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Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations

Biochemistry, ASAP ,
DOI: 10.1021/acs.biochem.6b01192 Download PDF

A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

ACS Catal., (2016) 6, 1853-1869
DOI: 10.1021/acscatal.5b02158 Download PDF

Ribozyme catalysis with a twist: the active state of the twister ribozyme in solution predicted from molecular simulation

J. Am. Chem. Soc., (2016) 138, 3058-3065
DOI: 10.1021/jacs.5b12061 Download PDF

Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn2+

Chem Commun (Camb)., (2016) 52, 4462-4465
DOI: 10.1039/C5CC10212J Download PDF

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

RNA, (2016) 22, 32-48
DOI: 10.1261/rna.053710.115 Download PDF

Force Field for Mg2+, Mn2+, Zn2+, and Cd2+ Ions That Have Balanced Interactions with Nucleic Acids

J. Phys. Chem. B., (2015) 119, 15460-15460
DOI: 10.1021/acs.jpcb.5b10423 Download PDF

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism

Biochim Biophys Acta, (2015) 1854, 1801-1808
DOI: 10.1016/j.bbapap.2015.04.022 Download PDF

Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects

Biochim. Biophys. Acta, (2015) 1854, 1795-1800
DOI: 10.1016/j.bbapap.2015.02.022. Download PDF

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

J. Am. Chem. Soc., (2015) 137, 14705-14715
DOI: 10.1021/jacs.5b08395 Download PDF

Competitive interaction of monovalent cations with DNA from 3D-RISM

Nucleic Acids Res., (2015) 43, 8405-8415
DOI: 10.1093/nar/gkv830 Download PDF

Determination of hepatitis delta virus ribozyme N(–1) nucleobase and functional group specificity using internal competition kinetics

Anal. Biochem., (2015) 483, 12-20
DOI: 10.1016/j.ab.2015.04.024 Download PDF

Assessment of Metal-Assisted Nucleophile Activation in the Hepatitis Delta Virus Ribozyme from Molecular Simulation and 3D-RISM

RNA, (2015) 21, 1-12
DOI: 10.1261/rna.051466.115 Download PDF

Nucleic acid reactivity: challenges for next-generation semiempirical quantum models

J. Comput. Chem., (2015) 36, 1370-1389
DOI: 10.1002/jcc.23933 Download PDF

Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

J. Chem. Theory Comput., (2015) 11, 373-377
DOI: 10.1021/ct500776j Download PDF

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

RNA, (2015) 21, 963-974
DOI: 10.1261/rna.047357.114 Download PDF

Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions

Chem. Eur. J., (2014) 20, 14336-14343
DOI: 10.1002/chem.201403862 Download PDF

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation

Curr. Opin. Chem. Biol., (2014) 21C, 96-102
DOI: 10.1016/j.cbpa.2014.06.010. Download PDF

Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path

J. Am. Chem. Soc., (2014) 136, 7789-7792
DOI: 10.1021/ja500180q Download PDF

Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods

J. Chem. Theory Comput., (2014) 10, 1538–1545
DOI: 10.1021/ct401013s Download PDF

Ion counting from explicit solvent simulations and 3D-RISM

Biophys. J., (2014) 106, 883-894
DOI: 10.1016/j.bpj.2014.01.021 Download PDF

Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

J. Chem. Theory Comput., (2014) 10, 24-34
DOI: 10.1021/ct400691f Download PDF

Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis

DOI: 10.1016/B978-0-12-381286-5.00002-0 Download PDF

Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation

Proc. Natl. Acad. Sci. USA, (2013) 110, 13002-13007
DOI: 10.1073/pnas.1215086110 Download PDF

Molecular Simulations of RNA 2′-O-Transesterification Reaction Models in Solution

J. Phys Chem. B, (2013) 117, 94-103
DOI: 10.1021/jp3084277 Download PDF

Mapping l1 ligase ribozyme conformational switch

J. Mol. Biol., (2012) 423, 106-122
DOI: 10.1016/j.jmb.2012.06.035 Download PDF

Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment

Angew. Chem. Int. Ed., (2012) 51, 647-651
DOI: 10.1002/anie.201104147 Download PDF

