Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble

Abstract

Conformational fluctuations in proteins have emerged as a potentially important aspect of biological function, although the precise relationship and the implications have yet to be fully explored. Numerous studies have reported that the binding of ligand can influence fluctuations. However, the role of the binding site in mediating these fluctuations is not known. Of particular interest is whether in addition to serving as structural scaffolds for recognition and catalysis, active-site residues may also play a role in modulating the cooperative network. To address this question, we employ an experimentally validated ensemble-based description of proteins to elucidate the extent to which perturbations at different sites can influence the cooperative network in the protein. Applying this method to a database of test proteins, it is found statistically that binding sites are located in regions most able to affect the cooperative network, even for cooperative interactions between residues distant to the binding sites. This indicates that the conformational manifold under native conditions is determined by the network of cooperative interactions within the protein and suggests that proteins have evolved to use these conformational fluctuations in carrying out their functions. Furthermore, because the energetic coupling pattern calculated for each protein is robust and relatively insensitive to sequence, these studies further suggest that binding sites evolved in regions of the protein that are inherently poised to take advantage of the fluctuations in the native structure.COREX analysis ͉ energetic coupling ͉ native state ensemble ͉ thermodynamic linkage B iological work in living organisms is mediated primarily through the use of protein molecules. Knowledge of the means by which proteins facilitate this work is of paramount importance to an understanding of function as well as the diseases that result from aberrant function. Of particular interest in recent years has been the observation that proteins are highly dynamic molecules that experience dramatic conformational excursions from the canonical high-resolution structure (1-3). In addition, it has also become clear that conformational dynamics play an important role in determining the ability of proteins to perform such diverse tasks as catalysis, allosterism, and signal transduction (4-6).The observation that protein conformational fluctuations play an important role in function suggests that functional sites in proteins may be uniquely coupled to structural fluctuations (7-9) and thus identifiable by how perturbations at these sites affect the conformational manifold. Here we use an ensemblebased model of the protein to explore this issue. By identifying a statistically significant difference in the response of the ensemble to perturbations at active sites of proteins, as determined from a representative test set, we find that binding sites play a unique role in influencing the cooperative network within proteins. This suggests that binding sites have been pre...

Computational Studies of Allosteric Regulation in the Hsp90 Molecular Chaperone: From Functional Dynamics and Protein Structure Networks to Allosteric Communications and Targeted Anti‐Cancer Modulators

“…Thermodynamicsbased approaches link structural perturbations and thermodynamically driven allosteric conformational changes with the free energy changes in conformational ensembles of pre-existing states. [23][24][25][26] The statistical ensemble-based models of protein allostery were recently generalized to model the effects of allosteric interactions in individual proteins on perturbations in signaling pathways, cellular functions, and disease states. [27][28][29][30][31] Most recently, the modern statistical view of protein allostery was further expanded to study disordered proteins, [32] the structure and dynamics of molecular networks, [33] and the mechanisms of allosteric protein inhibition in signaling networks.…”

Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

“…This ability of proteins to adopt multiple structures allows functional diversity without depending on the evolution of sequence diversity, and it can greatly facilitate the potential for rapidly evolving new functions and structures. Recently, Liu et al found that the conformational ensemble of native conditions is determined by the network of cooperative interactions within the protein and suggested that proteins have evolved to use these conformational fluctuations in carrying out their functions [29]. We have previously shown that Anisotropic Network Model (ANM) can be used to establish, a priori , the most likely conformational (transitional) changes of an enzyme starting from its unbound state to its three different bound states [30].…”

Monitoring Aromatic Picosecond to Nanosecond Dynamics in Proteins via 13C Relaxation: Expanding Perturbation Mapping of the Rigidifying Core Mutation, V54A, in Eglin c

“…Recently, native-state protein dynamics have been thought to be crucial for mediating allosteric signaling, or stated more generally, long-range communication (7)(8)(9)(10)(11)(12)(13)(14). One of the major challenges is the experimental characterization of dynamic processes relevant to intra- † This research was supported by NIH Grant GM066009 * To whom correspondence should be addressed: University of North Carolina, School of Pharmacy, Beard Hall, CB# 7360, Chapel Hill, NC 27599-7360. drewlee@unc.edu.…”