Abstract:
:The structure and alignment of the amphipathic alpha-helical antimicrobial peptide PGLa in a lipid membrane is determined with high accuracy by solid-state 2H-NMR. Orientational constraints are derived from a series of eight alanine-3,3,3-d3-labeled peptides, in which either a native alanine is nonperturbingly labeled (4x), or a glycine (2x) or isoleucine (2x) is selectively replaced. The concentration dependent realignment of the alpha-helix from the surface-bound "S-state" to a tilted "T-state" by 30 degrees is precisely calculated using the quadrupole splittings of the four nonperturbing labels as constraints. The remaining, potentially perturbing alanine-3,3,3-d3 labels show only minor deviations from the unperturbed peptide structure and help to single out the unique solution. Comparison with previous 19F-NMR constraints from 4-CF3-phenylglycine labels shows that the structure and orientation of the PGLa peptide is not much disturbed even by these bulky nonnatural side chains, which contain CF3 groups that offer a 20-fold better NMR sensitivity than CD3 groups.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Strandberg E,Wadhwani P,Tremouilhac P,Dürr UH,Ulrich ASdoi
10.1529/biophysj.105.073858subject
Has Abstractpub_date
2006-03-01 00:00:00pages
1676-86issue
5eissn
0006-3495issn
1542-0086pii
S0006-3495(06)72356-6journal_volume
90pub_type
杂志文章abstract::Green flagellates possess rhodopsin-like photoreceptors involved in control of their behavior via generation of photocurrents across the plasma membrane. Chlamydomonas mutants blocked in retinal biosynthesis are "blind," but they can be rescued by the addition of exogenous retinoids. Photosignaling by chlamyrhodopsin ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75930-9
更新日期:2001-11-01 00:00:00
abstract::The crystal structure of the Mycobacterium tuberculosis homolog of the bacterial mechanosensitive channel of large conductance (Tb-MscL) provides a unique opportunity to consider mechanosensitive signal transduction at the atomic level. Molecular dynamics simulations of the Tb-MscL channel embedded in an explicit lipi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75791-8
更新日期:2001-09-01 00:00:00
abstract::We present a new approach to probing single-particle dynamics that uses dynamic light scattering from a localized region. By scattering a focused laser beam from a micron-size particle, we measure its spatial fluctuations via the temporal autocorrelation of the scattered intensity. We demonstrate the applicability of ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77866-X
更新日期:1998-03-01 00:00:00
abstract::The effect of salt and pH titration on the selectivity of spin-labeled analogues of phosphatidic acid, phosphatidylserine, phosphatidylcholine, and stearic acid for the nicotinic acetylcholine receptor (nAcChoR) reconstituted into dioleoylphosphatidylcholine was examined at 0 degrees C using electron spin resonance sp...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81422-X
更新日期:1993-03-01 00:00:00
abstract::The molecular motor protein myosin VI moves toward the minus-end of actin filaments with a step size of 30-36 nm. Such large step size either drastically limits the degree of complex formation between dimer subunits to leave enough length for the lever arms, or requires an extension of the lever arms' crystallographic...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.05.010
更新日期:2011-06-22 00:00:00
abstract::At present, fluorescence recovery after photobleaching (FRAP) data are interpreted using various types of reaction-diffusion (RD) models: the model type is usually fixed first, and corresponding model parameters are inferred subsequently. In this article, we describe what we believe to be a novel approach for RD model...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.01.041
更新日期:2011-03-02 00:00:00
abstract::BP100 (KKLFKKILKYL-NH(2)) is a short cecropin A-melittin hybrid peptide, obtained through a combinatorial chemistry approach, which is highly effective in inhibiting both the in vitro and in vivo growth of economically important plant pathogenic Gram-negatives. The intrinsic Tyr fluorescence of BP100 was taken advanta...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.11.053
更新日期:2009-03-04 00:00:00
abstract::One of the most common swimming strategies employed by microorganisms is based on the use of rotating helical filaments, called flagella, that are powered by molecular motors. Determining the physical properties of this propulsive system is crucial to understanding the behavior of these organisms. Furthermore, the abi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.08.036
