Abstract:
:The Jun a 3 protein from mountain cedar (Juniperus ashei) pollen, a member of group 5 of the family of plant pathogenesis-related proteins (PR-proteins), reacts with serum IgE from patients with cedar hypersensitivity. We used the crystal structures of two other proteins of this group, thaumatin and an antifungal protein from tobacco, both approximately 50% identical in sequence to Jun a 3, as templates to build homology models for the allergen. The in-house programs EXDIS and FANTOM were used to extract distance and dihedral angle constraints from the Protein Data Bank files and determine energy-minimized structures. The mean backbone deviations for the energy-refined model structures from either of the templates is <1 A, their conformational energies are low, and their stereochemical properties (determined with PROCHECK) are acceptable. The circular dichroism spectrum of Jun a 3 is consistent with the postulated beta-sheet core. Tryptic fragments of Jun a 3 that reacted with IgE from allergic patients all mapped to one helical/loop surface of the models. The Jun a 3 models have features common to aerosol allergens from completely different protein families, suggesting that tertiary structural elements may mediate the triggering of an allergic response.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Soman KV,Midoro-Horiuti T,Ferreon JC,Goldblum RM,Brooks EG,Kurosky A,Braun W,Schein CHdoi
10.1016/S0006-3495(00)76410-1subject
Has Abstractpub_date
2000-09-01 00:00:00pages
1601-9issue
3eissn
0006-3495issn
1542-0086pii
S0006-3495(00)76410-1journal_volume
79pub_type
杂志文章abstract::The conformation of the polypeptide melittin in lipid membranes as determined by Raman spectroscopy is a bent alpha-helix formed by the mainly hydrophobic residues 1-21, and a nonhelical COOH-terminal segment of the hydrophilic residues 22-26. Fluorescence quenching experiments on residue Trp19 reveal that all COOH-te...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(86)83497-X
更新日期:1986-10-01 00:00:00
abstract::The relative contributions of the allosteric and affinity factors toward the change in p50 have been calculated for a series of effectors of hemoglobin (Hb). Shifts in the ligand affinity of deoxy Hb and the values for 50% ligand saturation (p50) were obtained from oxygen equilibrium data. Because the high-affinity pa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82556-X
更新日期:1990-03-01 00:00:00
abstract::We introduce dual-color time-integrated fluorescence cumulant analysis (TIFCA) to analyze fluorescence fluctuation spectroscopy data. Dual-color TIFCA utilizes the bivariate cumulants of the integrated fluorescent intensity from two detection channels to extract the brightness in each channel, the occupation number, a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.086181
更新日期:2006-10-01 00:00:00
abstract::Recent experimental studies (Pusch and Neher, 1988) and theoretical studies (Oliva et al., 1988) have found that the pipette tip is a significant barrier to diffusion in the whole cell patch clamp configuration. In this paper, we extend the theoretical analysis of fluxes between the pipette and cell to include transme...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82418-8
更新日期:1990-09-01 00:00:00
abstract::The structure and dynamics of soluble misfolded aggregates are poorly understood, despite their importance in protein science and disease. Water-soluble self-associated species that do not become insoluble over time are invaluable tools for high-resolution conformational studies aimed at dissecting the determinants of...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.12.3722
更新日期:2011-02-02 00:00:00
abstract::The binding mechanism of sweet proteins to their receptor, a G-protein-coupled receptor, is not supported by direct structural information. In principle, the key groups responsible for biological activity (glucophores) can be localized on a small structural unit (sweet finger) or spread on a larger surface area. A rec...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.073171
更新日期:2006-05-01 00:00:00
abstract::A variety of amphiphilic helical peptides have been shown to exhibit a transition from adsorbing parallel to a membrane surface at low concentrations to inserting perpendicularly into the membrane at high concentrations. Furthermore, this transition has been correlated to the peptides' cytolytic activities. X-ray lame...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80418-2
更新日期:1995-06-01 00:00:00
