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2007
Structural Basis of Effector Regulation and Signal Termination in Heterotrimeric G
2007
How do Receptors Activate G Proteins?
Publication date: 2007
Source:Advances in Protein Chemistry, Volume 74 Author(s): William M. Oldham, Heidi E. Hamm Heterotrimeric G proteins couple the activation of heptahelical receptors at the cell surface to the intracellular signaling cascades that mediate the physiological responses to extracellular stimuli. G proteins are molecular switches that are activated by receptor
2007
Some Mechanistic Insights into GPCR Activation from Detergent
2007
Activation of G Protein–Coupled Receptors
Publication date: 2007
Source:Advances in Protein Chemistry, Volume 74 Author(s): Xavier Deupi, Brian Kobilka G protein–coupled receptors (GPCRs) mediate responses to hormones and neurotransmitters, as well as the senses of sight, smell, and taste. These remarkably versatile signaling molecules respond to structurally diverse ligands. Many GPCRs couple to multiple G protein subtypes, and several have been shown to activate G protein–independent signaling pathways. Drugs acting on GPCRs exhibit efficacy profiles that may differ for different signaling cascades. The functional plasticity exhibited by GPCRs can be attributed to structural flexibility and the existence of multiple ligand
2007
Kinetic Analysis of G Protein–Coupled Receptor Signaling Using Fluorescence Resonance Energy Transfer in Living Cells
Publication date: 2007
Source:Advances in Protein Chemistry, Volume 74 Author(s): Martin J. Lohse, Carsten Hoffmann, Viacheslav O. Nikolaev, Jean
2007
Regulation of Rho Guanine Nucleotide Exchange Factors by G Proteins
Publication date: 2007
Source:Advances in Protein Chemistry, Volume 74 Author(s): Paul C. Sternweis, Angela M. Carter, Zhe Chen, Shahab M. Danesh, Ying
2007
Author Index
Publication date: 2007
Source:Advances in Protein Chemistry, Volume 74

This chapter lists the names of the authors who have contributed to volume 74 of the book Advances in Protein Chemistry, , such as L. Aris, S. Adams, L. Baisamy, A. Barac, I. Azpiazu, S. Bardin, andJ. A Ballesteros. Their names have been mentioned along with the page numbers in which their names appear in the book—for the ease of the reader.
2007
Subject Index
Publication date: 2007
Source:Advances in Protein Chemistry, Volume 74

This chapter lists the important terms that are discussed in the book Advances in Protein Chemistry (Volume 74) such as signal termination, protease-activated receptor, rapid mix flow cytometry, cysteines, catecholamine binding, Fourier transform, and cyan fluorescent protein. The terms are mentioned along with the page numbers in which they have appeared in the book—for the ease of the reader.
2007
Preface
Publication date: 2007
Source:Advances in Protein Chemistry, Volume 74 Author(s): Stephen Sprang This chapter focuses on recent developments in the efforts to understand the kinetic and structural basis of G protein signaling. It reviews structural and mechanistic aspects of signal transduction by G
2006
Contents
Publication date: 2007
Source:Advances in Protein Chemistry, Volume 74

2006
2006
2006
2006
Natural Triple
2006
Structure, Function, and Amyloidogenesis of Fungal Prions: Filament Polymorphism and Prion Variants
Publication date: 2006
Source:Advances in Protein Chemistry, Volume 73 Author(s): Ulrich Baxa, Todd Cassese, Andrey V. Kajava, Alasdair C. Steven Infectious proteins (prions) became an important medical issue when they were identified as agents of the transmissible spongiform encephalopathies. More recently, prions have been found in fungi and their investigation has been facilitated by greater experimental tractability. In each case, the normal form of the prion protein may be converted into the infectious form (the prion itself) in an autocatalytic process; conversion may either occur spontaneously or by transmission from an already infected cell. Four fungal prion proteins have been studied in some depth—Ure2p, Sup35p, and Rnq1p of Saccharomyces cerevisiae and HET
2006
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2006
From the Polymorphism of Amyloid Fibrils to their Assembly Mechanism and Cytotoxicity
Publication date: 2006
Source:Advances in Protein Chemistry, Volume 73 Author(s): Laurent Kreplak, Ueli Aebi Extracellular amyloid deposits are present in a variety of diseases. They contain amyloid fibrils that arise from the association of proteins or peptides. At the molecular level, all these fibrils share a common assembly principle based on a conformational change of the protein precursor leading to the formation of a cross
2006
Structural Models of Amyloid
2006
Contents
Publication date: 2006
Source:Advances in Protein Chemistry, Volume 73

