Advances in Protein Chemistry最新文献

{"title":"Elastin.","authors":"S. Mithieux, A. Weiss","doi":"10.32388/ik2i6m","DOIUrl":"https://doi.org/10.32388/ik2i6m","url":null,"abstract":"Elastin is a key extracellular matrix protein that is critical to the elasticity and resilience of many vertebrate tissues including large arteries, lung, ligament, tendon, skin, and elastic cartilage. Tropoelastin associates with multiple tropoelastin molecules during the major phase of elastogenesis through coacervation, where this process is directed by the precise patterning of mostly alternating hydrophobic and hydrophilic sequences that dictate intermolecular alignment. Massively crosslinked arrays of tropoelastin (typically in association with microfibrils) contribute to tissue structural integrity and biomechanics through persistent flexibility, allowing for repeated stretch and relaxation cycles that critically depend on hydrated environments. Elastin sequences interact with multiple proteins found in or colocalized with microfibrils, and bind to elastogenic cell surface receptors. Knowledge of the major stages in elastin assembly has facilitated the construction of in vitro models of elastogenesis, leading to the identification of precise molecular regions that are critical to elastin-based protein interactions.","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49467360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RETRACTED: Theory, Methods, and Applications of Coevolution in Protein Contact Prediction","authors":"Jianzhu Ma, Sheng Wang","doi":"10.1016/BS.APCSB.2015.07.003","DOIUrl":"https://doi.org/10.1016/BS.APCSB.2015.07.003","url":null,"abstract":"","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/BS.APCSB.2015.07.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54052018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Carrageenan and Furcellaran","authors":"A. Nussinovitch, Madoka Hirashima","doi":"10.1201/b15547-8","DOIUrl":"https://doi.org/10.1201/b15547-8","url":null,"abstract":"","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1201/b15547-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65987174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Activation of G protein-coupled receptors.","authors":"Xavier Deupi,&nbsp;Brian Kobilka","doi":"10.1016/S0065-3233(07)74004-4","DOIUrl":"https://doi.org/10.1016/S0065-3233(07)74004-4","url":null,"abstract":"<p><p>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-specific conformational states. This chapter will review our current understanding of the mechanism by which agonists bind and activate GPCRs.</p>","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(07)74004-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41036137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Some mechanistic insights into GPCR activation from detergent-solubilized ternary complexes on beads.","authors":"Tione Buranda,&nbsp;Anna Waller,&nbsp;Yang Wu,&nbsp;Peter C Simons,&nbsp;Sean Biggs,&nbsp;Eric R Prossnitz,&nbsp;Larry A Sklar","doi":"10.1016/S0065-3233(07)74003-2","DOIUrl":"https://doi.org/10.1016/S0065-3233(07)74003-2","url":null,"abstract":"<p><p>The binding of full and partial agonist ligands (L) to G protein-coupled receptors (GPCRs) initiates the formation of ternary complexes with G proteins [ligand-receptor-G protein (LRG) complexes]. Cyclic ternary complex models are required to account for the thermodynamically plausible complexes. It has recently become possible to assemble solubilized formyl peptide receptor (FPR) and beta(2)-adrenergic receptor (beta(2)AR) ternary complexes for flow cytometric bead-based assays. In these systems, soluble ternary complex formation of the receptors with G proteins allows direct quantitative measurements which can be analyzed in terms of three-dimensional concentrations (molarity). In contrast to the difficulty of analyzing comparable measurements in two-dimensional membrane systems, the output of these flow cytometric experiments can be analyzed via ternary complex simulations in which all of the parameters can be estimated. An outcome from such analysis yielded lower affinity for soluble ternary complex assembly by partial agonists compared with full agonists for the beta(2)AR. In the four-sided ternary complex model, this behavior is consistent with distinct ligand-induced conformational states for full and partial agonists. Rapid mix flow cytometry is used to analyze the subsecond dynamics of guanine nucleotide-mediated ternary complex disassembly. The modular breakup of ternary complex components is highlighted by the finding that the fastest step involves the departure of the ligand-activated GPCR from the intact G protein heterotrimer. The data also show that, under these experimental conditions, G protein subunit dissociation does not occur within the time frame relevant to signaling. The data and concepts are discussed in the context of a review of current literature on signaling mechanism based on structural and spectroscopic (FRET) studies of ternary complex components.