Dynamics polypeptides

Schreiber, H., Steinhauser, O. Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochem. 31 (1992) 5856-5860. 

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

Dlugosz M, Antosiewicz JM (2005) Effects of solute-solvent proton exchange on polypeptide chain dynamics A constant-pH molecular dynamics study. J Phys Chem B 109 13777-13784. 

Raman optical activity is an excellent technique for studying polypeptide and protein structure in aqueous solution since, as mentioned above, their ROA spectra are often dominated by bands originating in the peptide backbone that directly reflect the solution conformation. Furthermore, the special sensitivity of ROA to dynamic aspects of structure makes it a new source of information on order-disorder transitions. 

NMRrelaxation and diffusion experiments provide important insights into both the internal molecular dynamics and the overall hydrodynamic behavior of unfolded and partly folded states. Local variations in backbone dynamics are correlated with propensities for local compaction of the polypeptide chain that results in constriction of backbone motions (Eliezer et al., 1998, 2000). This can occur through formation of... 

Local Dynamics in Polypeptides Studied by Solid State 2H NMR Side Chain Dynamics of Poly(Y-benzyl L-glutamate) and Racemic Poly(Y-benzyl glutamate)... 

Solid state 2H NMR parameters are almost exclusively governed by the quadrupole interaction with the electric field gradient (EFG) tensor at the deuteron site.1 8 The EFG is entirely intramolecular in nature. Thus molecular order and mobility are monitored through the orientation of individual C-2H bond directions. Therefore, 2H NMR is a powerful technique for studying local molecular motions. It enables us to discriminate different types of motions and their correlation times over a wide frequency range. Dynamics of numerous polymers has been examined by solid state 2H NMR.1 3,7,9 Dynamic information on polypeptides by NMR is however limited,10 26 although the main-chain secondary structures of polypeptides in the solid have been extensively evaluated by 13C and 15N CP/MAS NMR.27,28... 

The long side chains of a homopolypeptide have remarkable motional freedom about multiple bonds, while the main chain forms the secondary regular conformation such as a-helix, /1-sheet, and turn, which are rigid structures. The macroscopic properties of the rigid a-helical polypeptide, therefore, highly depends on the dynamic structure of the side chains so that a lot of studies on the side chain dynamics of the a-helical polypeptides have been carried out in the solid and solution states.12,14,29 66... 

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