Modeling Insertion of Transmembrane Beta-barrels for Designing Outer Membrane Proteins PDF Download
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Author: Daniel Hsieh
Publisher:
ISBN:
Category : Bacterial proteins
Languages : en
Pages : 172
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Book Description
Outer membrane proteins (OMPs) perform a range of important functions in the cell biology of Gram-negative bacteria, mitochondria and chloroplasts. These functions include biogenesis, virulence, signal transduction, nutrient transport and apoptosis. In contrast to their inner membrane counterparts, OMPs have been more difficult to study due to the relative paucity of crystal structures. Although outer membrane proteins have been characterized and studied extensively by various structural and biophysical methods, our understanding of their folding, insertion and oligomerization is far behind that of inner membrane proteins. The goal of this study is to elucidate the folding and insertion mechanism of these transmembrane [beta]-barrel proteins (TMBs) and ultimately to provide guidelines for computationally designing OMP sequences that fold and insert efficiently. Using a subset of amino acids from thirty-five outer membrane proteins from Gram-negative bacteria and mitochondria, a propensity vs depth in membrane profile for each residue was derived. Although results indicate similar trends between amino acids of inner and outer membrane proteins, there are also differences that can be explained by differences in factors such as environment, secondary structural preferences, and folding/insertion pathway. The propensity profiles were converted into energies of insertion as a function of depth from the center of the membrane. This thesis explores the many ways of using the statistical potential to answer questions about OMP folding, insertion and oligomerization that could not have been framed due to the experimental limitations. We conclude with a discussion of ways to improve our potential, including the assumption of asymmetry of the lipid bilayer as well as incorporating homology model building.
Author: Daniel Hsieh
Publisher:
ISBN:
Category : Bacterial proteins
Languages : en
Pages : 172
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Book Description
Outer membrane proteins (OMPs) perform a range of important functions in the cell biology of Gram-negative bacteria, mitochondria and chloroplasts. These functions include biogenesis, virulence, signal transduction, nutrient transport and apoptosis. In contrast to their inner membrane counterparts, OMPs have been more difficult to study due to the relative paucity of crystal structures. Although outer membrane proteins have been characterized and studied extensively by various structural and biophysical methods, our understanding of their folding, insertion and oligomerization is far behind that of inner membrane proteins. The goal of this study is to elucidate the folding and insertion mechanism of these transmembrane [beta]-barrel proteins (TMBs) and ultimately to provide guidelines for computationally designing OMP sequences that fold and insert efficiently. Using a subset of amino acids from thirty-five outer membrane proteins from Gram-negative bacteria and mitochondria, a propensity vs depth in membrane profile for each residue was derived. Although results indicate similar trends between amino acids of inner and outer membrane proteins, there are also differences that can be explained by differences in factors such as environment, secondary structural preferences, and folding/insertion pathway. The propensity profiles were converted into energies of insertion as a function of depth from the center of the membrane. This thesis explores the many ways of using the statistical potential to answer questions about OMP folding, insertion and oligomerization that could not have been framed due to the experimental limitations. We conclude with a discussion of ways to improve our potential, including the assumption of asymmetry of the lipid bilayer as well as incorporating homology model building.
Author: Susan Buchanan
Publisher: Humana
ISBN: 9781493928705
Category : Science
Languages : en
Pages : 0
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Book Description
This volume is comprised of a collection of experimental protocols for common techniques and strategies used to study the biogenesis of b-barrel outer membrane proteins in Gram-negative bacteria. The BAM Complex: Methods and Protocols guides readers through methods on the function of the BAM complex, the roles played by each of the individual components, the expression and purification of the components, crystallization and structure determination of the components, and how the individual Bam components may assemble into a functional complex. 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. Authoritative and cutting-edge, The BAM Complex: Methods and Protocols will serve as an invaluable reference for those interested in studying the BAM complex.
