Abstract:
:A model alpha-helical peptide encapsulated in a reverse micelle is used to study the structure and dynamics of proteins under constrained environments that mimic the membrane-water environment in cells. Molecular dynamics simulations of the self assembly of systems composed of a peptide, sodium bis(2-ethylhexyl) sulfosuccinate (AOT), water, and isooctane show that the peptide prefers to be located at the water/AOT headgroups interface. We explore the effect of the AOT headgroup charge and the peptide charge and find that the peptides migrate to the interface in all cases. These results show that the peptides prefer the constrained hydration environment of the AOT headgroups. The driving force for this configuration is the gain in entropy by released water molecules that otherwise would solvate the protein and surfactant headgroups.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Tian J,Garcia AEdoi
10.1016/j.bpj.2009.03.014subject
Has Abstractpub_date
2009-05-20 00:00:00pages
L57-9issue
10eissn
0006-3495issn
1542-0086pii
S0006-3495(09)00750-4journal_volume
96pub_type
信件abstract::The classical cable equation, in which membrane conductance is considered constant, is modified by including the linearized effect of membrane potential on sodium and potassium ionic currents, as formulated in the Hodgkin-Huxley equations for the squid giant axon. The resulting partial differential equation is solved ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(69)86446-5
更新日期:1969-10-01 00:00:00
abstract::Five highly homologous epidermal growth factor receptor ligands were studied by mass spectral analysis, hydrogen/deuterium (H/D) exchange via attenuated total reflectance Fourier transform-infrared spectroscopy, and two-dimensional correlation analysis. These studies were performed to determine the order of events dur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.125856
更新日期:2008-05-15 00:00:00
abstract::We have established a quantum mechanics (QM)/molecular mechanics (MM) hybrid method for calculating the Raman spectra of protein-bound cofactors using the alpha-subunit of C-phycocyanin containing a phycocyanobilin (PCB) chromophore as a test case. The PCB cofactor was described with density functional theory, whereas...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.108878
更新日期:2007-09-15 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::Neuronal synapses are highly specialized structures for communication between nerve cells. Knowledge about their molecular organization and dynamics is still incomplete. The large multidomain protein Bassoon plays a major role in scaffolding and organizing the cytomatrix at the active zone of neurotransmitter release ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.111674
更新日期:2008-02-15 00:00:00
abstract::Shock waves are used clinically for breaking kidney stones and treating musculoskeletal indications. The mechanisms by which shock waves interact with tissue are still not well understood. Here, ultra-high-speed imaging was used to visualize the deformation of individual cells embedded in a tissue-mimicking phantom wh...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.09.042
更新日期:2018-03-27 00:00:00
abstract::Many membrane-bound molecules in cells form small clusters. It has been hypothesized that these clusters convert an analog extracellular signal into a digital intracellular signal and that this conversion increases signaling fidelity. However, the mechanism by which clusters digitize a signal and the subsequent effect...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.02.031
更新日期:2016-04-12 00:00:00
abstract::A new method of fluorescence microscopy for cell imaging has been developed that takes advantage of the spatial variations of fluorescence lifetimes in single cells as a source of image contrast, and thus it is named "fluorescence lifetime imaging microscopy (flimscopy)". Since time-resolved fluorescence measurements ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81427-9
更新日期:1993-03-01 00:00:00
abstract::The ryanodine receptor (RyR) of skeletal muscle contains two functional domains: a carboxyl-terminal hydrophobic domain that forms the putative conduction pore of the calcium release channel, and a large cytoplasmic domain that corresponds to the "foot structure." To understand the contribution of the foot structure t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78165-7
更新日期:1997-09-01 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::Nanopatterned surfaces are believed to kill bacteria through physical deformation, a mechanism that has immense potential against biochemical resistance. Because of its elusive nature, this mechanism is mostly understood through biophysical modeling. Problematically, accurate descriptions of the contact mechanics and ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.12.003
更新日期:2021-01-19 00:00:00
abstract::The freshwater polyp Hydra can regenerate from tissue fragments or random cell aggregates. We show that the axis-defining step ("symmetry breaking") of regeneration requires mechanical inflation-collapse oscillations of the initial cell ball. We present experimental evidence that axis definition is retarded if these o...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.09.062
更新日期:2009-02-18 00:00:00
abstract::More than 30 years ago, Nozaki and Tanford reported that the pK values for several amino acids and simple substances in 6 M guanidinium chloride differed little from the corresponding values in low salt (Nozaki, Y., and C. Tanford. 1967. J. Am. Chem. Soc. 89:736-742). This puzzling and counter-intuitive result hinders...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75980-2
更新日期:2001-12-01 00:00:00
abstract::Missense mutations in the membrane-binding actin-based motor protein, myosin-1a (Myo1a), have recently been linked to sensorineural deafness in humans. One of these mutations, E385D, impacts a residue in the switch II region of the motor domain that is present in virtually all members of the myosin superfamily. We sou...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1529/biophysj.107.122689