abstract::KATP channels assemble from four regulatory SUR1 and four pore-forming Kir6.2 subunits. At the single-channel current level, ATP-dependent gating transitions between the active burst and the inactive interburst conformations underlie inhibition of the KATP channel by intracellular ATP. Previously, we identified a slow...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74269-1
更新日期:2004-04-01 00:00:00
abstract::Relations describing threshold fluctuation phenomena in nerves are derived by calculating the approximate response of the Hodgkin-Huxley (HH) axon to electrical noise. We use FitzHugh's reduced phase space approximation and describe the dynamics of a noisy nerve by a two-dimensional brownian motion. The theory predict...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(71)86277-X
更新日期:1971-12-01 00:00:00
abstract::The structural features of SPM that control the transbilayer distribution of beta-GalCer in POPC vesicles were investigated by (13)C- and (31)P-NMR spectroscopy using lipid analogs that share physical similarities with GalCer or SPM. The SPM analogs included N-palmitoyl-4,5-dihydro-SPM, 3-deoxy-SPM, 1-alkyl-2-amidopho...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.057059
更新日期:2005-04-01 00:00:00
abstract::Nonlinear optical Stokes ellipsometric (NOSE) microscopy was demonstrated for the analysis of collagen-rich biological tissues. NOSE is based on polarization-dependent second harmonic generation imaging. NOSE was used to access the molecular-level distribution of collagen fibril orientation relative to the local fiber...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.05.055
更新日期:2016-10-04 00:00:00
abstract::Differentiation from a multipotent stem or progenitor state to a mature cell is an essentially irreversible process. The associated changes in gene expression patterns exhibit time-directionality. This "arrow of time" in the collective change of gene expression across multiple stable gene expression patterns (attracto...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.03.058
更新日期:2010-07-07 00:00:00
abstract::Endophilins are SH3- and BAR domain-containing proteins implicated in membrane remodeling and vesicle formation. Endophilins A1 and A2 promote the budding of endocytic vesicles from the plasma membrane, whereas endophilin B1 has been implicated in vesicle budding from intracellular organelles, including the trans-Golg...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.06.017
更新日期:2016-08-09 00:00:00
abstract::Polymers play an important role in many biological systems, so a fundamental understanding of their cross-links is crucial not only for the development of medicines but also for the development of biomimetic materials. The biomechanical movements of all mammals are aided by tendon fibrils. The self-organization and bi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.056747
更新日期:2005-07-01 00:00:00
abstract::Myoglobin (Mb) is a model system for ligand binding and migration. The energy barriers (ΔG) for ligand migration in Mb have been studied in the past by experiment and theory and significant differences between different approaches were found. From experiment, it is known that Mb can assume a large number of conformati...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.10.058
更新日期:2012-01-18 00:00:00
abstract::The use of the long-lived fluorescence probe coronene (mean value of tau(FL) approximately 200 ns) is described for investigating submicrosecond lipid dynamics in DPPC model bilayer systems occurring below the lipid phase transition. Time-resolved fluorescence emission anisotropy decay profiles, measures as a function...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79384-0
更新日期:1996-10-01 00:00:00
abstract::Outside-out patches of enzymatically dissociated adult and denervated mouse muscle fibers were superfused repetitively by pulses of acetylcholine (ACh) containing solution. Up to 300 channels opened simultaneously 300 microseconds after the beginning of a 1,000 microM ACh pulse corresponding to a peak current i of alm...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82138-5
更新日期:1991-11-01 00:00:00
abstract::In the photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides, light is absorbed by membrane-bound light-harvesting (LH) proteins LH1 and LH2. LH1 directly surrounds the reaction center (RC) and, together with PufX, forms a dimeric (RC-LH1-PufX)2 protein complex. In LH2-deficient Rba. sphaeroides mutants, RC-L...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.04.031
更新日期:2009-07-08 00:00:00
abstract::The aggregation of amyloid-β (Aβ) peptides plays a crucial role in the etiology of Alzheimer's disease (AD). Recently, it has been reported that an A2T mutation in Aβ can protect against AD. Interestingly, a nonpolar A2V mutation also has been found to offer protection against AD in the heterozygous state, although it...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.12.013
