Abstract:
:Small-angle x-ray scattering (SAXS) of biological macromolecules in solutions is a widely employed method in structural biology. SAXS patterns include information about the overall shape and low-resolution structure of dissolved particles. Here, we describe how to transform experimental SAXS patterns to feature vectors and how a simple k-nearest neighbor approach is able to retrieve information on overall particle shape and maximal diameter (Dmax) as well as molecular mass directly from experimental scattering data. Based on this transformation, we develop a rapid multiclass shape-classification ranging from compact, extended, and flat categories to hollow and random-chain-like objects. This classification may be employed, e.g., as a decision block in automated data analysis pipelines. Further, we map protein structures from the Protein Data Bank into the classification space and, in a second step, use this mapping as a data source to obtain accurate estimates for the structural parameters (Dmax, molecular mass) of the macromolecule under study based on the experimental scattering pattern alone, without inverse Fourier transform for Dmax. All methods presented are implemented in a Fortran binary DATCLASS, part of the ATSAS data analysis suite, available on Linux, Mac, and Windows and free for academic use.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Franke D,Jeffries CM,Svergun DIdoi
10.1016/j.bpj.2018.04.018subject
Has Abstractpub_date
2018-06-05 00:00:00pages
2485-2492issue
11eissn
0006-3495issn
1542-0086pii
S0006-3495(18)30464-8journal_volume
114pub_type
杂志文章abstract::Membrane potential of aortic endothelial cells under resting conditions is dominated by inward-rectifier K(+) channels belonging to the Kir 2 family. Regulation of endothelial Kir by membrane cholesterol was studied in bovine aortic endothelial cells by altering the sterol composition of the cell membrane. Our results...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75323-X
更新日期:2002-12-01 00:00:00
abstract::It has recently been shown that the highly protected segments 24-34 (S2) and 83-93 (S8) of each of the two 99-mers of human immunodeficiency virus type 1 protease play an essential role in the folding of the monomers, giving rise to the so-called (postcritical) folding nucleus ((FN) minimum condensation unit ensuring ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.106369
更新日期:2007-10-15 00:00:00
abstract::The primary drivers of yeast endocytosis are actin polymerization and curvature-generating proteins, such as clathrin and BAR domain proteins. Previous work has indicated that these factors may not be capable of generating the forces necessary to overcome turgor pressure. Thus local reduction of the turgor pressure, v...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.10.040
更新日期:2016-12-20 00:00:00
abstract::4',6-diamidino-2-phenylindole (DAPI), netropsin, and pentamidine are minor groove binders that have terminal -C(NH2)2+ groups. The hydration changes that accompany their binding to the minor groove of the (AATT)2 sequence have been studied using the osmotic stress technique with fluorescence spectroscopy. The affinity...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.097451
更新日期:2007-02-01 00:00:00
abstract::Dipole moment, enthalpy, and entropy changes were calculated for hypothetical structural units which control the opening and closing of ionic channels in axon membranes. The changes of these thermodynamic functions were calculated both for activation (transition to intermediate complex) and for the structural transfor...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(75)85815-2
更新日期:1975-03-01 00:00:00
abstract::An analysis of four 1-ns molecular dynamics trajectories for two different 15-bp oligonucleotides is presented. Our aim is to show which groups of atoms can be treated as rigid bodies within a bead representation of DNA, independently of the base sequence and for any conformations belonging to the A/B family. Five mod...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77074-8
更新日期:1999-11-01 00:00:00
abstract::The general formalism required to treat two-state sliding filament models of muscle contraction, including free energy considerations, is first reviewed and amplified. This formalism is then used to examine, and modify as needed, three models studied previously by Podolsky and Nolan, in which cross-bridge attachment-d...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(75)85823-1
更新日期:1975-04-01 00:00:00
