Insights into Protein—DNA Interactions, Stability and Allosteric Communications: A Computational Study of Mutsα-DNA Recognition Complexes

References

• Lahue , R. S. , Au , K. G. and Modrich , P. 1989 . Science , 245 : 160 – 164 .
   PubMed Web of Science ®Google Scholar
• Zhang , Y. , Yuan , F. , Presnell , S. R. , Tian , K. , Gao , Y. , Tomkinson , A. E. , Gu , L. and Li , G. M. 2005 . Cell , 122 : 693 – 705 .
   PubMed Web of Science ®Google Scholar
• Constantin , N. , Dzantiev , L. , Kadyrov , F. A. and Modrich , P. 2005 . J Biol Chem , 280 : 39752 – 39761 .
   PubMed Web of Science ®Google Scholar
• Gradia , S. , Subramanian , D. , Wilson , T. , Acharaya , S. , Makhov , A. , Griffith , J. and Fishel , R. 1999 . Mol Cell , 3 : 255 – 261 .
   PubMed Web of Science ®Google Scholar
• Blackwell , L. J. , Martik , D. , Bjornson , K. P. , Bjorson , E. S. and Modrich , P. 1998 . J Biol Chem , 273 : 32055 – 32062 .
   PubMed Web of Science ®Google Scholar
• Martik , D. , Baitinger , C. and Modrich , P. 2004 . J Biol Chem , 279 : 28402 – 28410 .
   PubMed Web of Science ®Google Scholar
• Wang , H. and Hays , J. B. 2003 . J Biol Chem , 278 : 28686 – 28693 .
   PubMed Web of Science ®Google Scholar
• Wang , H. and Hays , J. B. 2004 . EMBO J , 23 : 2126 – 2133 .
   PubMed Web of Science ®Google Scholar
• Young , L. and et al . 2003 . J Invest Dermatol , 121 : 876 – 880 .
   PubMed Web of Science ®Google Scholar
• Salsbury , F. R. and et al . 2006 . Nucleic Acids Res , 34 : 2173 – 2185 .
   PubMed Web of Science ®Google Scholar
• Vasilyeva , A. , Clodfelter , J. E. , Gorczynski , M. J. , Gerardi , A. R. , King , S. B. , Salsbury , F. R. and Scarpinato , K. D. 2010 . J Nucleic Acids ,
   PubMedGoogle Scholar
• Salsbury , F. R. 2010 . Curr Opin Pharmacol , 10 : 738 – 744 .
   PubMed Web of Science ®Google Scholar
• Warren , J. and et al . 2007 . Mol Cell , 26 : 579 – 592 .
   PubMed Web of Science ®Google Scholar
• Drotschmann , K. , Topping , R. P. , Clodfelter , J. E. and Salsbury , F. R. 2004 . DNA Repair (Amst.) , 3 : 729 – 742 .
   PubMed Web of Science ®Google Scholar
• Jiricny , J. 2006 . Nat Rev , 7 : 335 – 346 .
   Google Scholar
• Peltomaki , P. 2003 . J Clin Oncol , 21 : 1174 – 1179 .
   PubMed Web of Science ®Google Scholar
• Peltomaki , P. 2001 . Hum Mol Genetics , 10 : 735 – 740 .
   PubMed Web of Science ®Google Scholar
• Palombo , F. , Gallinari , P. , Iaccarino , I. , Lettieri , T. , Hughes , M. , D'Arrigo , A. , Truong , O. , Hsuan , J. J. and Jiricny , J. 1995 . Science , 30 : 1912 – 1914 .
   Web of Science ®Google Scholar
• Drummond , J. T. , Li , G. M. , Longley , M. J. and Modrich , P. 1995 . Science , 30 : 1909 – 1912 .
   Google Scholar
• Acharya , S. , Wilson , T. , Gradia , S. , Kane , M. F. , Guerrette , S. , Marsischky , G. T. , Kolodner , R. and Fishel , R. 1996 . Proc Natl Acad Sci U S A , 93 : 13629 – 13634 .
