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Mechanical Unfolding Response Of Proteins
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Book Synopsis Mechanical Unfolding Response of Proteins by : Ionel Popa
Download or read book Mechanical Unfolding Response of Proteins written by Ionel Popa and published by American Chemical Society. This book was released on 2023-06-16 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mechanical Unfolding Response of Proteins is a thermodynamically motivated overview of when, why, and how proteins respond to mechanical perturbations and the experimental techniques used to probe single protein biophysics. Relative newcomers to the field (new graduate students), and those starting from a biological background hoping for an introduction to the physics behind protein behavior, will benefit from reading this primer.
Book Synopsis Unfolding of Proteins: Thermal and Mechanical Unfolding by : Joe S. Hur
Download or read book Unfolding of Proteins: Thermal and Mechanical Unfolding written by Joe S. Hur and published by . This book was released on 2003 with total page 14 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past few decades, researchers have sequenced the human genome which is a blueprint for proteins. However, given only the information of the sequence we cannot yet accurately predict specific structural information such as the secondary and tertiary structure of a given protein, let alone its functionality in biological processes. Recent theoretical and experimental findings have shown that the topology or conformation of the native structure of small proteins plays a critical role in determining its biological function (Baker 2000; Alm & Baker 1999). In order to carry out their biological function properly, proteins must assume a shape, assembling themselves into an ordered structure. It is now well known that depending on the topology of proteins, for example, when proteins do not fold correctly, there can be serious medical complications, such as Parkinson's disease, Alzheimers to name a few. Furthermore, more biophysical manifestations of protein-protein interactions are reflected in processes related to phase equilibria such as crystallization, and in the marked dependence of the diffusion coefficients of macromolecules on their concentration (Price et al. 1999). The latter aspect is currently becoming of much interest to biologists and chemists with advances in techniques for monitoring protein diffusion in the crowded cellular environment (Dayel et al. 1999). With ever increasing areas of interest in biomedical applications as mentioned above, much effort has been put into understanding the mechanism of protein folding. However, at present, there exists neither a simple and universally applicable theoretical framework nor an efficient and accurate computational framework that can account for many experimental findings.
Book Synopsis Protein Mechanical Unfolding in Multiple Dimensions by : Edward William Thomas Causton
Download or read book Protein Mechanical Unfolding in Multiple Dimensions written by Edward William Thomas Causton and published by . This book was released on 2011 with total page 191 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mechanical Unfolding and Folding Studies on Proteins with High Sequence Identity But Different Conformations by : Jinliang Li
Download or read book Mechanical Unfolding and Folding Studies on Proteins with High Sequence Identity But Different Conformations written by Jinliang Li and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mechanical Unfolding and Confinement of Proteins Investigated Through an Ising-like Model by : Michele Caraglio
Download or read book Mechanical Unfolding and Confinement of Proteins Investigated Through an Ising-like Model written by Michele Caraglio and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Dynamics Simulations of the Mechanical Unfolding of Proteins by : Pai-Chi Li
Download or read book Molecular Dynamics Simulations of the Mechanical Unfolding of Proteins written by Pai-Chi Li and published by . This book was released on 2006 with total page 88 pages. Available in PDF, EPUB and Kindle. Book excerpt: A number of proteins perform load-bearing functions in living organisms and often have unique mechanical properties. In recent years, there has been considerable effort to understand the relationships between the molecular structure of such proteins and their mechanical response. Several of them have been studied in great detail through single molecule mechanical pulling experiments. Interpretation of these experiments requires the use of atomistic simulations. However typical simulation time scales are many orders of magnitude shorter than relevant experimental and/or physiological time scales. In this dissertation, we have developed a simulation methodology that provides a direct link between experiments and simulations and is capable of predicting the outcome of single molecule pulling experiments. By using this methodology, we have been able to understand the relationships between the molecular structure and the mechanical properties of a number of proteins. I report on our studies of the mechanical unfolding of the I27 domain of the muscle protein titin, ubiquitin, and protein G and compare them with the existing experimental data. The distribution of the unfolding force as well as its dependence on the pulling rate predicted by our simulations is found to be in good agreement with AFM experiments. We demonstrate that the mechanical unfolding pathway can be altered by changing the pulling geometry and that the presence of a hydrogen bonded clamp between terminal parallel strands of these domains is the key property that is responsible for their high mechanical stability. We have also extended our studies of single protein domains to protein dimers. Our replica-exchange molecular dynamics simulation study of the mechanical unfolding of a segment-swapped protein G dimer suggests that the mechanical resistance of a protein complex may be controlled not only by the mechanical stability of individual domains but also by the inter-chain interactions between domains.
