Abstract:
:A 250 ps molecular dynamics simulation of the dimyristoylphosphatidylcholine (DMPC)-based lipid bilayer, including explicit water molecules, is reported. The solvent environment of the head groups and other structural properties of the bilayer have been analyzed and compared with experimental results as well as our previous simulation of the dilauroylphosphatidylethanolamine (DLPE)-based bilayer. From this comparison we find that the solvent structure around the DMPC head group (clathrate shell) is significantly different than that around the DLPE head group (typical hydrogen bonding interactions). We have modeled the probable relationship between the different solvent environments around the R-N(CH3)3+ (DMPC) and R-NH3+ (DLPE) head groups and the different interlammelar distances in these systems by performing potential of mean force (PMF) simulations on two N(CH3)4+ and NH4+ ions in water. From the PMF simulations it appears that the differences in the hydration of the DMPC and DLPE head groups is not responsible for the differences in the hydration force observed for these systems. We also find that the orientational polarization of DLPE and DMPC is similar, which suggests that solvent polarization is not responsible for the differences in the hydration repulsion behavior observed in these systems. We also examined the order parameters for DMPC and found them to be in reasonable agreement with experiment. Given the different characteristics of the DLPE and DMPC head groups, we suggest an explanation of the differences in the interlammellar spacings of bilayers composed of these like-charged lipids. From our DLPE simulations we find that the R-NH3+ head groups can interact with the nonesterified oxygens of the phosphate group in an intraleaflet or an interleaflet manner. For the latter a "cross link" between two leaflets can be formed, which causes a stabilization of the interlamellar spacings at fairly short distances. Moreover, due to the strong intraleaflet interaction we find that the DLPE interface is relatively "flat" (as opposed to DMPC-based bilayers), which results in a surface that has regions of positive and negative charge that reside in the same plane along the bilayer normal. Based on this we propose that the DLPE bilayer interface can correlate itself with another DLPE interface by alignment of the regions of positive (or negative) charge on one leaflet with the opposite charges on the opposing leaflet.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Damodaran KV,Merz KM Jrdoi
10.1016/S0006-3495(94)80889-6subject
Has Abstractpub_date
1994-04-01 00:00:00pages
1076-87issue
4eissn
0006-3495issn
1542-0086pii
S0006-3495(94)80889-6journal_volume
66pub_type
杂志文章abstract::The actin cytoskeleton fulfills numerous key cellular functions, which are tightly regulated in activity, localization, and temporal patterning by actin binding proteins. Tropomyosins and gelsolin are two such filament-regulating proteins. Here, we investigate how the effects of tropomyosins are coupled to the binding...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.11.3812
更新日期:2018-02-27 00:00:00
abstract::Negatively charged phospholipids are an important component of biological membranes. The thermodynamic parameters governing self-assembly of anionic phospholipids are deduced here from isothermal titration calorimetry. Heats of demicellization were determined for dioctanoyl phosphatidylglycerol (PG) and phosphatidylse...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.01.049
更新日期:2012-03-07 00:00:00
abstract::Cartilage stiffness was measured ex vivo at the micrometer and nanometer scales to explore structure-mechanical property relationships at smaller scales than has been done previously. A method was developed to measure the dynamic elastic modulus, |E(*)|, in compression by indentation-type atomic force microscopy (IT A...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74375-1
更新日期:2004-05-01 00:00:00
abstract::The state of photosystem II core complex (PS II CC) in monolayer at the gas-water interface was investigated using in situ polarization-modulated infrared reflection absorption spectroscopy and x-ray reflectivity techniques. Two approaches for preparing and manipulating the monolayers were examined and compared. In th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77731-8
更新日期:1998-12-01 00:00:00
abstract::A recent theory for the long time dynamics of flexible chain molecules is applied for the first time to a peptide of biological importance, the neurotransmitter met-enkephalin. The dynamics of met-enkephalin is considerably more complicated than that of the previously studied glycine oligomers; met-enkephalin contains...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77185-7
