Helix twisting, dynamics

The dynamics of helix twisting has also been considered with equations for torsional rotation of the DNA being developed (Barkley and Zimm, 1979). Assuming that intercalated dyes reflect the motional properties of nucleic acids, indications are that this motion can account for most of the fluorescence depolarization decay of ethidium intercalated into DNA,... 

Noncovalent interactions play a key role in biodisciplines. A celebrated example is the secondary structure of proteins. The 20 natural amino acids are each characterized by different structures with more or less acidic or basic, hydrophilic or hydrophobic functionalities and thus capable of different intermolecular interactions. Due to the formation of hydrogen bonds between nearby C=0 and N-H groups, protein polypeptide backbones can be twisted into a-helixes, even in the gas phase in the absence of any solvent." A protein function is determined more directly by its three-dimensional structure and dynamics than by its sequence of amino acids. Three-dimensional structures are strongly influenced by weak non-covalent interactions between side functionalities, but the central importance of these weak interactions is by no means limited to structural effects. Life relies on biological specificity, which arises from the fact that individual biomolecules communicate through non-covalent interactions." " Molecular and chiral recognition rely on... 

T. Tarnai. We don t deal with dynamics it was a static calculation. We considered elastic bars, which are usually in sub-stress. We found the equilibrium configuration, under which the structure has a certain shape, and in this case we can find only the coordinates of the proper nodes. We found the planes of the curved members which are circular or curved, and whether or not you have twisted or bent elements. In this case the member forms a helix too, but we can make no further comment at this stage. 

H-type pseudoknot which sequesters the Shine-Dalgarno sequence, featuring an extended P4 hairpin which is dynamic on the ms-ps timescale, as revealed by Ti, Tip and RDC measurements. The authors present evidence that the extended helix of P4 introduces conformational disorder to hinder pseudoknot formation in the ligand-free state, whilst upon preQl binding a helical twist of P4 causes blocking of ligand exit and creates contacts which stabilise the bound-state triple helix. 

In order to obtain information on the poly(PDBF) molecular structure, molecular dynamics (MD) simulations were performed for a PDBF 20-mer model created on the basis of the DBF oligomer conformation in crystal (see X-ray Crystal Analyses section) under a constant NVT condition with COMPASS force field at 300 K for 8.6 ns. The simulation afforded the structure shown in Fig. 40 in which the neighboring fluorene moieties stack on top of each other in a chiral, slightly twisted arrangement. The entire chain formed a relatively long-pitched helical structure in the simulation. Hence, the local twist and the helix may contribute to the CD spectra. 

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