-
1
-
-
0035914444
-
Effects of spectator ligands on the specific recognition of intrastrand platinum-DNA cross-links by high mobility group box and TATA-binding proteins
-
Wei, M., Cohen, S. M., Silverman, A. P., and Lippard, S. J. (2001) Effects of spectator ligands on the specific recognition of intrastrand platinum-DNA cross-links by high mobility group box and TATA-binding proteins J. Biol. Chem. 276, 38774-38780
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 38774-38780
-
-
Wei, M.1
Cohen, S.M.2
Silverman, A.P.3
Lippard, S.J.4
-
2
-
-
36849089573
-
Conformation of DNA GG intrastrand cross-link of antitumor oxaliplatin and its enantiomeric analog
-
Malina, J., Novakova, O., Vojtiskova, M., Natile, G., and Brabec, V. (2007) Conformation of DNA GG intrastrand cross-link of antitumor oxaliplatin and its enantiomeric analog Biophys. J. 93, 3950-3962
-
(2007)
Biophys. J.
, vol.93
, pp. 3950-3962
-
-
Malina, J.1
Novakova, O.2
Vojtiskova, M.3
Natile, G.4
Brabec, V.5
-
3
-
-
38149004514
-
LEF-1 recognition of platinated GG sequences within double-stranded DNA. Influence of flanking bases
-
Chvalova, K., Sari, M. A., Bombard, S., and Kozelka, J. (2008) LEF-1 recognition of platinated GG sequences within double-stranded DNA. Influence of flanking bases J. Inorg. Biochem. 102, 242-250
-
(2008)
J. Inorg. Biochem.
, vol.102
, pp. 242-250
-
-
Chvalova, K.1
Sari, M.A.2
Bombard, S.3
Kozelka, J.4
-
4
-
-
10644245994
-
Recognition and processing of cisplatin- and oxaliplatin-DNA adducts
-
Chaney, S. G., Campbell, S. L., Bassett, E., and Wu, Y. (2005) Recognition and processing of cisplatin- and oxaliplatin-DNA adducts Crit. Rev. Oncol. Hematol. 53, L3-L11
-
(2005)
Crit. Rev. Oncol. Hematol.
, vol.53
-
-
Chaney, S.G.1
Campbell, S.L.2
Bassett, E.3
Wu, Y.4
-
5
-
-
0033600558
-
Effect of DNA polymerases and high mobility group protein 1 on the carrier ligand specificity for translesion synthesis past platinum-DNA adducts
-
Vaisman, A., Lim, S. E., Patrick, S. M., Copeland, W. C., Hinkle, D. C., Turchi, J. J., and Chaney, S. G. (1999) Effect of DNA polymerases and high mobility group protein 1 on the carrier ligand specificity for translesion synthesis past platinum-DNA adducts Biochemistry 38, 11026-11039
-
(1999)
Biochemistry
, vol.38
, pp. 11026-11039
-
-
Vaisman, A.1
Lim, S.E.2
Patrick, S.M.3
Copeland, W.C.4
Hinkle, D.C.5
Turchi, J.J.6
Chaney, S.G.7
-
6
-
-
30944466823
-
Increased expression of high mobility group box 1 (HMGB1) is associated with an elevated level of the antiapoptotic c-IAP2 protein in human colon carcinomas
-
Volp, K., Brezniceanu, M.-L., Bosser, S., Brabletz, T., Kirchner, T., Gottel, D., Joos, S., and Zornig, M. (2006) Increased expression of high mobility group box 1 (HMGB1) is associated with an elevated level of the antiapoptotic c-IAP2 protein in human colon carcinomas Gut 55, 234-242
-
(2006)
Gut
, vol.55
, pp. 234-242
-
-
Volp, K.1
Brezniceanu, M.-L.2
Bosser, S.3
Brabletz, T.4
Kirchner, T.5
Gottel, D.6
Joos, S.7
Zornig, M.8
-
7
-
-
0031864830
-
Oxaliplatin-mechanism of action and antineoplastic activity
-
Raymond, E., Faivre, S., Woynarowski, J. M., and Chaney, S. G. (1998) Oxaliplatin-mechanism of action and antineoplastic activity Semin. Oncol. 25, 4-12
-
(1998)
Semin. Oncol.
