scholarly journals Molecular Dynamics Simulation of the RNA Complex of a Double-Stranded RNA-Binding Domain Reveals Dynamic Features of the Intermolecular Interface and Its Hydration

2002 ◽  
Vol 83 (6) ◽  
pp. 3542-3552 ◽  
Author(s):  
Tiziana Castrignanò ◽  
Giovanni Chillemi ◽  
Gabriele Varani ◽  
Alessandro Desideri
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Rna Binding ◽  
Binding Domain ◽  
Dynamics Simulation ◽  
Dynamic Features ◽  
Double Stranded Rna ◽  
Rna Binding Domain ◽  
Rna Complex

scholarly journals Two functionally distinct RNA-binding motifs in the regulatory domain of the protein kinase DAI.

1995 ◽  
Vol 15 (1) ◽  
pp. 358-364 ◽  
Author(s):  
S R Green ◽  
L Manche ◽  
M B Mathews
Keyword(s):  
Amino Acid ◽  
Protein Kinase ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Alpha Helix ◽  
Binding Domain ◽  
Single Amino Acid ◽  
Double Stranded Rna ◽  
C Terminus ◽  
Rna Binding Domain

The RNA-binding domain of the protein kinase DAI, the double-stranded RNA inhibitor of translation, contains two repeats of a motif that is also found in a number of other RNA-binding proteins. This motif consists of 67 amino acid residues and is predicted to contain a positively charged alpha helix at its C terminus. We have analyzed the effects of equivalent single amino acid changes in three conserved residues distributed over each copy of the motif. Mutants in the C-terminal portion of either repeat were severely defective, indicating that both copies of the motif are essential for RNA binding. Changes in the N-terminal and central parts of the motif were more debilitating if they were made in the first motif than in the second, suggesting that the first motif is the more important for RNA binding and that the second motif is structurally more flexible. When the second motif was replaced by a duplicate of the first motif, the ectopic copy retained its greater sensitivity to mutation, implying that the two motifs have distinct functions with respect to the process of RNA binding. Furthermore, the mutations have the same effect on the binding of double-stranded RNA and VA RNA, consistent with the existence of a single RNA-binding domain for both activating and inhibitory RNAs.

scholarly journals Specificity of the Double-Stranded RNA-Binding Domain from the RNA-Activated Protein Kinase PKR for Double-Stranded RNA: Insights from Thermodynamics and Small-Angle X-ray Scattering

Biochemistry ◽  
2012 ◽  
Vol 51 (46) ◽  
pp. 9312-9322 ◽  
Author(s):  
Sunita Patel ◽  
Joshua M. Blose ◽  
Joshua E. Sokoloski ◽  
Lois Pollack ◽  
Philip C. Bevilacqua
Keyword(s):  
Protein Kinase ◽  
Small Angle ◽  
Rna Binding ◽  
Binding Domain ◽  
Double Stranded Rna ◽  
X Ray ◽  
X Ray Scattering ◽  
Rna Binding Domain ◽  
Ray Scattering

scholarly journals Identification of the gene encoding a type 1 RNase H with an N-terminal double-stranded RNA binding domain from a psychrotrophic bacterium

FEBS Journal ◽  
2007 ◽  
Vol 274 (14) ◽  
pp. 3715-3727 ◽  
Author(s):  
Takashi Tadokoro ◽  
Hyongi Chon ◽  
Yuichi Koga ◽  
Kazufumi Takano ◽  
Shigenori Kanaya
Keyword(s):  
Rna Binding ◽  
Rnase H ◽  
Binding Domain ◽  
Gene Encoding ◽  
Double Stranded Rna ◽  
Psychrotrophic Bacterium ◽  
Rna Binding Domain

scholarly journals Asymmetric Structural Motions of the Homomeric α7 Nicotinic Receptor Ligand Binding Domain Revealed by Molecular Dynamics Simulation

2003 ◽  
Vol 85 (5) ◽  
pp. 3007-3018 ◽  
Author(s):  
Richard H. Henchman ◽  
Hai-Long Wang ◽  
Steven M. Sine ◽  
Palmer Taylor ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ligand Binding ◽  
Nicotinic Receptor ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Dynamics Simulation ◽  
Receptor Ligand
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