2006
Author Index
Publication date: 2006
Source:Advances in Protein Chemistry, Volume 73

This chapter lists the names of the authors who have contributed to the book, Advances in Protein Chemistry, Volume 73, such as C. Abraham, P. Argos, M. Aguet, A. Amadei, M. Auger, and others. Their names have been mentioned along with the page numbers in which their names appear in the book—for the ease of the reader.
2005
Subject Index
Publication date: 2006
Source:Advances in Protein Chemistry, Volume 73

This chapter lists the important subjects that are discussed in the book, Advances in Protein Chemistry, Volume 73, such as crystallization and silk strength, familial disease, fibril formation, cooperative kinetics, protein data bank, and others. The terms are mentioned along with the page numbers in which they have appeared in the book—for the ease of the reader.
2005
Potential Functions for Hydrogen Bonds in Protein Structure Prediction and Design
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 72 Author(s): Alexandre V. Morozov, Tanja Kortemme Hydrogen bonds are an important contributor to free energies of biological macromolecules and macromolecular complexes, and hence an accurate description of these interactions is important for progress in biomolecular modeling. A simple description of the hydrogen bond is based on an electrostatic dipole–dipole interaction involving hydrogen
2005
Backbone–Backbone H
2005
Modeling Polarization in Proteins and Protein–ligand Complexes: Methods and Preliminary Results
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 72 Author(s): Richard A. Friesner This chapter discusses methods for modeling electronic polarization in proteins and protein–ligand complexes. Two different approaches are considered: explicit incorporation of polarization into a molecular mechanics force field and the use of mixed quantum mechanics/molecular mechanics methods to model polarization in a restricted region of the protein or protein–ligand complex. A brief description is provided of the computational methodology and parameterization protocols and then results from two preliminary studies are presented. The first study employs quantum mechanics/molecular mechanics (QM/MM) methods to improve the accuracy of protein–ligand docking; here, incorporation of polarization is shown to dramatically improve the robustness of the accuracy of structural prediction of the protein
2005
Hydrogen Bonds In Molecular Mechanics Force Fields
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 72 Author(s): Jan Hermans This chapter reviews formulation and parametrization of molecular mechanics force fields with special attention to technical and inherent problems. Most striking among the shortcomings is the inadequacy of the simple point charge description as a means to describe energy and forces of interactions between polar molecules and between polar groups in macromolecules, including hydrogen bonds. The current state of efforts to improve the description of polar interactions is discussed.
2005
Resonance Character of Hydrogen
2005
How Hydrogen Bonds Shape Membrane Protein Structure
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 72 Author(s): Stephen H. White The energetic cost of partitioning peptide bonds into membrane bilayers is prohibitive unless the peptide bonds participate in hydrogen bonds. However, even then there is a significant free energy penalty for dehydrating the peptide bonds that can only be overcome by favorable hydrophobic interactions. Membrane protein structure formation is thus dominated by hydrogen bonding interactions, which is the subject of this review.
2005
Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 72 Author(s): Wonpil Im, Jianhan Chen, Charles L. Brooks Since biomolecules exist in aqueous and membrane environments, the accurate modeling of solvation, and hydrogen bonding interactions in particular, is essential for the exploration of structure and function in theoretical and computational studies. In this chapter, we focus on alternatives to explicit solvent models and discuss recent advances in generalized Born (GB) implicit solvent theories. We present a brief review of the successes and shortcomings of the application of these theories to biomolecular problems that are strongly linked to backbone H-bonding and electrostatics. This discussion naturally leads us to explore existing areas for improvement in current GB theories and our approach towards addressing a number of the key issues that remain in the refinement of these models. Specifically, the critical importance of balancing solvation forces and intramolecular forces in GB models is illustrated by examining the influence of backbone hydrogen bond strength and backbone dihedral energetics on conformational equilibria of small peptids.
2005
Thermodynamics Of
2005
The Importance of Cooperative Interactions and a Solid
2005
New Directions in the Study of Peptide H
2005
Author Index
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 72

