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An Investigation Of Protein Interactions And The Relationship To Phase Behavior
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Book Synopsis An Investigation of Protein Interactions and the Relationship to Phase Behavior by : Darren Fredrick Rosenbaum
Download or read book An Investigation of Protein Interactions and the Relationship to Phase Behavior written by Darren Fredrick Rosenbaum and published by . This book was released on 1998 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Thermodynamic Modeling of Protein Interactions and Phase Behavior by : Leigh Quang
Download or read book Thermodynamic Modeling of Protein Interactions and Phase Behavior written by Leigh Quang and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein phase behavior encompasses the formation of dense phases, which include amorphous aggregates, gels, dense liquids, and crystals. The major solution variables that dictate the type of dense phase that is formed are pH, temperature, type of precipitant, precipitant concentration, and protein concentration. Because of the large parameter space and rich variety of phase transitions possible, protein phase behavior is a complex phenomenon. Fundamentally, macroscopic phase transitions are governed by the molecular interactions between proteins in solution. One promising way of quantifying protein-protein interactions and relating them to phase behavior is through the osmotic second virial coefficient B22, a dilute-solution property that characterizes two-particle interactions. The relationship of B22 to overall phase behavior of proteins is explored in this work. The goal of this thesis is to quantitatively relate protein-protein interactions to protein phase diagrams in order to develop predictive models of phase behavior under different solution conditions. A continuum-level approach is used initially to relate experimental B22 data and phase diagrams of proteins by appealing to existing thermodynamic models, with the expectation that a simple continuum model could provide a useful mechanistic framework for predicting protein phase behavior. The first approach attempted was to relate protein interactions and phase behavior within the Flory-Huggins theory of polymer solutions. The second approach utilized the model of Haas and Drenth, which is based on the free energy of mixing for hard spheres. Finally, phase equilibrium was predicted from virial coefficients using the osmotic virial equation. A qualitative relationship was found between B22 and phase behavior from these continuum models; however, quantitative agreement could not be obtained. The isotropic assumption shared among these models in addition to the orientationally-averaged nature of B22 suggests that the anisotropic character of protein interactions cannot be neglected, demonstrating the need for more detailed molecular-level models. The role of anisotropy in protein interactions was explored through analysis of "patch-antipatch" pairs in the computation of B22 in atomistic detail. Patch-antipatch pairs represent highly attractive orientations resulting from geometric complementarity between protein surfaces. Previous work used simple Monte Carlo integration for the calculation of B22 from atomistic models of proteins. However, the presence of patch-antipatch pairs led to significant numerical concerns. These concerns warranted a reexamination of the numerical methods for computing B22. A hybrid Monte Carlo/patch integration approach is utilized to calculate B22 for lysozyme and chymosin B. This method involves a combination of numerical integration techniques in an attempt to obtain better convergence in predicting B22. The overall B22 for the proteins studied was separated into three components: contributions from the excluded volume, from the patch-antipatch pairs, and from background configurations. The excluded volume component was found to be adequately determined using simple Monte Carlo integration. The contributions from individual patch-antipatch pairs were accounted for by carefully integrating the subregions of the configuration space occupied by these pairs using a globally adaptive integration routine. The background component to B22 was also calculated by simple Monte Carlo integration in which the regions of the configuration space occupied by the patch-antipatch pairs were excluded. The calculations performed that account for the full protein structure emphasize the importance of several features of protein interactions. First, the difference in the interaction behavior of the two proteins studied was found to be largely attributed to the charge anisotropy of patch-antipatch pairs. However, the relation of the results to experimental data is limited by the omission of accounting for the specific hydration of proteins. Hydration effects are known to affect, and usually attenuate, patch-antipatch configurations, and therefore would be expected to significantly impact the accurate prediction of B22. Classical colloidal as well as atomistic models that omit these important features are inadequate in providing a quantitative representation of protein interactions for a wide range of solution conditions.
