A theoretical study of polyelectrolyte effects in protein-DNA interactions: Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of .lambda. repressor-operator complex formation

1991 ◽  
Vol 113 (14) ◽  
pp. 5211-5215 ◽  
Author(s):  
B. Jayaram ◽  
F. M. DiCapua ◽  
David L. Beveridge
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Complex Formation ◽  
Theoretical Study ◽  
Dna Interactions ◽  
Lambda Repressor ◽  
Protein Dna Interactions ◽  
Energy Simulations

scholarly journals Site-Directed Mutagenesis Studies of Tn5 Transposase Residues Involved in Synaptic Complex Formation

2007 ◽  
Vol 189 (20) ◽  
pp. 7436-7441 ◽  
Author(s):  
Soheila Vaezeslami ◽  
Rachel Sterling ◽  
William S. Reznikoff
Keyword(s):  
Complex Formation ◽  
Catalytic Reactions ◽  
Site Directed Mutagenesis ◽  
Dna Interactions ◽  
Synaptic Complex ◽  
Biochemical Assays ◽  
Protein Dna Interactions ◽  
End Sequences ◽  
Tn5 Transposase ◽  
Cocrystal Structure

ABSTRACT Transposition (the movement of discrete segments of DNA, resulting in rearrangement of genomic DNA) initiates when transposase forms a dimeric DNA-protein synaptic complex with transposon DNA end sequences. The synaptic complex is a prerequisite for catalytic reactions that occur during the transposition process. The transposase-DNA interactions involved in the synaptic complex have been of great interest. Here we undertook a study to verify the protein-DNA interactions that lead to synapsis in the Tn5 system. Specifically, we studied (i) Arg342, Glu344, and Asn348 and (ii) Ser438, Lys439, and Ser445, which, based on the previously published cocrystal structure of Tn5 transposase bound to a precleaved transposon end sequence, make cis and trans contacts with transposon end sequence DNA, respectively. By using genetic and biochemical assays, we showed that in all cases except one, each of these residues plays an important role in synaptic complex formation, as predicted by the cocrystal structure.

scholarly journals Protein-DNA Interactions at the Opossum Npt2a Promoter are Dependent upon NHERF-1

2016 ◽  
Vol 39 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Barbara J. Clark ◽  
Rebecca D. Murray ◽  
Sarah A. Salyer ◽  
Samuel C. Tyagi ◽  
Cibi Arumugam ◽  
...  
Keyword(s):  
Complex Formation ◽  
Brush Border ◽  
Brush Border Membrane ◽  
Proximal Promoter ◽  
Mrna Levels ◽  
Dna Interactions ◽  
Phosphate Homeostasis ◽  
Protein Levels ◽  
Protein Dna Interactions ◽  
Mrna Half Life

Background/Aims: Phosphate homeostasis is controlled by the renal reabsorption of Pi by the type IIa sodium phosphate cotransporter, Npt2a, which is localized in the proximal tubule brush border membrane. Regulation of Npt2a expression is a key control point to maintain phosphate homeostasis with most studies focused on regulating protein levels in the brush border membrane. Molecular mechanisms that control Npt2a mRNA, however, remain to be defined. We have reported that Npt2a mRNA and protein levels correlate directly with the expression of the Na+/H+ exchanger regulatory factor 1 (NHERF-1) using opossum kidney (OK) cells and the NHERF-1-deficient OK-H cells. The goal of this study was to determine whether NHERF-1 contributes to transcriptional and/or post-transcriptional mechanisms controlling Npt2a mRNA levels. Methods: Npt2a mRNA half-life was compared between OK and NHERF-1 deficient OK-H cell lines. oNpt2a promoter-reporter gene assays and electrophoretic mobility shift assays (EMSA) were used identify a NHERF-1 responsive region within the oNpt2a proximal promoter. Results: Npt2a mRNA half-life is the same in OK and OK-H cells. The NHERF-1 responsive region lies within the proximal promoter in a region that contains a highly conserved CAATT box and G-rich element. Specific protein-DNA complex formation with the CAATT element is altered by the absence of NHERF-1 (OK v OK-H EMSA) although NHERF-1 does not directly contribute to complex formation. Conclusion: NHERF-1 helps maintain steady-state Npt2a mRNA levels in OK cells through indirect mechanisms that help promote protein-DNA interactions at the Npt2a proximal promoter.

Complex formation in solid deuterium in the presence of a ion

1987 ◽  
Vol 65 (1) ◽  
pp. 67-75 ◽  
Author(s):  
S. K. Bose ◽  
J. D. Poll
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Complex Formation ◽  
Infrared Absorption ◽  
Stationary Point ◽  
Theoretical Study ◽  
Supersonic Nozzle ◽  
Solid Deuterium ◽  
Nozzle Beam ◽  
Supersonic Nozzle Beam

Using the Metropolis scheme, we have carried out a Monte Carlo simulation of solid deuterium in the neighbourhood of a [Formula: see text] ion. The simulation is performed using a [Formula: see text] potential, which is based on the theoretical study of the stationary-point geometries of [Formula: see text] conformers by Yamaguchi et al. Complexes similar to [Formula: see text] clusters, as observed in the supersonic nozzle-beam experiments of van Deursen and Reuss, are found to form in the solid. Infrared absorption in solid deuterium due to the presence of such complexes is discussed.

Sign in / Sign up

Export Citation Format

Share Document