scholarly journals Interactions of theEscherichia coliDnaB−DnaC Protein Complex with Nucleotide Cofactors. 1. Allosteric Conformational Transitions of the Complex

Biochemistry ◽  
2009 ◽  
Vol 48 (29) ◽  
pp. 6712-6729 ◽  
Author(s):  
Anasuya Roychowdhury ◽  
Michal R. Szymanski ◽  
Maria J. Jezewska ◽  
Wlodzimierz Bujalowski
Keyword(s):  
Protein Complex ◽  
Conformational Transitions ◽  
Dnac Protein

scholarly journals Escherichia coliDnaB Helicase−DnaC Protein Complex: Allosteric Effects of the Nucleotides on the Nucleic Acid Binding and the Kinetic Mechanism of NTP Hydrolysis. 3

Biochemistry ◽  
2009 ◽  
Vol 48 (29) ◽  
pp. 6747-6763 ◽  
Author(s):  
Anasuya Roychowdhury ◽  
Michal R. Szymanski ◽  
Maria J. Jezewska ◽  
Wlodzimierz Bujalowski
Keyword(s):  
Nucleic Acid ◽  
Protein Complex ◽  
Kinetic Mechanism ◽  
Nucleic Acid Binding ◽  
Dnac Protein

Conformational Transitions in Escherichia coli Ribosomal RNAs as Visualized by Dedicated STEM

1988 ◽  
Vol 46 ◽  
pp. 176-177
Author(s):  
J.S. Wall ◽  
V. Maridiyan ◽  
S. Tumminia ◽  
J. Hairifeld ◽  
M. Boublik
Keyword(s):  
Ionic Strength ◽  
Three Dimensional ◽  
Conformational Transitions ◽  
Dark Field ◽  
Dimensional Structure ◽  
Ribosomal Rnas ◽  
Field Mode ◽  
Freeze Dried ◽  
High Resolution Images ◽  
Low Ionic Strength

The high contrast in the dark-field mode of dedicated STEM, specimen deposition by the wet film technique and low radiation dose (1 e/Å2) at -160°C make it possible to obtain high resolution images of unstained freeze-dried macromolecules with minimal structural distortion. Since the image intensity is directly related to the local projected mass of the specimen it became feasible to determine the molecular mass and mass distribution within individual macromolecules and from these data to calculate the linear density (M/L) and the radii of gyration.2 This parameter (RQ), reflecting the three-dimensional structure of the macromolecular particles in solution, has been applied to monitor the conformational transitions in E. coli 16S and 23S ribosomal RNAs in solutions of various ionic strength.In spite of the differences in mass (550 kD and 1050 kD, respectively), both 16S and 23S RNA appear equally sensitive to changes in buffer conditions. In deionized water or conditions of extremely low ionic strength both appear as filamentous structures (Fig. la and 2a, respectively) possessing a major backbone with protruding branches which are more frequent and more complex in 23S RNA (Fig. 2a).

High-Resolution electron crystallography of the light-harvesting chlorophyll-a/b protein complex from chloroplast membranes

1990 ◽  
Vol 48 (1) ◽  
pp. 610-610
Author(s):  
Werner Kühlbrandt ◽  
Da Neng Wang ◽  
K.H. Downing
Keyword(s):  
High Resolution ◽  
Electron Diffraction ◽  
Chlorophyll A ◽  
Protein Complex ◽  
Structural Integrity ◽  
Light Harvesting ◽  
Lhc Ii ◽  
Diffraction Patterns ◽  
Difference Fourier ◽  
2D Crystals

The light-harvesting chlorophyll-a/b protein complex (LHC-II) is the most abundant membrane protein in the chloroplasts of green plants where it functions as a molecular antenna of solar energy for photosynthesis. We have grown two-dimensional (2d) crystals of the purified, detergent-solubilized LHC-II . The crystals which measured 5 to 10 μm in diameter were stabilized for electron microscopy by washing with a 0.5% solution of tannin. Electron diffraction patterns of untilted 2d crystals cooled to 130 K showed sharp spots to 3.1 Å resolution. Spot-scan images of 2d crystals were recorded at 160 K with the Berkeley microscope . Images of untilted crystals were processed, using the unbending procedure by Henderson et al . A projection map of the complex at 3.7Å resolution was generated from electron diffraction amplitudes and high-resolution phases obtained by image processing .A difference Fourier analysis with the same image phases and electron diffraction amplitudes recorded of frozen, hydrated specimens showed no significant differences in the 3.7Å projection map. Our tannin treatment therefore does not affect the structural integrity of the complex.