Book Synopsis The Role of Protein-protein Interactions in the Phase Behavior of Aqueous Protein Solutions by : Camille O. Anderson
Download or read book The Role of Protein-protein Interactions in the Phase Behavior of Aqueous Protein Solutions written by Camille O. Anderson and published by . This book was released on 2001 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Interactions and Phase Behavior in Aqueous Solutions by : Andre C. Dumetz
Download or read book Protein Interactions and Phase Behavior in Aqueous Solutions written by Andre C. Dumetz and published by ProQuest. This book was released on 2008 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Dissertation Abstracts International by :
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2007 with total page 924 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Effects of Salts on the Phase Behavior of Proteins and Protein Mixtures by : Yu-Chia Cheng
Download or read book Effects of Salts on the Phase Behavior of Proteins and Protein Mixtures written by Yu-Chia Cheng and published by ProQuest. This book was released on 2008 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Separating proteins in aqueous solutions through fractional precipitation by addition of salts is one of the oldest protein separation methods, and it remains the only purification step for some industrial enzymes and an initial purification step for higher-value therapeutic proteins. However, despite its widespread application, the fundamental characteristics of protein precipitation by salt are still incompletely understood. The primary focus of this thesis is the experimental exploration of the phase behavior of single and binary protein systems during protein precipitation in concentrated ammonium sulfate and sodium chloride solutions, and the effect of solution conditions on protein interactions. Protein precipitation phase behavior of single protein systems was measured as a function of solution conditions for lysozyme and ovalbumin. X-ray powder diffraction (XRD) and optical microscopy were used to characterize the structure of the protein precipitates. These studies showed that crystallization after initial precipitation is feasible even at high ionic strengths if sufficient mixing time is allowed, and such behavior may be a more general phenomenon although different crystallization pathways may be found in some systems and under different conditions; for instance, different pathways are seen in ovalbumin-ammonium sulfate systems as a function of pH. A more important development is the interpretation that emerges of precipitation as a manifestation of a metastable liquid-liquid separation, with the precipitate being a kinetically trapped dense liquid phase. Furthermore, the diversity of possible dense phases (amorphous precipitate, crystal phases or gel) associated with liquid-liquid phase separation shows that understanding the effects of protein interactions of different kinds and at different ranges could have important consequences for the systematic control of protein phase behavior. The phase behavior in selective precipitation of lysozyme-ovalbumin binary mixtures was investigated at various conditions. The best combination of selectivity and recovery of lysozyme was achieved in pH 7 NaCl solutions. At an initial concentration of 30 mg/g H 2 O of lysozyme and 30 mg/g H 2 O of ovalbumin, more than 80% of the lysozyme was collected in precipitate form with 93% purity at ionic strengths above 3 m, while ovalbumin was collected in the supernatant at 80% purity. The purities of both proteins were therefore improved by at least 30% in one step. Moreover, crystallization following initial precipitation was observed in some binary precipitation experiments and indicates that binary precipitation, like single protein precipitation, is a metastable equilibrium state. The observations of selective precipitation behavior were correlated with values of the osmotic second virial coefficient, measured by cross-interaction chromatography (CIC). The results show that interaction measures such as protein self- and cross-interactions can be used as a predictor for general trends and/or inconsistencies in the separation behavior and for optimizing working conditions. Such a mechanistic relationship can obviate the need for extensive trial-and-error methods in order to optimize conditions for protein separations.
Book Synopsis Protein Self-Assembly by : Jennifer J. McManus
Download or read book Protein Self-Assembly written by Jennifer J. McManus and published by Humana. This book was released on 2020-08-08 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.
