Molecular dynamics simulation helix motion

Example Molecular dynamics simulations of selected portions of proteins can demonstrate the motion of an amino acid sequence while fixing the terminal residues. These simulations can probe the motion of an alpha helix, keeping the ends restrained, as occurs n atiirally m transmembrane proteins. You can also investigate the conformations of loops with fixed endpoints. 

For proteins with significant helical content it is possible to show that larger-scale displacements involve rigid-body motions of the helices. Two such proteins for which molecular dynamics simulations have been analyzed in terms of helix motions are the C-terminal fragment of the L7/L12 ribosomal protein of E. coli229 and myoglobin.230... 

V. Daggett, P. A. Kollman, and I. D. Kuntz, Biopolymers, 31, 1115 (1991). A Molecular Dynamics Simulation of Polyalanine An Analysis of Equilibrium Motions and Helix—Coil Transitions. 

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