Abstract:
:Molecular dynamics simulations of the tripeptide Ala-Phe-Ala-O-tert-butyl interacting with dimyristoylphosphatidylcholine lipid bilayers have been carried out. The lipid and aqueous environments of the peptide, the alkyl chain order, and the lipid and peptide dynamics have been investigated with use of density profiles, radial distribution functions, alkyl chain order parameter profiles, and time correlation functions. It appears that the alkyl chain region accommodates the peptides in the bilayer with minimal perturbation to this region. The peptide dynamics in the bilayer bound form has been compared with that of the free peptide in water. The peptide structure does not vary on the simulation time scale (of the order of hundreds of picoseconds) compared with the solution structure in which a random structure is observed.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Damodaran KV,Merz KM Jr,Gaber BPdoi
10.1016/S0006-3495(95)79997-0subject
Has Abstractpub_date
1995-10-01 00:00:00pages
1299-308issue
4eissn
0006-3495issn
1542-0086pii
S0006-3495(95)79997-0journal_volume
69pub_type
杂志文章abstract::Measurements were made of exchange rates of oxygen, carbon dioxide, and krypton-85 with blood at 37.5 degrees C. Gas transfer took place across a 1 mil silicone rubber membrane. The blood was in a rotating disk boundary layer flow, and the controlling resistance to transfer was the concentration boundary layer. Measur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(67)86624-4
更新日期:1967-11-01 00:00:00
abstract::A newly developed water-soluble phosphor suitable for measuring oxygen pressure in the blood (Green 2W) was used for noninvasive, in vivo imaging of oxygen distribution in the vascular systems of mice. Oxygen quenches the phosphorescence of Green 2W, measured in the presence of 2% albumin, according to the Stern-volme...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79764-3
更新日期:1996-04-01 00:00:00
abstract::Information processing and decision-making is based upon logic operations, which in cellular networks has been well characterized at the level of transcription. In recent years, however, both experimentalists and theorists have begun to appreciate that cellular decision-making can also be performed at the level of a s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.07.040
更新日期:2012-09-05 00:00:00
abstract::Experimental approaches such as fiber diffraction and cryo-electron microscopy reconstruction have defined regulatory positions of tropomyosin on actin but have not, as yet, succeeded at determining key atomic-level contacts between these proteins or fully substantiated the dynamics of their interactions at a structur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.05.017
更新日期:2020-07-07 00:00:00
abstract::We report constraints on the supramolecular structure of amyloid fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (A beta(1-40)) obtained from solid-state nuclear magnetic resonance (NMR) measurements of intermolecular dipole-dipole couplings between (13)C labels at 11 carbon s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75244-2
更新日期:2002-08-01 00:00:00
abstract::To investigate the mechanisms by which vesicles of pulmonary surfactant adsorb to an air-liquid interface, we measured the effect of different phospholipids and of their concentration both in the subphase and at the interface on this process. Adsorbing vesicles contained the hydrophobic surfactant proteins mixed with ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76589-1
更新日期:2000-01-01 00:00:00
abstract::Two modes of behavior of single human red cells in a shear field have been described. It is known that in low viscosity media and at shear rates less than 20 s-1, the cells rotate with a periodically varying angular velocity, in accord with the theory of Jeffery (1922) for oblate spheroids. In media of viscosity great...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(86)83734-1
更新日期:1986-05-01 00:00:00
abstract::Fatty acid binding proteins play an important role in the transportation of fatty acids. Despite intensive studies, how fatty acids enter the protein cavity for binding is still controversial. Here, a gap-closed variant of human intestinal fatty acid binding protein was generated by mutagenesis, in which the gap is lo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.12.005
更新日期:2020-01-21 00:00:00
abstract::A model is presented for the steric interaction between a plasma membrane protein and the membrane cytoskeleton in the human erythrocyte. The cytoskeleton is treated as a network of polymer chains attached to a flat bilayer, and the membrane protein is a hemisphere of effective radius R(e) with center on the bilayer e...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)79909-X
更新日期:1995-08-01 00:00:00
abstract::A-DNA is a stable alternative right-handed double helix that is favored by certain sequences (e.g., (dG)n.(dC)n) or under low humidity conditions. Earlier A-DNA structures of several DNA oligonucleotides and RNA.DNA chimeras have revealed some conformational variation that may be the result of sequence-dependent effec...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)79929-5
更新日期:1995-08-01 00:00:00
abstract::A first principles model for calculating hydrogen bonding interactions, previously applied to water, is here applied to the more difficult problem of interactions between DNA bases. We first consider the energetics and geometry for the A-T and the G-C basepairs, comparing our results to other calculated results as wel...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)79980-5
更新日期:1995-09-01 00:00:00
abstract::Protein solubility in aqueous solutions depends in a complicated and not well understood way on pH, salt type, and salt concentration. Why for instance does the use of two different monovalent salts, potassium thiocyanate and potassium chloride, produce such different results? One important and previously neglected so...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74512-3
更新日期:2003-08-01 00:00:00
abstract::The type 2a sarco/endoplasmic reticulum (ER) Ca2+-ATPase (SERCA2a) plays a key role in intracellular Ca2+ regulation in the heart. We have previously shown evidence of stable homodimers of SERCA2a in heterologous cells and cardiomyocytes. However, the functional significance of the pump dimerization remains unclear. H...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.08.025
更新日期:2020-10-06 00:00:00
