Using a combination of computational and experimental techniques to understand the molecular basis for protein allostery

Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects

How a protein propagates the conformational changes throughout its structure remains largely unknown. In thermosensitive TRP channels, this allosteric communication is triggered by ligand interaction or in response to temperature changes. Because dynamic allostery suggests a dynamic role of disordered regions, in this work we set out to thoroughly evaluate these regions in six thermosensitive TRP channels. Thus, by contrasting the intrinsic flexibility of the transmembrane region as a function of the degree of disorder in those proteins, we discovered several residues that do not show a direct correlation in both parameters. This kind of structural discrepancy revealed residues that are either reported to be dynamic, functionally relevant or are involved in signal propagation and probably part of allosteric networks. These discrepant, potentially dynamic regions are not exclusive of TRP channels, as this same correlation was found in the Kv Shaker channel.

MptpA Kinetics Enhanced by Allosteric Control of an Active Conformation

Understanding allostery in the Mycobacterium tuberculosis low molecular weight protein tyrosine phosphatase (MptpA) is a subject of great interest since MptpA is one of two protein tyrosine phosphatases (PTPs) from the pathogenic organism Mycobacterium tuberculosis expressed during host cell infection. Here, we combine computational modeling with solution NMR spectroscopy and we find that Q75 is an allosteric site. Removal of the polar side chain of Q75 by mutation to leucine results in a cascade of events that reposition the acid loop over the active site and relocates the catalytic aspartic acid (D126) at an optimal position for proton donation to the leaving aryl group of the substrate and for subsequent hydrolysis of the thiophosphoryl intermediate. The computational analysis is consistent with kinetic data, and NMR spectroscopy, showing that the Q75L mutant exhibits enhanced reaction kinetics with similar substrate binding affinity. We anticipate that our findings will motivate further studies on the possibility that MptpA remains passivated during the chronic state of infection and increases its activity as part of the pathogenic life cycle of M. tuberculosis possibly via allosteric means.

Feed Restriction Modulates Growth, Gut Morphology and Gene Expression in Zebrafish

A reduction in daily caloric or nutrient intake has been observed to promote health benefits in mammals and other vertebrates. Feed Restriction (FR), whereby the overall food intake of the organism is reduced, has been explored as a method to improve metabolic and immune health, as well as to optimize productivity in farming. However, less is known regarding the molecular and physiological consequences of FR. Using the model organism, Danio rerio, we investigated the impact of a short-term (month-long) FR on growth, gut morphology and gene expression. Our data suggest that FR has minimal effects on the average growth rates, but it may affect weight and size heterogeneity in a sex-dependent manner. In the gut, we observed a significant reduction in gut circumference and generally lower mucosal heights, whereas other parameters remained unchanged. Gene Ontology (GO), EuKaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified numerous metabolic, reproductive, and immune response pathways that were affected by FR. These results broaden our understanding of FR and contribute towards growing knowledge of its effects on vertebrate health.

Molecular insight into conformational transformation of human glucokinase: conventional and targeted molecular dynamics

Glucokinase (GK) plays a key role in the regulation of hepatic glucose metabolism. An unusual mechanism of positive cooperativity of monomeric GK containing only a single binding site for glucose is very interesting and still unclear. The activation process of GK is associated with a large-scale conformational change from the inactive to the active state. Here, conventional and targeted molecular dynamics simulations were used to study the conformational dynamics of GK in the stable configurations and in the transition from active to inactive state. Three phases of the structural reorganization of GK were detected. The first step is a transformation of GK from the active state to the intermediate structure, where the cleft between the domains is open, but alpha helix 13 is still inside the small domain. From this point, there are two alternative paths. One path leads to the inactive state through the release of helix 13 from the inside of small domain to the outside. Other path goes back to the active state. Simulation results reveal the critical role of helix 13 in the transformation of GK from the open state to inactive one and the influence of the loop 2 on the protein transformation between the open and the closed active states. Principal component analysis and covariance matrix analysis were carried out to analyze the dynamics of protein. Importance of hydrogen bonds in the stability of the closed conformation is shown. Overall, our simulations provide new information about the dynamics of GK and its structural transformation.Communicated by Ramaswamy H. Sarma.