abstract::A new method for the investigation of ion translocating membrane proteins is presented. Protein containing membrane fragments or vesicles are adsorbed to a solid supported membrane. The solid supported membrane consists of a lipid monolayer on a gold evaporated or gold sputtered glass substrate which is coated with a ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81379-1
更新日期:1993-02-01 00:00:00
abstract::The TRPV1 cation nonselective ion channel plays an essential role in thermosensation and perception of other noxious stimuli. TRPV1 can be activated by low extracellular pH, high temperature, or naturally occurring pungent molecules such as allicin, capsaicin, or resiniferatoxin. Its noxious thermal sensitivity makes ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.10.041
更新日期:2020-02-25 00:00:00
abstract::The organization of filamentous actin and myosin II molecular motor contractility is known to modify the mechanical properties of the cell cortical actomyosin cytoskeleton. Here we describe a novel method, to our knowledge, for using force spectroscopy approach curves with tipless cantilevers to determine the actomyos...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.04.034
更新日期:2016-06-07 00:00:00
abstract::Xenopus melanophores have pigment organelles or melanosomes which, in response to hormones, disperse in the cytoplasm or aggregate in the perinuclear region. Melanosomes are transported by microtubule motors, kinesin-2 and cytoplasmic dynein, and an actin motor, myosin-V. We explored the regulation of melanosome trans...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.067843
更新日期:2006-01-01 00:00:00
abstract::Protein conformational fluctuations modulate the catalytic powers of enzymes. The frequency of conformational fluctuations may modulate the catalytic rate at individual reaction steps. In this study, we modulated the rotary fluctuation frequency of F1-ATPase (F1) by attaching probes with different viscous drag coeffic...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.09.050
更新日期:2013-11-19 00:00:00
abstract::Evidence is presented for the existence of two forms of low-potential cytochrome a3. One appears to be similar to the low-spin form reported by Nicholls, P., and V. Hildebrandt (1978 Biochem. J. 173:65-72) and Wrigglesworth, J. M., J. Elsden, A. Chapman, N. Van der Water, and M. F. Grahn (1988. Biochim. Biophys. Acta....
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82633-3
更新日期:1990-06-01 00:00:00
abstract::We report molecular dynamics simulations in the explicit membrane environment of a small membrane-embedded protein, sarcolipin, which regulates the sarcoplasmic reticulum Ca-ATPase activity in both cardiac and skeletal muscle. In its monomeric form, we found that sarcolipin adopts a helical conformation, with a comput...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.02.025
更新日期:2009-05-06 00:00:00
abstract::A theory based on the Smolukowski analysis of colloid stability shows that the presence of charged, surface-active serum proteins at the alveolar air-liquid interface can severely reduce or eliminate the adsorption of lung surfactant from the subphase to the interface, consistent with the observations reported in the ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.062646
更新日期:2005-09-01 00:00:00
abstract::Kv1 potassium channels are widely distributed in mammalian tissues and are involved in a variety of functions from controlling the firing rate of neurons to maturation of T-lymphocytes. Here we show that the newly described KCNE4 beta-subunit has a drastic inhibitory effect on currents generated by Kv1.1 and Kv1.3 pot...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74585-8
更新日期:2003-09-01 00:00:00
abstract::The resonance Raman spectrum of the second intermediate in the bacteriorhodopsin cycle, bL550, is obtained by a simple flow technique. The Schiff base linkage in this intermediate appears to be protonated, contrary to previous suggestion. The fingerprint region of the spectrum of bL550 does not closely match those of ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(79)85269-8
更新日期:1979-06-01 00:00:00
abstract::Single-molecule methods provide direct measurements of macromolecular dynamics, but are limited by the number of degrees of freedom that can be followed at one time. High-resolution rotor bead tracking (RBT) measures DNA torque, twist, and extension, and can be used to characterize the structural dynamics of DNA and d...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.11.017
更新日期:2018-01-23 00:00:00
abstract::Synchronous neurotransmitter release is mediated by the opening of voltage-gated Ca(2+) channels and the build-up of submembrane Ca(2+) microdomains. Previous models of Ca(2+) microdomains have neglected possible electrostatic interactions between Ca(2+) ions and negative surface charges on the inner leaflet of the pl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.124909