   PubMed Web of Science ®Google Scholar
• Lamers , M. H. , Perrakis , A. , Enzlin , J. H. , Winterwerp , H. H. K. , de Wind , N. and Sixma , T. K. 2000 . Nature , 407 : 711 – 717 .
   PubMed Web of Science ®Google Scholar
• Westmoreland , J. , Porter , G. , Radman , M. and Resnick , M. A. 1997 . Genetics , 145 : 29 – 38 .
   PubMed Web of Science ®Google Scholar
• O'Brien , V. and Brown , R. 2006 . Carcinogenesis , 27 : 682 – 692 .
   PubMed Web of Science ®Google Scholar
• Cannavo , E. , Gerrlts , B. , Marra , G. and Jiricny , J. 2007 . J Biol Chem , 282 : 2976 – 2986 .
   PubMed Web of Science ®Google Scholar
• Gassman , N. R. , Clodfelter , J. E. , McCaulet , A. K. and et al . PLoS One , 6 e17907
   Google Scholar
• Brooks , B. R. , Bruccoleri , R. E. , Olafson , B. D. , States , D. J. , Swaminathan , S. and Karplus , M. 1983 . J Comput Chem , 4 : 187 – 217 .
   Web of Science ®Google Scholar
• Scheeff , E. D. , Briggs , J. M. and Howell , S. B. 1999 . Mol Pharmacol , 56 : 633 – 643 .
   PubMed Web of Science ®Google Scholar
• MacKerell , A. D. , Bashford , D. , Bellott , M. , Dunbrack , R. L. , Evanseck , J. D. , Field , M. J. , Fisher , S. , Gao , J. , Guo , H. , Ha , S. and et al . 1998 . J Phys Chem B , 102 : 3586 – 3616 .
   PubMed Web of Science ®Google Scholar
• MacKerell , D. A. Jr , Banavali , N. and Foloppe , N. 2001 . Biopolymers , 56 : 257 – 265 .
   Web of Science ®Google Scholar
• Jorgensen , W. L. , Chandsrasekhar , J. , Madura , J. D. , Impey , R. W. and Klein , M. L. 1983 . J Chem Phys , 79 : 926 – 935 .
   Web of Science ®Google Scholar
• Humphrey , W. , Dalke , A. and Schulten , K. 1996 . J Mol Graph , 14 : 33 – 38 .
   PubMed Web of Science ®Google Scholar
• Lee , M. S. , Salsbury , F. R. Jr. and Brooks , C. L. 2002 . J Chem Phys , 116 : 10606 – 10615 .
   Web of Science ®Google Scholar
• Lee , M. S. , Salsbury , F. R. Jr. and Olson , M. A. 2004 . J Comp Chem , 25 : 1967 – 1978 .
   PubMed Web of Science ®Google Scholar
• Salsbury , F. R. J. 2006 . Mol Phys , 104 : 1299 – 1309 .
   Web of Science ®Google Scholar
• Berendsen , H. J. C. , Postma , J. P. M. , van Gunsteren , W. F. , DiNola , A. and Haak , J. R. 1984 . J Chem Phys , 81 : 3684 – 3690 .
   Web of Science ®Google Scholar
• Kale , L. , Skeel , R. , Bhandarkar , M. , Brunner , R. , Gursoy , A. , Krawetz , N. , Phillips , J. , Shinozaki , A. , Varadarajan , K. and Schulten , K. 1999 . J Comp Phys , 15 : 1283 – 1312 .
   Google Scholar
• van Gunsteren , W. F. and Berendsen , H. J. C. 1977 . Mol Phys , 34 : 1311 – 1327 .
   Web of Science ®Google Scholar
• Darden , T. , York , D. and Pedersen , L. 1993 . J Chem Phys , 98 : 10089 – 10092 .
