
-
36.Record,M.T.,Jr.,Zhang,W.,andAnderson,C.F.(1998) Analysisofeffectsofsaltsandunchargedsolutesonproteinandnucleicacid equilibriaandprocesses:apractical,guide- recognizingandinterpretingpolyelectrolyteeffects,Hofmeistereffects, andosmoticeffectsofsalts,Adv.ProteinChem.51,281-353.(Pubitemid28252476)
-
(1998)
Advances in Protein Chemistry
, vol.51
, pp. 281-353
-
-
Record Jr., M.T.1
Zhang, W.2
Anderson, C.F.3
-
37
-
-
0018196563
-
Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions
-
Epstein, I. R. (1978) Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions, Biophys. Chem. 8, 327-339.
-
(1978)
Biophys. Chem.
, vol.8
, pp. 327-339
-
-
Epstein, I.R.1
-
38
-
-
20444458780
-
-) exclusion, in mixed salt solutions of polyanionic DNA using Monte Carlo and Poisson-Boltzmann calculations of ionpolyion preferential interaction coefficients
-
-) exclusion, in mixed salt solutions of polyanionic DNA using Monte Carlo and Poisson-Boltzmann calculations of ionpolyion preferential interaction coefficients. J. Phys. Chem. B 103, 3489-3504.
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 3489-3504
-
-
Ni, H.H.1
Anderson, C.F.2
Record Jr., M.T.3
-
39
-
-
0030932899
-
Competitive electrostatic binding of charged ligands to polyelectrolytes: Practical approach using the non-linear Poisson-Boltzmann equation
-
DOI 10.1016/S0301-4622(96)02231-4, PII S0301462296022314
-
39. Rouzina, I., and Bloomfield, V. A. (1997) Competitive electrostatic binding of charged ligands to polyelectrolytes: Practical approach, using the nonlinear Poisson-Boltzmann equation, Biophys. Chem. 64, 139-155. (Pubitemid 27148664)
-
(1997)
Biophysical Chemistry
, vol.64
, Issue.1-3
, pp. 139-155
-
-
Rouzina, I.1
Bloomfield, V.A.2
-
40
-
-
0030572245
-
Macroion attraction due to electrostatic correlation between screening counterions. 1. Mobile surface-adsorbed ions and diffuse ion cloud
-
40.Rouzina,I.,andBloomfield,V.A.(1996)Macroionattractiondue- electrostaticcorrelationbetweenscreeningcounterions0.1.Mobilesurface- adsorbedionsanddiffuseioncloud.J.Phys.Chem.100,9977-9989.(Pubitemid126788736)
-
(1996)
Journal of Physical Chemistry
, vol.100
, Issue.23
, pp. 9977-9989
-
-
Rouzina, I.1
Bloomfield, V.A.2
-
41
-
-
0026869974
-
Theory of delocalized ionic binding to polynucleotides-structural and excluded-volume effects
-
Ray, J., and Manning, G. S. (1992) Theory of delocalized ionic binding to polynucleotides-structural and excluded-volume effects. Biopolymers 32, 541-549.
-
(1992)
Biopolymers
, vol.32
, pp. 541-549
-
-
Ray, J.1
Manning, G.S.2
-
42
-
-
0026793123
-
Nonspecific ligand-DNA equilibrium binding parameters determined by fluorescence methods
-
Lohman, T. M., and Mascotti, D. P. (1992) Nonspecific ligand-DNA equilibrium binding parameters determined by fluorescence methods. Methods Enzymol. 212, 424-458.
-
(1992)
Methods Enzymol.
, vol.212
, pp. 424-458
-
-
Lohman, T.M.1
Mascotti, D.P.2
-
44
-
-
0029444946
-
Salt nucleic-acid interactions
-
Anderson, C. F., and Record, M. T., Jr. (1995) Salt nucleic-acid interactions, Annu. Rev. Phys. Chem. 46, 657-700.
-
(1995)
Annu. Rev. Phys. Chem.
