Global ETD Search
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Showing 1 to 20 of 49 for “"Allostery"”.
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UNDERSTANDING GENERALIZED ALLOSTERY IN THROMBIN
… enzyme, the exact mechanism of thrombin's allostery is still unclear and widely debated. This dissertation describes my application of molecular dynamics simulations and various quantitative methods to uncover thrombin's allostery. It discusses thrombin's allosteric responses upon different …
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Revisiting Allostery In Lac Repressor
… previously characterized to be critical for allostery. These dynamics are shown to be quenched in non-allosteric mutants which suggests functional relevance. Operator binding results in globally quenched dynamics and dramatic changes to the structure of the hinge. Inducer binding in the …
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Synthetic Transcription Factor Allostery Mapping and Analysis
… towards position linked factors integral in LacI allostery. Ultimately, this research seeks to establish a foundation for improved engineering strategies for synthetic transcription factors and to enhance the development of associated machine learning models by further elucidating the mechanistic …
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Structural And Functional Studies On Thrombin Allostery
Thrombin is an allosteric serine protease endowed with important physiological functions in the blood. Once activated, α-thrombin plays procoagulant, prothrombotic, and anticoagulant functions in blood. Its important role in blood coagulation can be emphasized by the fact that thrombin interacts …
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Coarse-grained models of biomolecule dynamics and allostery
… part of this thesis we investigate the “dynamic allostery” in dimeric proteins composed of two identical subunits. We demonstrate that cooperative effects upon binding of two identical ligands can arise purely through modification of slow global vibrational modes of the protein. We parameterise …
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Kinetic and Thermodynamic Allostery in the Ras Protein Family
The general metadata -- e.g., title, author, abstract, subject headings, etc. -- is publicly available, but access to the submitted files is restricted to UT Southwestern campus access and/or authorized UT Southwestern users.
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Allostery and GroEL: Exploring the Tenets of Nested Cooperativity
Despite a wealth of structural and biochemical studies on the functional cycle of the <i>E. coli</i> chaperonins GroEL and GroES, no model proposed to date accounts for all the effects seen experimentally by the various allosteric ligands: ATP, ADP, SP, GroES, and K+. The work in this dissertation …
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SERS-active peptide nanoparticles for investigating protein allostery and bionanoassembly
The tumour suppressor protein, p53, is either mutated or absent in over 50 % of cancers and is negatively regulated by the mouse double minute two protein, MDM2. This thesis presents a novel nanosensing approach to investigate full-length MDM2 interactions with p53, thus providing an allosteric …
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Examining the role of water and hydrophobicity in folding, aggregation, and allostery
Solvation and hydrophobicity drive many critical processes in nature, playing an important role in the folding of proteins, aggregation of surfactants into micelles, and in the disorder to order transitions that occur in some allosteric proteins upon ligand binding. Understanding how solvation and …
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The Structural Properties of Adaptation and Allostery in Proteins: A Case Study in a PDZ Domain
… in the protein structure, a phenomenon known as allostery. Where in the protein do these characteristics lie? Here, we address the sequence origins and structural properties of a) the adaptive capacity of proteins and b) allosteric communication within proteins. Understanding how proteins can …
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The Development and Application of Methods to Study the Evolution of Specificity, Allostery, and RNA -Protein Interactions in Translation
We have developed the sequence QR algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. These biasless profiles were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that …
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PLASTICITY IN PROTEIN SEQUENCE-FUNCTION RELATIONSHIPS
Allostery is defined as the functional regulation at one site in a protein by activity at a distant site. Because of the ubiquitous occurrence and diverse cellular roles of allosteric proteins, designing novel allosteric proteins is of great interest for applications in synthetic biological and …
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Leveraging Local Perturbations to Map Allosteric Networks of Phosphatases
<p>Allostery is central to regulation of protein function, but our mechanistic understanding remains incomplete. A deeper understanding of how redistributions of conformational states drive allostery in proteins could allow us to better grasp natural regulatory principles in cells and open new …
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Mechanistic Analysis of Microtubule Dynamics and Regulation
… in the lattice are tightly linked and provide allostery throughout the microtubule. Uncoupling the two cycles disrupts the allostery which greatly impacts the rapid transitions normally seen in dynamic instability that allow for fast and decisive structural rearrangements. In Chapter 3, I will …
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Insights into protein function from evolutionary and conformational dynamics
… engage in allosteric communication. To identify allostery we developed and tested two computational tools that operate on protein conformational dynamics data. These tools are useful for generating testable hypotheses about proteins with multiple functional sites for the design of non-competitive …
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Biophysical Analysis of S100A12 and the Nucleosome Core Particle
… the first part, we explore calcium mediated allostery in S100A12, focusing on the distinct roles of its two EF-hand calcium binding loops (EF-I and EF-II). Through a combination of isothermal titration calorimetry, NMR spectroscopy, and mutational analysis, we find that EF-II acts as the …
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Biochemical and Biophysical Characterization of the Allosteric Equilibrium of the Wiskott-Aldrich Syndrome Protein
… signaling proteins are regulated by a subset of allostery where intramolecular interactions modulate the conformational equilibrium between an uninhibited, inactive state and an active state. Relief of autoinhibition then requires that covalent modification or binding events shift the equilibrium …
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Molecular Dynamics Simulation Studies on Interfacial Dynamics of Proteins
… between globules mediate protein dynamics, allostery and charge transfer. Confined clusters of water molecules exhibit dynamics distinct from dynamics of water in the bulk or in the hydration layer around biomolecules. Here, we describe and compare the dynamics of water in the hydration …
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Building a rational model for the identification of allosteric sites
Allostery is the regulation of protein function, structure and/or flexibility that is induced by the binding of a ligand at a site distinct from the orthosteric site.1, 2 Interaction of a small molecule with these sites can bring greater selectivity as they are not conserved within a family and …
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UNIQUE ALLOSTERIC MECHANISM REGULATING PROTEIN-PROTEIN INTERACTION THROUGH PHOSPHORYLATION: A CASE STUDY OF THE CONFORMATIONAL CHANGES IN THE SYK TANDEM SH2 PROTEIN
… is regulated by a mechanism of dynamic allostery emerged.
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