Book Synopsis The Role of Protein - Protein Interactions in the Phase Behaviour of Aqueous Protein Solutions by :
Download or read book The Role of Protein - Protein Interactions in the Phase Behaviour of Aqueous Protein Solutions written by and published by . This book was released on 2006 with total page 197 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Simulations of the Effect of Cholesterol on Membrane-Mediated Protein-Protein Interactions by : Frédérick Jean-Marie De Meyer
Download or read book Molecular Simulations of the Effect of Cholesterol on Membrane-Mediated Protein-Protein Interactions written by Frédérick Jean-Marie De Meyer and published by . This book was released on 2010 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this work we use molecular simulations to investigate how cholesterol affects membrane-mediated protein-protein interactions. We consider a typical hydrated biological model membrane containing saturated phospholipids (for example, dimyris- toylphosphatidylcholine or DMPC), cholesterol, and trans-membrane proteins. We introduce a model in which the different molecules are coarse-grained, retaining their hydrophobic and hydrophilic properties together with their main structure and flexi- bility. The system is studied using a hybrid Monte-Carlo dissipative particle dynamics method. First we study lipid-mediated protein-protein interactions in a pure hydrated sat- urated phospholipid bilayer. The potential of mean force between the proteins show that hydrophobic forces drive long-range lipid-mediated protein-protein interactions and that the nature of these interactions depends on the length of the protein hy- drophobic segment, on the three-dimensional structure of the protein and on the properties of the lipid bilayer. The concept of hydrophilic shielding is introduced to gain insight into the nature of the computed potentials of mean force. To study the effect of cholesterol on the properties of a membrane, we extend our model to cholesterol. Structural and mechanical properties of the hydrated bi- layer containing a saturated lipid and cholesterol are studied at various temperatures and cholesterol concentrations. The properties studied are the area per lipid, con- densation, bilayer thickness, tail order parameters, bending modulus, and area com- pressibility. The model quantitatively reproduces most of the experimental effects of cholesterol on these properties and reproduces the main features of the experi- mental temperature-composition phase diagram. Based on the changes in structural properties a temperature-composition structure diagram is proposed, which is com- pared with the experimental phase and structure diagrams. The lateral organization of cholesterol in the bilayer is also discussed. In a second part, modifications of the cholesterol model are made to allow a better understanding of the cholesterol condensation effect. This condensation effect is further discussed in relation to the DMPC-cholesterol phase behavior. Finally, the effect of cholesterol on lipid-mediated protein-protein interactions is investigated. This is done in accordance with the results concerning the effect of cholesterol on the phase behavior of lipid bilayers. The calculations of the potential of mean force between proteins and protein clusters show that the addition of choles- terol gradually reduces repulsive lipid-mediated interactions between certain proteins. At a given cholesterol concentration, the interactions even become attractive. Hence, cholesterol significantly promotes protein aggregation. The role of protein-induced dynamical cholesterol-enriched and cholesterol-depleted shells in these effects is dis- cussed in detail.
Book Synopsis Molecular Thermodynamics of Protein Interactions and Phase Behavior in Aqueous Electrolyte Solution by : Christopher James Coen
Download or read book Molecular Thermodynamics of Protein Interactions and Phase Behavior in Aqueous Electrolyte Solution written by Christopher James Coen and published by . This book was released on 1995 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Measurement and Prediction of Protein Phase Behaviour and Protein-protein Interactions by : Cornelius Faber
Download or read book Measurement and Prediction of Protein Phase Behaviour and Protein-protein Interactions written by Cornelius Faber and published by . This book was released on 2006 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis American Doctoral Dissertations by :
Download or read book American Doctoral Dissertations written by and published by . This book was released on 2002 with total page 776 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Using Molecular Simulation to Explore Protein and Colloidal Phase Behavior in Bulk, Confinement, and Mixtures by : Thomas W. Rosch
Download or read book Using Molecular Simulation to Explore Protein and Colloidal Phase Behavior in Bulk, Confinement, and Mixtures written by Thomas W. Rosch and published by . This book was released on 2008 with total page 149 pages. Available in PDF, EPUB and Kindle. Book excerpt: Because of the ubiquity of colloidal solutions in everyday industrial applications such as papermaking and coatings there is a need to be able to efficiently design and manufacture these substances. A related issue concerns the connection between many physiological diseases and heath defects and the stability and phase behavior of certain proteins. It is imperative to understand the physical mechanisms that cause proteins to change their normal solution characteristics. To design colloidal solutions for specific applications as well as to produce preventative medicines and therapies an intimate knowledge of the connection between particle interactions and overall physical properties of the