Author: Raffaele Ieva
Publisher: Springer Nature
ISBN: 1071637347
Category :
Languages : en
Pages : 388
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Book Description
Author: Jos A.F. Op den Kamp
Publisher: Springer Science & Business Media
ISBN: 3642731848
Category : Science
Languages : en
Pages : 474
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Book Description
Many individual aspects of the dynamics and assembly of biological membranes have been studied in great detail. Cell biological approaches, advanced genetics, biophysics and biochemistry have greatly contributed to an increase in our knowledge in this field.lt is obvious however, that the three major membrane constituents - lipids, proteins and carbohydrates- are studied, in most cases separately and that a coherent overview of the various aspects of membrane biogenesis is not readily available. The NATO Advanced Study Institute on "New Perspectives in the Dynamics of Assembly of Biomembranes" intended to provide such an overview: it was set up to teach students and specialists the achievements obtained in the various research areas and to try and integrate the numerous aspects of membrane assembly into a coherent framework. The articles in here reflect this. Statting with detailed contributions on phospholipid structure, dynamics, organization and biogenesis, an up to date overview of the basic, lipidic backbone of biomembranes is given. Extensive progress is made in the research on membrane protein biosynthesis. In particular the post- and co-translational modification processes of proteins, the mechanisms of protein translocation and the sorting mechanisms which are necessary to direct proteins to their final, intra - or extracellular destination have been characterized in detail. Modern genetic approaches were indispensable in this research area: gene cloning, hybrid protein construction, site directed mutagenesis and sequencing techniques elucidated many functional aspects of specific nucleic acid and amino acid sequences.
Author:
Publisher:
ISBN: 9780815332183
Category : Cells
Languages : en
Pages : 0
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Book Description
Author: Martin Caffrey
Publisher: CRC Press
ISBN: 9780849389245
Category : Medical
Languages : en
Pages : 334
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Book Description
LIPIDAT is a convenient compilation of thermodynamic data and bibliographic information on lipids. Over 11,000 records in 15 information fields are provided. The book presents tabulations of all known mesomorphic and polymorphic phase transition types, temperatures, and enthalpies for synthetic and biologically derived lipids in dry, partially hydrated, and fully hydrated states. It also includes the effect of pH, protein, drugs, salt, and metal ion concentration on these thermodynamic values. Methods used in making the measurements and the experimental conditions are reported. Bibliographic information includes a complete literature reference and list of authors. The book will be an indispensable reference for biophysicists, chemical engineers, pharmaceutical and cosmetic researchers, dermatologists, nutritionists, biochemists, physiologists, food scientists, and fats and oils chemists.
Author: Vivien Yeh
Publisher: Springer
ISBN: 9811312389
Category : Science
Languages : en
Pages : 151
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Book Description
This book focuses on the study of how the properties of nanodiscs, such as lipid composition and size, influence the function of the embedding integral membrane protein, bacteriorhodopsin. The author performed systematic studies to show that the lipid composition and the charge of the hydrophobic head and the structure of hydrophilic tails affect the photocycle pathway of bacteriorhodopsin, which is closely associated with its proton-pumping activity. Furthermore, the author demonstrated a highly efficient method for extracting membrane proteins directly from the biological membrane, preserving protein conformation, function and essential native lipids. This book demonstrates optimization and sample preparation, and presents practical methods of preparing membrane protein-embedded nanodisc samples for biophysical studies, which benefit structural and functional studies in the field of membrane protein characterization, both.
Author: J.-M. Ghuysen
Publisher: Elsevier
ISBN: 0080860877
Category : Science
Languages : en
Pages : 607
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Book Description
Studies of the bacterial cell wall emerged as a new field of research in the early 1950s, and has flourished in a multitude of directions. This excellent book provides an integrated collection of contributions forming a fundamental reference for researchers and of general use to teachers, advanced students in the life sciences, and all scientists in bacterial cell wall research. Chapters include topics such as: Peptidoglycan, an essential constituent of bacterial endospores; Teichoic and teichuronic acids, lipoteichoic acids, lipoglycans, neural complex polysaccharides and several specialized proteins are frequently unique wall-associated components of Gram-positive bacteria; Bacterial cells evolving signal transduction pathways; Underlying mechanisms of bacterial resistance to antibiotics.
Author: Gunnar von Heijne
Publisher: R. G. Landes
ISBN:
Category : Science
Languages : en
Pages : 300
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Book Description
Author: Giovanna Ghirlanda
Publisher: Humana Press
ISBN: 9781627035842
Category : Science
Languages : en
Pages : 246
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Book Description
Focusing on model systems for the study of structure, folding, and association in the membrane, Membrane Proteins: Folding, Association, and Design presents an overview of methods that can be applied to these intricate systems. The volume is divided into four detailed sections, covering association of transmembrane helices, interactions with the lipid bilayer, NMR methods, as well as a variety of engineering approaches. Written for the highly successful Methods in Molecular Biology series, 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. Authoritative and practical, Membrane Proteins: Folding, Association, and Design serves as an ideal guide for researchers reaching for the tantalizing possibility of designing novel membrane proteins with tailored functionality.