更新日期:2019-10-01 00:00:00
abstract::We showed recently that the high-salt transition of poly[d(G-C)]. poly[d(G-C)] between B-DNA and Z-DNA (at [NaCl] = 2.25 M or [MgCl(2)] = 0.7 M) can be ascribed to the lesser electrostatic free energy of the B form, due to better immersion of the phosphates in the solution. This property was incorporated in cylindrica...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(00)76665-3
更新日期:2000-02-01 00:00:00
abstract::We used optical tweezers to analyze the effect of jasplakinolide and cyclodextrin on the force exerted by lamellipodia from developing growth cones (GCs) of isolated dorsal root ganglia (DRG) neurons. We found that 25 nM of jasplakinolide, which is known to inhibit actin filament turnover, reduced both the maximal exe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.04.036
更新日期:2012-06-06 00:00:00
abstract::There is no methodology for the estimation of the dynamic features of large-molecular-weight RNAs in homogeneous physiological media. In this report, a luminescence anisotropy-based method using a long-lifetime luminescent oligonucleotide probe for the estimation of the dynamic features of large-molecular-weight RNA i...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.062455
更新日期:2005-12-01 00:00:00
abstract::To map the binding sites involved in channel formation, synthetic peptides representing sequences of connexin 32 were tested for their ability to inhibit cell-cell channel formation. Both large peptides representing most of the two presumed extracellular loops of connexin32 and shorter peptides representing subsets of...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80663-0
更新日期:1994-11-01 00:00:00
abstract::The wormlike-chain (WLC) model is widely used to describe the energetics of DNA bending. Motivated by recent experiments, alternative, so-called subelastic chain models were proposed that predict a lower elastic energy of highly bent DNA conformations. Until now, no unambiguous verification of these models has been ob...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.05.050
更新日期:2012-07-18 00:00:00
abstract::Reconstruction of genome-scale metabolic networks is now possible using multiple different data types. Constraint-based modeling is an approach to interrogate capabilities of reconstructed networks by constraining possible cellular behavior through the imposition of physicochemical laws. As a result, a steady-state fl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.043000
更新日期:2004-10-01 00:00:00
abstract::The analysis of peptide and protein partitioning in lipid membranes is of high relevance for the understanding of biomembrane function. We used statistical thermodynamics analysis to demonstrate the effect of peptide mixing behavior on heat capacity profiles of lipid membranes with the aim to predict peptide aggregati...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)75047-4
更新日期:2003-04-01 00:00:00
abstract::In total internal reflection fluorescence microscopy (TIRFM), fluorophores near a surface can be excited with evanescent waves, which decay exponentially with distance from the interface. Penetration depths of evanescent waves from 60 nm to 300 nm were generated by varying the angle of incidence of a laser beam. With ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76808-1
更新日期:2000-05-01 00:00:00
abstract::The possibility that the chlorophyll (chl) ring distortions observed in the crystal structures of chl-protein complexes are involved in the transition energy modulation, giving rise to the spectral forms, is investigated. The out-of-plane chl-macrocycle distortions are described using an orthonormal set of deformation...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.104554
更新日期:2007-09-15 00:00:00
abstract::In this paper, we consider the effect of adding small carbohydrate solutes (small sugars) to DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) L(alpha) dispersions and the consequences on the force balance at zero osmotic pressure (maximal swelling). We show the importance of long incubations required to obtain sampl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75388-5
更新日期:2002-01-01 00:00:00
abstract::We study the stochastic dynamics of growth and shrinkage of single actin filaments taking into account insertion, removal, and ATP hydrolysis of subunits either according to the vectorial mechanism or to the random mechanism. In a previous work, we developed a model for a single actin or microtubule filament where hyd...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.12.4306
