Abstract:
:The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic acid 1:2 mixture in atomic detail. The simulations were performed at 350-370 K and mimicked the temperature- and pH-induced fusion of DPPC/palmitic acid vesicles from experiments by others. To make the calculations computationally feasible, a vesicle simulated at periodic boundary conditions was fused with its periodic image. Starting from a preformed stalk between the outer leaflets of the vesicle and its periodic image, a hemifused state formed within 2 ns. In one out of six simulations, a transient pore formed close to the stalk, resulting in the mixing of DPPC lipids between the outer and the inner leaflet. The hemifused state was (meta)stable on a timescale of up to 11 ns. Forcing a single lipid into the interior of the hemifusion diaphragm induced the formation and expansion of a fusion pore on a nanosecond timescale. This work opens the perspective to study a wide variety of mesoscopic biological processes in atomic detail.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Knecht V,Marrink SJdoi
10.1529/biophysj.106.103572subject
Has Abstractpub_date
2007-06-15 00:00:00pages
4254-61issue
12eissn
0006-3495issn
1542-0086pii
S0006-3495(07)71227-4journal_volume
92pub_type
杂志文章abstract::A novel system for measuring, simultaneously, ciliary beating and intracellular free calcium is presented. The advantages and dynamic nature of the system are demonstrated by measuring the effects of the calcium ionophore lonomycin and of extracellular ATP on ciliated rabbit trachea. The results are discussed with reg...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80492-8
更新日期:1994-07-01 00:00:00
abstract::The kinetics of force production in chemically skinned trabeculae from the guinea pig were studied by laser photolysis of caged ATP in the presence of Ca2+. Preincubation of the tissue during rigor with the enzyme apyrase was used to reduce the population of MgADP-bound cross-bridges (Martin and Barsotti, 1994). In un...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80676-9
更新日期:1994-11-01 00:00:00
abstract::We investigated the accessibility to protons and thiol-directed reagents of a cysteine substituted at position 338 in transmembrane segment 6 (TM6) of CFTR to test the hypothesis that T338 resides in the pore. Xenopus oocytes expressing T338C CFTR exhibited pH-dependent changes in gCl and I-V shape that were specific ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.050534
更新日期:2004-12-01 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::A kinetic model of the effect of agonist and anesthetics on ligand-gated ion channels, developed in earlier work, is further refined and used to predict traces observed in fast-perfusion electrophysiological studies on recombinant GABAA receptors under a wide range of agonist and/or anesthetic concentrations. The mode...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.12.052
更新日期:2015-03-10 00:00:00
abstract::A master equation theory is formulated to describe the dependence of the fluorescence yield (phi) in photosynthetic systems on the number of photons (Y) absorbed per photosynthetic unit (or domain). This theory is applied to the calculation of the dependence of the fluorescence yield on Y in (a) fluorescence induction...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(83)84278-7
更新日期:1983-10-01 00:00:00
abstract::Structures of truncated versions of the influenza A virus M2 proton channel have been determined recently by x-ray crystallography in the open conformation of the channel, and by NMR in the closed state. The structures differ in the position of the bound inhibitors. The x-ray structure shows a single amantadine molecu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.09.004
更新日期:2009-11-18 00:00:00
abstract::The temperature dependence of drug blockade of a calcium-dependent potassium channel K(Ca) has been studied in cultured CA1 hippocampal neurons. Channel openings from a 70-pS K+ channel were recorded when inside-out patches were exposed to a bath solution containing 140 mM K+ and 0.2 mM Ca2+. The mean open times of ch...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82161-0
更新日期:1991-11-01 00:00:00
abstract::Diacylglycerol kinase ε (DGKε) is a membrane-bound enzyme that catalyzes the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid (PA) in the phosphatidylinositol cycle. DGKε lacks a putative regulatory domain and has recently been reported to be regulated by highly curved membranes. To further st...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.09.008
更新日期:2020-02-25 00:00:00
abstract::Unlike most transmembrane proteins, phospholipids can migrate from one leaflet of the membrane to the other. Because this spontaneous lipid translocation (flip-flop) tends to be very slow, cells facilitate the process with enzymes that catalyze the transmembrane movement and thereby regulate the transbilayer lipid dis...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.01.016
更新日期:2019-03-05 00:00:00
abstract::The mathematics of the binomial model for quantal neurotransmitter release is considered in general terms, to explore what information might be extractable from statistical aspects of data. For an array of N statistically independent release sites, each with a release probability p, the compound binomial always pertai...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(97)78709-5
更新日期:1997-02-01 00:00:00
abstract::Mitochondria often reside in subcellular regions with high metabolic demands. We examined the mechanisms that can govern the relocation of mitochondria to these sites in respiratory neurons. Mitochondria were visualized using tetramethylrhodamineethylester, and their movements were analyzed by applying single-particle...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.092981
更新日期:2007-04-15 00:00:00
abstract::In this work, we present experimental data, supported by a quantitative model, on the generation and effect of potential gradients across a tethered bilayer lipid membrane (tBLM) with, to the best of our knowledge, novel architecture. A challenge to generating potential gradients across tBLMs arises from the tethering...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.11.1121
更新日期:2014-01-07 00:00:00
abstract::Results are presented of nonphotochemical-hole-burning experiments on the mitochondrial specific dye rhodamine 800 incubated with two human ovarian surface epithelial cell lines: OSE(tsT)-14 normal cells and OV167 carcinoma cells. This dye is selective for the plasma and inner membranes of the mitochondria, as shown b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74945-5
