Emerging computational approaches for the study of protein allostery

• We review computational approaches to study communication in allosteric proteins.
• Initial studies analyzed static structures from NMR and X-ray experiments.
• More recently, dynamics have been added via molecular dynamics simulations.
• Current challenges call for more systematic and transferable approaches.
• Combination with analytical techniques might increase predictability.

Allosteric regulation of protein function is key in controlling cellular processes so its underlying mechanisms are of primary concern to research in areas spanning protein engineering and drug design. However, due to the complex nature of allosteric mechanisms, a clear and predictive understanding of the relationship between protein structure and allosteric function remains elusive. Well established experimental approaches are available to offer a limited degree of characterization of mechanical properties within proteins, but the analytical capabilities of computational methods are evolving rapidly in their ability to accurately define the subtle and concerted structural dynamics that comprise allostery. This review includes a brief overview of allostery in proteins and an exploration of relevant experimental methods. An explanation of the transition from experimental toward computational methods for allostery is discussed, followed by a review of existing and emerging methods.