Abstract：
:Computational modeling of membrane proteins is critical to understand biochemical systems and to support chemical biology. In this work, we use a dataset of 448 non-redundant membrane protein chains to expose a "rule" that governs membrane protein structure: free cysteine thiols are not found accessible to oxidative compartments such as the extracellular space, but are rather involved in disulphide bridges. Taking as examples the 1018 three-dimensional models produced during the GPCR Dock 2008, 2010 and 2013 competitions and 390 models for a GPCR target in CASP13, we show that this rule was not accounted for by the modeling community. We thus highlight a new direction for model development that should lead to more accurate membrane protein models, especially in the loop domains.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Grazhdankin E,Stepniewski M,Xhaard Hdoi
10.1016/j.jsb.2019.10.002subject
Has Abstractpub_date
2020-01-01 00:00:00pages
107400issue
1eissn
1047-8477issn
1095-8657pii
S1047-8477(19)30211-4journal_volume
209pub_type
杂志文章abstract：:The 32 kDa hydrophilic and acidic enamelin, the most stable cleavage fragment of the enamel specific glycoprotein, is believed to play vital roles in controlling crystal nucleation or growth during enamel biomineralization. Circular dichroism and Fourier transform infrared spectra demonstrate that the secondary struct...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.04.007
更新日期：2008-07-01 00:00:00
abstract：:Polyketides such as the clinically-valuable antibacterial agent mupirocin are constructed by architecturally-sophisticated assembly lines known as trans-acyltransferase polyketide synthases. Organelle-sized megacomplexes composed of several copies of trans-acyltransferase polyketide synthase assembly lines have been o...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2015.12.011
更新日期：2016-03-01 00:00:00
abstract：:Protein tertiary structure modeling is a critical step for the interpretation of three dimensional (3D) election microscopy density. Our group participated the 2015/2016 EM Model Challenge using the MAINMAST software for a de novo main chain modeling. The software generates local dense points using the mean shifting a...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2018.07.013
更新日期：2018-11-01 00:00:00
abstract：:In many organisms, the ubiquitous second messenger cAMP is formed by at least one member of the adenylyl cyclase (AC) Class III. These ACs feature a conserved dimeric catalytic core architecture, either through homodimerization or through pseudo-heterodimerization of a tandem of two homologous catalytic domains, C1 an...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107534
更新日期：2020-08-01 00:00:00
abstract：:The nuclear lamina is a protein meshwork that lines the nuclear envelope in metazoan cells. It is composed largely of a polymeric assembly of lamins, which comprise a distinct sequence homology class of the intermediate filament protein family. On the basis of its structural properties, the lamina originally was propo...
journal_title：Journal of structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.jsb.2011.11.007
更新日期：2012-01-01 00:00:00
abstract：:Vibrio alginolyticus use flagella to swim. A flagellum consists of a filament, hook and basal body. The basal body is made up of a rod and several ring structures. This study investigates the structure of the T ring which is a unique component of the V. alginolyticus sodium ion-driven flagellar basal body. Using Zerni...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2010.08.004
更新日期：2011-01-01 00:00:00
abstract：:We present RIBFIND, a method for detecting flexibility in protein structures via the clustering of secondary structural elements (SSEs) into rigid bodies. To test the usefulness of the method in refining atomic structures within cryoEM density we incorporated it into our flexible fitting protocol (Flex-EM). Our benchm...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.10.011
更新日期：2012-02-01 00:00:00
abstract：:Tricorn protease from the archaeon Thermoplasma acidophilum acts "downstream" of the proteasome; in conjunction with its aminopeptidase cofactors it converts peptides generated by the proteasome into free amino acids. The basic functional unit of Tricorn is a homohexamer of the 121-kDa subunit, 20 of which can assembl...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1999.4169
更新日期：1999-12-01 00:00:00
abstract：:Ion mobility mass spectrometry was employed to study the structure of the βB2B3-crystallin heterodimer following oxidation through its increased exposure to hydroxyl radicals. The results demonstrate that the heterodimer can withstand limited oxidation through the incorporation of up to some 10 oxygen atoms per subuni...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.11.006
更新日期：2015-01-01 00:00:00
abstract：:Teeth sustain high loads over a lifetime and yet intact tooth failure is rare. The different structures of the tooth, jaw bone and the intervening soft periodontal ligament enable the tooth to endure repeated loading during mastication. Although mechanical and functional properties of the different components are thor...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.11.019
更新日期：2012-02-01 00:00:00
abstract：:The massive basal skeleton of a few remnant living hypercalcified sponges rediscovered since the 1960s are valuable representatives of ancient calcium carbonate biomineralization mechanisms in basal Metazoa. A multi-scale mineralogical characterization of the easily accessible Mediterranean living hypercalcified spong...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.08.008
更新日期：2011-12-01 00:00:00
abstract：:Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum (opium poppy), which belongs to the non-heme 2-oxoglutarate/Fe(II)-dependent dioxygenases (ODD) family, is a key enzyme in the morphine biosynthesis pathway. Initially, T6ODM was characterized as an enzyme catalyzing O-demethylation of thebaine to neopinone and ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2018.01.007
更新日期：2018-06-01 00:00:00
abstract：:Trypanosoma cruzi chagasin belongs to a recently discovered family of cysteine protease inhibitors found in lower eukaryotes and prokaryotes but not in mammals. Chagasin binds tightly to cruzain, the major lysosomal T. cruzi cysteine protease, involved with infectivity and survival of the parasite in mammalian host ce...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.07.017
更新日期：2007-02-01 00:00:00
abstract：:Here we introduce plusTipTracker, a Matlab-based open source software package that combines automated tracking, data analysis, and visualization tools for movies of fluorescently-labeled microtubule (MT) plus end binding proteins (+TIPs). Although +TIPs mark only phases of MT growth, the plusTipTracker software allows...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.07.009