更新日期:2008-01-15 00:00:00
abstract::Normal coordinate analyses and vibrational assignments are presented for the dimethyl phosphate anion [(CH3O)2PO2-] and its deuteriomethyl [(CD3O)2PO2-] and carbon-13 [(13CH3O)2PO2-] derivatives in the gauche-gauche conformation. The dimethyl phosphate anion, which is the simplest model for the nucleic acid phosphodie...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80767-2
更新日期:1994-01-01 00:00:00
abstract::Proteins that cross-link actin filaments can either form bundles of parallel filaments or isotropic networks of individual filaments. We have found that mixtures of actin filaments with alpha-actinin purified from either Acanthamoeba castellanii or chicken smooth muscle can form bundles or isotropic networks depending...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81059-2
更新日期:1993-07-01 00:00:00
abstract::We have applied two-dimensional infrared (2D IR) and betanu correlation spectroscopy to in-situ IR spectroscopy of pulmonary surfactant proteins SP-B and SP-C in lipid-protein monolayers at the air-water interface. For both SP-B and SP-C, a statistical windowed autocorrelation method identified two separate surface pr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(02)73973-8
更新日期:2002-10-01 00:00:00
abstract::We present here an efficient and accurate procedure for modeling of the three-dimensional structures of polypeptides in the explicit solvent water based on molecular dynamics calculations. Using the toxic domain analog of heat-stable enterotoxin as a model peptide, we examined the utilities of two molecular dynamics t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80975-0
更新日期:1994-06-01 00:00:00
abstract::The aquaglyceroporin GlpF is a transmembrane channel of Escherichia coli that facilitates the uptake of glycerol by the cell. Its high glycerol uptake rate is crucial for the cell to survive in very low glycerol concentrations. Although GlpF allows both influx and outflux of glycerol, its structure, similar to the str...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74718-3
更新日期:2003-11-01 00:00:00
abstract::In this study stereochemically pure d-erythro-sphingomyelins (SMs) with either 16:0 or 18:1(cisDelta9) as the N-linked acyl-chain were synthesized. Our purpose was to examine the properties of these sphingomyelins and acyl-chain matched racemic (d-erythro/l-threo) sphingomyelins in model membranes. Liquid-expanded d-e...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)76997-3
更新日期:1999-09-01 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::The GroE chaperonin system facilitates protein folding in an ATP-dependent manner. It has remained unclear why some proteins are obligate clients of the GroE system, whereas other closely related proteins are able to fold efficiently in its absence. Factors that cause folding to be slower affect kinetic partitioning b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.11.019
更新日期:2019-01-08 00:00:00
abstract::Fluorescent proteins are often used as reporters of transcriptional activity. Here we present a mathematical characterization of a novel fluorescent reporter that was recently engineered to have a short half-life (approximately 12 min). The advantage of this destabilized protein is that it can track the transient tran...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.122200
更新日期:2008-03-15 00:00:00
abstract::Intracellular transport of cargos along microtubules is often complicated by the topology of the underlying filament network. The fundamental building blocks for this complex arrangement are filament intersections. The navigation of cargos across microtubule intersections remains poorly understood. Here, we demonstrat...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.02.016
更新日期:2015-03-24 00:00:00
abstract::In response to external stimuli, cells modulate their adhesive state by regulating the number and intrinsic affinity of receptor/ligand bonds. A number of studies have shown that cell adhesion is dramatically reduced at room or lower temperatures as compared with physiological temperature. However, the underlying mech...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.06.037
更新日期:2010-09-08 00:00:00
abstract::We report that voltage-gated Na+ channels (Na(V)) from rat muscle (mu1) expressed in HEK293 cells exhibit anomalous rectification of whole-cell outward current under conditions of symmetrical Na+. This behavior gradually fades with time after membrane break-in, as if a diffusible blocking substance in the cytoplasm is...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76102-4
更新日期:2001-03-01 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::The sorting of lipids and proteins in cellular trafficking pathways is a process of central importance in maintaining compartmentalization in eukaryotic cells. However, the mechanisms behind these sorting phenomena are currently far from being understood. Among several mechanistic suggestions, membrane curvature has b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.11.067
更新日期:2009-04-08 00:00:00
abstract::We report on the application of two photon molecular excitation to fluorescence correlation spectroscopy. We demonstrate the first fluorescence correlation spectroscopy measurements of translational mobility in the cytoplasm of living cells. Two-photon excitation inherently excites small sample volumes in three dimens...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80230-4
更新日期:1995-02-01 00:00:00
abstract::Many proteins "bind" DNA through positively charged amino acids on their surfaces. However, to overcome significant energetic and topological obstacles, proteins that bend or package DNA might also modulate the stiffness that is generated by repulsions between phosphates within DNA. Much previous work describes how io...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.064667
更新日期:2005-10-01 00:00:00