scholarly journals A Coupled Base-Rotator Model for Structure and Dynamics of DNA: Local Fluctuations in Helical Twist Angles and Topological Solitons

1984 ◽  
Vol 72 (4) ◽  
pp. 679-693 ◽  
Author(s):  
S. Homma ◽  
S. Takeno
Keyword(s):  
Topological Solitons ◽  
Structure And Dynamics ◽  
Rotator Model ◽  
Helical Twist ◽  
Local Fluctuations

scholarly journals Solution structure and dynamics of the A-T tract DNA decamer duplex d(GGTAATTACC)2: implications for recognition by minor groove binding drugs

1999 ◽  
Vol 342 (1) ◽  
pp. 125-132 ◽  
Author(s):  
Clare E. BOSTOCK-SMITH ◽  
Charles A. LAUGHTON ◽  
Mark S. SEARLE
Keyword(s):  
Solution Structure ◽  
Minor Groove ◽  
Groove Width ◽  
Major Groove ◽  
Structure And Dynamics ◽  
Helical Twist ◽  
Distance Restraints ◽  
Dynamics Simulations ◽  
Stable Trajectory ◽  
Helical Parameters

The structure of the DNA decamer duplex d(GGTAATTACC)2 has been determined using NMR distance restraints and molecular dynamics simulations of 500 ps to 1 ns in aqueous solution at 300 K. Using both canonical A and canonical B starting structures [root-mean-square deviation (RMSD) 4.6 Å; 1 Å = 10-10 m], with and without experimental restraints, we show that all four simulations converge to a similar envelope of final conformations with B-like helical parameters (pairwise RMSD 1.27-2.03 Å between time-averaged structures). While the two restrained simulations reach a stable trajectory after 300-400 ps, the unrestrained trajectories take longer to equilibrate. We have analysed the dynamic aspects of these structures (sugar pucker, helical twist, roll, propeller twist and groove width) and show that the minor groove width in the AATT core of the duplex fluctuates significantly, sampling both wide and narrow conformations. The structure does not have the highly pre-organized narrow minor groove generally regarded as essential for recognition and binding by small molecules, suggesting that ligand binding carries with it a significant component of ‘induced-fit’. Our simulations show that there are significant differences in structure between the TpA step (where p = phosphate) and the ApA and ApT steps, where a large roll into the major groove at the TpA step appears to be an important factor in widening the minor groove at this position.

Discussion of the Oblique Rotator Model Cases Of 108 Aqr and x Serp.

1976 ◽  
Vol 32 ◽  
pp. 577-588
Author(s):  
C. Mégessier ◽  
V. Khokhlova ◽  
T. Ryabchikova
Keyword(s):  
Mathematical Formulation ◽  
The Other ◽  
Rotator Model ◽  
Oblique Rotator ◽  
First Results

My talk will be on the oblique rotator model which was first proposed by Stibbs (1950), and since received success and further developments. I shall present two different attempts at describing a star according to this model and the first results obtained in the framework of a Russian-French collaboration in order to test the precision of the two methods. The aim is to give the best possible representation of the element distributions on the Ap stellar surfaces. The first method is the mathematical formulation proposed by Deutsch (1958-1970) and applied by Deutsch (1958) to HD 125248, by Pyper (1969) to α2CVn and by Mégessier (1975) to 108 Aqr. The other one was proposed by Khokhlova (1974) and used by her group.

Peculiarity Parameters

1976 ◽  
Vol 32 ◽  
pp. 233-254
Author(s):  
H. M. Maitzen
Keyword(s):  
Magnetic Field ◽  
Magnetic Fields ◽  
Theoretical Work ◽  
Observational Evidence ◽  
Rotator Model ◽  
Peculiar Behaviour ◽  
Field Spectrum ◽  
Oblique Rotator ◽  
Ap Stars ◽  
The Way

Ap stars are peculiar in many aspects. During this century astronomers have been trying to collect data about these and have found a confusing variety of peculiar behaviour even from star to star that Struve stated in 1942 that at least we know that these phenomena are not supernatural. A real push to start deeper theoretical work on Ap stars was given by an additional observational evidence, namely the discovery of magnetic fields on these stars by Babcock (1947). This originated the concept that magnetic fields are the cause for spectroscopic and photometric peculiarities. Great leaps for the astronomical mankind were the Oblique Rotator model by Stibbs (1950) and Deutsch (1954), which by the way provided mathematical tools for the later handling pulsar geometries, anti the discovery of phase coincidence of the extrema of magnetic field, spectrum and photometric variations (e.g. Jarzebowski, 1960).

Nucleosome dynamics

2006 ◽  
Vol 73 ◽  
pp. 109-119 ◽  
Author(s):  
Chris Stockdale ◽  
Michael Bruno ◽  
Helder Ferreira ◽  
Elisa Garcia-Wilson ◽  
Nicola Wiechens ◽  
...  
Keyword(s):  
High Resolution ◽  
Chromatin Structure ◽  
Current Knowledge ◽  
Dynamic Properties ◽  
Structure And Dynamics ◽  
Nucleosome Dynamics ◽  
Sharp Focus ◽  
Recent Advances ◽  
Insight Into ◽  
Chromatin Structure And Dynamics

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.

Structure and dynamics of phosphate glasses

1998 ◽  
Vol 77 (2) ◽  
pp. 357-362 ◽  
Author(s):  
A. Matic, L. Borjesson
Keyword(s):  
Phosphate Glasses ◽  
Structure And Dynamics

Studies of the structure and dynamics of theDregion of the polar ionosphere during solar flares in April 2004

2006 ◽  
Vol 6 (2) ◽  
Author(s):  
V. D. Tereshchenko ◽  
E. B. Vasil'ev ◽  
O. F. Ogloblina ◽  
V. A. Tereshchenko ◽  
S. M. Chernyakov
Keyword(s):  
Solar Flares ◽  
Polar Ionosphere ◽  
Structure And Dynamics
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