2005
Subject Index
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 72

2005
Contents
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 72

2005
Comparative Motile Mechanisms in Cells
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71 Author(s): John M. Squire, David A.D. Parry Cell maintenance, cell division, and whole cell movement of the cell body involve a variety of molecular motors. Many of the myosin and kinesin motors are double-headed. Some of these motors, like myosin in muscle, are nonprocessive, whereas others, such as some double-headed nonmuscle myosins and the kinesins, are processive. Because many of these non-muscle motors may work in isolation, the double-headed motor systems can stay attached to their track by at least one of their two heads at all times so that they and their cargo can progress along the track. Whether the motors are processive or not depends on the careful control of the ATPase cycle. Some motile systems involve the aggregation of globular subunits into filaments. Actin and tubulin polymerization are well-documented examples of this. Finally, some of the proteins that help to process the necessary activities of nucleic acids in cells, the polymerases, also show motile features and are powered by ATP. The chapter summarizes the general structures of (1) myosin IIs, (2) kinesins, and (3) cytoplasmic dyneins—found in association with dynactin; and it discusses the way ATPases produces movement.
2005
Molecular Architecture in Muscle Contractile Assemblies
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71 Author(s): John M. Squire, Hind A. Al
2005
Titin and Its associated proteins: the third myofilament system of the sarcomere
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71 Author(s): Henk L. Granzier, Siegfried Labeit This chapter describes titin, the third myofilament of the sarcomere, and outlines the early history that led to the discovery of titin. The chapter also discusses the functional genomics of titin, including an extensive discussion of differential splicing in the I-band region of the molecule. This region is elastic and the molecular mechanism of this elasticity and the way it can be modulated by differential splicing and posttranslational modifications is reviewed in the chapter. Ultrastructural studies with antibodies specific to titin's I-band region have demonstrated that titin's central I-band region behaves extensibly on myofibrillar stretch. The analysis of titin's primary structure revealed specific motif families within its I-band region that act as molecular springs: (1) tandem Ig segments, (2) the PEVK segment, and (3) the N2B-Us segment. The first two elements are found in both skeletal muscle and cardiac muscle titins, but the N2B-Us is cardiac specific. The chapter discusses the titin-binding proteins, including the possible roles of titin-based protein complexes in cell signaling.
2005
Regulation of Muscle Contraction by Tropomyosin and Troponin: How Structure Illuminates Function
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71 Author(s): Jerry H. Brown, Carolyn Cohen This chapter provides a brief description of tropomyosin's periodic and aperiodic structural features related to their function. The chapter describes the structure of troponin and provides information on F-actin. The thin filaments of vertebrate striated muscle are periodic structures composed of three proteins with different designs that function together for the regulation of contraction. Tropomyosin displays two types of periodicity. In addition to a long-range
2005
The Molecular Mechanism of Muscle Contraction
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71 Author(s): Michael A. Geeves, Kenneth C. Holmes This chapter describes the analysis of the polymorphism of the myosin crossbridge and relates it to the Lymn–Taylor crossbridge cycle. Myosin from muscle (myosin II) consists of two long polypeptide chains (heavy chains) combined with four light chains. In cross-striated muscle, the tails of the molecules pack together to form the thick filaments, while the crossbridges that are ATPases point away from the thick filaments and cyclically interact with the actin filaments, moving them along by a kind of rowing action. The fuel for this process is provided by the hydrolysis of adenosine triphosphate (ATP). There are three primary conformations of the myosin crossbridge that can be associated with states in the Lymn–Taylor cycle. These are—namely, the post-rigor structure, the prepower stroke structure, and the rigor-like state. A comparison of these structures leads to the identification of various important conformationally flexible elements, such as (1) the positions of the converter domain, (2) the kink in the relay helix, and (3) the degree of twist of the central
2005
X
2005
Microtubules and Maps
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71 Author(s): Linda A. Amos, Daniel Schlieper Microtubules are very dynamic polymers whose assembly and disassembly is determined by whether their heterodimeric tubulin subunits are in a straight or curved conformation. Curvature is introduced by bending at the interfaces between monomers. Assembly and disassembly are primarily controlled by the hydrolysis of guanosine triphosphate (GTP) in a site that is completed by the association of two heterodimers. However, a multitude of associated proteins are able to fine
2005
The structure of microtubule motor proteins
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71 Author(s): A. Marx, J. M
2005
Rotary Molecular Motors
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71 Author(s): Stephan Wilkens The F
2005
Cytoskeleton Dynamics Powers Nematode Sperm Motility
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71 Author(s): Murray Stewart, Thomas M. Roberts Nematode sperm provide a simple and specialized system for studying the molecular mechanism of amoeboid cell motility. Locomotion is generated by the assembly dynamics of their cytoskeleton, which is based on the major sperm protein (MSP). Protrusive force is generated at the leading edge of the lamellipod by MSP filament formation and bundling, whereas the contractile force that drags the rearward cell body forward is generated by cytoskeleton disassembly. The dynamics of the system can be reconstituted in vitro using cell
2005
Structure and mechanism of DNA polymerases
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71 Author(s): Paul J. Rothwell, Gabriel Waksman DNA polymerases are molecular motors directing the synthesis of DNA from nucleotides. All polymerases have a common architectural framework consisting of three canonical subdomains termed the fingers, palm, and thumb subdomains. Kinetically, they cycle through various states corresponding to conformational transitions, which may or may not generate force. In this review, we present and discuss the kinetic, structural, and single
2005
Preface
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71

2005
Author Index
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71

2005
Subject Index
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71

2005
Contents
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 71


Series Editors
Publication date: 2005
Source:Advances in Protein Chemistry, Volume 70


view: 157

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