, vol.46
, pp. 657-700
-
-
Anderson, C.F.1
Record Jr., M.T.2
-
45
-
-
0000144150
-
Salt dependence of oligoion polyion binding-a thermodynamic description based on preferential interaction coefficients
-
Anderson, C. F., and Record, M. T., Jr. (1993) Salt dependence of oligoion polyion binding-a thermodynamic description based on preferential interaction coefficients. J. Phys. Chem. 97, 7116-7126.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 7116-7126
-
-
Anderson, C.F.1
Record Jr., M.T.2
-
47
-
-
0017820499
-
Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
-
Record, M. T., Jr., Anderson, C. F., and Lohman, T. M. (1978) Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 11, 103-178.
-
(1978)
Q. Rev. Biophys.
, vol.11
, pp. 103-178
-
-
Record Jr., M.T.1
Anderson, C.F.2
Lohman, T.M.3
-
48
-
-
0026323912
-
Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of sitespecific complexes between proteins and helical DNA
-
Record, M. T., Jr., Ha, J. H., and Fisher, M. A. (1991) Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of sitespecific complexes between proteins and helical DNA. Methods Enzymol. 208, 291-343.
-
(1991)
Methods Enzymol.
, vol.208
, pp. 291-343
-
-
Record Jr., M.T.1
Ha, J.H.2
Fisher, M.A.3
-
50
-
-
0001201675
-
The relationship between the Poisson-Boltzmann model and the condensation hypothesis: An analysis based on the low salt form of the Donnan coefficient
-
Anderson, C. F., and Record, M. T., Jr. (1980) The relationship between the Poisson-Boltzmann model and the condensation hypothesis: an analysis based on the low salt form of the Donnan coefficient, Biophys. Chem. 11, 353-360.
-
(1980)
Biophys. Chem.
, vol.11
, pp. 353-360
-
-
Anderson, C.F.1
Record Jr., M.T.2
-
51
-
-
11644276439
-
Limiting laws and counterion condensation in polyelectrolyte solutions I. Colligative properties
-
Manning, G. S. (1969) Limiting laws and counterion condensation in polyelectrolyte solutions I. Colligative properties. J. Chem. Phys. 51, 924-933.
-
(1969)
J. Chem. Phys.
, vol.51
, pp. 924-933
-
-
Manning, G.S.1
-
52
-
-
0014109212
-
Spectroscopic determination of tryptophan and tyrosine in proteins
-
Edelhoch, H. (1967) Spectroscopic determination of tryptophan and tyrosine in proteins, Biochemistry 6, 1948-1954.
-
(1967)
Biochemistry
, vol.6
, pp. 1948-1954
-
-
Edelhoch, H.1
-
53
-
-
3042626449
-
6 cationic peptide with short nucleic acid oligomers: Demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt
-
6 cationic peptide with short nucleic acid oligomers: demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt. Nucleic Acids Res. 32, 3271-3281.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 3271-3281
-
-
Ballin, J.D.1
Shkel, I.A.2
Record Jr., M.T.3
-
54
-
-
33745823525
-
Interactions of cationic ligands and proteins with small nucleic acids: Analytic treatment of the large Coulombic end effect on binding free energy as a function of salt concentration
-
Shkel, I. A., Ballin, J. D., and Record, M. T., Jr. (2006) Interactions of cationic ligands and proteins with small nucleic acids: analytic treatment of the large Coulombic end effect on binding free energy as a function of salt concentration, Biochemistry 45, 8411-8426.
-
(2006)
Biochemistry
, vol.45
, pp. 8411-8426
-
-
Shkel, I.A.1
Ballin, J.D.2
Record Jr., M.T.3
-
55
-
-
77957095245
-
Nonlinear least-squares analysis
-
Johnson, M. L., and Frasier, S. G. (1985) Nonlinear least-squares analysis. Methods Enzymol. 117, 301-342.
-
(1985)
Methods Enzymol.
, vol.117
, pp. 301-342
-
-
Johnson, M.L.1
Frasier, S.G.2
-
56
-
-
13244253556
-
Fitting models to biological data using linear and nonlinear regression
-
GraphPad Software, Inc., San Diego, CA.
-
Motulsky, H. Christopoulos, A. (2003) Fitting Models to Biological Data Using Linear and Nonlinear Regression, A. Practical Guide to Curve Fitting, GraphPad Software, Inc., San Diego, CA.
