Molecular dynamics , protein

Conformational Dynamics Simulations of Proteins molecular dynamics conformational flooding... 

This section covers the investigation of simple amino acids, proteins, lipids and nucleic acids. In particular, in proteins, molecular dynamics is an important link between molecular structure and function." " Among the hrst experimental approaches of... 

Keywords Prion protein Molecular dynamics simulation Protein dynamics Protein misfolding pH-induced misfolding Disease-related mutations... 

To follow the dynamics of the ions near the protein, molecular dynamics simulations were carried out in the presence of 6639 water molecules, and Na+ and Cl ions were added to a formal concentration of 30 and 120 mM. The simulations were carried out for a period of 10 ns, and the diffusion coefficients of the ions were calculated to be comparable with the values determined by experimental methods [85]. A great advantage of molecular dynamics calculations is the possibility to visualize the motion of each ion. On inspecting the various ions, it became evident that their spatial distribution was not random. There was a clear tendency of some anions and cations to remain in the vicinity of the protein, as if the local forces detained them next to the protein s surface. 

Caliment N, Schaefer M, Simonson T. Protein molecular dynamics with the general-ized/ACE solvent model. Proteins 2001 45 144-158. 

Karplus on protein molecular dynamics (1977), and so on (Todd 1983, Williams 1990). Quite a few small start-up companies banked on the public taste for natural products, for instance, in the form of herbal over-the-counter drugs (Anon. 1999). 

K+, and Ca2+ To address these questions properly requires a better understanding of the three-dimensional structure of transport enzymes, the identification of principal amino acids that participate in the translocation reaction, and an appreciation of the protein molecular dynamics that contribute to ion binding (and release) and movement in the translocation domain. 

Buck, M., Karplus, M. Internal and overall peptide group motion in proteins Molecular dynamics simulations for lysozyme compared with results from X-ray and NMR spectroscopy. J. Am. Chem. Soc. 1999, 121, 9645-58. 

Vibrational Energy Flow in Proteins Molecular Dynamics-Based Methods... 

Protein Molecular Dynamics with Electrostatic Force Entirely Determined by a Single Poisson-Boltzmann Calculation. 

Lindahl, E. Sansom, MS.P. (2008). Membrane proteins molecular dynamics simulations. Curr Opin Struct Biol, Vol.18, No.4, pp. 425-431... 

Water-membrane interfaces are discussed separately in this volume (see Environment of a Membrane Protein Molecular Dynamics Studies of Lipid Bilayers and Permeation of Lipid Membranes Molecular Dynamics Simulations). 

Proteins can be modeled as beads on a string, where each bead represents an amino acid residue (see Conformational Search Proteins Molecular Dynamics Techniques and Applications to Proteins and Protein Modeling Folding... 

B. Z. Lu, W. Z. Chen, C. X. Wang, and X. Xu, Proteins Struct. Funct. Genet., 48, 497 (2002). Protein Molecular Dynamics with Electrostatic Force Entirely Determined by a Single Poisson-Boltzmann Calculation. 

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