scholarly journals Specific Interaction between Catabolite Activator Protein and Cyclic AMP: Molecular Mechanics and Molecular Orbital Calculations

2005 ◽  
Vol 6 ◽  
pp. 67-82
Author(s):  
Haruhiko Nakamura ◽  
Ryo Usuki ◽  
Takayuki Natume ◽  
Noriyuki Kurita
Keyword(s):  
Cyclic Amp ◽  
Molecular Mechanics ◽  
Molecular Orbital ◽  
Specific Interaction ◽  
Molecular Orbital Calculations ◽  
Catabolite Activator Protein ◽  
Activator Protein

DENSITY FUNCTIONAL CALCULATIONS ON THE INTERACTION BETWEEN CATABOLITE ACTIVATOR PROTEIN AND CYCLIC AMP USING THE FRAGMENT MOLECULAR ORBITAL METHOD

2005 ◽  
Vol 04 (01) ◽  
pp. 183-195 ◽  
Author(s):  
SIN-ICHIRO SUGIKI ◽  
MAKOTO MATSUOKA ◽  
RYO USUKI ◽  
YASUO SENGOKU ◽  
NORIYUKI KURITA ◽  
...  
Keyword(s):  
Molecular Orbital ◽  
Density Functional ◽  
Specific Interaction ◽  
Cyclic Adenosine Monophosphate ◽  
Adenosine Monophosphate ◽  
Orbital Method ◽  
Molecular Orbital Method ◽  
Fragment Molecular Orbital ◽  
Catabolite Activator Protein ◽  
Activator Protein

The specific interaction between catabolite activator protein (CAP) and cyclic adenosine monophosphate (cAMP) was investigated using the fragment molecular orbital method based on density functional theory (FMO-DFT). One of the efficient tools of FMO-DFT is the analysis of effective pair interactions, which are the pairwise fragment interactions under the influence of electrostatic potentials from surrounding fragments. We investigated the specific interaction between CAP/mutated-CAP and cAMP/cGMP to elucidate the effect of amino-acid mutations in CAP on the CAP-cAMP as well as CAP-cGMP interactions.

scholarly journals Stable Structure for the Complex of Catabolite Activator Protein and Cyclic AMP: Molecular Mechanics Optimization by AMBER

2004 ◽  
Vol 5 ◽  
pp. 19-25
Author(s):  
Ryo Usuki ◽  
Yasuo Sengoku ◽  
Makoto Matsuoka ◽  
Shigenori Tanaka ◽  
Noriyuki Kurita
Keyword(s):  
Cyclic Amp ◽  
Molecular Mechanics ◽  
Stable Structure ◽  
Catabolite Activator Protein ◽  
Activator Protein

Molecular mechanics and all-electron fragment molecular orbital calculations on mutated polyglutamine peptides

2010 ◽  
Vol 944 (1-3) ◽  
pp. 12-20 ◽  
Author(s):  
Bryan M.B. Van Schouwen ◽  
Miki Nakano ◽  
Hirofumi Watanabe ◽  
Shigenori Tanaka ◽  
Heather L. Gordon ◽  
...  
Keyword(s):  
Molecular Mechanics ◽  
Molecular Orbital ◽  
Molecular Orbital Calculations ◽  
Fragment Molecular Orbital

scholarly journals Multiple Control of Flagellum Biosynthesis in Escherichia coli: Role of H-NS Protein and the Cyclic AMP-Catabolite Activator Protein Complex in Transcription of the flhDC Master Operon

1999 ◽  
Vol 181 (24) ◽  
pp. 7500-7508 ◽  
Author(s):  
O. Soutourina ◽  
A. Kolb ◽  
E. Krin ◽  
C. Laurent-Winter ◽  
S. Rimsky ◽  
...  
Keyword(s):  
Cyclic Amp ◽  
Transcriptional Start Site ◽  
Regulatory Region ◽  
Start Codon ◽  
Transcriptional Fusion ◽  
Multiple Control ◽  
Catabolite Activator Protein ◽  
Activator Protein ◽  
Flagellum Biosynthesis

ABSTRACT Little is known about the molecular mechanism by which histone-like nucleoid-structuring (H-NS) protein and cyclic AMP-catabolite activator protein (CAP) complex control bacterial motility. In the present paper, we show that crp and hns mutants are nonmotile due to a complete lack of flagellin accumulation. This results from a reduced expression in vivo of fliA and fliC, which encode the specific flagellar sigma factor and flagellin, respectively. Overexpression of the flhDC master operon restored, at least in part, motility in crp andhns mutant strains, suggesting that this operon is the main target for both regulators. Binding of H-NS and CAP to the regulatory region of the master operon was demonstrated by gel retardation experiments, and their DNA binding sites were identified by DNase I footprinting assays. In vitro transcription experiments showed that CAP activates flhDC expression while H-NS represses it. In agreement with this observation, the activity of a transcriptional fusion carrying the flhDC promoter was decreased in thecrp strain and increased in the hns mutant. In contrast, the activity of a transcriptional fusion encompassing the entire flhDC regulatory region extending to the ATG translational start codon was strongly reduced in both hnsand crp mutants. These results suggest that the region downstream of the +1 transcriptional start site plays a crucial role in the positive control by H-NS of flagellum biosynthesis in vivo. Finally, the lack of complementation of the nonmotile phenotype in acrp mutant by activation-deficient CAP mutated proteins and characterization of cfs, a mutation resulting in a CAP-independent motility behavior, demonstrate that CAP activatesflhDC transcription by binding to its promoter and interacting with RNA polymerase.

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