Abstract:
:Cryogenic electron microscopy (cryo-EM) and single-particle analysis enables determination of near-atomic resolution structures of biological molecules. However, large computational requirements limit throughput and rapid testing of new image processing tools. We developed PRIME, an algorithm part of the SIMPLE software suite, for determination of the relative 3D orientations of single-particle projection images. PRIME has primarily found use for generation of an initial ab initio 3D reconstruction. Here we show that the strategy behind PRIME, iterative estimation of per-particle orientation distributions with stochastic hill climbing, provides a competitive approach to near-atomic resolution single-particle 3D reconstruction. A number of mathematical techniques for accelerating the convergence rate are introduced, leading to a speedup of nearly two orders of magnitude. We benchmarked our developments on numerous publicly available data sets and conclude that near-atomic resolution ab initio 3D reconstructions can be obtained with SIMPLE in a matter of hours, using standard over-the-counter CPU workstations.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Reboul CF,Kiesewetter S,Eager M,Belousoff M,Cui T,De Sterck H,Elmlund D,Elmlund Hdoi
10.1016/j.jsb.2018.08.005subject
Has Abstractpub_date
2018-11-01 00:00:00pages
172-181issue
2eissn
1047-8477issn
1095-8657pii
S1047-8477(18)30201-6journal_volume
204pub_type
杂志文章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::The structures of many helical protein filaments can be derived from electron micrographs of their suspensions in thin films of vitrified aqueous solutions. The most successful and generally-applicable approach treats short segments of these filaments as independent "single particles", yielding near-atomic resolution ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2014.03.012
更新日期:2014-05-01 00:00:00
abstract::Titin is a giant protein responsible for passive-tension generation in muscle sarcomeres. Here, we used single-molecule AFM force spectroscopy to investigate the mechanical characteristics of a recombinant construct from the human cardiac-specific N2B-region, which harbors a 572-residue unique sequence flanked by two ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2006.02.017
更新日期:2006-08-01 00:00:00
abstract::We have studied two members of the family of morphogenetic factors or chaperonins, the GroEL-like factors from Escherichia coli and Bacillus subtilis, in order to determine the possible structural basis of their related function in promoting the correct and efficient assembly of biological oligomers. The main objectiv...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/1047-8477(91)90071-4
更新日期:1991-06-01 00:00:00
abstract::Seeding has been critical for obtaining diffraction-quality crystals for many structures. In this article, applications and recommendations for seeding are presented based on examples from our laboratory and other groups. The implementation of seeding in high-throughput crystallization, robotics, and other emerging te...
journal_title:Journal of structural biology
pub_type: 杂志文章,评审
doi:10.1016/s1047-8477(03)00039-x
更新日期:2003-04-01 00:00:00
abstract::Hypercalcified sponges, endowed with a calcium carbonate basal skeleton in addition to their spicules, form one of the most basal metazoan group engaged in extensive biomineralization. The Mediterranean species Petrobiona massiliana was used to investigate biological controls exerted on the biomineralization of its ba...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.04.004
更新日期:2012-06-01 00:00:00
abstract::The formation of amyloid is considered an intrinsic ability of most polypeptides. It is a structure adopted by many neuropeptides and neurohormones during the formation of dense core vesicles in secretory cells, yet the mechanisms mediating assembly and disassembly of these amyloids remain unclear. Neurokinin B is a n...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2019.09.011
更新日期:2019-12-01 00:00:00
abstract::Three-dimensional electron microscopy allows direct visualization of biological macromolecules close to their native state. The high impact of this technique in the structural biology field is highly correlated with the development of new image processing algorithms. In order to achieve subnanometer resolution, the si...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2008.09.009
更新日期:2009-01-01 00:00:00
abstract::To investigate the functional role of the nonhelical domains of the intermediate filament (IF) protein vimentin, we carried out transient transfection of constructs encoding fusion proteins of these domains with enhanced green fluorescent protein (EGFP). Expression of these fusion proteins did not have any effect on t...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2000.4315
更新日期:2000-11-01 00:00:00
abstract::This paper describes steps in the single-particle cryo-EM 3D structure determination of membrane proteins in their membrane environment. Using images of the Kv1.2 potassium-channel complex reconstituted into lipid vesicles, we describe procedures for the merging of focal-pairs of exposures and the removal of the vesic...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2016.01.012
更新日期:2016-04-01 00:00:00
abstract::Tobacco streak virus (TSV), the type member of Ilarvirus genus, is a major plant pathogen. TSV purified from infected plants consists of a ss-RNA genome encapsidated in spheroidal particles with diameters of 27, 30 and 33nm constructed from multiple copies of a single species of coat protein (CP) subunits. Apart from ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2015.12.007
更新日期:2016-02-01 00:00:00
abstract::Accurate image alignment is needed for computing three-dimensional reconstructions from transmission electron microscope tilt series. So far, the best results have been obtained by using colloidal gold beads as fiducial markers. If their use has not been possible for some reason, the only option has been the automatic...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2001.4443
更新日期:2001-12-01 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::Trypsin treatment of staphylococcal alpha-toxin cleaves the molecule into two roughly equally sized parts, which results in inactivation of the toxin. Tetragonal arrays of oligomers, closely resembling the native ones, can however be formed on lipid layers. From tilted views of negatively stained crystals a 3D structu...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/1047-8477(92)90024-5
更新日期:1992-05-01 00:00:00