更新日期:1999-01-01 00:00:00
abstract::Many aspects of chromatin biology are influenced by the nuclear compartment in which a locus resides, from transcriptional regulation to DNA repair. Further, the dynamic and variable localization of a particular locus across cell populations and over time makes analysis of a large number of cells critical. As a conseq...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.05.036
更新日期:2016-07-12 00:00:00
abstract::Biophysical understanding of membrane domains requires accurate knowledge of their structural details and elasticity. We report on a global small angle x-ray scattering data analysis technique for coexisting liquid-ordered (Lo) and liquid-disordered (Ld) domains in fully hydrated multilamellar vesicles. This enabled t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.11.3488
更新日期:2015-02-17 00:00:00
abstract::Myoplasmic free calcium transients were measured with antipyrylazo III in voltage clamped segments of frog skeletal muscle fibers and were used to calculate the rate of release (Rrel) of calcium from the sarcoplasmic reticulum. Intramembrane charge movement was measured for the same pulses in the same fibers. During a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(88)83050-9
更新日期:1988-12-01 00:00:00
abstract::The effects of the anionic tungsten carbonyl complex [W(CO)(5)SC(6)H(5)](-) and its fluorinated analog [W(CO)(5)SC(6)F(5)](-) on the electrical properties of the plasma membrane of mouse myeloma cells were studied by the single-cell electrorotation technique. At micromolar concentrations, both compounds gave rise to a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76400-9
更新日期:2000-09-01 00:00:00
abstract::We have measured the electronic circular dichroism (ECD) of the ferri- and ferro-states of several natural cytochrome c derivatives (horse heart, chicken, bovine, and yeast) and the Y67F mutant of yeast in the region between 300 and 750 nm. Thus, we recorded the ECD of the B- and Q-band region as well as the charge-tr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.095976
更新日期:2007-02-01 00:00:00
abstract::Enterococcus hirae V1-ATPase is a molecular motor composed of the A3B3 hexamer ring and the central stalk. In association with ATP hydrolysis, three catalytic AB pairs in the A3B3 ring undergo conformational changes, which lead to a 120° rotation of the central stalk. To understand how the conformational changes of th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.01.029
更新日期:2017-03-14 00:00:00
abstract::Effects of adducts of [PtCl(NH3)3]Cl or chlorodiethylenetriamineplatinum(II) on DNA stability were studied with emphasis on thermodynamic origins of that stability. Oligodeoxyribonucleotide duplexes (15-bp) containing the single, site-specific monofunctional adduct at G-residues of the central sequences TGT/ACA or 5'-...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.051771
更新日期:2005-02-01 00:00:00
abstract::A growth cone is a motile structure at the tips of axons that is driven by the actin network and guides axon extension. Low actin adhesion to the substrate creates a stationary actin treadmill that allows leading-edge protrusion when adhesion increases in response to guidance cues. We use experimental measurements in ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.03.003
更新日期:2012-04-04 00:00:00
abstract::Prion diseases are infectious fatal neurodegenerative diseases including Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy in cattle. The misfolding and conversion of cellular PrP in such mammals into pathogenic PrP is believed to be the key procedure. Rabbits are among the few mammalian species...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.08.018
更新日期:2011-09-21 00:00:00
abstract::The enzyme F1-adenosine triphosphatase (ATPase) is a molecular motor that converts the chemical energy stored in the molecule adenosine triphosphate (ATP) into mechanical rotation of its gamma-subunit. During steady-state catalysis, the three catalytic sites of F1 operate in a cooperative fashion such that at every in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.046128
更新日期:2004-11-01 00:00:00
abstract::Communication-deficient cells (the SKHep1 cell line) were stably transfected with a plasmid containing cDNA which encodes the major gap junction protein of rat liver, connexin32. Application of the dual whole-cell voltage clamp technique with patch electrodes to pairs of transfected SKHep1 cells revealed strong sensit...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82160-9
更新日期:1991-11-01 00:00:00
