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Author: Apratim Dhar
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Biomolecular dynamics and stability are predominantly investigated in vitro, and extrapolated to explain function in the living cell. In this thesis, we attempt to bridge this divide by performing studies of protein folding in in vitro crowded environments and in living cells. We begin by investigating the thermodynamic and kinetic behavior of the proteins in protein/carbohydrate matrices, and find significant differences compared to dilute, buffer solutions. We then develop Fast Relaxation Imaging (FReI) as a novel imaging technique to investigate protein folding dynamics inside living cells with millisecond temporal resolution and micrometer spatial resolution. We study the folding of the metabolic enzyme phosphoglycerate kinase (PGK) in U2OS (human osteosarcoma) cells and observe variations in folding kinetics within a single cell. FReI experiments carried out on an ensemble of 30 cells reveal large variations in folding time from cell to cell, which are analyzed to estimate the folding diffusion coefficient in vivo. Finally, we use short peptide tags to target PGK to the nucleus and endoplasmic reticulum of live cells and discern differential folding stability and kinetics in these organelles compared to protein folding in the cytoplasm.
Author: Apratim Dhar
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Biomolecular dynamics and stability are predominantly investigated in vitro, and extrapolated to explain function in the living cell. In this thesis, we attempt to bridge this divide by performing studies of protein folding in in vitro crowded environments and in living cells. We begin by investigating the thermodynamic and kinetic behavior of the proteins in protein/carbohydrate matrices, and find significant differences compared to dilute, buffer solutions. We then develop Fast Relaxation Imaging (FReI) as a novel imaging technique to investigate protein folding dynamics inside living cells with millisecond temporal resolution and micrometer spatial resolution. We study the folding of the metabolic enzyme phosphoglycerate kinase (PGK) in U2OS (human osteosarcoma) cells and observe variations in folding kinetics within a single cell. FReI experiments carried out on an ensemble of 30 cells reveal large variations in folding time from cell to cell, which are analyzed to estimate the folding diffusion coefficient in vivo. Finally, we use short peptide tags to target PGK to the nucleus and endoplasmic reticulum of live cells and discern differential folding stability and kinetics in these organelles compared to protein folding in the cytoplasm.
Author:
Publisher: Elsevier
ISBN: 0080522408
Category : Science
Languages : en
Pages : 516
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Book Description
This volume of Advances in Protein Chemistry provides a broad, yet deep look at the cellular components that assist protein folding in the cell. This area of research is relatively new--10 years ago these components were barely recognized, so this book is a particularly timely compilation of current information. Topics covered include a review of the structure and mechanism of the major chaperone components, prion formation in yeast, and the use of microarrays in studying stress response. Outlines preceding each chapter allow the reader to quickly access the subjects of greatest interest. The information presented in this book should appeal to biochemists, cell biologists, and structural biologists.
Author:
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Author: Robert L. Ellis
Publisher: Elsevier
ISBN: 0080528880
Category : Science
Languages : en
Pages : 339
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Book Description
The first of its kind, this volume presents the latest research findings on the chaperonins, the best studied family of a class of proteins known as molecular chaperones. These findings are changing our view of some fundamental cellular processes involving proteins, especially how proteins fold into their functional conformations. - Origins of the new view of protein folding - Prokaryotic chaperonins - Eukaryotic chaperonins - Evolution of the chaperonins - Refolding of denatured proteins - Organelle biosynthesis - Biomedical aspects
Author: Alexander Shekhtman
Publisher:
ISBN: 9783039282555
Category : Biology (General)
Languages : en
Pages : 152
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Book Description
This Special Issue examines state-of-the-art in-cell NMR spectroscopy as it relates to biological systems of increasing complexity. The compendia of research and recent innovations from prominent laboratories in the field of solid state and solution in-cell NMR spectroscopy, metabolomics and technology development are presented. The work establishes in-cell NMR spectroscopy as the premier method for determining the structures and interaction capabilities of biological molecules at high resolution within the delicately intricate interior of living cells, and the means of utilizing cells as living laboratories to directly assess the effects of exogenous and endogenous stimuli on cell physiology.].
Author:
Publisher: Academic Press
ISBN: 0128211377
Category : Science
Languages : en
Pages : 554
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Book Description
Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more. Includes comprehensive coverage on molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field
Author: Michael Charles Konopka
Publisher:
ISBN:
Category :
Languages : en
Pages : 198
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Book Description
Author: Mazahide Terazima
Publisher: Springer
ISBN: 4431558403
Category : Science
Languages : en
Pages : 276
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Book Description
In this monograph, the importance of fluctuations for biological reactions is discussed from various points of view. Understanding the biological reactions at the molecular level is one of the major targets in many scientific fields, including not only basic biology but also physics, physical chemistry, and medical science. One of the key factors in the process is “fluctuation”. Thermal energy causes biological molecules to be in constant fluctuation even while they are carrying out their biological functions. How do biological systems overcome the thermal fluctuations to realize the physiologically relevant reactions? Scientists in a number of fields—physics, chemistry, pharmacology, medicine, and others—have contributed chapters that elucidate the nature of the fluctuations and the relationship between fluctuations and biological functions. The fluctuations discussed in this volume are detected by the transient grating method, nuclear magnetic resonance, X-ray diffraction and scattering, and computer simulation, among other methods. The book presents various results of the studies of fluctuations in biological processes that were obtained with these methods by the leading scientists in their fields.
Author: Grace E. Orellana
Publisher: American Chemical Society
ISBN: 0841296383
Category : Science
Languages : en
Pages : 170
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Book Description
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.
Author: Donald B Wetlaufer
Publisher: Routledge
ISBN: 1000233154
Category : Social Science
Languages : en
Pages : 203
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Book Description
Proteins in living systems carry out a great variety of specific functions, each of which depends on the precise three-dimensional structure of a particular protein. Proteins are synthesized in the form of a flexible polypeptide chain that is capable of assuming a vast number of configurations; the transformation of this chain into a specific, relatively rigid three-dimensional structure is called folding--a remarkable process of self-organization. It is known that the amino acid sequences of some proteins have sufficient information to determine their three-dimensional structures. There are other proteins whose folding requires additional information beyond that found in the sequence of the mature protein. This book introduces the central problem of folding mechanisms as well as a number of other closely related issues. This book is neither a textbook nor a treatise. Rather, it is an attempt by several investigators to convey the excitement and challenges of those aspects of the folding problem in which they are actively engaged. The contributors give brief introductions to protein folding from the perspectives of molecular architecture, stability and dynamics, phage genetics, DNA exons, general physiology, and natural selection. They point out emerging new directions, including the suggestion of a class of diseases that result from protein folding defects.
