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 benchmark includes 13 pairs of protein structures in two conformations each, one of which is represented by a corresponding cryoEM map. Refining the structures in simulated and experimental maps at the 5-15Å resolution range using rigid bodies identified by RIBFIND shows a significant improvement over using individual SSEs as rigid bodies. For the 15Å resolution simulated maps, using RIBFIND-based rigid bodies improves the initial fits by 40.64% on average, as compared to 26.52% when using individual SSEs. Furthermore, for some test cases we show that at the sub-nanometer resolution range the fits can be further improved by applying a two-stage refinement protocol (using RIBFIND-based refinement followed by an SSE-based refinement). The method is stand-alone and could serve as a general interactive tool for guiding flexible fitting into EM maps.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Pandurangan AP,Topf Mdoi
10.1016/j.jsb.2011.10.011subject
Has Abstractpub_date
2012-02-01 00:00:00pages
520-31issue
2eissn
1047-8477issn
1095-8657pii
S1047-8477(11)00312-1journal_volume
177pub_type
杂志文章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：:Skeletal elements that are exposed to heavy mechanical loads may provide important insights into the evolutionary solutions to mechanical challenges. We analyzed the microscopic architecture of dactylus claws in the woodlice Porcellio scaber and correlated these observations with analyses of the claws' mineral composi...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.06.008
更新日期：2016-08-01 00:00:00
abstract：:We have used conical tomography to study the structure of integral proteins in their phospholipid bilayer environments. Complete conical series were collected from replicas of the water channel aquaporin-0 (AQP0), a 6.6 nm side tetramer with a molecular weight of approximately 120 kDa that was purified and reconstitut...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2004.09.004
更新日期：2005-01-01 00:00:00
abstract：:A characteristic feature of the dense phases formed by fiber-shaped molecules is their organization into parallel rods packed in a hexagonal or pseudo-hexagonal lateral network. This is typically the case for the collagen triple helices inside fibrils, as confirmed by recent X-ray diffraction experiments carried out o...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2010.11.018
更新日期：2011-02-01 00:00:00
abstract：:The concept of presenting antigens in a repetitive array to obtain high titers of specific antibodies is increasingly applied by using surface-engineered viruses or bacterial envelopes as novel vaccines. A case for this concept was made 25 years ago, when producing high-titer antisera against ordered arrays of gp23, t...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2003.08.004
更新日期：2003-09-01 00:00:00
abstract：:Understanding skeletal aging and predicting fracture risk is increasingly important with a growing elderly population. We hypothesized that when categorized by external bone size, the male femoral diaphysis would show different strength-age trajectories which can be explained by changes in morphology, composition and ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107650
更新日期：2020-12-01 00:00:00
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journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1997.3896
更新日期：1997-10-01 00:00:00
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journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2007.08.009
更新日期：2007-11-01 00:00:00
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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
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journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107573
更新日期：2020-10-01 00:00:00
abstract：:Single-axis cryo-electron tomography of vitrified specimens has become a method of choice to reconstruct in three dimensions macromolecular assemblies in their cellular context or prepared from purified components. Here, we asked how a dual-axis acquisition scheme would improve three-dimensional reconstructions of mic...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2012.11.004
更新日期：2013-02-01 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：: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：: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：:The morphology and structure of giant starch granules from the pseudo-bulbs of Phajus grandifolius were investigated, using a number of microscopy techniques together with synchrotron radiation microdiffration analysis. Most of the granules, which had sizes between 100 and 200 microm, occurred as ogival particles with...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.11.007
更新日期：2006-04-01 00:00:00
abstract：:Correlative light and electron microscopy is an increasingly popular technique to study complex biological systems at various levels of resolution. Fluorescence microscopy can be employed to scan large areas to localize regions of interest which are then analyzed by electron microscopy to obtain morphological and stru...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2012.12.004
更新日期：2013-03-01 00:00:00
