|
1.Verlet, L. Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Phys. Rev., (1967) 159, 98–103. 2.Van Holde, K. E., W. C. Johnson, and P. S. Ho. Principles of Physical Biochemistry, Upper Saddle River, (1999) NJ: Prentice Hall. 3.Yarbo, J. W., Kennedy, B. J., Barnum, C. P. Mithramycin inhibition of ribonucleic acid synthesis. Cancer Res. (1968) 26, 36. 4.Miller, D. M., Polansky, D. A., Thomas, S. D., Ray, R., Campbell, V. W., Sanchez, J., Koller, C. A. Mithramycin selectively inhibits transcription of G-C containing DNA. Am. J. Med. Sci. (1987) 294, 388–394. 5.Chakrabarti, S., Bhattacharyya, B., Dasgupta, D. Interaction of Mithramycin and Chromomycin A3 with d(TAGCTAGCTA)2: Role of Sugars in Antibiotic−DNA Recognition. J. Phys. Chem. B (2002) 106, 6947–6953. 6.Aich, P., Dasgupta, D. Role of Mg++ in the mithramycin-DNA interaction: Evidence for two types of mithramycin-Mg++ complex. Biochem. Biophys. Res. Commun. (1990) 173, 689–692. 7.Aich, P., Sen, R., Dasgupta D. Interaction between antitumor antibiotic chromomycin A3 and Mg2+. I. Evidence for the formation of two types of chromomycin A3-Mg2+ complexes. Chem.-Biol. Interact. (1992) 83, 23–33. 8.Aich, P., Sen, R., Dasgupta, D. Role of magnesium ion in the interaction between chromomycin A3 and DNA: binding of chromomycin A3-Mg2+ complexes with DNA. Biochemistry (1992) 31, 2988–2997. 9.Aich, P., Dasgupta, D. Role of magnesium ion in mithramycin-DNA interaction: binding of mithramycin-Mg2+ complexes with DNA. Biochemistry (1995) 34, 1376–1385. 10. Chakrabarti, S., Mir, M. A., Dasgupta, D. Differential interactions of antitumor antibiotics chromomycin A(3) and mithramycin with d(TATGCATA)(2) in presence of Mg(2+). Biopolymers (2001) 62, 131–140. 11. Banville, D. L., Keniry, M. A., Shafer, R. H. NMR studies of the interaction of chromomycin A3 with small DNA duplexes. Binding to GC-containing sequences. Biochemistry (1990) 29, 6521–6534. 12. Banville, D. L., Keniry, M. A., Shafer, R. H. NMR investigation of mithramycin A binding to d(ATGCAT)2: a comparative study with chromomycin A3. Biochemistry (1990) 29, 9294–9304. 13. Gao, X., Patel, D. J. Solution structure of the chromomycin-DNA complex. Biochemistry (1989) 28, 751–762. 14. Sastry, M., Patel, D. J. Solution structure of the mithramycin dimer-DNA complex. Biochemistry (1993) 32, 6588–6604. 15. Majee, S., Sen, R., Guha, S., Bhattacharyya, D., Dasgupta, D. Differential interactions of the Mg2+ complexes of chromomycin A3 and mithramycin with poly(dG-dC) x poly(dC-dG) and poly(dG) x poly(dC). Biochemistry (1997) 36, 2291–2299. 16. Gao, X., Patel, D. J. Chromomycin dimer-DNA oligomer complexes. Sequence selectivity and divalent cation specificity. Biochemistry (1990) 29, 10940–10956. 17. Sastry, M., Fiala, R., Patel, D. J. Solution structure of mithramycin dimers bound to partially overlapping sites on DNA. J. Mol. Biol. (1995) 251, 674–689. 18.Chambers HF. In B. G. Katzung (ed.), Basic and clinical pharmacology, 9th ed. McGraw–Hill, (2004) New York, 764–772. 19.Fourmy D, Recht MI, Blanchard SC, Puglisi JD. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science (1996) 274, 1367–1371. 20.Fourmy D, Yoshizawa S, Puglisi JD. Paromomycin binding induces a local conformational change in the A–site of 16 s rRNA. J. Mol. Biol. (1998) 277, 333–345. 21.Yoshizawa S, Fourmy D, Puglisi JD. Structural origins of gentamicin antibiotic action. EMBO J. (1998) 17, 6437–6448. 22.Carter AP, Clemons WM, Brodersen DE, Morgan–Warren RJ, Wimberly BT, Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature (2000) 407, 340–348. 23.Vicens Q, Westhof E. Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Structure (2001) 9, 647–658. 24.Vicens Q, Westhof E. Crystal structure of geneticin bound to a bacterial 16 S ribosomal RNA A site oligonucleotide. J. Mol. Bio. (2003) 326, 1175–1188. 