Download or read book Identification and Analysis of the Folding Determinants of Membrane Proteins written by Fiona Cunningham and published by . This book was released on 2011 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: Membrane proteins are responsible for a variety of key cellular functions including transport of essential substrates across the membrane, signal transduction, and maintenance of cellular morphology. However, given the size and high hydrophobicity of membrane proteins, along with demanding expression and solubilization protocols that often preclude biophysical studies, novel approaches must be devised for studies of their structure and function. This thesis addresses these issues through several sets of inter-related experiments. We first examine sequence motifs directing alpha-helix packing, wherein the determinants of glycophorin A (GpA) dimerization were identified via TOXCAT assay and the evaluation of GpA-derived peptides. We found that (i) conservative mutations can have significant effects on the oligomerization of glycophorin A; and (ii) residues that introduce more efficiently packed structures that are poorly solvated by lipid leads to improved transmembrane segment dimerization. In a further study, we inquired into the criteria for selection of membrane-spanning alpha-helices by cellular machinery through investigation of hydrophobic helical segments (termed delta-helices) that we identified in soluble proteins. We found that the number and location of charged residues in a given hydrophobic helix are related to their insertion propensity as membrane-spanning segments. When we applied this criterion to delta-helices in their intact protein structures, we successfully determined the extent of delta-helix mutations necessary to convert a soluble protein, in part, to a membrane-inserted protein. Finally, using a three-transmembrane segment construct from the cystic fibrosis transmembrane conductance regulator (CFTR), we performed experiments aimed at optimizing criteria for protein overexpression, including construct design, choice of expression system, growth media, and expression temperature. The overall findings are interpreted in terms of progress towards defining the fundamental characteristics of membrane-spanning alpha-helices - from their primary amino acid sequence to the helix-helix interactions they display in the assembly of biologically-functional membrane protein structures.
Download or read book Determinants of Membrane Protein Folding written by Rachel Marie Johnson and published by . This book was released on 2007 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to the challenges of insolubility, aggregation, and purification presented by membrane proteins in structure determination, it is important to develop alternative methods for elucidating their final folds. In particular, since few membrane protein high-resolution structures are available, it would be of value to be able to predict the three-dimensional conformation arising from the transmembrane (TM) helical segment(s) of a membrane protein largely on the basis of the protein primary sequence. In order to predict this structure and its stability, it is necessary to evaluate the principal energetic contributions in the folding process, including helix-helix, helix-lipid, and lipid-lipid interactions. To this end, this thesis examines sequence motifs and packing interactions both between TM helices, and between the TM helix and the lipid acyl chains of the surrounding phospholipid bilayer. By using a de novo designed hydrophobic hairpin as a model, it was found that helix-helix association exists as a delicate balance of forces consisting predominantly of electrostatic and van der Waals interactions. In situations where hydrophobic van der Waals packing energy between helices is sufficient to prevent significant rotation about the major axes of interacting helices, we found that intra-hairpin side chain - side chain hydrogen bond formation occurred mainly when pairs of polar residues were interfacially located and proximal. The role of lipid in helix-helix associations was also addressed; we showed a strong inverse correlation between non-polar group lipid accessibility and dimer affinity in both glycophonn A (GpA) and M13 coat protein (MCP) Gly-xxx-Gly (GG4) motif-mediated homodimers, suggesting that lipid can act as a poor membrane protein solvent---conceptually analogous to water in soluble protein folding---and thus can contribute to dimer stability. In a further study of both GpA and MCP homodimers, we demonstrated that centrally located GG4 motifs are capable of stronger helix-helix interactions than those proximal to TM helix ends even while surrounding interfacial residues are maintained, indicating that relative importance of the TM context of GG4 motifs in stabilizing helix-helix interactions. These overall findings are interpreted in terms of progress toward prediction of helix-helix interaction strength in the folding and assembly of membrane proteins.
Download or read book Determinants of Membrane Protein Structure Probed by de Novo Design written by Holly Gratkowski and published by . This book was released on 2002 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Folds written by Henrik Bohr and published by CRC Press. This book was released on 1995-10-20 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by outstanding scientists in physics and molecular biology, this book addresses the most recent advances in the analysis of the protein folding processes and protein structure determination. Emphasis is also placed on modelling and presentation of experimental results of structural membrane bound proteins. Many color plates help to illustrate structural aspects covered including: Defining folds of protein domains Structure determination from sequence Distance geometry Lattice theories Membrane proteins Protein-Ligand interaction Topological considerations Docking onto receptors All analysis is presented with proven theory and experimentation. Protein Folds: A Distance-Based Approach is an excellent text/reference for biotechnologists and biochemists as well as graduate students studying in the research sciences.
