The forces and energetic principles that guide molecular structure and dynamics in cellular lipid bilayers are poorly understood, largely due to limited familiarity with physical chemistry outside of water. We strive to enhance our fundamental chemical intuition concerning membrane proteins because their biochemical behavior within lipid membranes governs critical cellular processes and dictates health or disease. Likewise, this intuition paired with the ability manipulate membrane protein structure and function using computational modeling, theoretical calculations, and molecular design are instrumental to the engineering of new therapeutics. The work described here focuses on using protein design and integrative computational approaches to dissect the fundamental biophysical principles underlying protein interactions and folding within the lipid environment, spanning studies of both natural and totally synthetic proteins. Chapter 1 describes the design and experimental characterization of a family of simple synthetic model membrane proteins that rely entirely on the steric packing of lipid-embedded apolar sidechains for their stabilization and folding. This work reveals new fundamental principles governing van der Waals forces for proteins in lipid which should dictate protein structure, function, and evolution. Chapter 2 reports discovery of an evolutionarily conserved interaction motif within the transmembrane (TM) domains of integrin family proteins regulating their biochemical function. This discovery was driven by molecular modeling and all-atom dynamics simulations paired with co-workers' optical tweezer force spectroscopy experiments. Chapter 3 details the development and application of software to design lipid-soluble peptides that target the transmembrane domains of proteins. We report several molecules that activate integrin Îł5Îø1 in human endothelial cell culture, and one with binding specificity for the Îø1 subunit. Chapter 4 outlines a second campaign with similar software to engineer small synthetic transmembrane proteins that bind and inhibit signal-amplifying erythropoietin receptor (EpoR), a canonical cytokine family receptor. Here, we demonstrate computational design can be used to target membrane-soluble molecules to specifically adopt custom, non-native binding modes to engage targeted regions of protein embedded in lipid. Thus, the efforts described represent leaps in our capacity to compute designer tool molecules entirely from scratch useful for manipulating membrane-spanning regions. These works together define progress in our fundamental biophysical understanding of protein interactions and folding in lipid, as well as our ability to dissect membrane protein structure and function with in silico molecular modeling algorithms and novel chemical biology tools.

Studies of receptors, ion channels, and other membrane proteins require a solid understanding of the structural principles of these important biomolecules. Membrane protein structure is, however, a very challenging field. The structures of only three types of transmembrane proteins have been determined to moderate or high resolution during the last two decades, a period during which the amino acid sequences of hundreds, if not thousands, of membrane proteins have been reported. As a result, the creation of structural models to serve as guides for studies of receptors, channels, and other membrane proteins has become crucially important. This book has been assembled in order to share the experiences and findings of expert researchers in protein structure and structure-prediction methods as well as membrane biophysics and lipid physical chemistry, whose work establishes the basis for the development of suitable model structures. The reviews presented here emphasize fundamental ideas and provide an entry to the diverse and complex literature. The four major sections deal with the general nature of the membrane protein structure problem, biochemical and molecular biological approaches to protein topology, direct structural methods, and model and physicochemical approaches. The work will be of interest to physiologists, cellular and molecular biologists, biophysicists, and biochemists working on the function of membrane proteins such as receptors, ion channels, and transporters, as well as senior graduate students and independent investigators.

This book reviews current techniques used in membrane protein structural biology, with a strong focus on practical issues. The study of membrane protein structures not only provides a basic understanding of life at the molecular level but also helps in the rational and targeted design of new drugs with reduced side effects. Today, about 60% of the commercially available drugs target membrane proteins and it is estimated that nearly 30% of proteins encoded in the human genome are membrane proteins. In recent years much effort has been put towards innovative developments to overcome the numerous obstacles associated with the structure determination of membrane proteins. This book reviews a variety of recent techniques that are essential to any modern researcher in the field of membrane protein structural biology. The topics that are discussed are not commonly found in textbooks. The scope of this book includes: Expression screening using fluorescent proteins The use of detergents in membrane protein research The use of NMR Synchrotron developments in membrane protein structural biology Visualisation and X-ray data collection of microcrystals X-ray diffraction data analysis from multiple crystals Serial millisecond crystallography Serial femtosecond crystallography Membrane protein structures in drug discovery The information provided in this book should be of interest to anyone working in the area of structural biology. Students will find carefully prepared overviews of basic ideas and advanced protein scientists will find the level of detail required to apply the material directly to their day to day work. Chapters 4, 5, 6, 8 and 9 of this book are published open access under a CC BY 4.0 license at link.springer.com.

Membrane proteins, representing nearly 40% of all proteins, are key components of cells involved in many cellular processes, yet only a small number of their structures have been determined. Membrane Protein Structure Determination: Methods and Protocols presents many detailed techniques for membrane protein structure determination used today by bringing together contributions from top experts in the field. Divided into five convenient sections, the book covers various strategies to purify membrane proteins, approaches to get three dimensional crystals and solve the structure by x-ray diffraction, possibilities to gain structural information for a membrane protein using electron microscopy observations, recent advances in nuclear magnetic resonance (NMR), and molecular modelling strategies that can be used either to get membrane protein structures or to move from atomic structure to a dynamic understanding of a molecular functioning mechanism. Written in the highly successful Methods in Molecular BiologyTM 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. Comprehensive and easy to use, Membrane Protein Structure Determination: Methods and Protocols serves as an ideal reference for scientists seeking to further our knowledge of these vital and versatile proteins as well as our overall understanding of the complicated world of cell biology.

Computer-based design and modeling, computational approaches, and instrumental methods for elucidating molecular mechanisms of protein folding and ligand-acceptor interactions are included in Volumes 202 and 203, as are genetic and chemical methods for the production of functional molecules including antibodies and antigens, enzymes, receptors, nucleic acids and polysaccharides, and drugs.

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.