</p>","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(07)74003-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41036136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of Rho guanine nucleotide exchange factors by G proteins.","authors":"Paul C Sternweis,&nbsp;Angela M Carter,&nbsp;Zhe Chen,&nbsp;Shahab M Danesh,&nbsp;Ying-Fan Hsiung,&nbsp;William D Singer","doi":"10.1016/S0065-3233(07)74006-8","DOIUrl":"https://doi.org/10.1016/S0065-3233(07)74006-8","url":null,"abstract":"<p><p>Monomeric Rho GTPases regulate cellular dynamics through remodeling of the cytoskeleton, modulation of immediate signaling pathways, and longer-term regulation of gene transcription. One family of guanine nucleotide exchange factors for Rho proteins (RhoGEFs) provides a direct pathway for regulation of RhoA by cell surface receptors coupled to heterotrimeric G proteins. Some of these RhoGEFs also contain RGS domains that can attenuate signaling by the G(12) and G(13) proteins. The regulation provided by these RhoGEFs is defined by their selective regulation by specific G proteins, phosphorylation by kinases, and potential localization with signaling partners. Evidence of their physiological importance is derived from gene knockouts in Drosophila and mice. Current understanding of the basic regulatory mechanisms of these RhoGEFs is discussed. An overview of identified interactions with other signaling proteins suggests the growing spectrum of their involvement in numerous signaling pathways.</p>","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(07)74006-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41036139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How do receptors activate G proteins?","authors":"William M Oldham,&nbsp;Heidi E Hamm","doi":"10.1016/S0065-3233(07)74002-0","DOIUrl":"https://doi.org/10.1016/S0065-3233(07)74002-0","url":null,"abstract":"<p><p>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-catalyzed GTP for GDP exchange on the G protein alpha subunit, which is the rate-limiting step in the activation of all downstream signaling. Despite the important biological role of the receptor-G protein interaction, relatively little is known about the structure of the complex and how it leads to nucleotide exchange. This chapter will describe what is known about receptor and G protein structure and outline a strategy for assembling the current data into improved models for the receptor-G protein complex that will hopefully answer the question as to how receptors flip the G protein switch.</p>","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(07)74002-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41036135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural basis of effector regulation and signal termination in heterotrimeric Galpha proteins.","authors":"Stephen R Sprang,&nbsp;Zhe Chen,&nbsp;Xinlin Du","doi":"10.1016/S0065-3233(07)74001-9","DOIUrl":"https://doi.org/10.1016/S0065-3233(07)74001-9","url":null,"abstract":"<p><p>This chapter addresses, from a molecular structural perspective gained from examination of x-ray crystallographic and biochemical data, the mechanisms by which GTP-bound Galpha subunits of heterotrimeric G proteins recognize and regulate effectors. The mechanism of GTP hydrolysis by Galpha and rate acceleration by GAPs are also considered. The effector recognition site in all Galpha homologues is formed almost entirely of the residues extending from the C-terminal half of alpha2 (Switch II) together with the alpha3 helix and its junction with the beta5 strand. Effector binding does not induce substantial changes in the structure of Galpha*GTP. Effectors are structurally diverse. Different effectors may recognize distinct subsets of effector-binding residues of the same Galpha protein. Specificity may also be conferred by differences in the main chain conformation of effector-binding regions of Galpha subunits. Several Galpha regulatory mechanisms are operative. In the regulation of GMP phospodiesterase, Galphat sequesters an inhibitory subunit. Galphas is an allosteric activator and inhibitor of adenylyl cyclase, and Galphai is an allosteric inhibitor. Galphaq does not appear to regulate GRK, but is rather sequestered by it. GTP hydrolysis terminates the signaling state of Galpha. The binding energy of GTP that is used to stabilize the Galpha:effector complex is dissipated in this reaction. Chemical steps of GTP hydrolysis, specifically, formation of a dissociative transition state, is rate limiting in Ras, a model