TY - BOOK
T1 - Ligand-induced propagation of entropic signals across proteins
AU - Moorman, Veronica R.
N1 - Protein-ligand interactions are of paramount importance to the field of biochemistry. They are ubiquitous across biological systems and are at the core of structural, enzymatic and signaling processes. While much is known, only recently have the nature and role of the entropic component of these protein-ligand binding events been of concern.
PY - 2012/1/1
Y1 - 2012/1/1
N2 - Protein-ligand interactions are of paramount importance to the field of biochemistry. They are ubiquitous across biological systems and are at the core of structural, enzymatic and signaling processes. While much is known, only recently have the nature and role of the entropic component of these protein-ligand binding events been of concern. As entropy can be defined by the number of possible microstates, measures of dynamics can be used to proxy for protein conformational entropy. This dissertation utilizes nuclear magnetic resonance (NMR)-based nuclear spin relaxation experiments to illuminate site-resolved changes in backbone (viewed through N-H amide relaxation) and side-chain (viewed through CH2D deuterium or CHD2 carbon relaxation) motions for two protein-ligand systems: the model enzyme hen egg white lysozyme binding to a small, inhibitory sugar (chitotriose) and the GTPase Cdc42Hs binding to a 46-residue peptide derived from a p21-activating kinase (PBD46). Notably, both systems demonstrate a dependence of the variance of motional change upon ligand binding on the distance to the bound ligand. Moreover, a general distance dependence is seen across a variety of protein-ligand interactions described in the literature. Upon binding a ligand, the precise directionality and magnitude in the dynamical change of each methyl probe is context-dependent and appears to have complex underpinnings, but the variance of the dynamical response falls off with the distance from the binding interface. This decay fits to a double exponential function, indicating that both a fast-decaying local response and a slow-decaying long-range response appear to be present. The existence of this slower decay rate suggests that thermodynamic motional coupling can propagate across entire proteins and potentially be utilized by nature for allosteric-type processes. Individual proteins appear to take advantage of this property in different ways, seemingly to optimize biological function, as illustrated by the bifurcation of dynamical changes in Cdc42Hs upon binding PBD46 and the core rigidification in HEWL in response to binding chitotriose. This work provides evidence of the raw material necessary for dynamically-mediated protein allostery, and therefore illustrates the potential relevance of and emphasizes the need for consideration of fast timescale methyl motions when studying protein-ligand thermodynamics.
AB - Protein-ligand interactions are of paramount importance to the field of biochemistry. They are ubiquitous across biological systems and are at the core of structural, enzymatic and signaling processes. While much is known, only recently have the nature and role of the entropic component of these protein-ligand binding events been of concern. As entropy can be defined by the number of possible microstates, measures of dynamics can be used to proxy for protein conformational entropy. This dissertation utilizes nuclear magnetic resonance (NMR)-based nuclear spin relaxation experiments to illuminate site-resolved changes in backbone (viewed through N-H amide relaxation) and side-chain (viewed through CH2D deuterium or CHD2 carbon relaxation) motions for two protein-ligand systems: the model enzyme hen egg white lysozyme binding to a small, inhibitory sugar (chitotriose) and the GTPase Cdc42Hs binding to a 46-residue peptide derived from a p21-activating kinase (PBD46). Notably, both systems demonstrate a dependence of the variance of motional change upon ligand binding on the distance to the bound ligand. Moreover, a general distance dependence is seen across a variety of protein-ligand interactions described in the literature. Upon binding a ligand, the precise directionality and magnitude in the dynamical change of each methyl probe is context-dependent and appears to have complex underpinnings, but the variance of the dynamical response falls off with the distance from the binding interface. This decay fits to a double exponential function, indicating that both a fast-decaying local response and a slow-decaying long-range response appear to be present. The existence of this slower decay rate suggests that thermodynamic motional coupling can propagate across entire proteins and potentially be utilized by nature for allosteric-type processes. Individual proteins appear to take advantage of this property in different ways, seemingly to optimize biological function, as illustrated by the bifurcation of dynamical changes in Cdc42Hs upon binding PBD46 and the core rigidification in HEWL in response to binding chitotriose. This work provides evidence of the raw material necessary for dynamically-mediated protein allostery, and therefore illustrates the potential relevance of and emphasizes the need for consideration of fast timescale methyl motions when studying protein-ligand thermodynamics.
UR - https://repository.upenn.edu/dissertations/AAI3542832/
M3 - Doctoral Thesis
ER -