   Web of Science ®Google Scholar
• Sethna , J. P. 2010 . Statistical Mechanics: Entropy, Order parameters and Complexity (Clarendon Press)
   Google Scholar
• Louise-May , S. , Auffinger , P. and Wsthof , E. 1996 . Curr Opin Struct Biol , 6 : 289 – 298 .
   PubMed Web of Science ®Google Scholar
• Auffinger , P. , Louise-May , S. and Westhof , E. 1995 . J Am Chem Soc , 117 : 6720 – 6726 .
   Web of Science ®Google Scholar
• Vaiana , A. C. , Westhof , E. and Auffinger , P. 2006 . Biochimie , 88 : 1061 – 1073 .
   PubMed Web of Science ®Google Scholar
• Salsbury , F. R. J. , Crowder , M. W. , Kingsmore , S. F. and et al . 2009 . J Mol Modeling , 15 : 133 – 145 .
   PubMed Web of Science ®Google Scholar
• Karpen , M. E. , Tobias , D. J. and Brooks , C. L. III . 1993 . Biochemistry , 32 : 412 – 420 .
   PubMed Web of Science ®Google Scholar
• 2010 . Matlab v.7.10.0 Natick , Massachusetts : (The Math Works Inc. .
   Google Scholar
• Tiwari , A. and Panigrahi , S. K. 2007 . In Silico Biol , 7 : 651 – 661 .
   PubMedGoogle Scholar
• Panigrahi , S. K. and Desiraju , G. R. 2007 . Proteins , 67 : 128 – 142 .
   PubMed Web of Science ®Google Scholar
• Sarkhel , S. and Desiraju , G. R. 2004 . Proteins , 54 : 247 – 259 .
   PubMed Web of Science ®Google Scholar
• Takahara , P. M. , Rosenzweig , A. C. , Frederick , C. A. and Lippard , S. J. 1995 . Nature , 377 : 649 – 652 .
   PubMed Web of Science ®Google Scholar
• Takahara , P. M. , Frederick , C. A. and Lippard , S. J. 1996 . J Am Chem Soc , 118 : 12309 – 12321 .
   Web of Science ®Google Scholar
• Kartalou , M. and Essigmann , J. M. 2001 . Mutat Res , 478 : 1 – 21 .
   PubMed Web of Science ®Google Scholar
• Gelasco , A. and Lippard , S. J. 1998 . Biochemistry , 37 : 9230 – 9239 .
   PubMed Web of Science ®Google Scholar
• Rosenberg , B. , Camp , L. and Van Krigas , T. 1965 . Nature , 205 : 698 – 699 .
   PubMed Web of Science ®Google Scholar
• Duckett , D. R. , Drummond , J. T. , Murchie , A. I. , Reardon , J. T. , Sancar , A. , Lilley , D. M. and Modrich , P. 1996 . Proc Natl Acad Sci U S A , 93 : 6443 – 6447 .
   PubMed Web of Science ®Google Scholar
• Yamada , M. , O'Regan , E. , Brown , R. and Karran , P. 1997 . Nucleic Acids Res , 25 : 491 – 496 .
   PubMed Web of Science ®Google Scholar
• Jeffrey , G. A. and Saenger , W. 1991 . Hydrogen Bonding in Biological Structures (Springer Verlag)
   Google Scholar
• Taylor , R. and Kennard , O. 1982 . J Am Chem Soc , 104 : 5063 – 5070 .
   Web of Science ®Google Scholar
• Lin , P. D. , Wang , Y. , Scherer , S. J. , Clark , A. B. , Yang , K. , Avdievich , E. , Jin , B. and et al . 2004 . Cancer Res , 64 : 517 – 522 .
   PubMed Web of Science ®Google Scholar
• Yang , W. 2008 . Cell Research , 18 : 184 – 197 .
   PubMed Web of Science ®Google Scholar
• Salsbury , F. R. 2010 . Protein Pept Lett , 17 : 744 – 750 .
   PubMed Web of Science ®Google Scholar