abstract：:Cryo-electron tomography of vitreous sections is currently the most promising technique for visualizing arbitrary regions of eukaryotic cells or tissue at molecular resolution. Despite significant progress in the sample preparation techniques over the past few years, the three dimensional reconstruction using electron...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/S1047-8477(08)00060-9
更新日期：2008-03-01 00:00:00
abstract：:COVID-19 pandemic, caused by SARS-CoV-2, has drastically affected human health all over the world. After the emergence of the pandemic the major focus of efforts to attenuate the infection has been on repurposing the already approved drugs to treat COVID-19 adopting a fast-track strategy. However, to date a specific r...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107690
更新日期：2020-12-29 00:00:00
abstract：:To date, the calcareous tubes of serpulid marine worms have not been studied extensively in a biomineralization context. The structure and composition of the tube shell and adhesive cement of the marine tubeworm Hydroides dianthus were studied using a variety of characterization techniques, including powder XRD, FTIR,...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2009.09.008
更新日期：2010-02-01 00:00:00
abstract：:Third harmonic generation microscopy is shown to be a robust method for obtaining structural information on a variety of biological specimens. Its nature allows depth-resolved imaging of inhomogeneities with virtually no background from surrounding homogeneous media. With an appropriate illumination geometry, third ha...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/S1047-8477(03)00125-4
更新日期：2004-07-01 00:00:00
abstract：:The carboxy-terminal region of the KCNH family of potassium channels contains a cyclic-nucleotide binding homology domain (CNBHD) that is important for channel gating and trafficking. The solution structure of the CNBHD of the KCNH potassium of zebrafish was determined using solution NMR spectroscopy. This domain exis...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.03.008
更新日期：2014-04-01 00:00:00
abstract：:Upon illumination the visual receptor rhodopsin (Rho) transitions to the activated form Rho(∗), which binds the heterotrimeric G protein, transducin (Gt) causing GDP to GTP exchange and Gt dissociation. Using succinylated concanavalin A (sConA) as a probe, we visualized native Rho dimers solubilized in 1mM n-dodecyl-β...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2013.02.014
更新日期：2013-05-01 00:00:00
abstract：:To characterize the spatial and temporal occurrence of programmed cell death (PCD) in Lilium anther tissues, we used both microscopical and molecular markers of apoptosis for developmental stages from meiosis to pollen release. The first hallmarks of PCD include cell condensation and shrinkage of the cytoplasm, separa...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.07.011
更新日期：2005-11-01 00:00:00
abstract：:Vateritic deformities occurring in the invasive heterodont bivalve Corbicula fluminea from several locations in the UK were characterised in detail for the first time using scanning electron microscopy, X-ray diffraction and different geochemical techniques (electron microprobe, ICP-AES, and mass spectrometry). Large ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.02.002
更新日期：2011-05-01 00:00:00
abstract：:An approach to automated acquisition of cryoEM image data from lacey carbon grids using the Leginon program is described. Automated liquid nitrogen top up of the specimen holder dewar was used as a step towards full automation, without operator intervention during the course of data collection. During cryoEM studies o...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2010.08.014
更新日期：2010-12-01 00:00:00
abstract：:Human alpha 2-macroglobulin (alpha 2M), a large tetrameric plasma glycoprotein, inhibits a wide spectrum of proteinases by a particular "trapping" mechanism resulting from the proteolysis of peptide bonds at specific "bait" regions. This induces the hydrolysis of four thiol esters triggering both the possible covalent...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(91)90060-a
更新日期：1991-02-01 00:00:00
abstract：:Like in most Crustacea, the cuticle of terrestrial isopods is hardened by a calcareous mineral phase. This rigid cuticle is frequently shed during a process called moulting. To reduce calcium loss, Porcellio scaber eats the shed cuticle, the exuviae, and absorb the calcium from it through large tubular diverticula of ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107613
更新日期：2020-11-01 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
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更新日期：2016-04-01 00:00:00
abstract：:Poly(A)-binding protein (PABP) is an RNA-binding protein that binds specifically to the poly(A) tail of messenger RNAs in eukaryotes. The PABP/poly(A) tail complex has been implicated as being important in promoting the efficient initiation of translation as well as in maintaining the integrity of the mRNA. PABP binds...
journal_title：Journal of structural biology
pub_type： 杂志文章
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更新日期：1997-07-01 00:00:00
abstract：:Infection of plants by Zucchini Yellow Mosaic Virus (ZYMV) induces severe ultrastructural changes. The aim of this study was to investigate ultrastructural changes during ZYMV-infection in Cucurbita pepo L. plants on the two and three dimensional (2D and 3D) level and to correlate these changes with the spread of ZYMV...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.03.006
更新日期：2014-05-01 00:00:00