, vol.25
, pp. 4-12
-
-
Raymond, E.1
Faivre, S.2
Woynarowski, J.M.3
Chaney, S.G.4
-
8
-
-
0000460127
-
Oxaliplatin, tetraplatin, cisplatin, and carboplatin: Spectrum of activity in drug-resistant cell lines and in the cell lines of the National Cancer Institute's Anticancer Drug Screen panel
-
Rixe, O., Ortuzar, W., Alvarez, M., Parker, R., Reed, E., Paull, K., and Fojo, T. (1996) Oxaliplatin, tetraplatin, cisplatin, and carboplatin: Spectrum of activity in drug-resistant cell lines and in the cell lines of the National Cancer Institute's Anticancer Drug Screen panel Biochem. Pharmacol. 52, 1855-1865
-
(1996)
Biochem. Pharmacol.
, vol.52
, pp. 1855-1865
-
-
Rixe, O.1
Ortuzar, W.2
Alvarez, M.3
Parker, R.4
Reed, E.5
Paull, K.6
Fojo, T.7
-
9
-
-
0037432325
-
Nature of Full-Length HMGB1 Binding to Cisplatin-Modified DNA
-
Jung, Y. and Lippard, S. J. (2003) Nature of Full-Length HMGB1 Binding to Cisplatin-Modified DNA Biochemistry 42, 2664-2671
-
(2003)
Biochemistry
, vol.42
, pp. 2664-2671
-
-
Jung, Y.1
Lippard, S.J.2
-
10
-
-
0034727674
-
Intercalating residues determine the mode of HMG1 domains A and B binding to cisplatin-modified DNA
-
He, Q., Ohndorf, U. M., and Lippard, S. J. (2000) Intercalating residues determine the mode of HMG1 domains A and B binding to cisplatin-modified DNA Biochemistry 39, 14426-14435
-
(2000)
Biochemistry
, vol.39
, pp. 14426-14435
-
-
He, Q.1
Ohndorf, U.M.2
Lippard, S.J.3
-
11
-
-
0029131298
-
Structural basis for DNA bending by the architectural transcription factor LEF-1
-
Love, J. J., Li, X., Case, D. A., Giese, K., Grosschedl, R., and Wright, P. E. (1995) Structural basis for DNA bending by the architectural transcription factor LEF-1 Nature 376, 791-795
-
(1995)
Nature
, vol.376
, pp. 791-795
-
-
Love, J.J.1
Li, X.2
Case, D.A.3
Giese, K.4
Grosschedl, R.5
Wright, P.E.6
-
12
-
-
0029075461
-
Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex
-
Werner, M. H., Huth, J. R., Gronenborn, A. M., and Clore, G. M. (1995) Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex Cell 81, 705-714
-
(1995)
Cell
, vol.81
, pp. 705-714
-
-
Werner, M.H.1
Huth, J.R.2
Gronenborn, A.M.3
Clore, G.M.4
-
13
-
-
0033578010
-
Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins
-
Ohndorf, U.-M., Rould, M. A., He, Q., Pabo, C. O., and Lippard, S. J. (1999) Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins Nature 399, 708-712
-
(1999)
Nature
, vol.399
, pp. 708-712
-
-
Ohndorf, U.-M.1
Rould, M.A.2
He, Q.3
Pabo, C.O.4
Lippard, S.J.5
-
14
-
-
35148827661
-
Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics
-
Sharma, S., Gong, P., Temple, B., Bhattacharyya, D., Dokholyan, N. V., and Chaney, S. G. (2007) Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics J. Mol. Biol. 373, 1123-1140
-
(2007)