25.Fran�帙is B, Russell RJ, Murray JB, Aboul–ela F, Masquida B, Vicens Q, Westhof E. Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic Acid Res. (2005) 33, 5677–5690. 26.Vicens Q, Westhof E. Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding A site. Chem. Biol. (2002) 9, 747–755. 27.Kaul M, Pilch DS. Thermodynamics of aminoglycoside–rRNA recognition: The binding of neomycin–Class aminoglycosides to the A site of 16S rRNA. Biochemistry (2002) 41, 7695–7706. 28.Pilch DS, Kaul M, Barbieri CM, Kerrigan JE. Thermodynamics of aminoglycoside–rRNA recognition. Biopolymers (2003) 70, 58–79. 29.Yang G, Trylska J, Tor Y, McCammon JA. Binding of aminoglycosidic antibiotics to the oligonucleotide A–site model and 30S ribosomal subunit: Poisson–Boltzmann model, thermal denaturation, and fluorescence studies. J. Med. Chem. (2006) 49, 5478–5490. 30.Kaul M, Barbieri CM, Kerrigan JE, Pilch DS. Coupling of drug protonation to the specific binding of aminoglycosides to the A site of 16 S rRNA: elucidation of the number of drug amino groups involved and their identities. J. Mol. Biol. (2003) 326, 1373–1387. 31.Yoshizawa S, Fourmy D, Puglisi JD. Recognition of the codon–anticodon helix by ribosomal RNA. Science (1999) 285, 1722–1725. 32.Kaul M, Barbieri CM, Pilch DS. Aminoglycoside–induced reduction in nucleotide mobility at the ribosomal RNA A–site as a potentially key determinant of antibacterial activity. J. Am. Chem. Soc. (2006) 128, 1261–1271. 33.Sanbonmatsu KY. Energy landscape of the ribosomal decoding center. Biochimie (2006) 88, 1053–1059. 34.Vaiana AC, Sanbonmatsu KY. Stochastic Gating and Drug–Ribosome Interactions. J. Mol. Biol. (2009) 386, 648–661. 35.Meroueh SO, Mobashery S. Conformational transition in the aminoacyl t–RNA site of the bacterial ribosome both in the presence and absence of an aminoglycoside antibiotic. Chem. Biol. Drug. Des. (2007) 69, 291–297. 36.Vaiana AC, Westhof E, Auffinger P. A molecular dynamics simulation study of an aminoglycoside/A–site RNA complex: conformational and hydration patterns. Biochimie. (2006) 88, 1061–1073. 37.Romanowska J, Setny P, Trylska J. Molecular dynamics study of the ribosomal A–site. J. Phys. Chem. B (2008) 112, 15227–15243. 38.Berveridge, D. L., McConnell, K. J. Nucleic acids: theory and computer simulation, Y2K. Curr. Opin. Struct. Biol. (2000) 10, 182. 39.Cheatham, T. E., III, Kollman, P. A. Molecular dynamics simulation of nucleic acids. Annu. ReV. Phys. Chem. (2000) 51, 435. 40.Auffinger, P. & Vaiana, A. C. Molecular dynamics simulations of RNA systems. In Handbook of RNA biochemistry (Westhof, Bindereif, Schon & Hartmann, eds.) (2005) 560–576. Willey-VCH, Manheim. 41.Durante-Mangoni E, Grammatikos A, Utili R, Falagas ME. Do we still need the aminoglycosides? Int J Antimicrob Agents. (2009) 33, 201–205. 42.Wang J, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (resp) model perform in calculating conformational energies of organic and biological molecules. J. Comput. Chem. (2000) 21, 1049–1074. 43.Jorgensen WL, Chandrasekhar J, Madura J, Impley RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. (1983) 79, 926–935. 44.Bayly CI, Cieplak P, Cornell WD, Kollman PA. A well–behaved electrostatic potential based method using charge restraints for determining atom–centered charges: the RESP model. J. Phys. Chem. (1993) 97, 10269–10280. 45.Pathiaseril A, Woods RJ. Relative energies of binding for antibody–carbohydrate–antigen complexes computed from free–energy simulations. J. Am. Chem. Soc. (2000) 122, 331–338. 46.Recht MI, Fourmy D, Blanchard SC, Dahlquist KD, Puglisi JD. RNA sequence determinants for aminoglycoside binding to an A–site rRNA model oligonucleotide. J. Mol. Biol. (1996) 262, 421–436. 