The Earliest Stages of a Protein's Life Influence Its Long-term Solubility and Structural Accuracy

The Earliest Stages of a Protein's Life Influence Its Long-term Solubility and Structural Accuracy
Author: Matthew Dalphin
Publisher:
Total Pages: 426
Release: 2020
Genre:
ISBN:

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Despite its fundamental importance for life, many details regarding how the cell promotes the solubility and structural accuracy of proteins remains poorly understood. This lack of knowledge poses serious challenges in basic science, biotechnology and medicine as the inability to prevent inclusion body formation limits the efficient overproduction of recombinant proteins and protein-based therapeutics. In this thesis, experimental and computational approaches were combined to explore factors that help discriminate folding and aggregation pathways at various stages of a protein's life in the cell. If folded properly, the native states of many proteins, including apomyoglobin and the soluble E. coli proteome, were shown to be kinetically-trapped from stable aggregate states under physiologically-relevant conditions. However, kinetic simulations suggest that this kinetic trapping can be circumvented at high protein concentrations and, importantly, in the presence of small pre-nucleated aggregate seeds capable of further elongation. In order to further explore how the intracellular environment further influences protein folding and aggregation, we developed a novel bacterial Hsp70 inhibitor which targets and inhibits DnaK. This inhibitor is functional in dilute buffer and cell-free systems. Importantly, it does not also inhibit nascent protein biosynthesis. Our novel inhibitor was then used to probe how the ribosome and DnaK coordinate co- and post-translational events which ultimately support proper protein folding. The ribosome was observed to act as a powerful facilitator of protein solubility during the earliest stages of translation and upon ribosome release. However, it requires additional help from molecular chaperones (e.g. DnaK) to ensure the soluble proteins produced are structurally accurate. Kinetic simulations further highlight that this chaperone requirement for proper folding increases for proteins which are slow to fold at the end of translation. This highlights the synergistic, yet distinct, roles of the ribosome and DnaK required to produce soluble, properly folded proteins which would otherwise be aggregation-prone on their own. Taken together, the work highlighted in this thesis sheds light on the unique mechanism by which the cell shapes, and ultimately traps, proteins into their native state during the earliest stages of protein life.

Critical Beginnings

Critical Beginnings
Author: Rachel Beth Hutchinson
Publisher:
Total Pages: 0
Release: 2022
Genre:
ISBN:

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Protein folding is essential for the survival of all organisms. Early co- and post-translational folding stages are critical because they determine a protein's ability to function for the remainder of its life. When these early folding steps go awry, proteins form harmful aggregates that cause deadly maladies and render protein production costly in the basic-research, biotechnology, and pharmaceutical settings. However, it is not well understood how proteins avoid aggregation and reach their native state in the cell. In this thesis, fluorescence lifetimes and frequency-domain fluorescence depolarization decays were exploited to determine how proteins attain their functional state within the cellular environment. We first explored co-translational folding. We demonstrate that ribosome-bound globin proteins have a compact region containing only 60-80 amino acids (40-50% of the full-length protein). Remaining residues may interact with the ribosome. We identify chain-length dependent interactions between ribosome-bound proteins and ribosomal proteins, trigger factor, and Hsp70. The size of the compact region demonstrates that at least half the sequence folds post-translationally. Upon release from the ribosome, proteins form either the functional native state or harmful aggregates. These states are kinetically trapped from each other, demonstrating the critical importance of the early folding steps for long-term protein health and function. We show that the Hsp70 molecular chaperone acts during the immediately post-translational folding period to grant solubility to aggregation-prone protein variants. Surprisingly, the soluble fraction contains undesirable soluble aggregates, and higher Hsp70 chaperone concentrations are required to prevent their formation, relative to insoluble aggregates. Finally, much higher than physiologically relevant concentrations of Hsp70 are sometimes required to prevent soluble-aggregate formation. We then identified the Hsp70 binding sites in 2,258 E. coli proteins and found that 99% of these proteins contain at least one binding site. Many Hsp70 client proteins do not require chaperones assistance for solubility, but Hsp70 may enable these proteins to form the native structure. The solvent exposure of Hsp70 binding sites suggests proteins may begin folding while bound to the chaperone. In all, this work provides fundamental insights about cellular function and informs the future development of targeted strategies to overcome deleterious protein-aggregation.