solution is needed. To probe this issue four types of systems are examined. In each system solution conditions are altered affecting the nature and strength of the particle interactions. Our goal is to understand the physics behind the evolution of fluid properties that occurs because of changes in microscopic interactions. The method we employ in this pursuit is grand canonical transition matrix Monte Carlo. We examine an embedded point charge protein model of lysozyme in bulk, mixed with polymer, as well as in confinement. We find that in bulk the model is able to capture qualitatively experimental trends for changes in critical temperature and evolution of the fluid phase diagram with changing solution conditions such as salt concentration and pH. Quantitatively the model predicts a relatively narrow coexistence curve compared to experimental values. It is found that the osmotic second virial coefficient remains relatively constant over a broad range of solutions conditions suggesting a universal magnitude of attraction needed to induce phase separation. We examine a simple system consisting of hard sphere colloids with added Gaussian core polymers. Decreasing the size of the polymers relative to colloids as well as increasing the energetic repulsion between polymers upon overlap results in an overall stabilization of the mixture. Unlike bulk solutions containing molecules of the Carlsson et al. lysozyme model, the osmotic second virial coefficient at the critical point for model colloid-polymer mixtures is not constant but depends on polymer size and interaction. Increasing polymer size or decreasing polymer repulsion results in a larger negative value. Overall the model fails to capture the experimental behavior of polymer excluded volume interactions because its inability to describe the polymers capability of deformation around the colloid. We extend our analysis to a mixture containing the embedded charge model for lysozyme and Gaussian core polymers. Overall, the system exhibited a strong dependence on pH and salt concentration that qualitatively followed experimental trends. Increase of salt concentration or decrease in protein charge decreases the number of polymers needed to induce phase separation. This trend was not sensitive to the size of the polymer relative to the protein. Finally we examine the effect surface interactions have on the phase behavior for the lysozyme model as well as a simple square well model. Both systems exhibited a distinctly non-monotonic variation of its critical temperature as a function of fluid-wall interaction strength. A maximum occurs at an intermediate strength. We introduce two metrics that enable one to predict the location of this maximum. The first is related to the contact angle a fluid makes with the confining substrate while the second is based upon virial coefficient information. Because similar trends are exhibited in both systems we believe that the results should be general in nature.
Book Synopsis Molecular Recognition in Gas Phase by : Andrey Dyachenko
Download or read book Molecular Recognition in Gas Phase written by Andrey Dyachenko and published by . This book was released on 2013 with total page 163 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the present thesis we have explored different factors that impede accurate quantitative description of non-covalent protein-protein and protein-ligand interactions and design of new potent and specific binders from the scratch. Firstly, we addressed the role of solvent in the mechanism of non-covalent interactions. Secondly, we tackled the question about the intrinsic conformational flexibility of the protein molecules and the part it plays in weak interactions between proteins. In the first part of the thesis we studied the interactions of vascular endothelial growth factor (VEGF) protein with five cyclic peptides in solution and gas phase. The results showed that affinities of five ligands to VEGF in solution and gas phase are ranked in inversed order. That is, the that has the highest affinity in solution (as shown by chemical shift perturbation NMR and isothermal titration calorimetry) forms the weakest complex with VEGF in gas phase, and vice versa. We compared gas-phase and solution binding affinities of of five peptides and made qualitative conclusions about the role of the solvent in protein-ligand interactions. In order to obtain more quantitative information about the gas-phase behavior of non-covalent complexes we have developed a combined experimental/theoretical approach to study the energetics of collisional activation of the ion prior to dissociation. We applied developed strategy to model CID in traveling wave ion guide (TWIG) collision cell. We validated the model on the CID of leu-enkephalin peptide and then applied developed strategy to five non-covalent protein-peptide complexes and found activation energies of their dissociation reactions. Next we applied ESI native MS to study the allosteric interactions between the molecular chaperonin GroEL and ATP. The obtained data allowed to construct a scheme of conformational transition of GroEL upon binding of ATP and distinguish between two different cooperativity models, providing strong arguments in favor of Monod-Wyman-Changeux (MWC) model. Finally, be studied the backbone dynamics of VEGF with a combination of NMR relaxation and all-atom force-field based normal mode analysis (NMA). We showed that combination of experimental and computational approach allows to identify flexible zones with higher level of confidence. We also found out that residues, that are involved VEGF-receptor interactions, reside in or close to the flexible zones, suggesting the critical role conformational plasticity plays in the non-covalent protein-protein interactions.
