Trapped water molecules are essential to structural dynamics and function of a ribozyme. - Wikidata - awgldk - TriplyDB

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

http://www.wikidata.org/entity/Q35037250

about

Biomolecular electrostatics and solvation: a computational perspective Single molecule fluorescence approaches shed light on intracellular RNAs A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization Solvent Structure and Hammerhead Ribozyme Catalysis Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme Identification of an Imino Group Indispensable for Cleavage by a Small Ribozyme iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.The role of conserved waters in conformational transitions of Q61H K-ras.The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting".Coupling of fast and slow modes in the reaction pathway of the minimal hammerhead ribozyme cleavage.Molecular dynamics simulations of RNA: an in silico single molecule approach.Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation.Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition.Multiscale methods for computational RNA enzymology.Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases RNA dynamics: it is about time.Ribozyme catalysis revisited: is water involved?Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.Free energy calculation of modified base-pair formation in explicit solvent: A predictive model.The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (β/α)(8) barrel enzymes.The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch Allosteric activation via kinetic control: potassium accelerates a conformational change in IMP dehydrogenase.QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.Direct structural analysis of modified RNA by fluorescent in-line probing Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in Pressure modulates the self-cleavage step of the hairpin ribozyme.Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations.The Small Ribozymes: Common and Diverse Features Observed through the FRET Lens.Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme.General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility.

P2860

Q26853115-E12ECAFB-E20C-4BC5-A20E-8765EA091DFF Q26999350-1FF1A04A-069D-4A40-8199-E7BF97362272 Q27644728-A3494CD0-3509-493F-ADA5-418ADC196DA1 Q27650351-1FEC2F0C-5E54-4F49-BE4B-565A98E551BE Q27651015-A4DFF50E-A959-4381-B8E0-5C9466B49214 Q27654589-85E5AD5C-F61B-4E7E-899D-1E50E1DAB94F Q30479670-02859FCF-10D6-4B8C-A065-6C9A941AF47D Q33967967-76308952-2C66-427A-9A2F-6A06DBCBF94B Q34167863-F0640222-97FD-4646-AE58-BD3E3370DC94 Q35804539-FCE9E887-7F6F-4A76-BCBB-35798F7D696C Q35921595-40D35DF1-396B-4A50-852D-45E74FDFFC3C Q35972956-9051A98F-FE9F-4EBD-B1AD-E45190CCE3E3 Q36058510-B0DFCDC5-208B-46D3-A1F7-19B10EF13F60 Q36124795-A95A0C52-95ED-4A5D-A1A0-FF76781F9BC5 Q36176609-E8596BAC-CF42-4FD1-BBC7-A9A88457C91B Q36351119-1C7BEEFA-AC35-45CB-B8F1-072E11BE8DF1 Q36372186-A7CF7230-CCEF-4964-BC1D-38E70BFC0C3C Q36540017-231CEAC4-4554-4268-AE6B-8A3A4D636FF0 Q36800450-812A1953-C800-4212-A823-D4C812DF680B Q36967162-67135521-1852-4F42-9A47-427ECD368085 Q37045038-0CB682A8-2105-4426-A5E1-8079384A5AFC Q37127249-46DA6EF7-CC11-4EC4-ADB9-2F235AA40EF1 Q37142097-59863B0D-F741-42CB-8007-709B031D953F Q37366654-01F653BE-9004-4C11-A2A9-0D6D95F2AA3C Q37426610-23B710F0-D989-4CFD-9C93-9E1A5A2AF3FD Q37983899-172502CE-58DF-42F1-8BDA-D7CF8FE7FBBD Q38052698-45DF78E1-28C3-4E01-84AB-D7CD354F7957 Q38352038-88998497-49F9-4FFF-BCDE-04FF1BC64DDE Q38618632-2082FEB1-E604-4D90-A4A9-121D9D43963B Q39354341-73B8CD97-4CCB-472C-9F85-B8600EAB9795 Q40395128-ADF93310-B310-41EB-9E5E-E526C0D7BCB1 Q40623105-05B53D17-BABF-442F-B064-91D0EE3B12C3 Q41335361-BC3415B2-2AB8-45D6-ADA0-ECBB869F1F68 Q41809931-609345DC-1128-4EC1-9FB2-84C3DBB713BD Q41915155-6BCC2AD6-7B3C-4D9E-8A8F-4E4638B0E13A Q42292919-D4DCCF1F-AD09-4096-86E0-5E0605E34016 Q42362871-91433F24-123E-450D-9CCD-2332D29082A3 Q42839458-C46C124F-7EAD-4BDF-AAF9-7DF37D7FA86B Q43143817-0543706F-1D3F-43B8-9E3B-B52C16442003 Q43201948-CECF7408-62B1-4AC0-AAF4-F144BF19DA77

