Abstract：
:Although the fundamental steps in Fourier-based image analysis of electron micrographs of helical structures have not changed significantly since the techniques were developed 30 years ago, there have been developments which aid both the analysis itself and the interpretation of results. Increases in computational resources have allowed the automation of many of the repetitive steps in image processing. We describe here a set of computer programs which have been developed at Brandeis University over the past 10 or more years. These programs, referred to as the Brandeis Helical Package, are designed to operate independently of each other with a simple and more uniform protocol for the flow of information between them. The programs are now easier to understand and to use and therefore represent a good tool for the analysis of helical structures.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Owen CH,Morgan DG,DeRosier DJdoi
10.1006/jsbi.1996.0027subject
Has Abstractpub_date
1996-01-01 00:00:00pages
167-75issue
1eissn
1047-8477issn
1095-8657pii
S1047-8477(96)90027-1journal_volume
116pub_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：: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：:Beam damage is the main resolution-limiting factor when biological particles are observed by cryoelectron microscopy in a thin vitrified solution film. Furthermore, the low contrast of the specimen frequently makes observation difficult and limits the possibility of image processing. Cryo-negative staining, in which t...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/s1047-8477(02)00035-7
更新日期：2002-06-01 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：:Uptake and metabolism of silicon by diatoms are studied by the combined use of solid-state 29Si NMR spectroscopy and confocal laser fluorescence microscopy especially with respect to the presence and nature of an intracellular silicon-storage pool. Cells of the marine diatom Thalassiosira pseudonana were synchronized ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2007.09.010
更新日期：2008-01-01 00:00:00
abstract：:We describe here a set of procedures and algorithms that may be used as an aid in determining the indexing rule of a helical specimen. Crystallizing macromolecules into helical arrays has the potential to speed up and simplify the process of three-dimensional reconstruction of the macromolecular structure. The process...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2003.10.008
更新日期：2003-10-01 00:00:00
abstract：:The mature dentinoenamel junction (DEJ) is viewed by some investigators and the current authors, not as a fossilized, sharp transition between enamel and dentin, but as a relatively broad structural transition zone including the mantle dentin and the inner aprismatic enamel. In this study, the DEJ structure in bovine ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2007.10.006
更新日期：2008-02-01 00:00:00
abstract：:Helicases are proteins that use the energy of ATP hydrolysis to open double-stranded DNA, RNA, or RNA-DNA hybrids into two single strands. Based upon sequence analysis, at least 12 helicases exist in Escherichia coli. We know that these proteins play important roles in DNA replication, recombination, repair, and trans...
journal_title：Journal of structural biology
pub_type： 杂志文章,评审
doi：10.1006/jsbi.1998.4050
更新日期：1998-12-15 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：:CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm whi...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2015.08.008
更新日期：2015-11-01 00:00:00
abstract：:In order to understand further the mechanism of bone fracture repair, and thus to innovate better operative treatment for bone fracture and to design new implant materials for bone repair, microstructures of external periosteal callus (EPC) of repaired femoral fracture in both children and adults were investigated by ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1996.0084
更新日期：1996-11-01 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：:In many microorganisms, menaquinone is an essential lipid-soluble electron carrier. Recently, an alternative menaquinone biosynthetic pathway was found in some microorganisms [Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H., Dairi, T., 2008. An alternative menaquinone biosynthetic pathway ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2009.07.007
更新日期：2009-12-01 00:00:00
abstract：:While cryo-electron tomography (cryo-ET) can reveal biological structures in their native state within the cellular environment, it requires the production of high-quality frozen-hydrated sections that are thinner than 300nm. Sample requirements are even more stringent for the visualization of membrane-bound protein c...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.07.010
更新日期：2017-02-01 00:00:00
abstract：:This is the first crystal structure of a carbohydrate induced dimer of phospholipase A(2) (PLA(2)). This is an endogenous complex formed between two PLA(2) molecules and two mannoses. It was isolated from Krait venom (Bungarus caeruleus) and crystallized as such. The complete amino acid sequence of PLA(2) was determin...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2004.11.011