abstract::The use of one-dimensional electron density strip models in interpreting low-angle X-ray data from planar and concentric multilayered structures is described. Diffraction formulas for an n-strip model are given. Fourier transforms, normalization constants, and Patterson functions are derived for certain strip models. ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(69)86381-2
更新日期:1969-02-01 00:00:00
abstract::Tropomyosin (Tm) paracrystal formation induced by Mg2+ was studied by monitoring increases in light scattering. Paracrystals formed above a critical Tm concentration with lag phases in the time courses at pH 7.5 and 6.0, indicating that condensation polymerization processes are involved. The kinetic data at pH 7.5 rea...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(89)82655-4
更新日期:1989-07-01 00:00:00
abstract::The cellular response to external mechanical forces has important effects on numerous biological phenomena. The sequences of molecular events that underlie the observed changes in cellular properties have yet to be elucidated in detail. Here we have detected the responses of a cultured cell against locally applied cyc...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.12.3693
更新日期:2011-02-02 00:00:00
abstract::Dendritic shaft (Zd) and spine (Zsp) input impedances were computed numerically for sites on hippocampal neurons, using a segmental format of cable calculations. The Zsp values for a typical spine appended onto a dendritic shaft averaged less than 2% higher than the Zd values for the adjacent dendritic shaft. Spine sy...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84001-1
更新日期:1984-07-01 00:00:00
abstract::Electrorotation of fixed red blood cells has been investigated in the frequency range between 16 Hz and 30 MHz. The rotation was studied as a function of electrolyte conductivity and surface charge density. Between 16 Hz and 1 kHz, fixed red blood cells undergo cofield rotation. The maximum of cofield rotation occurs ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77918-4
更新日期:1998-04-01 00:00:00
abstract::Distinct lipid environments, including lipid rafts, are increasingly recognized as a crucial factor affecting membrane protein function in plasma membranes. Unfortunately, an understanding of their role in membrane protein activation and oligomerization has remained elusive due to the challenge of characterizing these...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.08.040
更新日期:2011-10-05 00:00:00
abstract::The vibrational spectroscopy and population dynamics of excited singlet (2(1)Ag), excited triplet (3B u), and the ground (1Ag) electronic states of carotenoids in chromatophores of Chromatium vinosum (mainly spirilloxanthin and rhodopin) and of the same carotenoids in benzene solutions are examined by picosecond time-...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82047-1
更新日期:1991-07-01 00:00:00
abstract::Ceramides have been implicated in the initiation of apoptosis by permeabilizing the mitochondrial outer membrane to small proteins, including cytochrome c. In addition, ceramides were shown to form large metastable channels in planar membranes and liposomes, indicating that these lipids permeabilize membranes directly...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.071977
更新日期:2006-04-01 00:00:00
abstract::We have studied the low-resolution solution conformation of a Holliday (or four-way) DNA junction by using small-angle x-ray scattering, sedimentation velocity, and computational modeling techniques. The scattering data were analyzed in two independent ways: firstly, by rigid-body modeling of the scattering data using...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(04)74355-6
更新日期:2004-05-01 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::We present a method for calculating the configurational-dependent diffusion coefficient of a globular protein as a function of the global folding process. Using a coarse-grained structure-based model, we determined the diffusion coefficient, in reaction coordinate space, as a function of the fraction of native contact...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.04.041
更新日期:2010-07-21 00:00:00
abstract::Electrically excitable channels were expressed in Chinese hamster ovary cells using a vaccinia virus vector system. In cells expressing rat brain IIA Na+ channels only, brief pulses (< 1 ms) of depolarizing current resulted in action potentials with a prolonged (0.5-3 s) depolarizing plateau; this plateau was caused b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81153-6
更新日期:1993-09-01 00:00:00
abstract::The engulfment function of macrophages relies on complex molecular interactions involving both lipids and proteins. In particular, the clearance of apoptotic bodies (efferocytosis) is enabled by externalization on the cell target of phosphatidylserine lipids, which activate receptors on macrophages, suggesting that (l...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.12.036
更新日期:2014-02-04 00:00:00
abstract::Hormones are released from neuroendocrine cells by passing through an exocytotic pore that forms after vesicle and plasma membrane fusion. An elegant way to study this process at the single-vesicle level is to use styryl dyes, which stain not only the membrane, but also the matrix of individual vesicles in some neuroe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.054098
更新日期:2005-04-01 00:00:00
abstract::Mislocalization and aggregation of the huntingtin protein are related to Huntington's disease. Its first exon-more specifically the first 17 amino acids (Htt17)-is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin's activity through posttranslational modifications and serv...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.02.001
更新日期:2015-03-10 00:00:00
abstract::Are protein nonpolar cavities filled with water molecules? Although many experimental and theoretical investigations have been done, particularly for the nonpolar cavity of IL-1 beta, the results are still conflicting. To study this problem from the thermodynamic point of view, we calculated hydration free energies of...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.01.029
更新日期:2010-06-16 00:00:00
abstract::Multiconformation membrane proteins are mechanosensitive (MS) if their conformations displace different bilayer areas. Might MS closed-closed transitions serve as tension buffers, that is, as membrane "spandex"? While bilayer expansion is effectively instantaneous, transitions of bilayer-embedded MS proteins are stoch...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.08.054
更新日期:2009-11-18 00:00:00