Molecular Biology of The Cell

Molecular Biology of The Cell
Author: Bruce Alberts
Publisher:
Total Pages: 0
Release: 2002
Genre: Cytology
ISBN: 9780815332183

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Basic Sciences in Ophthalmology

Basic Sciences in Ophthalmology
Author: Josef Flammer
Publisher: Springer Science & Business Media
Total Pages: 253
Release: 2013-02-19
Genre: Medical
ISBN: 3642322611

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Basic Sciences in Ophthalmology aims to link clinical ophthalmology directly to its basic science roots. This first volume describes the physics and chemistry required for a sound understanding of modern ophthalmology. The book opens with an extensive discussion of the interaction of light with matter and the way in which light is used in ophthalmic examinations and treatments. After describing traditional methods of imaging, particular emphasis is placed on modern instrumentation such as OCT. The interaction between light and tissues in different types of laser treatment is also addressed. The chemistry section focuses on compounds particularly relevant to the eye, such as oxygen and water. The origin and consequences of oxidative stress are reviewed, and the physical behavior of chemical compounds in the eye is explained. Understanding is facilitated through the use of many examples taken from the field of ophthalmology. The text is complemented by about 450 figures.

Proteins

Proteins
Author: James J. L'Italien
Publisher: Springer Science & Business Media
Total Pages: 780
Release: 2012-12-06
Genre: Science
ISBN: 1461317878

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This volume surveys the current status of many of the important methods and approaches which are central to the study of protein structure and function. Many of the articles in this volume are written to emphasize the general utility of the method or approach which is at its core, and to provide sufficient literature references to enable the reader to adapt the method or approach to other applications. It is hoped that this volume will provide a source from which newcomers as well as experienced scient ists may becom& more familiar with recent developments and future trends in some of the important areas of protein research. The articles which comprise this book are selected proceedings from the Symposium of American Protein Chemists, which was held in San Diego, California, September 30 to October 3, 1985. The goal of the organizers of this first symposium was to provide a forum for discussion and inter action among scientists whose interests span the broad spectrum of protein structure and function research. The concept and timing of the symposium well received as evidenced by the approximately 500 delegates to the was symposium. The inaugural meeting was marked by a strong scientific pro gram with over 140 papers presented in either a lecture or poster format.

Protein Design

Protein Design
Author: Raphael Guerois
Publisher: Humana
Total Pages: 300
Release: 2006-06-01
Genre: Science
ISBN: 9781588295859

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Protein Design: Methods and Applications presents the most up-to-date protein design and engineering strategies so that readers can undertake their own projects with a maximum chance of success. The authors present integrated computational approaches that require various degrees of computational complexity, and the major accomplishments that have been achieved in the design and structural characterization of helical peptides and proteins.

Nature's Robots

Nature's Robots
Author: Charles Tanford
Publisher: OUP Oxford
Total Pages: 312
Release: 2003-11-27
Genre: Science
ISBN: 0191578517

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Proteins are amazingly versatile molecules. They make the chemical reactions happen that form the basis for life, they transmit signals in the body, they identify and kill foreign invaders, they form the engines that make us move, and they record visual images. All of this is now common knowledge, but it was not so a hundred years ago. Nature's Robots is an authoritative history of protein science, from the origins of protein research in the nineteenth century, when the chemical constitution of 'protein' was first studied and heatedly debated and when there was as yet no glimmer of the functional potential of substances in the 'protein' category, to the determination of the first structures of individual proteins at atomic resolution - when positions of individual atoms were first specified exactly and bonding between neighbouring atoms precisely defined. Tanford and Reynolds, who themselves made major contributions to the golden age of protein science, have written a remarkably vivid account of this history. It is a fascinating story, involving heroes from the past, working mostly alone or in small groups, usually with little support from formal research groups. It is also a story that embraces a number of historically important scientific controversies. Written in clear and accessible prose, Nature's Robots will appeal to general readers with an interest in popular science, in addition to professional scientists and historians of science.