Book Synopsis Folding/unfolding Kinetics of Lattice Proteins by Applying a Simple Statistical Mechanical Model for Protein Folding by : Hiroshi Wako
Download or read book Folding/unfolding Kinetics of Lattice Proteins by Applying a Simple Statistical Mechanical Model for Protein Folding written by Hiroshi Wako and published by Nova Biomedical Books. This book was released on 2011 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The folding/unfolding kinetics of a three-dimensional lattice protein was studied using a simple statistical mechanical model for protein folding that was previously developed. The model considers the specificity of an amino acid sequence and the native structure of a given protein. The characteristic relaxation rate on the free energy surface was calculated starting from a completely unfolded structure (or native structure) that is assumed to associate with a folding rate (or an unfolding rate). To elucidate the roles of individual amino acid residues in protein folding/unfolding kinetics, the kinetic properties for all possible single amino acid substitutions of these proteins were calculated and their responses were examined. This book presents and discusses research results in the kinetics of protein folding/unfolding.
Book Synopsis Macromolecular Crowding Effects in the Mechanical Unfolding Forces of Proteins by : Marisa B. Roman
Download or read book Macromolecular Crowding Effects in the Mechanical Unfolding Forces of Proteins written by Marisa B. Roman and published by . This book was released on 2012 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Macromolecules can occupy a large fraction of the volume of a cell and this crowded environment influences the behavior and properties of the proteins, such as mechanical unfolding forces, thermal stability and rates of folding and diffusion. Although much is already known about molecular crowding, it is not well understood how it affects a protein's resistance to mechanical stress in a crowded environment and how the size of the crowders affect those changes. An atomic force microscope-based single molecule method was used to measure the effects of the crowding on the mechanical stability of a model protein, in this case I-27. As proteins tend to aggregate, single molecule methods provided a way to prevent aggregation because of the very low concentration of proteins in the solution under study. Dextran was used as the crowding agent with three different molecular weights 6kDa, 10 kDa and 40 kDa, with concentrations varying from zero to 300 grams per liter in a pH neutral buffer solution at room temperature. Results showed that the forces required to unfold biomolecules were increased when a high concentration of crowder molecules were added to the buffer solution and that the maximum force required to unfold a domain was when the crowder size was 10 kDa, which is comparable to the protein size. Unfolding rates obtained from Monte Carlo simulations showed that they were also affected in the presence of crowders. As a consequence, the energy barrier was also affected. These effects were most notable when the size of the crowder was 10 kDa, comparable to the size of the protein. On the other hand, distances to the transition state did not seem to change when crowders were added to the solution. The effect of Dextran on the energy barrier was modeled by using established theories such as Ogston's and scaled particle theory, neither of which was completely convincing at describing the results. It can be hypothesized that the composition of Dextran plays a role in the deviation of the predicted behavior with respect to the experimental data.
Book Synopsis Mechanical Unfolding of Membrane Proteins Captured with Single Molecule AFM Techniques by : Natalya Baltrukovich
Download or read book Mechanical Unfolding of Membrane Proteins Captured with Single Molecule AFM Techniques written by Natalya Baltrukovich and published by . This book was released on 2008 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Advanced Techniques in Biophysics by : José Luis R. Arrondo
Download or read book Advanced Techniques in Biophysics written by José Luis R. Arrondo and published by Springer Science & Business Media. This book was released on 2007-04-21 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technical advancements are basic elements in our life. In biophysical studies, new applications and improvements in well-established techniques are being implemented every day. This book deals with advancements produced not only from a technical point of view, but also from new approaches that are being taken in the study of biophysical samples, such as nanotechniques or single-cell measurements. This book constitutes a privileged observatory for reviewing novel applications of biophysical techniques that can help the reader enter an area where the technology is progressing quickly and where a comprehensive explanation is not always to be found.
Book Synopsis Calcium and Cell Function by : Wai Yiu Cheung
Download or read book Calcium and Cell Function written by Wai Yiu Cheung and published by . This book was released on 1980 with total page 536 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Handbook of Molecular Force Spectroscopy by : Aleksandr Noy
Download or read book Handbook of Molecular Force Spectroscopy written by Aleksandr Noy and published by Springer Science & Business Media. This book was released on 2007-12-03 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: Researchers in academia and industry who are interested in techniques for measuring intermolecular forces will find this an essential text. It presents a review of modern force spectroscopy, including fundamentals of intermolecular forces, technical aspects of the force measurements, and practical applications. The handbook begins with a review of the fundamental physics of loading single and multiple chemical bonds on the nanometer scale. It contains a discussion of thermodynamic and kinetic models of binding forces and dissipation effects in nanoscale molecular contacts, covers practical aspects of modern single-molecule level techniques, and concludes with applications of force spectroscopy to chemical and biological processes. Computer modeling of force spectroscopy experiments is also addressed.