J. Mol. Biol.
, vol.373
, pp. 1123-1140
-
-
Sharma, S.1
Gong, P.2
Temple, B.3
Bhattacharyya, D.4
Dokholyan, N.V.5
Chaney, S.G.6
-
15
-
-
65849293705
-
Structural basis for the sequence-dependent effects of platinum-DNA adducts
-
Ramachandran, S., Temple, B. R., Chaney, S. G., and Dokholyan, N. V. (2009) Structural basis for the sequence-dependent effects of platinum-DNA adducts Nucleic Acids Res. 37, 2434-2448
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 2434-2448
-
-
Ramachandran, S.1
Temple, B.R.2
Chaney, S.G.3
Dokholyan, N.V.4
-
16
-
-
80051496112
-
Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG) cross-links
-
Bhattacharyya, D., Ramachandran, S., Sharma, S., Pathmasiri, W., King, C. L., Baskerville-Abraham, I., Boysen, G., Swenberg, J. A., Campbell, S. L., Dokholyan, N. V., and Chaney, S. G. (2011) Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG) cross-links PLoS One 6, e23582
-
(2011)
PLoS One
, vol.6
, pp. 23582
-
-
Bhattacharyya, D.1
Ramachandran, S.2
Sharma, S.3
Pathmasiri, W.4
King, C.L.5
Baskerville-Abraham, I.6
Boysen, G.7
Swenberg, J.A.8
Campbell, S.L.9
Dokholyan, N.V.10
Chaney, S.G.11
-
17
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., and Kollman, P. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 24, 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
18
-
-
0029011701
-
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
-
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 117, 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
19
-
-
0000936259
-
A molecular mechanics AMBER-type force field for modeling platinum complexes of guanine derivatives
-
Yao, S., Plastaras, J. P., and Marzilli, L. G. (1994) A molecular mechanics AMBER-type force field for modeling platinum complexes of guanine derivatives Inorg. Chem. 33, 6061-6077
-
(1994)
Inorg. Chem.
, vol.33
, pp. 6061-6077
-
-
Yao, S.1
Plastaras, J.P.2
Marzilli, L.G.3
-
20
-
-
0032866230
-
Molecular modeling of the intrastrand guanine-guanine DNA adducts produced by cisplatin and oxaliplatin
-
Scheeff, E. D., Briggs, J. M., and Howell, S. B. (1999) Molecular modeling of the intrastrand guanine-guanine DNA adducts produced by cisplatin and oxaliplatin Mol. Pharmacol. 56, 633-643
-
(1999)
Mol. Pharmacol.
, vol.56
, pp. 633-643
-
-
Scheeff, E.D.1
Briggs, J.M.2
Howell, S.B.3
-
21
-
-
34247186195
-
-
University of California, San Francisco.
-
Case, D. A., Darden, T. A., Cheatham, T. E., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Merz, K. M., Jr., Pearlman, D. A., Crowley, M., Walker, R. C., Zhang, W., Wang, B., Hayik, S., Roitberg, A. E., Seabra, G., Wong, K. F., Paesani, F., Wu, X., Brozell, S., Tsui, V., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Beroza, P., Mathews, D. H., Schafmeister, C. E. A. F., Ross, W. S., and Kollman, P. A. (2006) AMBER 9, University of California, San Francisco.
-
(2006)
AMBER 9
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz Jr., K.M.8
Pearlman, D.A.9
Crowley, M.10
Walker, R.C.11
Zhang, W.12
Wang, B.13
Hayik, S.14
Roitberg, A.E.15
Seabra, G.16
Wong, K.F.17
Paesani, F.18
Wu, X.19
Brozell, S.20
Tsui, V.21
Gohlke, H.22
Yang, L.23
Tan, C.24
Mongan, J.25
Hornak, V.26
Cui, G.27
Beroza, P.28
Mathews, D.H.29
Schafmeister, C.E.A.F.30
Ross, W.S.31
Kollman, P.A.32
more..