47.Case DA, Darden TA, Cheatham ITE, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Brozell S, Tsui V, Gohlke H, Mongan J, Hornak B, Cui G, Beroza P, Scafmeister C, Caldwell JW, Ross WS, Kollman PA. AMBER8. (2004) San Francisco: University of California. 48.Darden, T., York, D., Pedersen, L. Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J. Chem. Phys. (1993) 98, 10089–10092. 49.Ryckaert, J. P., Ciccotti, G., Berendsen, H. J. C. Numerical integration of the Cartesian equations of motion of a system with constraints; molecular dynamics of n–alkanes. J. Comput. Phys. (1977) 23, 237. 50.Tsui V, Case DA. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers (2001) 56, 275–291. 51.McQuarrie DA. Statistical mechanics. (1976) New York: Harper and Row. 52.Schlitter J. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem. Phys. Lett. (1993) 215, 617–621. 53.Kitao A, Go N. Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol. (1999) 9, 164–169. 54.Berendsen HJ, Hayward S. Collective protein dynamics in relation to function. Curr. Opin. Struct. Biol. (2000) 10, 165–169. 55.Amadei A, Linssen AB, Berendsen HJ. Essential dynamics of proteins. Proteins (1993) 17, 412–425. 56.Lavery R, Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. (1988) 6, 63–91. 57.Berendsen HJ, Van der Spoel D, Van Drunen R. GROMACS: A message–passing parallel molecular dynamics implementation. Comp. Phys. Comm. (1995) 91, 43–56. 58.Ceruso MA, Amadei A, Di Nola A. Mechanics and dynamics of B1 domain of protein G: role of packing and surface hydrophobic residues. Protein. Sci. (1999) 8, 147–160. 59.van Aalten DM, Conn DA, de Groot BL, Berendsen HJ, Findlay JB, Amadei A. Protein dynamics derived from clusters of crystal structures. Biophys. J. (1997) 73, 2891–2896. 60.de Groot BL, Hayward S, van Aalten DM, Amadei A, Berendsen HJ. Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data. Proteins (1998) 31, 116–127. 61.Sorin E.J., Rhee Y.M., Pande V.S. Does water play a structural role in the folding of small nucleic acids? Biophys. J. (2005) 88, 2516–2524. 62.Simone De A., Dodson G.G., Verma C.S., ZagariA., Fraternali F. Prion and water: tight and dynamical hydration sites have a key role in structural stability. Proc. Natl. Acad. Sci. USA (2005) 102, 7535–7540. 63.Rhodes M.M, R�繅lov�� K, Sponer J, Walter N.G. Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proc. Natl. Acad. Sci. USA (2006) 103, 13380–13385. 64.Papoian G.A., Ulander J., Eastwood M.P., Luthey-Schulten Z., Wolynes P.G. Water in protein structure prediction. Proc. Natl. Acad. Sci. USA (2004) 101, 3352–3357. 65.Petrone P.M., Garcia A.E. MHC-peptide binding is assisted by bound water molecules. J. Mol. Biol. (2004) 338, 419–435. 66.Verdonk M.L., ChessariG., Cole J.C., Hartshorn M.J., Murray C.W., Nissink J.W., Taylor R.D., Taylor R. Modeling water molecules in protein–ligand docking using GOLD. J. Med. Chem. (2005) 48, 6504–6515. 67.Henchman R.H., McCammon J.A. Extracting hydration sites around proteins from explicit water simulations. J. Comput. Chem. (2002) 23, 861–869. 68.Harris S. A., Gavathiotis E., Searle M. S., Orozco M., Laughton, C. A. Cooperativity in drug-DNA recognition: a molecular dynamics study. J. Am. Chem. Soc. (2001) 123, 12658–12663. 69.Schaefer M, Froemmel C. A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution. J. Mol. Biol. (1990) 216, 1045–1066. 70.Schaefer M, Karplus M. A comprehensive analytical treatment of continuum electrostatics. J. Phys. Chem. (1996) 100, 1578–1599. 71.Bashford D, Case DA. Generalized born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. (2000) 51, 129–152. 72.Recht MI, Douthwaite S, Puglisi JD. Basis for prokaryotic specificity of action of aminoglycoside antibiotics. EMBO J. (1999) 18, 3133–3138.
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