更新日期:2010-04-21 00:00:00
abstract::In rat mesenteric arteries, smooth muscle cells exhibit intercellular calcium waves in response to local phenylephrine stimulation. These waves have a velocity of approximately 20 cells/s and a range of approximately 80 cells. We analyze these waves in a theoretical model of a population of coupled smooth muscle cells...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.04.031
更新日期:2010-07-21 00:00:00
abstract::The Green's function technique is applied to a study of breathing modes in a DNA double helix which contains a region of different base pairs from the rest of the double helix. The calculation is performed on a G-C helix in the B conformation with four consecutive base pairs replaced by A-T. The average stretch in hyd...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82570-4
更新日期:1990-03-01 00:00:00
abstract::We have constructed a model of the upper part of the glycolysis in the pancreatic beta-cell. The model comprises the enzymatic reactions from glucokinase to glyceraldehyde-3-phosphate dehydrogenase (GAPD). Our results show, for a substantial part of the parameter space, an oscillatory behavior of the glycolysis for a ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74460-9
更新日期:2003-07-01 00:00:00
abstract::One of the disadvantages of the sucrose-gap method for measuring membrane potentials with extracellular electrodes is a membrane hyperpolarization of the order of 30 to 60 mv, as compared with the resting potential obtained with intracellular microelectrodes in the absence of a sucrose-gap. In the present study the co...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(66)86669-9
更新日期:1966-07-01 00:00:00
abstract::Given some simple kinetic models of the photocycle of bacteriorhodopsin (bR) and data taken at many wavelengths and under conditions that avoid photoselection and steady-state cycling complications, it is shown how to extract the apparent rate constants and the spectra of the intermediates. Special consideration was g...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(82)84543-8
更新日期:1982-05-01 00:00:00
abstract::We describe the use of asymmetric Ru-ligand complexes as a new class of luminescent probes that can be used to measure rotational motions of proteins. These complexes are known to display luminescent lifetimes ranging from 10 to 4000 ns. In this report, we show that the asymmetric complex Ru(bpy)2(dcbpy) (PF6)2 displa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80193-1
更新日期:1995-01-01 00:00:00
abstract::A simple method of generating electric field-induced concentration gradients in planar supported bilayers has been developed. Gradients of charged, fluorescently labeled probes were visualized by epifluorescence microscopy and could be observed at field strengths as low as 1 V/cm. Steady-state concentration gradients ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80067-6
更新日期:1995-11-01 00:00:00
abstract::When cells migrate through constricting pores, they incur DNA damage and develop genomic variation. Experiments show that this damage is not due to DNA breakage from mechanical stress on chromatin in the deformed nucleus. Here we propose a model for a mechanism by which nuclear deformation can lead to DNA damage. We t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.04.037
更新日期:2017-06-06 00:00:00
abstract::Measurements of voltage relaxations following brief charge-pulses applied to lipid bilayers have been performed at different hydrostatic pressures in the presence of the neutral carriers cyclo (D-Val-L-Pro-L-Val-D-Pro)3(PV) and valinomycin. From double-exponential relaxations observed in membranes containing PV-K+ com...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(86)83443-9
更新日期:1986-07-01 00:00:00
abstract::Structural changes in frog skeletal muscle were studied using x-ray diffraction with a time resolution of 0.53-1.02 ms after a single electrical stimulus at 8 degrees C. Tension began to drop at 6 ms (latency relaxation), reached a minimum at 8 ms, and then twitch tension developed. The intensity of the meridional ref...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74925-X
更新日期:2003-02-01 00:00:00
abstract::Coupled folding-binding is central to the function of many intrinsically disordered proteins, yet not fully understood. With a continuous three-letter protein model, we explore the free-energy landscape of pairs of interacting sequences and how it is impacted by 1), variations in the binding mechanism; and 2), the add...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.12.008
更新日期:2012-02-08 00:00:00