-
1
-
-
0033574510
-
Protein-DNA interactions: A structural analysis
-
Jones, S., P. van Heyningen, H. M. Berman, and J. M. Thornton. 1999. Protein-DNA interactions: a structural analysis. J. Mol. Biol. 287:877-896.
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 877-896
-
-
Jones, S.1
Van Heyningen, P.2
Berman, H.M.3
Thornton, J.M.4
-
2
-
-
0033573827
-
Structural features of protein-nucleic acid recognition sites
-
Nadassy, K., S. J. Wodak, and J. Janin. 1999. Structural features of protein-nucleic acid recognition sites. Biochemistry. 38:1999-2017.
-
(1999)
Biochemistry
, vol.38
, pp. 1999-2017
-
-
Nadassy, K.1
Wodak, S.J.2
Janin, J.3
-
3
-
-
0030736323
-
Protein-DNA recognition complexes: Conservation of structure and binding energy in the transition state
-
Jen-Jacobson, L. 1997. Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state. Biopolymers. 44:153-180.
-
(1997)
Biopolymers
, vol.44
, pp. 153-180
-
-
Jen-Jacobson, L.1
-
4
-
-
0034049693
-
Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition
-
Oda, M., and H. Nakamura. 2000. Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition. Genes Cells. 5:319-326.
-
(2000)
Genes Cells
, vol.5
, pp. 319-326
-
-
Oda, M.1
Nakamura, H.2
-
5
-
-
0034556938
-
Thermodynamic parameters of specific and non-specific protein-DNA binding
-
Jen-Jacobson, L., L. E. Engler, J. T. Ames, M. R. Kurpiewski, and A. Grigorescu. 2000. Thermodynamic parameters of specific and non-specific protein-DNA binding. Supramol. Chem. 12:143-160.
-
(2000)
Supramol. Chem.
, vol.12
, pp. 143-160
-
-
Jen-Jacobson, L.1
Engler, L.E.2
Ames, J.T.3
Kurpiewski, M.R.4
Grigorescu, A.5
-
6
-
-
0028210087
-
Protein-DNA recognition: New perspectives and underlying themes
-
von Hippel, P. H. 1994. Protein-DNA recognition: new perspectives and underlying themes. Science. 263:769-770.
-
(1994)
Science
, vol.263
, pp. 769-770
-
-
Von Hippel, P.H.1
-
7
-
-
0035883723
-
Structure and function of type II restriction endonucleases
-
Pingoud, A., and A. Jeltsch. 2001. Structure and function of type II restriction endonucleases. Nucleic Acids Res. 29:3705-3727.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 3705-3727
-
-
Pingoud, A.1
Jeltsch, A.2
-
9
-
-
0028283502
-
A thermodynamic study of the trp repressor-operator interaction
-
Ladbury, J. E., J. G. Wright, J. M. Sturtevant, and P. B. Sigler. 1994. A thermodynamic study of the trp repressor-operator interaction. J. Mol. Biol. 238:669-681.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 669-681
-
-
Ladbury, J.E.1
Wright, J.G.2
Sturtevant, J.M.3
Sigler, P.B.4
-
10
-
-
0029044394
-
Calorimetric analysis of lambda cI repressor binding to DNA operator sites
-
Merabet, E., and G. K. Ackers. 1995. Calorimetric analysis of lambda cI repressor binding to DNA operator sites. Biochemistry. 34:8554-8563.
-
(1995)
Biochemistry
, vol.34
, pp. 8554-8563
-
-
Merabet, E.1
Ackers, G.K.2
-
11
-
-
0031576995
-
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, D. E., R. M. Saecker, J. P. Bond, M. W. Capp, O. V. Tsodikov, S. E. Melcher, M. M. Levandoski, and M. T. Record Jr. 1997. 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. J. Mol. Biol. 267:1186-1206.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 1186-1206
-
-
Frank, D.E.1
Saecker, R.M.2
Bond, J.P.3
Capp, M.W.4
Tsodikov, O.V.5
Melcher, S.E.6
Levandoski, M.M.7
Record Jr., M.T.8
-
13
-
-
0028961741
-
Water release associated with specific binding of gal repressor
-
Garner, M. M., and D. C. Rau. 1995. Water release associated with specific binding of gal repressor. EMBO J. 14:1257-1263.
-
(1995)
EMBO J.