P2860

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

http://www.wikidata.org/entity/Q35037250

description

2006 nî lūn-bûn

@nan

2006 թուականի Օգոստոսին հրատարակուած գիտական յօդուած

@hyw

2006 թվականի օգոստոսին հրատարակված գիտական հոդված

@hy

2006年の論文

@ja

2006年学术文章

@wuu

2006年学术文章

@zh-cn

2006年学术文章

@zh-hans

2006年学术文章

@zh-my

2006年学术文章

@zh-sg

2006年學術文章

@yue

name

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

@ast

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

@en

type

label

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

@ast

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

@en

prefLabel

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

@ast

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

@en

P1433

Q35037250-7EE48FBC-A28B-46DC-B5A6-1DF19B70BC78

P1476

Q35037250-77FEEC2C-1036-41E9-8F97-48B7CDF6EE32

P2093

Q35037250-568ED3D8-6C4D-476A-835D-AAC2619E9721

Q35037250-58AFD23D-01E8-4DD9-95B7-ECAD538095F5

Q35037250-B2BC860D-B542-4D47-A6E9-5EF280DD166F

Q35037250-F0DD4FAD-251D-49A0-A5B0-F5DE6A130750

P2860

Q35037250-047958E1-F7D6-484C-BC90-0E3D69FE1EFD

Q35037250-0722208E-955C-469A-B78A-07A283487FEF

Q35037250-0BFA5769-AB27-42CD-85F8-6B07DB273AFA

Q35037250-1640BF8B-F82A-416C-B27F-3C09F15C94C1

Q35037250-195E959F-EC16-41A6-90C4-EC52F84EA966

Q35037250-2024C6D2-AE0E-4868-BC52-211732C32566

Q35037250-22081C49-88AE-4825-8A77-C06CE1F3C438

Q35037250-23AA3A02-1F55-4DFE-9CA7-99A75BBCBF1D

Q35037250-2AAD7D70-1E0B-4DC9-A1DC-0C0BAE3AD420

Q35037250-31A72FDF-D53E-4281-8625-72A640CD0F8B

P304

Q35037250-8024B0D3-1E8E-4549-ADEA-CEE6FE3D295F

P31

Q35037250-13E0FC34-B95D-47EF-AD9C-737B20A00884

P356

Q35037250-B840A244-9F28-4BB1-A1B8-EE5510D4E6CC

P407

Q35037250-8B2D6AD4-0DBD-42AA-92CA-DEAB0B086197

P433

Q35037250-70B039DE-16ED-4836-8796-266764BD0C68

P478

Q35037250-CF78332A-A210-4FCA-9CAD-36959FC706BD

P577

Q35037250-F42211C6-A64A-476E-B566-645DE7F6BDA4

P5875

Q35037250-B777C446-85FB-49FB-9113-071C92EAAB62

P698

Q35037250-37D61034-B6DF-4B86-9B4F-F66BDE66DFC3

P921

Q35037250-DFB476FA-839B-41FD-8036-49897044781B

P932

Q35037250-C0B3D72C-4FD0-40DA-86CC-176C79B9D6C5

P356

PNAS.0605090103

P1433

Proceedings of the National Academy of Sciences of the United States of America

P1476

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

@en

P2093

Jirí Sponer

http://www.w3.org/2001/XMLSchema#string

Kamila Réblová

http://www.w3.org/2001/XMLSchema#string

Maria M Rhodes

http://www.w3.org/2001/XMLSchema#string

Nils G Walter

http://www.w3.org/2001/XMLSchema#string

P2860

Molecular dynamics simulations of sarcin-ricin rRNA motif.

Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis

Transition state stabilization by a catalytic RNA

The transcriptional landscape of the mammalian genome

The RNA world on ice: a new scenario for the emergence of RNA information

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone

Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer

Functional involvement of G8 in the hairpin ribozyme cleavage mechanism.

Ribo-gnome: the big world of small RNAs

Energetics and cooperativity of tertiary hydrogen bonds in RNA structure.

P304

13380-13385

http://www.w3.org/2001/XMLSchema#string

P31

scholarly article

P356

10.1073/PNAS.0605090103

http://www.w3.org/2001/XMLSchema#string

P407

P433

36

http://www.w3.org/2001/XMLSchema#string

P478

103

http://www.w3.org/2001/XMLSchema#string

P577

2006-08-24T00:00:00Z

http://www.w3.org/2001/XMLSchema#dateTime

P5875

6849575

http://www.w3.org/2001/XMLSchema#string

P698

16938834

http://www.w3.org/2001/XMLSchema#string

P921

P932

1569172

http://www.w3.org/2001/XMLSchema#string