Characterizing the function of unstructured proteins: Simulations of charged polymers under confinement

Experimental findings that some polypeptides may be unstructured and behave as entropically driven polymeric spacers in biological systems motivates a study of confined polymers. Here we examine the confinement of neutral, polyampholyte, and polyelectrolyte polymers between two parallel surfaces using course grained models and molecular dynamics. Forces between the confining surfaces are determined for different polymer classes and as a function of chain length, charge sequence (pattern) and degree of confinement. Changes in chain properties are also evaluated under these conditions. The results reinforce the significance of length and net charge for predicting chain properties. In addition the clustering of charge along the chain appears to be critical, and changes in cluster size and distribution produce dramatic changes in chain behavior. (C) 2001 American Institute of Physics.