PROTEINS <I>IN VACUO</I>. A MORE EFFICIENT MEANS OF CALCULATING ORIENTATIONALLY-AVERAGED COLLISION CROSS SECTIONS OF PROTEIN IONS

Abstract

With the aim of understanding solvent effects in protein folding, unfolding, stability and dynamic behavior, studies of protein ions in vacuo have become popular in recent years. One experimental descriptor which gives a general overview of ionic structure is the orientationally-averaged collision cross section , which is obtained from ion drift mobility (IDM) and other kinds of measurements. In modelling protein structures in vacuo with molecular dynamics simulations, it is necessary to calculate for a plurality of model structures for comparison with experiments. The collision cross section is sensitive to the roughness (concavity) of the protein surface because of the possibility of multiple collisions during an encounter between a given bath gas particle and the protein. Calculations of , though in principle straightforward, are time consuming. In the work presented below, it was investigated whether a more efficient calculation scheme can be employed without sacrificing too much accuracy. In the new scheme, atomic-scale protein surface granularity is smoothed out by a collected-atoms approach, while large-scale concavity of the protein is essentially preserved.


(Received August 31, 2001; revised December 26, 2001)


Bull.Chem.Soc.Ethiop. 2001, 15(2), 157-166