  The paradigm that the primary amino acid sequence prescribes structure and
thus function has for a long time been central to the understanding of protein
science. Though the theory is supported by the behaviour of most structured
proteins, it loses much of its applicability when discussing intrinsically
disordered proteins (IDPs). These peculiar proteins, whose tertiary structure
constantly interconverts between a series of energetically favourable
conformations, are the root of many current, pressing scientific mechanisms.
Many biological processes that are still yet to be elucidated--the mechanisms
of of protein folding, ligand binding, and general protein dynamics--involve
IDPs. Because most dynamic protein events are on such short time scales, using
experimental methods to observe their action often times doesn't yield useful
data. As well, the data resulting from scientific techniques developed for
structured, "static proteins" must be presented in conjunction with data from
methods tailored specifically to IDPs in order to have significance. A method
that models IDPs with shocking accuracy is computer simulation, particularly
Molecular Dynamics (MD) simulations. With computational power only recently
increasing enough to encompass the timescale needed for protein dynamics, MD
simulations are still fairly novel in their implementations. This paper will
discuss and consolidate the current methods, problems, and solutions of using
MD simulation to model IDPs. Which simulation parameters can be altered to more
precisely describe observed biological behaviour? How can one accurately use MD
simulation to answer questions that, when using experimental methods, have no
answer? How can the data resulting from MD simulation be analyzed and
quantified to support the conclusions being drawn?
