Triple helix structures: sequence dependence, flexibility and mismatch effects

J Sun, JL Mergny, R Lavery… - Journal of …, 1991 - Taylor & Francis
By means of molecular modelling, electrostatic interactions are shown to play an important
role in the sequence-dependent structure of triple helices formed by a homopyrimidine …

The flexibility of the nucleic acids:(I)“SIR”, a novel approach to the variation of polymer geometry in constrained systems

H Sklenar, R Lavery, B Pullman - Journal of Biomolecular Structure …, 1986 - Taylor & Francis
A novel and powerful methodology is developed which allows the alteration of molecular
structures subjected to constraints and its application to polynucleotides with …

[HTML][HTML] Activation of the edema factor of Bacillus anthracis by calmodulin: Evidence of an interplay between the EF-calmodulin interaction and calcium binding

E Laine, L Martínez, A Blondel, TE Malliavin - Biophysical journal, 2010 - cell.com
Calmodulin (CaM) is a remarkably flexible protein which can bind multiple targets in
response to changes in intracellular calcium concentration. It contains four calcium-binding …

Computer simulations of x‐ray scattering curves: Gelation and crystallization process in amylose solutions

JJ Müller, C Gernat, W Schulz, EC Müller… - Biopolymers …, 1995 - Wiley Online Library
Small-and wide-angle x-ray scattering is used for structural characterization of amylose
solutions and gets. Recently published coordinates determined by x-ray fiber structure …

An application of the Miertus‐Scrocco‐Tomasi solvation model in molecular mechanics and dynamics simulations

AA Varnek, G Wipff, AS Glebov… - Journal of Computational …, 1995 - Wiley Online Library
The point-chart approximation of the Miertus-Scrocco-Tomasi solvation model (MST-PC)
based on a continuum representation of the solvent has been incorporated in force field …

Structural Characterization of the 1:1 Adduct Formed between the Antitumor Antibiotic Hedamycin and the Oligonucleotide Duplex d(CACGTG)2 by 2D NMR …

S Pavlopoulos, W Bicknell, DJ Craik, G Wickham - Biochemistry, 1996 - ACS Publications
2D NMR spectroscopic methods have been used to determine the structure of the adduct
formed between the antitumor antibiotic hedamycin and the oligodeoxyribonucleotide …

Investigations on the dynamic structures of adenine-and thymine-containing DNA

S Brahms, V Fritsch, JG Brahms, E Westhof - Journal of molecular biology, 1992 - Elsevier
The structures of poly (dA-dT), poly (dA-dBr 5 U) and of poly (dA)· poly (dT) have been
investigated in solution and in fibers, by Raman spectroscopy. Both the alternating poly (dA …

Molecular dynamics simulations of poly (dA)· poly (dT): comparisons between implicit and explicit solvent representations

V Fritsch, G Ravishanker, DL Beveridge… - … Original Research on …, 1993 - Wiley Online Library
The program AMBER 3.0 has been used to generate molecular dynamics trajectories of a
poly (dA)· poly (dT) decamer. The simulations were performed using different methods to …

Photophysical Consequences of Coupling Bacteriochlorophyll a with Serine and its Resulting Solubility in Water¶

I Eichwurzel, H Stiel, K Teuchner… - Photochemistry and …, 2000 - Wiley Online Library
We investigated the dependence on solvents of optical absorption and emission of the
bacteriochlorophyll a‐serine (BChl‐ser), a water soluble bacteriochlorophyll (BChl) …

Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions

M Zacharias, H Sklenar - Biophysical journal, 1997 - cell.com
A combination of conformational search, energy minimization, and energetic evaluation
using a continuum solvent treatment has been employed to study the stability of various …