更新日期:2008-09-01 00:00:00
abstract::The unfolding and folding of protein barnase has been extensively investigated in bulk conditions under the effect of denaturant and temperature. These experiments provided information about structural and kinetic features of both the native and the unfolded states of the protein, and debates about the possible existe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.11.015
更新日期:2016-01-05 00:00:00
abstract::The electrophysiological properties of the cation channel of the purified nicotinic acetylcholine receptor (AChR) reconstituted in planar lipid bilayers were characterized. Single-channel currents were activated by acetylcholine, carbamylcholine and suberyldicholine. The single channel conductance (28 pS in 0.3 M NaCl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84145-4
更新日期:1984-01-01 00:00:00
abstract::Protein-mediated membrane remodeling is a ubiquitous and critical process for proper cellular function. Inverse Bin/Amphiphysin/Rvs (I-BAR) domains drive local membrane deformation as a precursor to large-scale membrane remodeling. We employ a multiscale approach to provide the molecular mechanism of unusual I-BAR dom...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.06.025
更新日期:2019-08-06 00:00:00
abstract::We manipulate lipid bilayer surface charge and gauge its influence on gramicidin A channel conductance by two strategies: titration of the lipid charge through bulk solution pH and dilution of a charged lipid by neutral. Using diphytanoyl phosphatidylserine (PS) bilayers with CsCl aqueous solutions, we show that the e...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77620-9
更新日期:1998-10-01 00:00:00
abstract::A one-dimensional version of the model recently proposed by Läuger (1988) to explain the closed-time distribution of ionic channels in cell membranes is solved analytically. While the probability density f(t) for closed-time lengths may show a well-defined exponential behavior at short times, a power-law decay is pred...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(89)82890-5
更新日期:1989-05-01 00:00:00
abstract::Collective action by inverse-Bin/Amphiphysin/Rvs (I-BAR) domains drive micron-scale membrane remodeling. The macroscopic curvature sensing and generation behavior of I-BAR domains is well characterized, and computational models have suggested various mechanisms on simplified membrane systems, but there remain missing ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.11.019
更新日期:2021-01-05 00:00:00
abstract::Recent studies have demonstrated that caffeine can act as an antimutagen and inhibit the cytoxic and/or cytostatic effects of some DNA intercalating agents. It has been suggested that this inhibitory effect may be due to complexation of the DNA intercalator with caffeine. In this study we employ optical absorption, fl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79587-5
更新日期:1996-01-01 00:00:00
abstract::Hydrophobic interactions between a bilayer and its embedded membrane proteins couple protein conformational changes to changes in the packing of the surrounding lipids. The energetic cost of a protein conformational change therefore includes a contribution from the associated bilayer deformation energy (DeltaGdef0), w...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77252-8
更新日期:1999-02-01 00:00:00
abstract::Computations on sodium channel gating were conducted using a closed-open-inactivated coupled kinetic scheme. The time constant of inactivation (tauh) derives a voltage dependency from coupling to voltage-dependent activation even when rate constants between inactivated and other states are strictly voltage independent...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77408-4
更新日期:1999-05-01 00:00:00
abstract::Rearrangement of tertiary structure in response to mechanical force (termed tertiary structure elasticity) in the tandem Ig chain is the first mode of elastic response for muscle protein titin. Tertiary structure elasticity occurs at low stretching forces (few tens of pN), and was described at atomic resolution in a r...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1016/j.bpj.2011.01.019
更新日期:2011-02-16 00:00:00
abstract::Many organisms are able to survive subzero temperatures at which bodily fluids would normally be expected to freeze. These organisms have adapted to these lower temperatures by synthesizing antifreeze proteins (AFPs), capable of binding to ice, which make further growth of ice energetically unfavorable. To date, the s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75821-3
更新日期:2001-09-01 00:00:00