It will be obvious from this discussion that the view of protein−protein interactions that emerges is very different from that implicit in colloidal studies, since we place particular emphasis on specific types of atomic interactions. We begin by briefly reviewing the structural basis of protein−protein interactions as deduced from crystallographic studies of protein complexes. Because of this, one of our main hopes in writing this work is to provide a description of the methods used in more atomically detailed studies, that is sufficiently accessible that it will serve as a useful primer both for theoreticians more familiar with DLVO type models and for experimentalists interested in understanding protein−protein simulation techniques. Second, even a cursory reading of the extant literature reveals that the distance between the two fields in terms of language is often embarrassingly large: an exchange of papers between workers from the two areas can in many cases be safely accomplished without any meaningful transfer of information.
First, the total breadth spanned by the two fields combined is so large as to defy adequate coverage in the allotted space. Although these studies are often of great interest, we restrict our attention here to studies of the first type. Studies of the latter type are typically aimed at describing the effects of macromolecular interactions on the meso- or macroscopic properties of protein solutions, such as their diffusional behavior (see, e.g., ref 11).
Although simulation techniques are many and varied, they can be broadly divided into two areas: (1) those that describe the proteins involved in atomic or near-atomic detail, with the aim of investigating the roles played by specific amino acids in the interactions, (2) those that treat proteins as simple geometric shapes (generally spheres), interacting by potential functions such as the DLVO potential, 10 derived for treating colloidal suspensions. The purpose of this article is to outline the uses of computer simulations for describing protein−protein interactions.
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