-
(2003)
A. Practical Guide to Curve Fitting
-
-
Motulsky, H.1
Christopoulos, A.2
-
57
-
-
70349119250
-
Regression and time series model selection in small samples
-
Hurvich, C. M., and Tsai, C. L. (1989) Regression and time series model selection in small samples, Biometrika 76, 297-307.
-
(1989)
Biometrika
, vol.76
, pp. 297-307
-
-
Hurvich, C.M.1
Tsai, C.L.2
-
58
-
-
0023229226
-
A general method of analysis of ligand-macromolecule equilibria using a spectroscopic signal from the ligand to monitor binding. Application to Escherichia coli single-strand binding protein-nucleic acid interactions
-
DOI 10.1021/bi00385a023
-
58. Bujalowski, W., and Lohman, T. M. (1987) A general method of analysis of ligand-macromolecule equilibria using a spectroscopic signal from the ligand to monitor binding. Application to Escherichia coli single-strand binding protein-nucleic acid interactions. Biochemistry 20, 3099-3106. (Pubitemid 17087843)
-
(1987)
Biochemistry
, vol.26
, Issue.11
, pp. 3099-3106
-
-
Bujalowski, W.1
Lohman, T.M.2
-
59
-
-
0028030641
-
Conformational transitions of duplex and triplex nucleic acid helices: Thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients
-
Bond, J. P., Anderson, C. F., and Record, M. T., Jr. (1994) Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients, Biophys. J. 67, 825-836.
-
(1994)
Biophys. J.
, vol.67
, pp. 825-836
-
-
Bond, J.P.1
Anderson, C.F.2
Record Jr., M.T.3
-
60
-
-
0033862774
-
Salt effects on ionization equilibria of histidines in myoglobin
-
Kao, Y. H., Fitch, C. A., Bhattacharya, S., Sarkisian, C. J., Lecomte, J. T. J., and Garcia-Moreno E, B. (2000) Salt effects on ionization equilibria of histidines in myoglobin, Biophys. J. 79, 1637-1654.
-
(2000)
Biophys. J.
, vol.79
, pp. 1637-1654
-
-
Kao, Y.H.1
Fitch, C.A.2
Bhattacharya, S.3
Sarkisian, C.J.4
Lecomte, J.T.J.5
Garcia-Moreno, E.B.6
-
61
-
-
0037197681
-
Electrostatic effects in highly charged proteins: Salt sensitivity of ptfl values of histidines in Staphylococcal nuclease
-
Lee, K. K., Fitch, C. A., Lecomte, J. T. J., and Garcia-Moreno E, B. (2002) Electrostatic effects in highly charged proteins: salt sensitivity of ptf(l values of histidines in Staphylococcal nuclease, Biochemistry 41, 5656-5667.
-
(2002)
Biochemistry
, vol.41
, pp. 5656-5667
-
-
Lee, K.K.1
Fitch, C.A.2
Lecomte, J.T.J.3
Garcia-Moreno, E.B.4
-
62
-
-
0016688895
-
Electrostatic effects in myoglobin. Application of the modified Tanford-Kirkwood theory to myoglobins from horse, California grey whale, harbor seal, and California sea lion
-
Shire, S., Hanania, G., and Gurd, F. (1975) Electrostatic effects in myoglobin. Application of the modified Tanford-Kirkwood theory to myoglobins from horse, California grey whale, harbor seal, and California sea lion. Biochemistry 14, 1352-1358.
-
(1975)
Biochemistry
, vol.14
, pp. 1352-1358
-
-
Shire, S.1
Hanania, G.2
Gurd, F.3
-
63
-
-
0016207302
-
Electrostatic effects in myoglobin. Hydrogen ion equilibria in sperm whale ferrimyoglobin
-
Shire, S., Hanania, G., and Gurd, F. (1974) Electrostatic effects in myoglobin. Hydrogen ion equilibria in sperm whale ferrimyoglobin. Biochemistry 13, 2967-2974.