-
22
-
-
46049096322
-
Ab initio folding of proteins with all-atom discrete molecular dynamics
-
Ding, F., Tsao, D., Nie, H., and Dokholyan, N. V. (2008) Ab initio folding of proteins with all-atom discrete molecular dynamics Structure 16, 1010-1018
-
(2008)
Structure
, vol.16
, pp. 1010-1018
-
-
Ding, F.1
Tsao, D.2
Nie, H.3
Dokholyan, N.V.4
-
23
-
-
0037045235
-
Origin of attraction and directionality of the π/π interaction: Model chemistry calculations of benzene dimer interaction
-
Tsuzuki, S., Honda, K., Uchimaru, T., Mikami, M., and Tanabe, K. (2002) Origin of attraction and directionality of the π/π interaction: Model chemistry calculations of benzene dimer interaction J. Am. Chem. Soc. 124, 104-112
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 104-112
-
-
Tsuzuki, S.1
Honda, K.2
Uchimaru, T.3
Mikami, M.4
Tanabe, K.5
-
24
-
-
66749109882
-
Evidence for Stabilization of DNA/RNA-Protein Complexes Arising from Nucleobase-Amino Acid Stacking and T-Shaped Interactions
-
Rutledge, L. R., Durst, H. F., and Wetmore, S. D. (2009) Evidence for Stabilization of DNA/RNA-Protein Complexes Arising from Nucleobase-Amino Acid Stacking and T-Shaped Interactions J. Chem. Theory Comput. 5, 1400-1410
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1400-1410
-
-
Rutledge, L.R.1
Durst, H.F.2
Wetmore, S.D.3
-
25
-
-
4344598766
-
Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction
-
Misura, K. M., Morozov, A. V., and Baker, D. (2004) Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction J. Mol. Biol. 342, 651-664
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 651-664
-
-
Misura, K.M.1
Morozov, A.V.2
Baker, D.3
-
26
-
-
0025878347
-
π-π interactions: The geometry and energetics of phenylalanine-phenylalanine interactions in proteins
-
Hunter, C. A., Singh, J., and Thornton, J. M. (1991) π-π interactions: The geometry and energetics of phenylalanine-phenylalanine interactions in proteins J. Mol. Biol. 218, 837-846
-
(1991)
J. Mol. Biol.
, vol.218
, pp. 837-846
-
-
Hunter, C.A.1
Singh, J.2
Thornton, J.M.3
-
27
-
-
34247491471
-
Role of aromatic amino acids in protein-nucleic acid recognition
-
Baker, C. M. and Grant, G. H. (2007) Role of aromatic amino acids in protein-nucleic acid recognition Biopolymers 85, 456-470
-
(2007)
Biopolymers
, vol.85
, pp. 456-470
-
-
Baker, C.M.1
Grant, G.H.2
-
28
-
-
33745242847
-
Structure of a complex of tandem HMG boxes and DNA
-
Stott, K., Tang, G. S., Lee, K. B., and Thomas, J. O. (2006) Structure of a complex of tandem HMG boxes and DNA J. Mol. Biol. 360, 90-104
-
(2006)
J. Mol. Biol.
, vol.360
, pp. 90-104
-
-
Stott, K.1
Tang, G.S.2
Lee, K.B.3
Thomas, J.O.4
-
29
-
-
0027504913
-
Crystal structure of a yeast TBP/TATA-box complex
-
Kim, Y., Geiger, J. H., Hahn, S., and Sigler, P. B. (1993) Crystal structure of a yeast TBP/TATA-box complex Nature 365, 512-520
-
(1993)
Nature
, vol.365
, pp. 512-520
-
-
Kim, Y.1
Geiger, J.H.2
Hahn, S.3
Sigler, P.B.4
|