Protein Force Fields

Proteins are arguably the most chemically, structurally, and functionally diverse of the biologically relevant macromolecules. In biological systems, amino acids, the smallest common subunit of proteins, function as intermediates for a variety of biosynthetic pathways, can be diverted for use as sources of energy, and function as neurotransmitters. Polypeptides, containing from two to approximately fifty amino acids, also function as neurotransmitters as well as hormones involved in the regulation of many physiological processes. Novel physiologically relevant polypeptides are still being discovered at a high rate. Proteins, which contain from approximately 50 to over 1000 amino acids, contribute to physiological function in an almost unimaginable number of ways. To date, a large percentage of the experimental and theoretical studies of proteins have focused on their role as enzymes, catalyzing reactions at rates, in certain cases, that are ultimately limited by the rate of diffusion of the substrates to the enzyme. Other roles of proteins, however, are equally important. They include roles in such functions as mechanical support, transport, storage, motion, immune protection, signal transduction, growth, and differentiation. Importantly, a large number of disease states are associated with polypeptides and proteins and a significant percentage of pharmaceutical agents act on protein targets. This wide variety of function associated with proteins has motivated a huge number of research efforts to elucidate the relationship of their biological function to their structure. Biochemical studies are effective at investigating phenomenological aspects of protein function, including substrate specificity, kinetic mechanisms of action, and regulation by endogenous agents. These approaches can also be used to identify individual amino acid residues important for function. Rigorous studies of structure function relationships in proteins require three-dimensional structures of the proteins, generally based on X-ray crystallography and NMR spectroscopy.1 Three-dimensional structures from these techniques, however, are predominately presented as static in nature. Information on mobility is often included only as isotropic temperature factors, although NMR experiments provide a variety of information on motions2 and Laue-based diffraction techniques have produced time resolved images of proteins in certain instances.3 More recently, nanotechnology based techniques such as optical tweezers and atomic force microscopy have allowed for forces acting on individual molecules to be measured.4 All of these experimental techniques allow for ‘snapshots’ of events occurring during, for example, the catalytic cycle to be taken; however, a continuous ‘movie’ of events is not yet available. In addition, only minimal information concerning the relationship of structure to energetics are experimentally accessible. Theoretical studies of proteins based on empirical force field calculations offer a methodology to overcome both of these limitations allowing for detailed structure function studies to be performed. In addition, these approaches offer the potential for making predications on alterations in protein structures prior to actual production of the modified protein.5,6 Effective application of empirical force field based methodologies is based, in part, on the accuracy of the force field. The present article describes the functional forms of force fields used for the study of proteins. This is followed by information on the methods used for optimization of the force field parameters and how those parameters are tested. A brief conclusion includes a summary and an outlook of theoretical developments which may influence future protein force fields. The present article does not present a rigorous comparison of currently available force fields. Rather, it emphasizes the approaches used in the optimization and testing of protein force fields in order to allow the reader to select the most appropriate force field for the particular problem they are addressing. While not a complete list, a number of parameter sets appropriate for protein studies may be found in the following references.7 22 Finally, it should be noted that the intimacy of the author with the CHARMM22 all-hydrogen protein parameter set excludes a totally unbiased presentation of the aspects of protein force fields discussed below.