RNA crystallography

Holbrook, Stephen R.; Kim, Sung‐Hou

doi:10.1002/(sici)1097-0282(1997)44:1<3::aid-bip2>3.0.co;2-z

Cited by 74 publications

(16 citation statements)

References 82 publications

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“…MD simulations and free energy calculations have long been applied to DNAprotein complexes. The theoretical study of RNA-protein complexes, however, is a fairly new and emerging field concurrent with the explosion of RNA-protein structures determined by both crystallography and NMR (32,36,65,162). Often, the assembly of RNA-protein complexes requires extensive conformational rearrangement or induced-fit.…”

Section: Rna-protein Complexesmentioning

confidence: 99%

Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions

Wang

Donini

Reyes

et al. 2001

Annu. Rev. Biophys. Biomol. Struct.

514

436

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Computer modeling has been developed and widely applied in studying molecules of biological interest. The force field is the cornerstone of computer simulations, and many force fields have been developed and successfully applied in these simulations. Two interesting areas are (a) studying enzyme catalytic mechanisms using a combination of quantum mechanics and molecular mechanics, and (b) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE) calculation methods. Enzyme catalysis involves forming and breaking of covalent bonds and requires the use of quantum mechanics. Noncovalent interactions appear ubiquitously in biology, but here we confine ourselves to review only noncovalent interactions between protein and protein, protein and ligand, and protein and nucleic acids.

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Section: Rna-protein Complexesmentioning

confidence: 99%

Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions

Wang

Donini

Reyes

et al. 2001

Annu. Rev. Biophys. Biomol. Struct.

514

436

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“…For instance, the standard C1 0 -C1 0 distance between Watson-Crick base-pairs is 10.7 Å for GC and 10.4 Å for AU, whereas the distance for UU is 9.9 Å and for water-mediated UC is 11.7 Å . 35 The larger distance for the UC base-pair represents the fact that the water-mediated bridge increases the distance between the bases. The average distances between C1 0 -C1 0 atoms in the helix obtained from Hydrogen bond occupancy in percentage computed over 20 ns for the wild-type hairpin structure calculated using the GB method, DKC-mutated hairpin structure calculated using the GB method, and the wild-type hairpin structure calculated using the PME method.…”

Section: Base-pairing In Telomerasementioning

confidence: 99%

Dynamic Behavior of the Telomerase RNA Hairpin Structure and its Relationship to Dyskeratosis Congenita

Yingling¹,

Shapiro²

2005

Journal of Molecular Biology

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“…Coaxial stacking is the end-to-end stacking of separate helical RNA parts to form long quasi-continuous helical structures (see as example h16/h17 in 30S or H34/H35 in domain II of 50S in H. marismortui [64,67]). Stacking of nucleic acids is driven by the highly energetically favored stacking interactions between the -electron system of the nucleic acid bases [68].…”

Section: Coaxial Stackingmentioning

confidence: 99%