G protein GTPase, even in the presence of a GAP; however, the energy of enzyme reorganization to produce a catalytically active conformation appears to be substantial. It is possible that the collapse of the switch regions, associated with Galpha deactivation, also encounters a kinetic barrier, and is coupled to product (Pi) release or an event preceding formation of the GDP*Pi complex. Evidence for a catalytic intermediate, possibly metaphosphate, is discussed. Galpha GAPs, whether exogenous proteins or effector-linked domains, bind to a discrete locus of Galpha that is composed of Switch I and the N-terminus of Switch II. This site is immediately adjacent to, but does not substantially overlap, the Galpha effector binding site. Interactions of effectors and exogenous GAPs with Galpha proteins can be synergistic or antagonistic, mediated by allosteric interactions among the three molecules. Unlike GAPs for small GTPases, Galpha GAPs supply no catalytic residues, but rather appear to reduce the activation energy for catalytic activation of the Galpha catalytic site.</p>","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(07)74001-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41036134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kinetic analysis of G protein-coupled receptor signaling using fluorescence resonance energy transfer in living cells.","authors":"Martin J Lohse,&nbsp;Carsten Hoffmann,&nbsp;Viacheslav O Nikolaev,&nbsp;Jean-Pierre Vilardaga,&nbsp;Moritz Bünemann","doi":"10.1016/S0065-3233(07)74005-6","DOIUrl":"https://doi.org/10.1016/S0065-3233(07)74005-6","url":null,"abstract":"<p><p>We describe and review methods for the kinetic analysis of G protein-coupled receptor (GPCR) activation and signaling that are based on optical methods. In particular, we describe the use of fluorescence resonance energy transfer (FRET) as a means of analyzing conformational changes within a single protein (for example a receptor) or between subunits of a protein complex (such as a G protein heterotrimer) and finally between distinct proteins (such as a receptor and a G protein). These methods allow the analysis of signaling kinetics in intact cells with proteins that retain their essential functional properties. They have produced a number of unexpected results: fast receptor activation kinetics in the millisecond range, similarly fast kinetics for receptor-G protein interactions, but much slower activation kinetics for G protein activation.</p>","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(07)74005-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41036138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Natural triple beta-stranded fibrous folds.","authors":"Anna Mitraki,&nbsp;Katerina Papanikolopoulou,&nbsp;Mark J Van Raaij","doi":"10.1016/S0065-3233(06)73004-2","DOIUrl":"https://doi.org/10.1016/S0065-3233(06)73004-2","url":null,"abstract":"<p><p>A distinctive family of beta-structured folds has recently been described for fibrous proteins from viruses. Virus fibers are usually involved in specific host-cell recognition. They are asymmetric homotrimeric proteins consisting of an N-terminal virus-binding tail, a central shaft or stalk domain, and a C-terminal globular receptor-binding domain. Often they are entirely or nearly entirely composed of beta-structure. Apart from their biological relevance and possible gene therapy applications, their shape, stability, and rigidity suggest they may be useful as blueprints for biomechanical design. Folding and unfolding studies suggest their globular C-terminal domain may fold first, followed by a \"zipping-up\" of the shaft domains. The C-terminal domains appear to be important for registration because peptides corresponding to shaft domains alone aggregate into nonnative fibers and/or amyloid structures. C-terminal domains can be exchanged between different fibers and the resulting chimeric proteins are useful as a way to solve structures of unknown parts of the shaft domains. The following natural triple beta-stranded fibrous folds have been discovered by X-ray crystallography: the triple beta-spiral, triple beta-helix, and T4 short tail fiber fold. All have a central longitudinal hydrophobic core and extensive intermonomer polar and nonpolar interactions. Now that a reasonable body of structural and folding knowledge has been assembled about these fibrous proteins, the next challenge and opportunity is to start using this information in medical and industrial applications such as gene therapy and nanotechnology.</p>","PeriodicalId":51216,"journal":{"name":"Advances in Protein Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0065-3233(06)73004-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26461783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}