Use of Antibody to aid Visualization of Protein at the Termini of Bacteriophage Ø29 DNA

1980 ◽  
Vol 38 ◽  
pp. 540-541
Author(s):  
Dwight Anderson ◽  
Charlene Peterson ◽  
Gursaran Notani ◽  
Bernard Reilly
Keyword(s):  
Electron Microscopy ◽  
Bacillus Subtilis ◽  
Dna Synthesis ◽  
Restriction Endonuclease ◽  
Protein Complex ◽  
Protein Product ◽  
Viral Dna ◽  
Small Proteins ◽  
Antibody Labeling ◽  
Subtilis Bacteriophage

The protein product of cistron 3 of Bacillus subtilis bacteriophage Ø29 is essential for viral DNA synthesis and is covalently bound to the 5’-termini of the Ø29 DNA. When the DNA-protein complex is cleaved with a restriction endonuclease, the protein is bound to the two terminal fragments. The 28,000 dalton protein can be visualized by electron microscopy as a small dot and often is seen only when two ends are in apposition as in multimers or in glutaraldehyde-fixed aggregates. We sought to improve the visibility of these small proteins by use of antibody labeling.

ASSOCIATION BEHAVIOUR OF THE OESTRADIOL-BINDING PROTEIN COMPLEX WITH THE NUCLEAR FRACTION

1972 ◽  
Vol 71 (2_Suppla) ◽  
pp. S420-S438 ◽  
Author(s):  
David L. Williams ◽  
Jack Gorski
Keyword(s):  
Binding Site ◽  
Protein Complex ◽  
Binding Protein ◽  
Nuclear Fraction ◽  
Site Saturation ◽  
Total Binding

ABSTRACT A number of studies have been carried out to examine the distribution of the oestradiol-binding protein complex between cytosol and nuclear fractions as a function of total binding site saturation. The results of these studies suggest that each binding protein has one binding site for the hormone. In addition, these studies suggest that the interaction of the oestradiol-binding protein complex with the nucleus involves a large number of low affinity association sites.

Protein Flexibility Catalyzes a Cell Signaling Reaction of the Ras-GAP Complex

2019 ◽  
Author(s):  
Keiei Kumon ◽  
Masahiro Higashi ◽  
Shinji Saito ◽  
Shigehiko Hayashi
Keyword(s):  
Cell Signaling ◽  
Conformational Changes ◽  
Catalytic Reaction ◽  
Protein Complex ◽  
Enzyme Mechanism ◽  
Activation Free Energy ◽  
Chemical Catalysis ◽  
Simple Chemical ◽  
A Cell ◽  
Enzyme Molecules

Many enzyme molecules exhibit characteristic global and slow dynamics which furnish them with allostery realizing remarkable molecular functionalities more than simple chemical catalysis. However, molecular mechanism of a catalytic reaction associated with the molecular flexibility of enzymes is not well-understood. Here we report a hybrid molecular simulation study on GTPase activity of a Ras-GAP protein complex for cell signaling termination. We unveiled that extensive conformational changes of the protein complex and exclusion of internal water molecules are induced upon the transition state (TS) formation in the catalytic reaction and significantly lower the reaction activation free energy. We also revealed that tumor-related mutations perturb those conformational changes upon the TS formation, leading to reduction of the catalytic activity. The findings of the remarkably dynamic protein conformation directly linking to the catalytic reaction have broad implications for understanding of enzyme mechanism and for developments of allosteric drugs and novel catalysts.

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