abstract::The baculum is an extraskeletal bone located in the penis of a few species in several orders of mammals such as carnivores, insectivores, rodents, bats and primates. This study aims to describe the structure, architecture and mechanical properties of the canine baculum. To this end canine bacula from castrated and unc...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.06.006
更新日期:2011-09-01 00:00:00
abstract::A simple, fast and efficient noise-reduction protocol for three-dimensional electron tomographic reconstructions of biological material is presented. The approach is based on iterative application of median filtering and shows promise for automatic noise reduction as a pre-processor for automated data analysis tools w...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2006.10.030
更新日期:2007-05-01 00:00:00
abstract::Bacterial two-component regulatory systems (TCS) play important roles in sensing environmental stimuli and responding to them by regulating gene expression. VbrK/VbrR, a TCS in Vibrio parahaemolyticus, confers resistance to β-lactam antibiotics through activating a β-lactamase gene. Its periplasmic sensor domain was p...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2020.107610
更新日期:2020-11-01 00:00:00
abstract::The structural remodeling of collagen is important in biological processes such as fibrosis, developmental morphogenesis and wound repair. Highly ordered collagen macromolecules produce second harmonic generation signals without the need for any exogenous label. Conversely, the cellular components stained with exogeno...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2009.07.023
更新日期:2010-01-01 00:00:00
abstract::The yeast Saccharomyces cerevisiae mitochondrial matrix factor Mmf1, a member in the YER057c/Yigf/Uk114 family, participates in isoleucine biosynthesis and mitochondria maintenance. Mmf1 physically interacts with another mitochondrial matrix protein Mam33, which is involved in the sorting of cytochrome b₂ to the inter...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.05.005
更新日期:2011-09-01 00:00:00
abstract::The transcriptional regulator CpxR mediates an adaptive response to envelope stress, tightly linked to virulence and antibiotics resistance in several Gammaproteobacteria pathogens. In this work, we integrated crystallographic and small-angle X-ray scattering data to gain insights into the structure and conformational...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2018.08.001
更新日期:2018-11-01 00:00:00
abstract::The configuration of the active site of E2 ligases, central enzymes in the ubiquitin/ubiquitin-like protein (Ub/Ubl) conjugation systems, has long puzzled researchers. Taking advantage of the wealth of newly available structures and sequences of E2s from diverse organisms, we performed a large-scale comparative analys...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.12.006
更新日期:2008-05-01 00:00:00
abstract::We have previously used cryo-electron tomography combined with sub-volume averaging and classification to obtain 3D structures of macromolecular assemblies in cases where a single dominant species was present, and applied these methods to the analysis of a variety of trimeric HIV-1 and SIV envelope glycoproteins (Env)...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.01.004
更新日期:2012-05-01 00:00:00
abstract::Integral membrane proteins are involved in virtually every cellular process. Precisely regulating these machineries would allow controlling many human and vertebrate diseases. Embedded into cellular membranes, membrane proteins establish molecular interactions that sensitively react to environmental changes and to mol...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.02.010
更新日期:2007-08-01 00:00:00
abstract::A novel type 1 ribosome-inactivating protein (RIP) designated cucurmosin was isolated from the sarcocarp of Cucurbita moschata (pumpkin). Besides rRNA N-glycosidase activity, cucurmosin exhibits strong cytotoxicities to three cancer cell lines of both human and murine origins, but low toxicity to normal cells. Plant g...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2008.06.011
更新日期:2008-10-01 00:00:00
abstract::The fumarate reductase (flavocytochrome c(3)) from Shewanella frigidimarina (formerly S. putrefaciens) NCIMB400 has been crystallized in the space group P2(1), with cell dimensions of a = 45.447 A, b = 92.107 A, c = 78.311 A, and beta = 91.038 degrees and one molecule per asymmetric unit. A native data set has been co...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1999.4139
更新日期:1999-08-01 00:00:00
abstract::The Membrane Attack Complex-Perforin (MACPF) family is ubiquitously found in all kingdoms. They have diverse cellular roles, however MACPFs with pore-forming toxic function in venoms and poisons are very rare in animals. Here we present the structure of PmPV2, a MACPF toxin from the poisonous apple snail eggs, that ca...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2020.107531
更新日期:2020-08-01 00:00:00
abstract::The hyaluronate receptor CD44 plays role in cell adhesion and migration and is involved in tumor metastasis. The extracellular domain of CD44 comprises the hyaluronate-binding domain (HABD) and the membrane-proximal stem region; the short intracellular portion interacts with adaptor proteins and triggers signaling pat...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2015.06.005
更新日期:2015-08-01 00:00:00
abstract::Folding and self-assembly of amyloid beta (Abeta) peptide are linked to Alzheimer's disease. To understand the initial stage of amyloid-beta peptide aggregation, conformational characteristics of monomers of wild-type (WT) Abeta(28-35) and its mutant peptides A30G and A30I were investigated using density functional th...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2010.02.017
更新日期:2010-06-01 00:00:00
abstract::The Caliciviridae is a family of nonenveloped, icosahedral, positive-sense single-stranded RNA viruses. This family of viruses consists of both animal and human pathogens. Adapting human caliciviruses to cell culture has not been successful, whereas some animal caliciviruses, including San Miguel sea lion virus, have ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/s1047-8477(02)00583-x
更新日期:2003-02-01 00:00:00
abstract::DNA-dependent protein kinase (DNA-PK) is part of the eukaryotic DNA double strand break repair pathway and as such is crucial for maintenance of genomic stability, as well as for V(D)J (variable-diversity-joining) recombination. The catalytic subunit of DNA-PK (DNA-PKcs) belongs to the phosphatidylinositol-3 (PI-3) ki...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2003.11.024
更新日期:2004-03-01 00:00:00