A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197

Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I.; Gould, Ian R.; Merz, Kenneth M.; Ferguson, David M.; Spellmeyer, David C.; Fox, Thomas; Caldwell, and James W.; Kollman, Peter A.

doi:10.1021/ja955032e

Cited by 1,300 publications

(1,535 citation statements)

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“…Thus, the present work indicates RNA and DNA•RNA hybrids to have greater local flexibility than DNA, consistent with crystallographic, NMR and fluorescence experiments. The contrast of the present results with those of Noy et al appear to be associated with the use of the AMBER force field 60,61 in that study versus the CHARMM27 force field in the present work. Further studies are required to investigate this force field difference in greater detail.…”

Section: Structural and Dynamic Characteristicscontrasting

confidence: 99%

Atomic Detail Investigation of the Structure and Dynamics of DNA•RNA Hybrids: A Molecular Dynamics Study

MacKerell

2008

J. Phys. Chem. B

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DNA•RNA hybrid duplexes are biologically important molecules and are shown to have potential therapeutic properties. To investigate the relationship between structures, energetics, solvation and RNase H activity of hybrid duplexes in comparison with pure DNA and RNA duplexes, a molecular dynamics study using the CHARMM27 force field was undertaken. The structural properties of all the four nucleic acids are in very good agreement with the experimental data. The backbone dihedral angles and the puckering of the (deoxy)ribose indicate that the purine rich strands retain their A/B like properties but the pyrimidine rich DNA strand undergoes A-B conformational transitions. The minor groove widths of the hybrid structures are narrower than in the RNA duplex a requirement for RNase H binding. In addition, sampling of noncanonical phosphodiester backbone dihedrals by the DNA strands, differential solvation properties and helical properties, most notably rise, are suggested to contribute to hybrids being RNase H substrates. Differential RNase H activity towards hybrids containing purine vs. pyrimidine rich RNA strands is suggested to be due to sampling of values of the phosphodiester backbone dihedrals in the DNA strands. Notably, the present results indicate that hybrids have decreased flexibility as compared to RNA, in contrast to previous reports.

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Section: Structural and Dynamic Characteristicscontrasting

confidence: 99%

Atomic Detail Investigation of the Structure and Dynamics of DNA•RNA Hybrids: A Molecular Dynamics Study

MacKerell

2008

J. Phys. Chem. B

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“…We note this range of interaction parameter is smaller than found in typical empirical force fields for protein-hydrocarbon side chains and lipids. 25 Water behavior in this zone of solute-solvent interaction is reminiscent of that observed in many earlier studies where either a hard sphere model or a vdW model with a very small attraction for the solute was considered. 5,6,15,27-31 As mentioned, Patey and co-workers first observed 6 that in between two, infinite, hard walls even a simple LJ fluid near bulk-phase coexistence can undergo a dewetting transition.…”

Section: Resultsmentioning

confidence: 52%

The Dewetting Transition and The Hydrophobic Effect

2007

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A molecular-level description of the behavior of water in hydrophobic spaces is presented in terms of the coupled effects of solute size and atomic solute-solvent interactions. For model solutes with surface areas near those of protein contacts, we identify three different regions of solute-water interaction to be associated with three distinctly different structural characteristics of water in the intersolute region: dry, oscillating, and wet. A first orderlike phase transition is confirmed from the wet to dry state bridged by a narrow region with liquid-vapor oscillations in the intersolute region as the strength of the solute-water attractive dispersion interaction decreases. We demonstrate that the recent idea that cavitation in the intersolute region of nanoscopic solutes is preceded by the formation of a vapor layer around an individual solute is not the general case. The appearance of density waves pulled up around and outside of a nanoscopic plate occurs at lower interaction strengths than are required to obtain a wet state between such plates. We further show that chemically reasonable estimates of the interaction strength lead to a microscopically wet state and a hydrophobic interaction characterized by traps and barriers to association and not by vacuum induced collapse.

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“…The computational treatment of this QM region employed the Vosko-WilkNusair local density approximation (VWN-LDA) 37 and the gradient corrections of Becke 38 and Perdew 39 for exchange and correlation, respectively, along with the ADF IV basis set (triple ζ with polarization on all heavy atoms). Alternatively, the atoms of the corrin ring substituents that have merely steric/electrostatic influences on the cofactor geometry were treated at the MM level using the Amber 95 force field 40 and were coupled to the QM region using the multipole derived charge analysis model as implemented in ADF. 41 QM/MM geometries were updated using the BFGS Hessian scheme in optimizations carried out with an integration constant of 4.0 on a cluster of Pentium Xeon processors (ACE Computers).…”

Section: Methodsmentioning

confidence: 99%

Spectroscopic Studies of the Corrinoid/Iron−Sulfur Protein from Moorella thermoacetica

et al. 2006

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Methyl transfer reactions are important in a number of biochemical pathways. An important class of methyltransferases uses the cobalt cofactor cobalamin, which receives a methyl group from an appropriate methyl donor protein to form an intermediate organometallic methyl-Co bond that subsequently is cleaved by a methyl acceptor. Control of the axial ligation state of cobalamin influences both the mode (i.e., homolytic vs heterolytic) and the rate of Co-C bond cleavage. Here we have studied the axial ligation of a corrinoid iron-sulfur protein (CFeSP) that plays a key role in energy generation and cell carbon synthesis by anaerobic microbes, such as methanogenic archaea and acetogenic bacteria. This protein accepts a methyl group from methyltetrahydrofolate forming Me-Co 3+ CFeSP that then donates a methyl cation (Me) from Me-Co 3+ CFeSP to a nickel site on acetyl-CoA synthase. To unambiguously establish the binding scheme of the corrinoid cofactor in the CFeSP, we have combined resonance Raman, magnetic circular dichroism, and EPR spectroscopic methods with computational chemistry. Our results clearly demonstrate that the MeCo 3+ and Co 2+ states of the CFeSP have an axial water ligand like the free MeCbi + and Co 2+ Cbi + cofactors; however, the Co-OH 2 bond length is lengthened by about 0.2 Å for the protein-bound cofactor. Elongation of the Co-OH 2 bond of the CFeSP-bound cofactor is proposed to make the cobalt center more "Co 1+ -like", a requirement to facilitate heterolytic Co-C bond cleavage.

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197

Cited by 1,300 publications

References 0 publications

Atomic Detail Investigation of the Structure and Dynamics of DNA•RNA Hybrids: A Molecular Dynamics Study

Atomic Detail Investigation of the Structure and Dynamics of DNA•RNA Hybrids: A Molecular Dynamics Study

The Dewetting Transition and The Hydrophobic Effect

Spectroscopic Studies of the Corrinoid/Iron−Sulfur Protein from Moorella thermoacetica

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