更新日期：2005-03-01 00:00:00
abstract：:Using a combination of atomic force, scanning and transmission electron microscopy, we found that avian erythrocytes infected with the avian malaria parasite Plasmodium gallinaceum develop approximately 60 nm wide and approximately 430 nm long furrow-like structures on the surface. Furrows begin to appear during the e...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.03.005
更新日期：2008-06-01 00:00:00
abstract：:We describe here a set of multiresolution visualization and docking procedures that we refer to as the Situs package. The package was developed to provide an efficient and robust method for the fitting of atomic structures into low-resolution data. The current release was optimized specifically for the visualization a...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2000.4350
更新日期：2001-02-01 00:00:00
abstract：:Sickle hemoglobin (HbS) polymerization initiates in the deoxy state with the binding of hydrophobic patch formed by the isopropyl group of βVal6 residue of a hemoglobin tetramer with the hydrophobic pocket of another tetramer, whose hydrophobic patch binds to the hydrophobic groove of a third molecule. Subsequent elon...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2017.04.009
更新日期：2017-07-01 00:00:00
abstract：:AVS (Application Visualization System) is commercially available software for analyzing and viewing data. AVS is primarily used in the physical sciences and engineering, and here we describe the application of AVS for examining three-dimensional density maps generated by electron microscopy and image processing. For t...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1996.0017
更新日期：1996-01-01 00:00:00
abstract：:We have solved a crystal structure from Melanocarpus albomyces laccase expressed in the filamentous fungus Trichoderma reesei (rMaL) at 1.3A resolution by using synchrotron radiation at 100K. At the moment, this is the highest resolution that has been attained for any multicopper oxidase. The present structure confirm...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2007.12.003
更新日期：2008-04-01 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：:The bacterial type II protein secretion (T2S) and type IV piliation (T4P) systems share several common features. In particular, it is well established that the T2S system requires the function of a pilus-like structure, called pseudopilus, which is built upon assembly of pilin-like subunits, called pseudopilins. Pilin...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2009.09.003
更新日期：2010-01-01 00:00:00
abstract：:The small icosahedral plant RNA nepovirus Grapevine fanleaf virus (GFLV) is specifically transmitted by a nematode and causes major damage to vineyards worldwide. To elucidate the molecular mechanisms underlying the recognition between the surface of its protein capsid and cellular components of its vector, host and v...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.02.007
更新日期：2011-05-01 00:00:00
abstract：:Brain deposition of Aβ in the form of amyloid plaques is a pathological hallmark of Alzheimer's disease. There are two major species of Aβ in the brain: Aβ42 and Aβ40. Although Aβ40 is several-fold more abundant than Aβ42 in soluble form, Aβ42 is the major component of amyloid plaques. Structural knowledge of Aβ42 fib...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.01.013
更新日期：2016-04-01 00:00:00
abstract：:Null-mutation in Drosophila importin-alpha2, such as the deficiency imp-alpha2(D14), causes recessive female sterility with the formation of dumpless eggs. In imp-alpha2(D14) the transfer of nurse cell components to the oocyte is interrupted and the Kelch protein, an oligomeric ring canal actin organizer, is normally ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.12.007
更新日期：2006-04-01 00:00:00
abstract：:Control of tissue composition and organization will be a key feature in the development of successful products through tissue engineering. However, the mechanism of collagen fibril formation, growth, and organization is not yet fully understood. In this study we have examined collagen fibril formation in a wound heali...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2002.4460
更新日期：2002-01-01 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
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：:Sub-nanometer resolution structure determination is becoming a common practice in electron cryomicroscopy of macromolecular assemblies. The data for these studies have until now been collected on photographic film. Using cytoplasmic polyhedrosis virus (CPV), a previously determined structure, as a test specimen, we sh...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2004.02.004
更新日期：2004-08-01 00:00:00
abstract：:AAA+ proteins remodel target substrates in an ATP-dependent manner, an activity that is of central importance for a plethora of cellular processes. While sharing a similar hexameric structure AAA+ proteins must exhibit differences in substrate recognition to fulfil their diverse biological functions. Here we describe ...
journal_title：Journal of structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.jsb.2003.10.009
更新日期：2004-04-01 00:00:00