更新日期：2011-11-01 00:00:00
abstract：:Gap junctions containing extensive, highly ordered crystalline arrays of hexagonally packed connexons have been isolated from the hepatopancreas of the arthropod, Homarus americanus (American lobster). The structure of such junctions has been studied to a resolution of approximately 25 A in three dimensions by electro...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(91)90075-8
更新日期：1991-06-01 00:00:00
abstract：:Four-helical bundles are the most abundant topological motif among helical folds. Their constituent helices show crossing angles that mainly cluster around +20 degrees (aligned) or -50 degrees (orthogonal). Bundles with all helices aligned are called 'square' and comprise four-helical coiled coils as their structurall...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2010.01.023
更新日期：2010-05-01 00:00:00
abstract：:Formation of filaments by the Ure2 protein constitutes the molecular mechanism of the [URE3] prion in yeast. According to the "amyloid backbone" model, the N-terminal asparagine-rich domains of Ure2p polymerize to form an amyloid core fibril that is surrounded by C-terminal domains in their native conformation. Protea...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.02.007
更新日期：2005-05-01 00:00:00
abstract：:The use of electron tomography has allowed the three-dimensional membrane topography of the mitochondrion to be better understood. The most striking feature of this topology is the crista junction, a structure that may serve to divide functionally the inner membrane and intermembrane spaces. In situ these junctions se...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/s1047-8477(02)00012-6
更新日期：2002-04-01 00:00:00
abstract：:Ribonucleic acids (RNAs) play a key role in many fundamental life processes. These polymers are often found complexed with proteins in extremely large particles whose molecular mass may reach several millions of daltons (e.g., ribosomes, spliceosomes, and viruses). Structural studies of such RNA-protein complexes shou...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1999.4134
更新日期：1999-09-01 00:00:00
abstract：:In COPII mediated vesicle formation, Sec13/Sec31 heterotetramers play a role in organizing the membranes into a spherical vesicle. There they oligomerize into a cage that interacts with the other COPII proteins to direct vesicle formation and concentrate cargo into a bud. In this role they must be flexible to accommod...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2018.08.016
更新日期：2018-11-01 00:00:00
abstract：:The crystallographic structures of the adducts of salicylate 1,2-dioxygenase (SDO) with substrates salicylate, gentisate and 1-hydroxy-2-naphthoate, obtained under anaerobic conditions, have been solved and analyzed. This ring fission dioxygenase from the naphthalenesulfonate-degrading bacterium Pseudaminobacter salic...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.11.026
更新日期：2012-02-01 00:00:00
abstract：:The unsupervised segmentation method proposed in the current study follows the evolutional ability of human vision to extrapolate significant structures in an image. In this work we adopt the perceptual grouping strategy by selecting the spectral clustering framework, which is known to capture perceptual organization ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2013.10.013
更新日期：2013-12-01 00:00:00
abstract：:We have shown by in vitro development of staged follicles in the presence of tritiated proline, as well as by immunoblot analysis, that the Dvs19 and DVS15 chorion proteins of Drosophila virilis are synthesized by the follicular epithelium and are incorporated in the chorion at the terminal stages of choriogenesis. Li...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1998.4999
更新日期：1998-10-01 00:00:00
abstract：:The purified glucocorticoid receptor (GR) from rat liver has been visualised by electron microscopy. The specimens were prepared by spreading on thin carbon support and negatively stained using uranyl acetate. Two forms of GR, the monomeric and the dimeric forms, were identified based on size, chromatographic distribu...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(91)90030-z
更新日期：1991-08-01 00:00:00
abstract：:Mononuclear macrophages are important immune cells in the organisms. The complicated membrane structure underlying the diverse functions of mononuclear-macrophage has been largely unresolved. As a representative of monocyte-derived macrophages, the membrane structure of PMA differentiated THP-1 cells was comprehensive...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2019.04.002
更新日期：2019-06-01 00:00:00
abstract：:A new era has begun for single particle cryo-electron microscopy (cryoEM) which can now compete with X-ray crystallography for determination of protein structures. The development of direct detectors constitutes a revolution that has led to a wave of near-atomic resolution cryoEM reconstructions. However, regardless o...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.09.008
更新日期：2014-11-01 00:00:00
abstract：:Nacre is the iridescent inner lining of many mollusk shells, with a unique lamellar structure at the sub-micron scale, and remarkable resistance to fracture. Despite extensive studies, nacre formation mechanisms remain incompletely understood. Here we present 20-nm, 2°-resolution polarization-dependent imaging contras...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2013.10.002
更新日期：2013-12-01 00:00:00
abstract：:F-plasmid-mediated bacterial conjugation was studied with hfr (traDts) and tra I mutant Escherichia coli donor strains. This allowed us to observe a statistically significant number of conjugation-specific contacts by video and electron microscopy. Single mating events between E. coli were observed in real time by vid...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(91)90018-r
更新日期：1991-10-01 00:00:00
abstract：:Titin is a giant protein that spans half of the striated muscle sarcomere. The I-band portion of titin extends as the sarcomere is stretched, developing what is known as passive force. This portion of the molecule is composed mainly of tandem immunoglobulin (Ig) segments, consisting of serially linked Ig-like domains,...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1998.3984
更新日期：1998-01-01 00:00:00
abstract：:Early electron microscope studies of developing wool and hair established that trichocyte (hard alpha-) keratin fibers have a composite structure in which filaments, subsequently shown to belong to the class of intermediate filaments (IF), were embedded in a matrix of sulfur-rich proteins. These studies also showed th...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/s1047-8477(03)00027-3
更新日期：2003-05-01 00:00:00