Book Synopsis PROBING GAS-PHASE PEPTIDE STRUCTURE AND PROTEIN-PROTEIN INTERACTIONS USING MASS SPECTROMETRIC TECHNIQUES. by :
Download or read book PROBING GAS-PHASE PEPTIDE STRUCTURE AND PROTEIN-PROTEIN INTERACTIONS USING MASS SPECTROMETRIC TECHNIQUES. written by and published by . This book was released on 2009 with total page 640 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presented in this dissertation are studies on the gas-phase structural features of peptides and peptide fragment ions using mass spectrometry (MS), hydrogen/deuterium (H/D) exchange, infrared multiphoton dissociation (IRMPD) spectroscopy, and computational modeling. Additional studies are presented on the mechanism of hydrogen/deuterium exchange using a model amino acid system. The application of chemical cross-linking to investigate the interaction between two proteins, LexA and RecA, is also presented. Gas-phase structural features can be probed using a number of techniques, and several of the studies presented in this dissertation involve the use of gas-phase H/D exchange. Although the basic mechanism for exchange has been determined, the factors that affect the rate and extent of exchange are not well understood. A computational modeling study of the exchange behavior of asparagine and its methyl ester demonstrated that exchange will occur preferentially at sites of more similar basicity. The distinctive exchange behavior of a model histidine-containing pentapeptide, HAAAA, prompted further studies into the structural features that result in five fast exchanging hydrogens and one slower exchange. Peptide analogues were used to identify the sites of exchange, and IRMPD spectroscopy combined with computational modeling indicated that exchange may occur because interaction with water at those sites results in lower energy structures compared to the other sites. Structural studies were also performed to determine whether the b2+ion from HAAAA is an oxazolone or diketopiperazine. The IRMPD spectrum showed bands that matched both a diketopiperazine and an oxazolone structure. H/D exchange and fragmentation studies further supported the presence of a mixture of species. Protein-protein interactions perform a vital role in regulating cellular processes. Despite extensive mutational analysis, the binding interaction between LexA and RecA, two proteins involved in the SOS response, is unclear. Chemical cross-linking experiments were undertaken to help target future mutational studies, and these studies identified two possible interactions. The first potential binding interaction is located in the cleft of RecA, and the second interaction may be caused by a LexA dimer binding across the RecA helical groove. The presence of two different binding interactions suggests that LexA may have redundant binding modes for RecA interaction.
Download or read book Research Awards Index written by and published by . This book was released on 1988 with total page 874 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein-Lipid Interactions by : C.Reyes Mateo
Download or read book Protein-Lipid Interactions written by C.Reyes Mateo and published by Springer Science & Business Media. This book was released on 2008-09-30 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological membranes have long been identified as key elements in a wide variety of cellular processes including cell defense communication, photosynthesis, signal transduction, and motility; thus they emerge as primary targets in both basic and applied research. This book brings together in a single volume the most recent views of experts in the area of protein–lipid interactions, providing an overview of the advances that have been achieved in the field in recent years, from very basic aspects to specialized technological applications. Topics include the application of X-ray and neutron diffraction, infrared and fluorescence spectroscopy, and high-resolution NMR to the understanding of the specific interactions between lipids and proteins within biological membranes, their structural relationships, and the implications for the biological functions that they mediate. Also covered in this volume are the insertion of proteins and peptides into the membrane and the concomitant formation of definite lipid domains within the membrane.