, vol.14
, pp. 1257-1263
-
-
Garner, M.M.1
Rau, D.C.2
-
14
-
-
0029910813
-
Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences
-
Sidorova, N. Y., and D. C. Rau. 1996. Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences. Proc. Natl. Acad. Sci. USA. 93:12272-12277.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 12272-12277
-
-
Sidorova, N.Y.1
Rau, D.C.2
-
15
-
-
0025780755
-
Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA
-
Luisi, B. F., W. X. Xu, Z. Otwinowski, L. P. Freedman, K. R. Yamamoto, and P. B. Sigler. 1991. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature. 352:497-505.
-
(1991)
Nature
, vol.352
, 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
-
16
-
-
0027159254
-
The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments
-
Winkler, F. K., D. W. Banner, C. Oefner, D. Tsemoglou, R. S. Brown, S. P. Heathman, R. K. Bryan, P. D. Martin, K. Petratos, and K. S. Wilson. 1993. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12:1781-1795.
-
(1993)
EMBO J.
, vol.12
, pp. 1781-1795
-
-
Winkler, F.K.1
Banner, D.W.2
Oefner, C.3
Tsemoglou, 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
-
17
-
-
0031873125
-
Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: Possible implications for nonspecific binding by the wild-type protein
-
Albright, R. A., M. C. Mossing, and B. W. Matthews. 1998. Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-type protein. Protein Sci. 7:1485-1494.
-
(1998)
Protein Sci.
, vol.7
, pp. 1485-1494
-
-
Albright, R.A.1
Mossing, M.C.2
Matthews, B.W.3
-
18
-
-
0033634983
-
Structure of BamHI bound to nonspecific DNA: A model for DNA sliding
-
Viadiu, H., and A. K. Aggarwal. 2000. Structure of BamHI bound to nonspecific DNA: a model for DNA sliding. Mol. Cell. 5:889-895.
-
(2000)
Mol. Cell
, vol.5
, pp. 889-895
-
-
Viadiu, H.1
Aggarwal, A.K.2
-
19
-
-
3142657230
-
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes
-
Kalodimos, C. G., N. Biris, A. M. Bonvin, M. M. Levandoski, M. Guennuegues, R. Boelens, and R. Kaptein. 2004. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science2E 305:386-389.
-
(2004)
Science
, vol.305
, pp. 386-389
-
-
Kalodimos, C.G.1
Biris, N.2
Bonvin, A.M.3
Levandoski, M.M.4
Guennuegues, M.5
Boelens, R.6
Kaptein, R.7
-
20
-
-
0026323912
-
Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA
-
Record, M. T. Jr., J. H. Ha, and M. A. Fisher. 1991. Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific 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
-
21
-
-
0034850147
-
A structural basis for processivity
-
Breyer, W. A., and B. W. Matthews. 2001. A structural basis for processivity. Protein Sci. 10:1699-1711.
-
(2001)
Protein Sci.
, vol.10
, pp. 1699-1711
-
-
Breyer, W.A.1
Matthews, B.W.2
-
22
-
-
0029899865
-
Sequence-specific DNA-binding dominated by dehydration
-
Lundback, T., and T. Hard. 1996. Sequence-specific DNA-binding dominated by dehydration. Proc. Natl. Acad. Sci. USA. 93:4754-4759.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 4754-4759
-
-
Lundback, T.1
Hard, T.2
-
23
-
-
0032478266
-
Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease
-
Robinson, C. R., and S. G. Sligar. 1998. Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease. Proc. Natl. Acad. Sci. USA. 95:2186-2191.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 2186-2191
-
-
Robinson, C.R.1
Sligar, S.G.2
-
24
-
-
0030911133
-
Recognition and cleavage of DNA by type-11 restriction endonucleases
-
Pingoud, A., and A. Jeltsch. 1997. Recognition and cleavage of DNA by type-11 restriction endonucleases. Eur. J. Biochem. 246:1-22.
-
(1997)
Eur. J. Biochem.
, vol.246
, pp. 1-22
-
-
Pingoud, A.1
Jeltsch, A.2
-
25
-
-
0028298842
-
Structure of restriction endonuclease BamHI and its relationship to EcoRI
-
Newman, M., T. Strzelecka, L. F. Dorner, I. Schildkraut, and A. K. Aggarwal. 1994. Structure of restriction endonuclease BamHI and its relationship to EcoRI. Nature. 368:660-664.
-
(1994)
Nature
, vol.368
, pp. 660-664
-
-
Newman, M.1
Strzelecka, T.2
Dorner, L.F.3
Schildkraut, I.4
Aggarwal, A.K.5
-
26
-
-
0029048413
-
Structure of BamHI endonuclease bound to DNA: Partial folding and unfolding on DNA binding
-
Newman, M., T. Strzelecka, L. F. Dorner, I. Schildkraut, and A. K. Aggarwal. 1995. Structure of BamHI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science. 269:656-663.