-
(1974)
Biochemistry
, vol.13
, pp. 2967-2974
-
-
Shire, S.1
Hanania, G.2
Gurd, F.3
-
64
-
-
25444493135
-
Free energy contributions to direct readout of a DNA sequence
-
Ferreiro, D. U., Dellarole, M., Nadra, A. D., and de Prat-Gay, G. (2005) Free energy contributions to direct readout of a DNA sequence. J. Biol. Chem. 280, 32480-32484.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 32480-32484
-
-
Ferreiro, D.U.1
Dellarole, M.2
Nadra, A.D.3
De Prat-Gay, G.4
-
65
-
-
0003836971
-
-
Oxford University Press, New York.
-
Dawson, R. M. C., Elliott, D. C., Elliot, W. H., Jones, K. M. (1995) Data for Biochemical Research, Oxford University Press, New York.
-
(1995)
Data for Biochemical Research
-
-
Dawson, R.M.C.1
Elliott, D.C.2
Elliot, W.H.3
Jones, K.M.4
-
66
-
-
0019886912
-
Ion effects on the lac repressor-operator equilibrium
-
Barkley, M. D., Lewis, P. A., and Sullivan, G. E. (1981) Ion effects on the lac repressor-operator equilibrium, Biochemistry 20, 3842-3851.
-
(1981)
Biochemistry
, vol.20
, pp. 3842-3851
-
-
Barkley, M.D.1
Lewis, P.A.2
Sullivan, G.E.3
-
67
-
-
3142657230
-
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes
-
DOI 10.1126/science.1097064
-
67. Kalodimos, C. G., Biris, N., Bonvin, A. M. J. J., Levandoski, M. M., Guennuegues, M., Boelens, R., and Kaptein, R. (2004) Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305, 386-389. (Pubitemid 38938152)
-
(2004)
Science
, vol.305
, Issue.5682
, pp. 386-389
-
-
Kalodimos, C.G.1
Biris, N.2
Bonvin, A.M.J.J.3
Levandoski, M.M.4
Guennuegues, M.5
Boelens, R.6
Kaptein, R.7
-
68
-
-
33744795425
-
Structural and thermodynamic basis for the enhanced transcriptional control by the human papillomavirus strain-16 E2 protein
-
DOI 10.1021/bi060123h
-
68. Cicero, D. O., Nadra, A. D., Eliseo, T., Dellarole, M., Paci, M., and de Prat-Gay, G. (2006) Structural and thermodynamic basis for the enhanced transcriptional control by the human papillomavirus strain-16 E2 protein, Biochemistry 45, 6551-6560. (Pubitemid 43833155)
-
(2006)
Biochemistry
, vol.45
, Issue.21
, pp. 6551-6560
-
-
Cicero, D.O.1
Nadra, A.D.2
Eliseo, T.3
Dellarole, M.4
Paci, M.5
De Prat-Gay, G.6
-
69
-
-
0027159254
-
The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments
-
69.Winkler,F.K.,Banner,D.W.,Oefner,C.,Tsernoglou,D.,Brown,R.S.,Heathman, S.P.,Bryan,R.K.,Martin,P.D.,Petratos,K.,andWilson,K.S.(1993) ThecrystalstructureofEcoRVendonucleaseandofitscomplexeswithcognateandnon cognateDNAfragments.EMBOJ.12,1781-1795.(Pubitemid23157693)
-
(1993)
EMBO Journal
, vol.12
, Issue.5
, pp. 1781-1795
-
-
Winkler, F.K.1
Banner, D.W.2
Oefner, C.3
Tsernoglou, D.4
Brown, R.S.5
Heathman, S.P.6
Bryan, R.K.7
Martin, P.D.8
Petratos, K.9
Wilson, K.S.10
-
70
-
-
0029010368
-
The basis for half-site specificity explored through, a noncognate steroid receptor-DNA complex
-
Gewirth, D. T., and Sigler, P. B. (1995) The basis for half-site specificity explored through, a noncognate steroid receptor-DNA complex, Nat. Struct. Mol. Biol. 2, 386-394.
-
(1995)
Nat. Struct. Mol. Biol.