Book Synopsis Single-molecule Studies of Proteins by : Andres F. Oberhauser
Download or read book Single-molecule Studies of Proteins written by Andres F. Oberhauser and published by Springer Science & Business Media. This book was released on 2012-11-09 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Single Molecule Studies of Proteins, expert researchers discuss the successful application of single-molecule techniques to a wide range of biological events, such as the imaging and mapping of cell surface receptors, the analysis of the unfolding and folding pathways of single proteins, the analysis interaction forces between biomolecules, the study of enzyme catalysis or the visualization of molecular motors in action. The chapters are aimed at established investigators and post-doctoral researchers in the life sciences wanting to pursue research in the various areas in which single-molecule approaches are important; this volume also remains accessible to advanced graduate students seeking similar research goals.
Download or read book Protein Folding written by Alka Dwevedi and published by Springer. This book was released on 2014-12-01 with total page 61 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book will discuss classes of proteins and their folding, as well as the involvement of bioinformatics in solving the protein folding problem. In vivo and in vitro folding mechanisms are examined, as well as the failures of in vitro folding, a mechanism helpful in understanding disease caused by misfolding. The role of energy landscapes is also discussed and the computational approaches to these landscapes.
Book Synopsis Elasticity and Mechanical Unfolding of Globular Protein Domains by : Rebecca C. Zinober-Moore
Download or read book Elasticity and Mechanical Unfolding of Globular Protein Domains written by Rebecca C. Zinober-Moore and published by . This book was released on 2005 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Folding by : Grace E. Orellana
Download or read book Protein Folding written by Grace E. Orellana and published by American Chemical Society. This book was released on 2024-05-08 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Life as we know it would not exist if proteins did not fold into functional three-dimensional structures, where α-helices, loops, and β-sheets act together to form active sites that drive a myriad of biochemical reactions in the cell. The failure of this process is linked to the pathology of various diseases, such as neurodegenerative disorders like Alzheimer’s, genetic conditions (like cystic fibrosis), and cancer. It is no wonder that close to $2 billion in worldwide research funding has been devoted over the last five years (2019–2025) to helping scientists understand the molecular details of protein folding, how it can fail in ways that promote disease in humans, and clinical paths to treat or prevent diseases linked to protein misfolding. This primer is prerequisite reading to the literature on this important topic for readers new to the field. Chapter one provides exposure to the three-dimensional structure of proteins; readers will learn how to identify secondary structures, protein motifs, and domains involved in biological function. Chapter two introduces methodologies to determine the three-dimensional structure of proteins; readers will learn modern techniques to determine the secondary structure composition and the orientation of atoms in three-dimensional space. By providing exposure to how the physical environment (i.e., chemical denaturants, pH, pressure, and temperature) controls protein denaturation, readers will learn how such information can be used to study the biophysical characteristics of proteins through various probes and methodologies.
Book Synopsis Elastic Filaments of the Cell by : H.L. Granzier
Download or read book Elastic Filaments of the Cell written by H.L. Granzier and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 427 pages. Available in PDF, EPUB and Kindle. Book excerpt: Elastic filaments refer mainly to titin, the largest of all known proteins. Titin was discovered initially in muscle cells, where it interconnects the thick filament with the Z-line. Titin forms a molecular spring that is responsible for maintaining the structural integrity of contracting muscle, ensuring efficient muscle contraction. More recently, it has become clear that titin is not restricted to muscle cells alone. For example, titin is found in chromosomes of neurons and also in blood platelets. This topic is fast becoming a focal point for research in understanding viscoelastic properties at the molecular, cellular, and tissue levels. In titin may lie a generic basis for biological viscoelasticity. It has become clear that titin may hold the key to certain clinical anomalies. For example, it is clear that titin-based ventricular stiffness is modulated by calcium and that titin is responsible for the altered stiffness in cardiomyopathies. It is also clear from evidence from a group of Finnish families that titin mutations may underlie some muscular dystrophies and that with other mutations chromatids fail to separate during mitosis. Thus, it is clear that this protein will have important clinical implications stemming from its biomechanical role. One aspect of this field is the bringing together of bioengineers with clinical researchers and biologists. Genetic and biochemical aspects of titin-related proteins are being studied together with front-line engineering approaches designed to measure the mechanics of titin either in small aggregates or in single molecules.