-
(1995)
Science
, vol.269
, pp. 656-663
-
-
Newman, M.1
Strzelecka, T.2
Dorner, L.F.3
Schildkraut, I.4
Aggarwal, A.K.5
-
27
-
-
0031717755
-
The role of metals in catalysis by the restriction endonuclease BamHI
-
Viadiu, H., and A. K. Aggarwal. 1998. The role of metals in catalysis by the restriction endonuclease BamHI. Nat. Struct. Biol. 5:910-916.
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 910-916
-
-
Viadiu, H.1
Aggarwal, A.K.2
-
28
-
-
0038297676
-
Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex
-
Sun, J., H. Viadiu, A. K. Aggarwal, and H. Weinstein. 2003. Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex. Biophys. J. 84:3317-3325.
-
(2003)
Biophys. J.
, vol.84
, pp. 3317-3325
-
-
Sun, J.1
Viadiu, H.2
Aggarwal, A.K.3
Weinstein, H.4
-
29
-
-
0035937250
-
The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC
-
Engler, L. E., P. Sapienza, L. F. Dorner, R. Kucera, I. Schildkraut, and L. Jen-Jacobson. 2001. The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC. J. Mol. Biol. 307:619-636.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 619-636
-
-
Engler, L.E.1
Sapienza, P.2
Dorner, L.F.3
Kucera, R.4
Schildkraut, I.5
Jen-Jacobson, L.6
-
30
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization and dynamics calculations
-
Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J. Comput. Chem. 4:187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
31
-
-
84893016902
-
Grand canonical Monte Carlo study of dense liquid Lenard-Jones, soft spheres and water
-
Mezei, M. 1987. Grand canonical Monte Carlo study of dense liquid Lenard-Jones, soft spheres and water. Mol. Phys. 61:565-582.
-
(1987)
Mol. Phys.
, vol.61
, pp. 565-582
-
-
Mezei, M.1
-
32
-
-
0001120964
-
Grand canonical Monte Carlo simulation of water position in crystal hydrates
-
Resat, H., and M. Mezei. 1994. Grand canonical Monte Carlo simulation of water position in crystal hydrates. J. Am. Chem. Soc. 116:7451-7452.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 7451-7452
-
-
Resat, H.1
Mezei, M.2
-
33
-
-
0029781535
-
Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate
-
Resat, H., and M. Mezei. 1996. Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate. Biophys. J. 71:1179-1190.
-
(1996)
Biophys. J.
, vol.71
, pp. 1179-1190
-
-
Resat, H.1
Mezei, M.2
-
34
-
-
84988080188
-
Generic solvation sites in a crystal
-
Mezei, M., and D. L. Beveridge. 1984. Generic solvation sites in a crystal. J. Comput. Chem. 6:523-527.
-
(1984)
J. Comput. Chem.
, vol.6
, pp. 523-527
-
-
Mezei, M.1
Beveridge, D.L.2
-
35
-
-
0242657029
-
-
John Wiley and Sons Inc., New York
-
Berge, C. 1962. The Theory of Graphs. John Wiley and Sons Inc., New York.
-
(1962)
The Theory of Graphs
-
-
Berge, C.1
-
36
-
-
0022462967
-
Structural chemistry of biomolecular hydration via computer simulation: The proximity criterion
-
Mezei, M., and D. L. Beveridge. 1986. Structural chemistry of biomolecular hydration via computer simulation: the proximity criterion. Methods Enzymol. 127:21-47.
-
(1986)
Methods Enzymol.
, vol.127
, pp. 21-47
-
-
Mezei, M.1
Beveridge, D.L.2
-
37
-
-
0012834310
-
Modified proximity criterion for the analysis of the solvation environment of a polyfunctional solute
-
Mezei, M. 1988. Modified proximity criterion for the analysis of the solvation environment of a polyfunctional solute. Mol. Simul. 1:327-332.
-
(1988)
Mol. Simul.
, vol.1
, pp. 327-332
-
-
Mezei, M.1
-
38
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Jr., D. Bashford, R. L. Bellot, R. L. Dunbrack Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnik, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher 3rd, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellot, R.L.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnik, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
39
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., J. Chandrashekar, J. D. Madura, R. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrashekar, J.2
Madura, J.D.3
Impey, R.4
Klein, M.L.5
-
40
-
-
0037351013
-
A new method for mapping macromolecular topography
-
Mezei, M. 2003. A new method for mapping macromolecular topography. J. Mol. Graph. Model. 21:463-472.