, vol.2
, pp. 386-394
-
-
Gewirth, D.T.1
Sigler, P.B.2
-
71
-
-
0034495086
-
Backbone dynamics of sequence specific recognition and binding by the yeast Pho4 bHLH domain probed by NMR
-
71.Cave,J.W.,Kremer,W.,andWemmer,D.E(2000) BackbonedynamicsofsequencespecificrecognitionandbindingbytheyeastPho4bHLH domainprobedbyNMR.ProteinSci.9,2354-2365.(Pubitemid32105718)
-
(2000)
Protein Science
, vol.9
, Issue.12
, pp. 2354-2365
-
-
Cave, J.W.1
Kremer, W.2
Wemmer, D.E.3
-
72
-
-
66249112873
-
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions
-
Gao, M., and Skolnick, J. (2009) From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PLoS Comput. Biol. 5, e1000341.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Gao, M.1
Skolnick, J.2
-
73
-
-
0031722426
-
An analysis of the relationship between hydration and protein-DNA interactions
-
73.Woda,J.,Schneider,B.,Patel,K.,Mistry,K.,andBerman,H.M.(1998) Ananalysisoftherelationshipbetweenhydration,andprotein-DNAinteractions,Biophys. J.75,2170-2177.(Pubitemid28492099)
-
(1998)
Biophysical Journal
, vol.75
, Issue.5
, pp. 2170-2177
-
-
Woda, J.1
Schneider, B.2
Patel, K.3
Mistry, K.4
Berman, H.M.5
-
74
-
-
70350513011
-
Interactions of the osmolyte glycine betaine with molecular surfaces in water: Thermodynamics, structural interpretation, and prediction of m-values
-
Capp, M. W., Pegram, L. M., Saecker, R. M., Kratz, M., Riccardi, D., Wendorff, T., Cannon, J. G., and Record, M. T., Jr. (2009) Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values. Biochemistry 48, 10372-10379.
-
(2009)
Biochemistry
, vol.48
, pp. 10372-10379
-
-
Capp, M.W.1
Pegram, L.M.2
Saecker, R.M.3
Kratz, M.4
Riccardi, D.5
Wendorff, T.6
Cannon, J.G.7
Record Jr., M.T.8
-
75
-
-
39649115803
-
Formation of a wrapped DNA-protein interface: Experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA
-
Meulen, K. A. V., Saecker, R. M., and Record, M. T., Jr. (2008) Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA. J. Mol. Biol. 377, 9-27.
-
(2008)
J. Mol. Biol.
, vol.377
, pp. 9-27
-
-
Meulen, K.A.V.1
Saecker, R.M.2
Record Jr., M.T.3
-
77
-
-
49649112395
-
Thermodynamic origin of Hofmeister ion effects
-
Pegram, L. M., and Record, M. T., Jr. (2008) Thermodynamic origin of Hofmeister ion effects. J. Phys. Chem. B 112, 9428-9436.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9428-9436
-
-
Pegram, L.M.1
Record Jr., M.T.2
-
78
-
-
0029816432
-
Binding of ionic ligands to polyelectrolytes
-
Stigter, D., and Dill, K. A. (1996) Binding of ionic ligands to polyelectrolytes. Biophys. J. 71, 2064-2074.
-
(1996)
Biophys. J.
, vol.71
, pp. 2064-2074
-
-
Stigter, D.1
Dill, K.A.2
-
79
-
-
0023664206
-
Aggregation of DNA by analogs of spermidine; enzymatic and structural studies
-
Srivenugopal, K., Wemmer, D., and Morris, D. (1987) Aggregation of DNA by analogs of spermidine; enzymatic and structural studies. Nucleic Acids Res. 15, 2563-2580.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 2563-2580
-
-
Srivenugopal, K.1
Wemmer, D.2
Morris, D.3
-
80
-
-
0022429605
-
Nuclear magnetic resonance studies of polyamine binding to a defined DNA sequence
-
Wemmer, D. E., Srivenugopal, K. S., Reid, B. R., and Morris, D. R. (1985) Nuclear magnetic resonance studies of polyamine binding to a defined DNA sequence. J. Mol. Biol. 185, 457-459.
-
(1985)
J. Mol. Biol.
, vol.185
, pp. 457-459
-
-
Wemmer, D.E.1
Srivenugopal, K.S.2
Reid, B.R.3
Morris, D.R.4
|