Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
about
Solvent Structure and Hammerhead Ribozyme CatalysisActive-Site Monovalent Cations Revealed in a 1.55-Å-Resolution Hammerhead Ribozyme StructureCrystal structure and mechanistic investigation of the twister ribozymeMolecular modeling of nucleic acid structure: energy and samplingA Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme ActivationComputational mutagenesis studies of hammerhead ribozyme catalysis.Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis.Protein-responsive ribozyme switches in eukaryotic cells.Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme.Insight into the phosphodiesterase mechanism from combined QM/MM free energy simulations.Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path.Ground-state coordination of a catalytic metal to the scissile phosphate of a tertiary-stabilized Hammerhead ribozyme.Folding of the hammerhead ribozyme: pyrrolo-cytosine fluorescence separates core folding from global folding and reveals a pH-dependent conformational change.Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulationsMapping L1 ligase ribozyme conformational switch.Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.Multiscale methods for computational RNA enzymology.Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids.Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization.Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation.Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes.Model systems: how chemical biologists study RNA.Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction.Molecular modeling of nucleic acid structure: energy and sampling.Nucleic acid catalysis: metals, nucleobases, and other cofactors.Structural evaluation of the DNA aptamer for ATP DH25.42 by AFM.Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations.Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes.The structure of a nucleolytic ribozyme that employs a catalytic metal ion.Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides.The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents.Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformationsProtonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme.Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions.Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations.RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
P2860
Q27650351-0E23D654-19A5-414A-A9C5-847055264916Q27678350-3E519ED7-7454-4F6C-9DE8-E170DDEC67DAQ27694565-411CA9B4-C649-40B4-9348-1996E6441CF3Q28386410-16699241-7620-448D-A06E-4C884F9DE5DEQ28821468-BB5A1F0D-E137-403F-A70B-4336D799A3EFQ30496830-1CF993D1-9839-4A66-9307-750326126EE3Q34267439-AA60D6E1-2F97-43A3-A95C-E9BB1A541099Q34510072-4801E5B6-737A-4E57-AFC6-2D76A8842914Q34615599-24524D7B-0FAF-4C67-A429-189DA21DEACCQ35083854-2F223FC2-499D-4314-9807-A4F9E093C814Q35628399-A5AA2060-B9A8-480B-BF7A-7A6F39718F0DQ35682190-9FCA75E8-0040-4C14-B48D-8C9BE8632819Q35775781-0FABDD85-1525-4422-9121-0F213573846CQ36404547-AADA9401-85C7-429E-9005-D54E1A79E784Q36433589-2933EC5B-3FC6-413C-B646-0AB60F4F1904Q36455539-F803B416-E2B0-4F63-9A1E-5D264CBA6CA4Q36540017-826C9D9A-4F84-4587-8901-7F617C02CC45Q36561838-A804C383-96A0-4546-9D9D-AC00EBAF4FEEQ36604456-0342F1CA-6807-4025-B655-C8D64381C6D0Q37142097-790CE96A-194F-4F75-BFC4-FC1F1107712AQ37151359-55C92F64-C975-4800-B7E7-0EFE4CCAF380Q37275350-29FEEB43-438B-43CE-B0DA-992281361BB4Q37366654-05E698ED-08DD-4093-ACF8-CD2959F49EC1Q37399660-A4E85C46-23D1-48C4-9A7A-8F2F2774DD49Q37455511-6717027F-BA4A-4863-8A25-8934764DA89AQ37946428-9AC85A6C-0721-40BF-A021-4EDD9BA0EBDBQ38186666-F822C5FD-25E8-4EFF-85F8-EFFE459FB2D5Q38204496-E1B0044D-68D9-48C7-B657-47A051316397Q38308629-F491D0CB-696E-4C7F-B2B0-CDE5464AA6C3Q38771778-F365D916-3326-4356-A462-AD993BBD5B35Q38820529-19E7322D-6798-4E2B-B1FD-6D2A1D745BD7Q38926821-A77BF383-A092-4261-966D-6A52DFF31925Q38959329-B9B00E8C-A790-4056-9468-2564439376D2Q39310715-CCBA1B62-06CF-4186-A5DB-C0E018BFE469Q41335361-428E7A84-9490-4875-B304-40BBAE45136FQ41809931-4BC64A21-2DA9-43AA-A4DC-7DAFD3FD97BEQ42021708-B476928B-80B6-401B-A673-40F91A53D947Q42040369-239F77A1-CDBA-4334-B08B-BCDEB59235DEQ45075632-C2ED8C83-329E-4078-A750-29E00DD2D38BQ47235409-03DE61DE-0041-4F4E-A83F-AC800A2D7AD3
P2860
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
description
2008 nî lūn-bûn
@nan
2008年の論文
@ja
2008年論文
@yue
2008年論文
@zh-hant
2008年論文
@zh-hk
2008年論文
@zh-mo
2008年論文
@zh-tw
2008年论文
@wuu
2008年论文
@zh
2008年论文
@zh-cn
name
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
@en
type
label
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
@en
prefLabel
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
@en
P2860
P50
P356
P1476
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
@en
P2093
Monika Martick
William G Scott
P2860
P304
P356
10.1021/JA076529E
P407
P577
2008-02-14T00:00:00Z