Characterization of the structure and dynamics of the HDV ribozyme in different stages along the reaction path

J. Phys. Chem. Lett., (2011) 2, 2538-2543
DOI: 10.1021/jz201106y Download PDF

Active participation of Mg2+ ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozymes

DOI: 10.1021/ct100467t Download PDF

Computational mutagenesis studies of hammerhead ribozyme catalysis

J. Am. Chem. Soc., (2010) 132, 13505-13518
DOI: 10.1021/ja105956u Download PDF

Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations

DOI: 10.1016/S1574-1400(10)06001-9 Download PDF

Molecular dynamics simulation of bovine pancreatic ribonuclease A - CpA and transition state-like complexes

J. Phys. Chem. B, (2010) 21, 7371-7382
DOI: 10.1021/jp909004y Download PDF

Identification of dynamical hinge points of the L1 ligase molecular switch

RNA, (2010) 16, 769-780
DOI: 10.1261/rna.1897810 Download PDF

Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation

J. Mol. Biol., (2009) 388, 195-206
DOI: 10.1016/j.jmb.2009.02.054 Download PDF

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

RNA, (2008) 14, 1501-1507
DOI: 10.1261/rna.863108 Download PDF

Origin of Mutational Effects at the C3 and G8 Positions on Hammerhead Ribozyme Catalysis from Molecular Dynamics Simulations

J. Am. Chem. Soc., (2008) 130, 7168-7169
DOI: 10.1021/ja711242b Download PDF

Quantum mechanical/molecular mechanical simulation study of the mechanism of Hairpin ribozyme catalysis

J. Am. Chem. Soc., (2008) 130, 4680-4691
DOI: 10.1021/ja0759141 Download PDF

Solvent structure and hammerhead ribozyme catalysis

Chem. Biol., (2008) 15, 332-342
DOI: 10.1016/j.chembiol.2008.03.010 Download PDF

Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

J. Am. Chem. Soc., (2008) 130, 3053-3064
DOI: 10.1021/ja076529e Download PDF

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

J. Comput. Chem., (2007) 28, 495-507
DOI: 10.1002/jcc.20474 Download PDF

Density-functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification

J. Phys. Chem. B., (2005) 109, 19987-20003
DOI: 10.1021/jp053146z Download PDF

Theoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: solvent effects, thio effects, and implications for enzymatic reactions

J. Phys. Chem. B, (2005) 109, 13827-13834
DOI: 10.1021/jp051042i Download PDF

Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

Chemistry, (2005) 11, 2081-2093
DOI: 10.1002/chem.200400790 Download PDF

The contribution of phosphate-phosphate repulsions to the free energy of DNA bending

Nucleic Acids Res., (2005) 33, 1257-1268
DOI: 10.1093/nar/gki272 Download PDF

Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis

Chem. Phys. Chem., (2004) 5, 1045-1049
DOI: 10.1002/cphc.200400091 Download PDF

Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

J. Am. Chem. Soc., (2004) 126, 7504–7513
DOI: 10.1021/ja031815l Download PDF

Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods

J. Mol. Biol., (2003) 330, 993-1004
DOI: 10.1016/S0022-2836(03)00658-2 Download PDF

Quantum Mechanical Characterization of Nucleic Acids in Solution:  A Linear-Scaling Study of Charge Fluctuations in DNA and RNA

J. Phys. Chem. B, (2002) 106, 7693-7703
DOI: 10.1021/jp0146667 Download PDF

Theoretical studies on the hydrolysis of phosphate diesters in the gas phase, solution, and RNase A

Int. J. Quantum Chem., (2002) 86, 10-26
DOI: 10.1002/qua.1601 Download PDF

Application of Linear-Scaling Electronic Structure Methods to the Study of Polarization of Proteins and DNA in Solution

ACS Symposium Series, (1998) 712, 275-287
DOI: 10.1021/bk-1998-0712.ch018 Download PDF