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Folding Kinetics written by Bengt Nölting and published by Springer Science & Business Media. This book was released on 2005-12-05 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: First methods book which includes many detailed descriptions Absolutely needed and thus timely for the scientific community Comprises 15% more content and includes the mentioned special features
Download or read book Membrane Protein Assembly written by Gunnar von Heijne and published by R. G. Landes. This book was released on 1997 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Topological Analysis of Membrane Proteins in Bacteria and Studies of Factors Involved in Protein Folding written by Saravanamuttu Gnaneshan and published by . This book was released on 2000 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Identifying Determinants of Folding and Activity for a Protein of Unknown Structure written by James Ulrich Bowie and published by . This book was released on 1989 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Membrane Structural Biology written by Mary Luckey and published by Cambridge University Press. This book was released on 2014-02-24 with total page 427 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook provides a strong foundation and a clear overview for students of membrane biology and an invaluable synthesis of cutting-edge research for working scientists. The text retains its clear and engaging style, providing a solid background in membrane biochemistry, while also incorporating the approaches of biophysics, genetics and cell biology to investigations of membrane structure, function and biogenesis to provide a unique overview of this fast-moving field. A wealth of new high resolution structures of membrane proteins are presented, including the Na/K pump and a receptor-G protein complex, offering exciting insights into how they function. All key tools of current membrane research are described, including detergents and model systems, bioinformatics, protein-folding methodology, crystallography and diffraction, and molecular modeling. This comprehensive and up-to-date text, emphasising the correlations between membrane research and human health, provides a solid foundation for all those working in this field.
Download or read book The Determinants of Polypeptide Partitioning Between Water and Membranes written by Charles John Russell and published by . This book was released on 1998 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Biophysics of Membrane Proteins written by Carmen Domene and published by Royal Society of Chemistry. This book was released on 2016-11-30 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exploring current themes in modern computational and membrane protein biophysics, this book presents a comprehensive account of the fundamental principles underlying different methods and techniques used to describe the intriguing mechanisms by which membrane proteins function. The book discusses the experimental approaches employed to study these proteins, with chapters reviewing recent crucial structural advances that have allowed computational biophysicists to discern how these molecular machines work. The book then explores what computational methods are available to researchers and what these have taught us about three key families of membrane proteins: ion channels, transporters and receptors. The book is ideal for researchers in computational chemistry and computational biophysics.
Download or read book Investigation of Folding Stability and Function of Alpha Helical Membrane Proteins Under Native Condition written by Ruiqiong Guo and published by . This book was released on 2018 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Membrane Proteins written by Giovanna Ghirlanda and published by Humana. This book was released on 2016-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Folding Stability and Degradation of Membrane Protein in the Bilayer written by Fathima Shaima Muhammed Nazaar and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein quality control involves the regulation of functional protein concentration at an optimal level in cells. To achieve this cellular need, a variety of biomolecular phenomena including protein synthesis, protein folding, chaperone action, and protein turnover are coordinated and balanced. While many studies on protein quality control focus on water-soluble proteins, it is not well understood how the quality control of membrane proteins is maintained. However, this question has been challenging to address due to difficulties in establishing tractable model systems in the lipid bilayer environment. This dissertation aims to answer two specific problems in membrane biology: 1) How does the lipid bilayer influence the folding and cooperativity of membrane proteins? 2) How do the intrinsic folding properties of membrane proteins influence their susceptibility to degradation? Using the intramembrane protease GlpG as a model, I find that, compared to micelles, the lipid bilayer enhances the stability of the protein by facilitating residue burial in the protein interior and strengthening the cooperative interaction network. Also, I find that conformational stability is not a major determinant of degradation rates of membrane proteins, and rather, the hydrophobicity of transmembrane segments or the conformational distribution of denatured state ensembles impact more. This finding suggests that the rate-limiting step of FtsH-mediated degradation of membrane proteins is not substrate denaturation but the dislocation of the hydrophobic transmembrane segments from the membrane to water. My studies will contribute to the fundamental understanding of the lipid bilayer as a solvent mediating folding, function, and quality control of membrane proteins.
Download or read book Membrane Protein Topology Acquisition and Folding Through the Transition State written by Nicholas Woodall and published by . This book was released on 2016 with total page 125 pages. Available in PDF, EPUB and Kindle. Book excerpt: The folding mechanisms of helical membrane proteins remain largely uncharted. Here we examine two of the primary events during membrane protein folding: insertion/topology acquisition into the lipid bilayer and the assembly of alpha helices into their native state. Towards this goal we characterize the kinetics of bacteriorhodopsin folding and employ -value analysis to explore the folding transition state. We were able to obtain reliable -values for 16 mutants of bacteriorhodopsin well distributed throughout the protein. Every -value was less than 0.4, indicating the transition state is not uniquely structured. We suggest that the transition state is a loosely organized ensemble of conformations. Before the final folding of the alpha helices, the transmembrane segments must be properly aligned in the lipid bilayer. The topology of helical membrane proteins is generally defined during insertion of the transmembrane helices. It is now clear, however, that topology can remain malleable in some cases. We show that the entire EmrE protein can indeed invert topology after the full protein is translated and inserted. Wholesale topology flipping is remarkable given the physical constraints of the membrane and exposes new avenues to envision folding pathways, both productive and detrimental.
Download or read book Biogenesis of Fatty Acids Lipids and Membranes written by Otto Geiger and published by Springer. This book was released on 2019-01-29 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concise chapters, written by experts in the field, cover a wide spectrum of topics on lipid and membrane formation in microbes (Archaea, Bacteria, eukaryotic microbes).All cells are delimited by a lipid membrane, which provides a crucial boundary in any known form of life. Readers will discover significant chapters on microbial lipid-carrying biomolecules and lipid/membrane-associated structures and processes.