Determinants of human glucokinase activation and implications for small molecule allosteric control

Glucokinase (GK) is an enzyme that catalyzes the ATP-dependent phosphorylation of glucose to form glucose-6-phosphate, and it is a tightly regulated checkpoint in glucose homeostasis. GK is known to undergo substantial conformational changes upon glucose binding. The monomeric enzyme possesses a highly exotic kinetic activity profile with an unusual sigmoidal dependence on glucose concentration. In this interdisciplinary study, which draws on small angle X-ray scattering (SAXS) integrated with 250 ns of atomistic molecular dynamics (MD) simulations and experimental glucose binding thermodynamics, we reveal that the critical regulation of this glucose sensor is due to a solvent controlled "switch". We demonstrate that the "solvent switch" is driven by specific protein structural dynamics, which leads to an enzyme structure that has a much more favorable solvation energy than most of the protein ensemble. These findings uncover the physical workings of an agile and flexible protein scaffold, which derives its long-range allosteric control through specific regions with favorable solvation energy. The physiological framework presented herein provides insights that have direct implications for the design of small molecule GK activators as anti-diabetes therapeutics as well as for understanding how proteins can be designed to have built-in regulatory functions via solvation energy dynamics.

Paradoxes and wonders of intrinsic disorder: Complexity of simplicity

At first glance it may seem that intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are simpler than ordered proteins and domains on multiple levels. However, such multilevel simplicity equips these proteins with the ability to have very complex behavior.

Allosteric communication pathways and thermal rectification in PDZ-2 protein: a computational study

Allosteric communication in proteins is a fundamental and yet unresolved problem of structural biochemistry. Previous findings, from computational biology ( Ota, N.; Agard, D. A. J. Mol. Biol. 2005 , 351 , 345 - 354 ), have proposed that heat diffuses in a protein through cognate protein allosteric pathways. This work studied heat diffusion in the well-known PDZ-2 protein, and confirmed that this protein has two cognate allosteric pathways and that heat flows preferentially through these. Also, a new property was also observed for protein structures: heat diffuses asymmetrically through the structures. The underling structure of this asymmetrical heat flow was a normal length hydrogen bond (∼2.85 Å) that acted as a thermal rectifier. In contrast, thermal rectification was compromised in short hydrogen bonds (∼2.60 Å), giving rise to symmetrical thermal diffusion. Asymmetrical heat diffusion was due, on a higher scale, to the local, structural organization of residues that, in turn, was also mediated by hydrogen bonds. This asymmetrical/symmetrical energy flow may be relevant for allosteric signal communication directionality in proteins and for the control of heat flow in materials science.

On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

Implicit methods for modeling protein electrostatics require dielectric properties of the system to be known, in particular, the value of the dielectric constant of protein. While numerous values of the internal protein dielectric constant were reported in the literature, still there is no consensus of what the optimal value is. Perhaps this is due to the fact that the protein dielectric constant is not a “constant” but is a complex function reflecting the properties of the protein’s structure and sequence. Here, we report an implementation of a Gaussian-based approach to deliver the dielectric constant distribution throughout the protein and surrounding water phase by utilizing the 3D structure of the corresponding macromolecule. In contrast to previous reports, we construct a smooth dielectric function throughout the space of the system to be modeled rather than just constructing a “Gaussian surface” or smoothing molecule–water boundary. Analysis on a large set of proteins shows that (a) the average dielectric constant inside the protein is relatively low, about 6–7, and reaches a value of about 20–30 at the protein’s surface, and (b) high average local dielectric constant values are associated with charged residues while low dielectric constant values are automatically assigned to the regions occupied by hydrophobic residues. In terms of energetics, a benchmarking test was carried out against the experimental pK_a’s of 89 residues in staphylococcal nuclease (SNase) and showed that it results in a much better RMSD (= 1.77 pK) than the corresponding calculations done with a homogeneous high dielectric constant with an optimal value of 10 (RMSD = 2.43 pK).

Unusual biophysics of intrinsically disordered proteins

Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the "turned-out" response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the "edge of chaos" systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.