更新日期:2003-02-01 00:00:00
abstract::The electrical membrane potential (Vm) is one of the components of the electrochemical potential of protons across the biological membrane (proton motive force), which powers many vital cellular processes. Because Vm also plays a role in signal transduction, measuring it is of great interest. Over the years, a variety...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.10.030
更新日期:2020-01-07 00:00:00
abstract::We measured isotonic sliding distance of single skinned fibers from rabbit psoas muscle when known and limited amounts of ATP were made available to the contractile apparatus. The fibers were immersed in paraffin oil at 20 degrees C, and laser pulse photolysis of caged ATP within the fiber initiated the contraction. T...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80020-2
更新日期:1995-10-01 00:00:00
abstract::An algorithm needed for computer simulation of immunodiffusion has been deduced from existing theories of the in vitro reaction between antibody and antigen. The "Goldberg most probable polymer distribution" theory provides a formula that gives the amount of free antibody, free antigen, and diffusible complexes from e...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(73)85996-X
更新日期:1973-05-01 00:00:00
abstract::Von Willebrand factor (VWF) is a multimeric plasma glycoprotein involved in both hemostasis and thrombosis. VWF conformational changes, especially unfolding of the A2 domain, may be required for efficient enzymatic cleavage in vivo. It has been shown that a single A2 domain unfolds at most probable unfolding forces of...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.12.4324
更新日期:2010-04-21 00:00:00
abstract::Whether proteins or lipids are the primary target sites for general anesthetic action has engendered considerable debate. Recent in vivo studies have shown that the S(+) and R(-) enantiomers of isoflurane are not equipotent, implying involvement of proteins. Bovine serum albumin (BSA), a soluble protein devoid of lipi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79599-1
更新日期:1996-01-01 00:00:00
abstract::Aquaporin (AQP) functions as a water-conducting pore. Mercury inhibits the water permeation through AQP. Although site-directed mutagenesis has shown that mercury binds to Cys189 during the inhibition process, it is not fully understood how this inhibits the water permeation through AQP1. We carried out 40 ns molecula...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.12.4310
更新日期:2010-04-21 00:00:00
abstract::In a relaxed muscle fiber at low ionic strength, the cross-bridges may well be in states comparable to the one that precedes the cross-bridge power stroke (Schoenberg, M. 1988. Adv. Exp. Med. Biol. 226:189-202). Using electron paramagnetic resonance (EPR) and (saturation transfer) electron paramagnetic resonance (ST-E...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82093-8
更新日期:1991-09-01 00:00:00
abstract::Deuterium and phosphorus nuclear magnetic resonance (NMR) has been used to investigate the dynamics of slow motional processes induced in bilayer cardiolipin upon binding with cytochrome c. 31P NMR line shapes suggest that protein binding induces less restricted, isotropic-like motions in the lipid phosphates within t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81048-8
更新日期:1993-07-01 00:00:00
abstract::In this work we have designed a simple system to investigate empirically the image contrast of tapping-mode atomic force microscopy (TMAFM). We modified the cantilever tips with protein molecules (bovine serum albumin or goat anti-biotin antibody) and used these protein-modified cantilevers to scan poly-L-lysine films...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78354-1
更新日期:1997-12-01 00:00:00
abstract::Using a method they developed, Stamatoff and Krimm (1976) have phased swelling data from nerve myelin. Although most phases agree with those I determined previously, there are a few differences. In this letter the two different phasings, theirs and my own, are used to compute the corresponding electron-density profile...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(79)85242-X
更新日期:1979-04-01 00:00:00
abstract::Tagging of individual proteins with genetically encoded fluorescent proteins (FPs) has been used extensively to study localization and interactions in live cells. Recent developments in single-molecule localization microscopy have enabled the dynamic visualization of individual tagged proteins inside living cells. How...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.05.047
更新日期:2016-07-12 00:00:00
abstract::Cyclic 3'5' adenosine monophosphate (cAMP)-dependent-protein kinase (PKA) signaling is a fundamental regulatory pathway for mediating cellular responses to hormonal stimuli. The pathway is activated by high-affinity association of cAMP with the regulatory subunit of PKA and signal termination is achieved upon cAMP dis...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.07.050
更新日期:2014-09-16 00:00:00
abstract::The dynamics of protein distribution in endocytic membranes are relevant for many cellular processes, such as protein sorting, organelle and membrane microdomain biogenesis, protein-protein interactions, receptor function, and signal transduction. We have developed an assay based on Fluorescence Resonance Energy Micro...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74500-7
更新日期:2003-07-01 00:00:00
abstract::Understanding the fundamentals of genome packaging in viral capsids is important for finding effective antiviral strategies and for utilizing benign viral particles for gene therapy. While the structure of encapsidated genomic materials has been routinely characterized with experimental techniques such as cryo-electro...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.08.021
更新日期:2015-10-20 00:00:00
abstract::The relationship between calcium current and transmitter release was studied in squid giant synapse. It was found that the voltage-dependent calcium current triggers the release of synaptic transmitter in direct proportion to its magnitude and duration. Transmitter release occurs with a delay of approximately 200 mus ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(81)84899-0
更新日期:1981-03-01 00:00:00
abstract::Using homonuclear (1)H NOESY spectra, with chemical shifts, (3)JH(N)H(α) scalar couplings, residual dipolar couplings, and (1)H-(15)N NOEs, we have optimized and validated the conformational ensembles of the amyloid-β 1-40 (Aβ40) and amyloid-β 1-42 (Aβ42) peptides generated by molecular dynamics simulations. We find t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.04.056
更新日期:2013-06-18 00:00:00