Date of Award


Document Type


Degree Name

Master of Science (MS)



Committee Chair/Advisor

Dr. Brian Dominy

Committee Member

Dr. Dvora Perahia

Committee Member

Dr. Steve Stuart

Committee Member

Dr. Hugo Sanabria

Committee Member

Dr. Emil Alexov


Allostery (1) is the process through which proteins self-regulate in response to various stimuli. Allosteric interactions occur between nonadjacent spatially distant residues (1), and they are exhibited through the correlated motions (2) and momenta of participating residues. The location of allosteric sites in proteins can be determined experimentally but computational methods to predict the location of allosteric sites are being developed as well (2-4, 10). Experimental and computational methodologies for locating allosteric sites can be used to design specific targeted drug delivery (5-6, 19), but these methods have not yet fully explained a mechanism for allosteric communications.

An allosteric pathway is a chain of residues that “communicate” by frequently colliding into one another. The frequency of collisions causes members of the chain to transfer kinetic energy amongst each other preferentially (3-4). Allosteric pathways begin and end at protein binding sites. An allosteric event occurs when an external molecule interacts with a binding site. An allosteric process is triggered by an allosteric event (7-9), and it is a consequence of a protein’s free energy landscape changing in response to the stimuli (12). The protein begins to assume a new conformation due to the changes in its free energy landscape, and as its structure changes its functionality also changes as the system approaches a new equilibria. At equilibrium, a protein’s conformational ensemble remains stable, and the residues participating in an allosteric pathway remain fairly constant (3).

The frequent collisions along allosteric pathways lead to quantifiable mathematical patterns in the physical states (position, momentum, internal energy) of allosteric pathway residues over time. Non-allosteric pathway residues also collide with other residues but will not display a discernable pattern in physical state with other residues over time. Current computational methods for quantifying patterns in physical state to identify allosteric pathways utilize Percolation Theory (3), Isotropic Heat Diffusion (4), Direct Cross Correlation (2), and Information Theory (11, 13). This work strives to enhance the Information Theoretic approach for locating allosteric sites and use this new perspective to develop a model to describe protein communication. The Information Theoretic approach has been chosen due to its ability to capture dynamic, nonlinear relationships, at relevant biological temperatures. Mutual Information (MI) quantifies the information that two variables share (5), and it will be used in this work to examine signaling relationships between a protein’s residues at equilibrium. There is evidence to suggest that allosteric signals travel along energy pathways through transfers of kinetic energy between colliding residues (3-4). This work hypothesizes that a pattern of collisions forms during equilibria via repetitive kinetic energy transfers between residues along an allosteric pathway. If the energy transferred during this process functions as a repetitive biological ‘signal’ then there will be quantifiable patterns in physical state data that Mutual Information can be used to characterize analytically.



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