更新日期:2015-02-03 00:00:00
abstract::The outer membrane porin OmpF from Escherichia coli has been reconstituted into lipid bilayers of defined composition, and fluorescence spectroscopy is used to characterize its interaction with the surrounding lipid. OmpF is a trimer within the membrane. It contains two Trp residues per monomer, Trp(214) at the lipid-...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76454-X
更新日期:2000-10-01 00:00:00
abstract::Inositol 1,4,5-trisphosphate (InsP(3)) receptors (InsP(3)Rs) are intracellular Ca(2+) channels gated by the second messenger InsP(3). Here we describe a novel approach for recording single-channel currents through recombinant InsP(3)Rs in mammalian cells that applies patch-clamp electrophysiology to nuclei isolated fr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(01)75685-8
更新日期:2001-07-01 00:00:00
abstract::An interactive program is described for calculating the second virial coefficient contribution to the thermodynamic nonideality of solutions of rigid macromolecules based on their triaxial dimensions. The FORTRAN-77 program, available in precompiled form for the PC, is based on theory for the covolume of triaxial elli...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77398-4
更新日期:1999-05-01 00:00:00
abstract::Heart surface optical mapping of transmembrane potentials has been widely used in studies of normal and pathological heart rhythms and defibrillation. In these studies, three-dimensional spatio-temporal events can only be inferred from two-dimensional surface potential maps. We present a novel optical system that enab...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75910-3
更新日期:2001-11-01 00:00:00
abstract::Fusion is a crucial event in the infection of animal cells by enveloped viruses (e.g., HIV or influenza). Viral fusion is mediated by glycoproteins, spanning the viral envelope, which attach to a membrane surface and induce fusion of the viral envelope to the cellular membrane. Influenza fusion protein (hemagglutinin)...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78175-X
更新日期:1997-09-01 00:00:00
abstract::Magic-angle spinning nuclear magnetic resonance is well suited for the study of membrane proteins in the nativelike lipid environment. However, the natural cellular membrane is invariably more complex than the proteoliposomes most often used for solid-state NMR (SSNMR) studies, and differences may affect the structure...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.02.018
更新日期:2015-04-07 00:00:00
abstract::The muscle nicotinic receptor (AChR) is a pentamer of four different subunits, each of which contains four transmembrane domains (M1-M4). We recently showed that channel opening and closing rates of the AChR depend on a hydrogen bond involving a threonine at position 14' of the M4 domain in the alpha-subunit. To deter...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75541-0
更新日期:2002-04-01 00:00:00
abstract::The potassium selective, inward rectifier current (IK1) is known to be responsible for maintaining the resting membrane potential of quiescent ventricular myocytes. However, the contribution of this current to the different phases of the cardiac action potential has not been adequately established. In the present stud...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82187-7
更新日期:1991-12-01 00:00:00
abstract::We report here several unusual features of inactivation of the rat Kv2.1 delayed rectifier potassium channel, expressed in Xenopus oocytes. The voltage dependence of inactivation was U-shaped, with maximum inactivation near 0 mV. During a maintained depolarization, development of inactivation was slow and only weakly ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77888-9
更新日期:1998-04-01 00:00:00
abstract::Neutrophils rely on rapid changes in morphology to ward off invaders. Time-resolved dynamics of spreading human neutrophils after activation by the chemoattractant fMLF (formyl methionyl leucyl phenylalanine) was observed by RICM (reflection interference contrast microscopy). An image-processing algorithm was develope...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.080382
更新日期:2006-12-15 00:00:00
abstract::Fast Ca(2+) release kinetics were measured in cardiac sarcoplasmic reticulum vesicles actively loaded with Ca(2+). Release was induced in solutions containing 1.2 mM free ATP and variable free [Ca(2+)] and [Mg(2+)]. Release rate constants (k) were 10-fold higher at pCa 6 than at pCa 5 whereas Ryanodine binding was hig...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)75037-1
更新日期:2003-04-01 00:00:00