A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns.
作者： A VAIANA , E WESTHOF , P AUFFINGER
DOI: 10.1016/J.BIOCHI.2006.06.006
关键词:
摘要: … On the contrary, the group formed by sites w6, w9, and w11 is characterized by low residence times (less than 0.25 ns) in both binding pockets as well as high exchange rates. …
archives-ouvertes.fr
elsevier.com
sci-hub.se 参考文章(61)
Pascal Auffinger, Molecular Dynamics Simulations of RNA Systems: Importance of the Initial Conditions Computational Studies of RNA and DNA. pp. 283- 300 ,(2006) , 10.1007/978-1-4020-4851-3_11
Berghuis Am, Wright Gd, Mobashery S, Aminoglycoside antibiotics. Structures, functions, and resistance. Advances in Experimental Medicine and Biology. ,vol. 456, pp. 27- 69 ,(1998)
G. A. Papoian, J. Ulander, M. P. Eastwood, Z. Luthey-Schulten, P. G. Wolynes, Water in protein structure prediction Proceedings of the National Academy of Sciences of the United States of America. ,vol. 101, pp. 3352- 3357 ,(2004) , 10.1073/PNAS.0307851100
Pascal Auffinger, Andrea C. Vaiana, Molecular Dynamics Simulations of RNA Systems Wiley‐VCH Verlag GmbH & Co. KGaA. pp. 560- 576 ,(2008) , 10.1002/9783527619504.CH34
Handbook of RNA biochemistry Wiley-VCH. ,(2005) , 10.1002/9783527619504
Liem X. Dang, Mechanism and Thermodynamics of Ion Selectivity in Aqueous Solutions of 18-Crown-6 Ether: A Molecular Dynamics Study Journal of the American Chemical Society. ,vol. 117, pp. 6954- 6960 ,(1995) , 10.1021/JA00131A018
Juan Luis Asensio, Ana Hidalgo, Igor Cuesta, Carlos González, Javier Cañada, Cristina Vicent, Jose Luis Chiara, Gabriel Cuevas, Jesús Jiménez-Barbero, Experimental evidence for the existence of non-exo-anomeric conformations in branched oligosaccharides: NMR analysis of the structure and dynamics of aminoglycosides of the neomycin family. Chemistry: A European Journal. ,vol. 8, pp. 5228- 5240 ,(2002) , 10.1002/1521-3765(20021115)8:22<5228::AID-CHEM5228>3.0.CO;2-L
Pascal Auffinger, Shirley Louise-May, Eric Westhof, Molecular Dynamics Simulations of the Anticodon Hairpin of tRNAAsp: Structuring Effects of C−H···O Hydrogen Bonds and of Long-Range Hydration Forces Journal of the American Chemical Society. ,vol. 118, pp. 1181- 1189 ,(1996) , 10.1021/JA952494J
Chiansan Ma, Nathan A. Baker, Simpson Joseph, J. Andrew McCammon, Binding of Aminoglycoside Antibiotics to the Small Ribosomal Subunit: A Continuum Electrostatics Investigation Journal of the American Chemical Society. ,vol. 124, pp. 1438- 1442 ,(2002) , 10.1021/JA016830+
C. S. Poornima, P. M. Dean, Hydration in drug design. 2. Influence of local site surface shape on water binding. Journal of Computer-aided Molecular Design. ,vol. 9, pp. 513- 520 ,(1995) , 10.1007/BF00124322