QCRNA 1.0: A database of quantum calculations for RNA catalysis

Giese, Timothy J.; Gregersen, Brent A.; Liu, Yun; Nam, Kwangho; Mayaan, Evelyn; Moser, Adam; Range, Kevin; Faza, Olalla Nieto; López, Carlos Silva; Lera, Ángel R. de; Schaftenaar, Gijs; López, Xabier; T, Lee; Karypis, George; York, Darrin M.

doi:10.1016/j.jmgm.2006.02.011

Cited by 27 publications

(46 citation statements)

References 88 publications

(85 reference statements)

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“…5 compares the polarizabilities of DFTB2, DFTB2+CPEQ, and DFTB2+CPE0 to standard B3LYP/6-31++G** results. The comparisons include 33 anionic, 142 neutral, and 35 cationic molecules taken from the QCRNA database [80]. The molecules were selected for having contained some combination of H, C, N, and O, but no other elements.…”

Section: Methodsmentioning

confidence: 99%

Density-functional expansion methods: grand challenges

Giese

York

2012

Theor Chem Acc

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We discuss the source of errors in semiempirical density functional expansion (VE) methods. In particular, we show that VE methods are capable of well-reproducing their standard Kohn-Sham density functional method counterparts, but suffer from large errors upon using one or more of these approximations: the limited size of the atomic orbital basis, the Slater monopole auxiliary basis description of the response density, and the one- and two-body treatment of the core-Hamiltonian matrix elements. In the process of discussing these approximations and highlighting their symptoms, we introduce a new model that supplements the second-order density-functional tight-binding model with a self-consistent charge-dependent chemical potential equalization correction; we review our recently reported method for generalizing the auxiliary basis description of the atomic orbital response density; and we decompose the first-order potential into a summation of additive atomic components and many-body corrections, and from this examination, we provide new insights and preliminary results that motivate and inspire new approximate treatments of the core-Hamiltonian.

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Section: Methodsmentioning

confidence: 99%

Density-functional expansion methods: grand challenges

Giese

York

2012

Theor Chem Acc

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“…All calculations were performed in accord with the standardized protocol, previously detailed,40 used to construct the QCRNA database, a recently developed on-line database of quantum calculations for RNA catalysis 41. In brief, all structures were optimized in the gas phase with with B3LYP/6–31++G** as implemented in the Gaussian03 suite of programs 42.…”

Section: Methodsmentioning

confidence: 99%

Density functional study of the influence of C5 cytosine substitution in base pairs with guanine

et al. 2008

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The present study employs density-functional electronic structure methods to investigate the effect of chemical modification at the C5 position of cytosine. A series of experimentally motivated chemical modifications are considered, including alkyl, halogen, aromatic, fused ring, and strong σ and π withdrawing functional groups. The effect of these modifications on cytosine geometry, electronic structure, proton affinities, gas phase basicities, cytosine-guanine base-pair hydrogen bond network and corresponding nucleophilicity at guanine are examined. Ultimately, these results play a part in dissecting the effect of endogenous cytosine methylation on the reactivity of neighboring guanine toward carcinogens and DNA alkylating agents.

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“… f As additional benchmark, all (19) RNA model reactions with the overall charge of −1 are selected from the QCRNA database from the York group;[78] these include 56 reaction energies and 47 barriers. These systems were consistently calculated at the B3LYP/6-311++G(3df,2p) level for energy and B3LYP/6-31++G(d,p) for structure by the York group.…”

Section: Figures and Tablementioning

confidence: 99%

Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin

Yang¹,

Yu²,

Cui³

2008

Journal of Molecular Biology

114

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Conventional myosin is representative of biomolecular motors in which the hydrolysis of Adenosine triphosphate (ATP) is coupled to large-scale structural transitions both in and remote from the active site. The mechanism that underlies such “mechanochemical coupling”, especially the causal relationship between the hydrolysis and the allosteric structural changes, has remained elusive despite extensive experimental and computational analyses. In this study, using combined quantum mechanical and molecular mechanical (QM/MM) simulations and different conformations of the myosin motor domain, we provide evidence to support that regulation of ATP hydrolysis activity is not limited to residues in the immediate environment of the γ phosphate. Specifically, we illustrate that efficient hydrolysis of ATP depends not only on the proper orientation of the lytic water but also the structural stability of several nearby residues, especially the Arg238-Glu459 salt-bridge (the numbering of residues follows the myosin II in Dictyostelium discoideum) and the water molecule that spans this salt-bridge and the lytic water. More importantly, by comparing the hydrolysis activity in two motor conformations with very similar active site (i.e., Switch-I and II) configurations, which distinguishes this work from our previous study, the results clearly indicate that the ability of these residues to make their crucial electrostatic stabilization relies on the configuration of residues in the nearby N-terminus of the relay helix and the “wedge loop”. Without the structural support from those motifs, residues in a closed active site in the post-rigor motor domain undergo subtle structural variations that lead to consistently higher calculated ATP hydrolysis barriers than in the pre-powerstroke state. In other words, starting from the post-rigor state, turning on the ATPase activity requires not only displacement of Switch II to close the active site but also structural transitions in the N-terminus of the relay helix and the “wedge loop”, which have been proposed previously to be ultimately coupled to the rotation of the converter subdomain 40 Å away.

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QCRNA 1.0: A database of quantum calculations for RNA catalysis

Cited by 27 publications

References 88 publications

Density-functional expansion methods: grand challenges

Density-functional expansion methods: grand challenges

Density functional study of the influence of C5 cytosine substitution in base pairs with guanine

Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin

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