A Framework for K-12 Science Education

A Framework for K-12 Science Education
Author: National Research Council
Publisher: National Academies Press
Total Pages: 400
Release: 2012-02-28
Genre: Education
ISBN: 0309214459

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Science, engineering, and technology permeate nearly every facet of modern life and hold the key to solving many of humanity's most pressing current and future challenges. The United States' position in the global economy is declining, in part because U.S. workers lack fundamental knowledge in these fields. To address the critical issues of U.S. competitiveness and to better prepare the workforce, A Framework for K-12 Science Education proposes a new approach to K-12 science education that will capture students' interest and provide them with the necessary foundational knowledge in the field. A Framework for K-12 Science Education outlines a broad set of expectations for students in science and engineering in grades K-12. These expectations will inform the development of new standards for K-12 science education and, subsequently, revisions to curriculum, instruction, assessment, and professional development for educators. This book identifies three dimensions that convey the core ideas and practices around which science and engineering education in these grades should be built. These three dimensions are: crosscutting concepts that unify the study of science through their common application across science and engineering; scientific and engineering practices; and disciplinary core ideas in the physical sciences, life sciences, and earth and space sciences and for engineering, technology, and the applications of science. The overarching goal is for all high school graduates to have sufficient knowledge of science and engineering to engage in public discussions on science-related issues, be careful consumers of scientific and technical information, and enter the careers of their choice. A Framework for K-12 Science Education is the first step in a process that can inform state-level decisions and achieve a research-grounded basis for improving science instruction and learning across the country. The book will guide standards developers, teachers, curriculum designers, assessment developers, state and district science administrators, and educators who teach science in informal environments.

Biochar for Environmental Management

Biochar for Environmental Management
Author: Johannes Lehmann
Publisher: Routledge
Total Pages: 450
Release: 2012-05-16
Genre: Business & Economics
ISBN: 1136571205

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Biochar is the carbon-rich product when biomass (such as wood, manure or crop residues) is heated in a closed container with little or no available air. It can be used to improve agriculture and the environment in several ways, and its stability in soil and superior nutrient-retention properties make it an ideal soil amendment to increase crop yields. In addition to this, biochar sequestration, in combination with sustainable biomass production, can be carbon-negative and therefore used to actively remove carbon dioxide from the atmosphere, with major implications for mitigation of climate change. Biochar production can also be combined with bioenergy production through the use of the gases that are given off in the pyrolysis process. This book is the first to synthesize the expanding research literature on this topic. The book's interdisciplinary approach, which covers engineering, environmental sciences, agricultural sciences, economics and policy, is a vital tool at this stage of biochar technology development. This comprehensive overview of current knowledge will be of interest to advanced students, researchers and professionals in a wide range of disciplines.

Strengthening Forensic Science in the United States

Strengthening Forensic Science in the United States
Author: National Research Council
Publisher: National Academies Press
Total Pages: 348
Release: 2009-07-29
Genre: Law
ISBN: 0309142393

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Scores of talented and dedicated people serve the forensic science community, performing vitally important work. However, they are often constrained by lack of adequate resources, sound policies, and national support. It is clear that change and advancements, both systematic and scientific, are needed in a number of forensic science disciplines to ensure the reliability of work, establish enforceable standards, and promote best practices with consistent application. Strengthening Forensic Science in the United States: A Path Forward provides a detailed plan for addressing these needs and suggests the creation of a new government entity, the National Institute of Forensic Science, to establish and enforce standards within the forensic science community. The benefits of improving and regulating the forensic science disciplines are clear: assisting law enforcement officials, enhancing homeland security, and reducing the risk of wrongful conviction and exoneration. Strengthening Forensic Science in the United States gives a full account of what is needed to advance the forensic science disciplines, including upgrading of systems and organizational structures, better training, widespread adoption of uniform and enforceable best practices, and mandatory certification and accreditation programs. While this book provides an essential call-to-action for congress and policy makers, it also serves as a vital tool for law enforcement agencies, criminal prosecutors and attorneys, and forensic science educators.