37 research outputs found
Protein tyrosine phosphatases: structure, signaling and drug discovery/ Lalima G. Ahuja.
No full textIncludes bibliographical references and index.Protein tyrosine phosphatases remove phosphates from the phosphotyrosine residues of target proteins and reverse the action of various protein tyrosine kinases. This essential interplay between the opposing actions of protein tyrosine phosphatases and protein tyrosine kinases forms the basis of signaling networks that underlie the cellular workings of human physiology. Initially passed-off as housekeeping genes; these proteins were only acknowledged to maintain a steady background of phosphotyrosine levels in the cell. However, recent progress in studying their role in embryonic development and human disease has established their importance as regulators of signal regulation. Convincing evidence shows the role of mutations in these proteins to cause and/or intensify the severity of various diseases including metabolic and neurological disorders and also cancer. Protein tyrosine phosphatases have slowly, yet convincingly become crucial targets for therapeutic intervention of various human pathophysiologies. This book describes these signaling enzymes using the molecular details of their structure and mechanistic function. Various subtypes of cysteine-based Class I, II, III and the Haloacid dehalogenase related Class IV protein tyrosine phosphatases have been illustrated and explained. The superfamily of proteins is also described vis-a-vis its complimentary protein phosphoserine/phosphoserine phosphatases. Membrane bound receptor forms and the cytosolic non-receptor protein tyrosine phosphatases have been described for their biological function. This book serves as a reference for any reader looking to understand the sequence features, structural elements, molecular mechanism and cellular function of this superfamily of signaling enzymes.Frontmatter -- Preface -- About The Author -- Contents -- 1.Tyrosine Phosphorylation In Cell Signaling: Discovery And Beyond -- 2.Protein Phosphatases: Classification And Domain Architecture -- 3.Protein Tyrosine Phosphatases: Molecular Structure And Mechanism -- 4.The Receptor Protein Tyrosine Phosphatases: Structure And Function -- 5.The Double-Domain Receptor Protein Tyrosine Phosphatases -- 6 The Non-Receptor Protein Tyrosine Phosphatases: Part I -- 7.The Non-Receptor Protein Tyrosine Phosphatases: Part Ii -- 8.Protein Tyrosine Phosphatases: Strategies For Drug Development -- Index1 online resource (xiv, 282 pages
Tuning the “violin” of protein kinases: The role of dynamics‐based allostery
No full textThe intricacies of allosteric regulation of protein kinases continue to engage the research community. Allostery, or control from a distance, is seen as a fundamental biomolecular mechanism for proteins. From the traditional methods of conformational selection and induced fit, the field has grown to include the role of protein motions in defining a dynamics-based allosteric approach. Harnessing of these continuous motions in the protein to exert allosteric effects can be defined by a "violin" model that focuses on distributions of protein vibrations as opposed to concerted pathways. According to this model, binding of an allosteric modifier causes global redistribution of dynamics in the protein kinase domain that leads to changes in its catalytic properties. This model is consistent with the "entropy-driven allostery" mechanism proposed by Cooper and Dryden in 1984 and does not require, but does not exclude, any major structural changes. We provide an overview of practical implementation of the violin model and how it stands amidst the other known models of protein allostery. Protein kinases have been described as the biomolecules of interest. © 2019 IUBMB Life, 71(6):685-696, 2019
A Catalytically Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation
No full textTyrosine kinases are enzymes playing a critical role in cellular signaling. Molecular dynamics umbrella sampling potential of mean force computations are used to quantify the impact of activating and inactivating mutations of c-Src kinase. The potential of mean force computations predict that a specific double mutant can stabilize c-Src kinase into an active-like conformation while disabling the binding of ATP in the catalytic active site. The active-like conformational equilibrium of this catalytically dead kinase is affected by a hydrophobic unit that connects to the hydrophobic spine network via the C-helix. The αC-helix plays a crucial role in integrating the hydrophobic residues, making it a hub for allosteric regulation of kinase activity and the active conformation. The computational free-energy landscapes reported here illustrate novel design principles focusing on the important role of the hydrophobic spines. The relative stability of the spines could be exploited in future efforts to artificially engineer active-like but catalytically dead forms of protein kinases
Rescue of catalytic activity through a G-loop mutation.
No full textA. Molecular modeling of β3K/A+(GL)G-K mutant. B. Western blot of the different mutants showing the expression (PKA-C) and autophosphorylation state of the AL and C-tail (pT197 and pS338, respectively). C. Level of radioactive phosphoryl transfer of the different mutants as compared to the WT-C data represents the mean and standard deviation shown in S1 Table. D. Thermal shift assay capturing the conformational changes depicting the transition from the open to the intermediate and from the intermediate to the closed conformation through the addition of ATP and ATP + substrate. Data shown in S5 Table. E. Western blot of the different mutants showing the expression (PKA-C) and autophosphorylation state of the AL and C-tail (pT197 and pS338, respectively). F. Level of radioactive phosphoryl transfer of the different mutants as compared to the WT-C data represents the mean and standard deviation shown in S1 Table.</p
A Catalytically Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation
No full textAn Allosteric Region of Src Tyrosine Kinase Allows for Stabilization of Its Active-Like Conformation
No full textMutation of a kinase allosteric node uncouples dynamics linked to phosphotransfer
No full textThe expertise of protein kinases lies in their dynamic structure, wherein they are able to modulate cellular signaling by their phosphotransferase activity. Only a few hundreds of protein kinases regulate key processes in human cells, and protein kinases play a pivotal role in health and disease. The present study dwells on understanding the working of the protein kinase-molecular switch as an allosteric network of "communities" composed of congruently dynamic residues that make up the protein kinase core. Girvan-Newman algorithm-based community maps of the kinase domain of cAMP-dependent protein kinase A allow for a molecular explanation for the role of protein conformational entropy in its catalytic cycle. The community map of a mutant, Y204A, is analyzed vis-à-vis the wild-type protein to study the perturbations in its dynamic profile such that it interferes with transfer of the γ-phosphate to a protein substrate. Conventional biochemical measurements are used to ascertain the effect of these dynamic perturbations on the kinetic profiles of both proteins. These studies pave the way for understanding how mutations far from the kinase active site can alter its dynamic properties and catalytic function even when major structural perturbations are not obvious from static crystal structures