-
(2003)
J. Mol. Graph. Model.
, vol.21
, pp. 463-472
-
-
Mezei, M.1
-
41
-
-
0031887345
-
Solvation studies of DMP323 and A76928 bound to HIV protease: Analysis of water sites using grand canonical Monte Carlo simulations
-
Marrone, T. J., H. Resat, C. N. Hodge, C. H. Chang, and J. A. McCammon. 1998. Solvation studies of DMP323 and A76928 bound to HIV protease: analysis of water sites using grand canonical Monte Carlo simulations. Protein Sci. 7:573-579.
-
(1998)
Protein Sci.
, vol.7
, pp. 573-579
-
-
Marrone, T.J.1
Resat, H.2
Hodge, C.N.3
Chang, C.H.4
McCammon, J.A.5
-
42
-
-
23444450909
-
Coupling of local folding to site-specific binding of proteins to DNA
-
Spolar, R. S., and M. T. Record Jr. 1994. Coupling of local folding to site-specific binding of proteins to DNA. Science. 263:777-784.
-
(1994)
Science
, vol.263
, pp. 777-784
-
-
Spolar, R.S.1
Record Jr., M.T.2
-
43
-
-
0024378717
-
Role of hydrophobic effect in the stability of site-specific protein-DNA complexes
-
Ha, J. H., R. S. Spolar, and M. T. J. Record. 1989. Role of hydrophobic effect in the stability of site-specific protein-DNA complexes. J. Mol. Biol. 209:801-816.
-
(1989)
J. Mol. Biol.
, vol.209
, pp. 801-816
-
-
Ha, J.H.1
Spolar, R.S.2
Record, M.T.J.3
-
44
-
-
0035976713
-
Do water molecules mediate protein-DNA recognition?
-
Reddy, C. K., A. Das, and B. Jayaram. 2001. Do water molecules mediate protein-DNA recognition? J. Mol. Biol. 314:619-632.
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 619-632
-
-
Reddy, C.K.1
Das, A.2
Jayaram, B.3
-
45
-
-
0020692923
-
Ordered water structure around a B-DNA dodecamer. A quantitative study
-
Kopka, M. L., A. V. Fratini, H. R. Drew, and R. E. Dickerson. 1983. Ordered water structure around a B-DNA dodecamer. A quantitative study. J. Mol. Biol. 163:129-146.
-
(1983)
J. Mol. Biol.
, vol.163
, pp. 129-146
-
-
Kopka, M.L.1
Fratini, A.V.2
Drew, H.R.3
Dickerson, R.E.4
-
46
-
-
0026624859
-
Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G
-
Quintana, J. R., K. Grzeskowiak, K. Yanagi, and R. E. Dickerson. 1992. Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. J. Mol. Biol. 225:379-395.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 379-395
-
-
Quintana, J.R.1
Grzeskowiak, K.2
Yanagi, K.3
Dickerson, R.E.4
-
47
-
-
0028823008
-
Hydration of the DNA bases is local
-
Schneider, B., and H. M. Berman. 1995. Hydration of the DNA bases is local. Biophys. J. 69:2661-2669.
-
(1995)
Biophys. J.
, vol.69
, pp. 2661-2669
-
-
Schneider, B.1
Berman, H.M.2
-
48
-
-
0023061930
-
Structure and dynamics of water surrounding biomolecules
-
Saenger, W. 1987. Structure and dynamics of water surrounding biomolecules. Annu. Rev. Biophys. Biophys. Chem. 16:93-114.
-
(1987)
Annu. Rev. Biophys. Biophys. Chem.
, vol.16
, pp. 93-114
-
-
Saenger, W.1
-
49
-
-
0033525668
-
Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation
-
Feig, M., and B. M. Pettitt. 1999. Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation. J. Mol. Biol. 286:1075-1095.
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 1075-1095
-
-
Feig, M.1
Pettitt, B.M.2
-
50
-
-
0034255123
-
Speeding molecular recognition by using the folding funnel: The fly-casting mechanism
-
Shoemaker, B. A., J. J. Portman, and P. G. Wolynes. 2000. Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc. Natl. Acad. Sci. USA. 97:8868-8873.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 8868-8873
-
-
Shoemaker, B.A.1
Portman, J.J.2
Wolynes, P.G.3
|