abstract::Embryo and oocyte cryopreservation is a widely used technology for cryopreservation of genetic resources. One limitation of cryopreservation is the low tolerance to freezing observed for oocytes and embryos rich in lipid droplets. We apply Raman spectroscopy to investigate freezing of lipid droplets inside cumulus-ooc...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.06.019
更新日期:2018-08-07 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::Clostridium difficile (C. diff) is one of the most common and most severe hospital-acquired infections; its consequences range from lengthened hospital stay to outright lethality. C. diff causes cellular damage through the action of two large toxins TcdA and TcdB. Recently, there has been increased effort toward devel...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.05.031
更新日期:2013-07-16 00:00:00
abstract::The viral genome and replicative enzymes of the human immunodeficiency virus are encased in a shell consisting of assembled mature capsid protein (CA). The core shell is a stable, effective protective barrier, but is also poised for dissolution on cue to allow transmission of the viral genome into its new host. In thi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75725-6
更新日期:2001-07-01 00:00:00
abstract::As sketched in Fig. 1, a current molecular dynamics computer simulation of a lipid bilayer fails to capture significant features of the macroscopic system, including long wavelength undulations. Such fluctuations are intrinsically connected to the value of the macroscopic (or thermodynamic) surface tension (cf. Eqs. 1...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79337-2
更新日期:1996-09-01 00:00:00
abstract::A study on clonal growth in Chinese hamster ovary (CHO) cells was conducted after exposure to optical trapping wavelengths using Nd:YAG (1064 nm) and tunable titanium-sapphire (700-990 nm) laser microbeam optical traps. The nuclei of cells were exposed to optical trapping forces at various wavelengths, power densities...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79716-3
更新日期:1996-03-01 00:00:00
abstract::RNA functions are often kinetically controlled. The folding kinetics of RNAs involves global structural changes and local nucleotide movement, such as base flipping. The most elementary step in RNA folding is the closing and opening of a basepair. By integrating molecular dynamics simulation, master equation, and kine...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.09.017
更新日期:2019-11-05 00:00:00
abstract::The energy transfer processes between carotenoids and Chls have been studied by femtosecond transient absorption in the CP29-WT complex, which contains only two carotenoids per polypeptide located in the L1 and L2 sites, and in the CP29-E166V mutant in which only the L1 site is occupied. The comparison of these two sa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)75057-7
更新日期:2003-04-01 00:00:00
abstract::An innovative method is presented to measure the mechanical driving point impedance of biological structures up to at least 40 kHz. The technique employs an atomic force cantilever with a ferromagnetic coating and an external magnetic field to apply a calibrated force to the cantilever. Measurement of the resulting ca...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.103.037184
更新日期:2004-08-01 00:00:00
abstract::In the studies of force-induced conformational transitions of biomolecules, the large timescale difference from experiments presents the challenge of obtaining convergent sampling for molecular dynamics simulations. To circumvent this fundamental problem, an approach combining the replica-exchange method and umbrella ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.11.004
更新日期:2010-02-17 00:00:00
abstract::Cell spreading is involved in many physiological and pathological processes. The spreading behavior of a cell significantly depends on its microenvironment, but the biochemomechanical mechanisms of geometry-confined cell spreading remain unclear. A dynamic model is here established to investigate the spreading of cell...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.04.044
更新日期:2017-06-06 00:00:00
abstract::Ion channels assist and control the diffusion of ions through biological membranes. The conduction process depends on the structural characteristics of these nanopores, among which are the hydrophobicity and the afforded diameter of the conduction pathway. In this contribution, we use full atomistic free-energy molecu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.087437
更新日期:2006-08-01 00:00:00
abstract::Apparent diffusion coefficient (ADC) measurement in the lung using gas magnetic resonance imaging is a promising technique with potential for reflecting changes in lung microstructure. Despite some recent impressive human applications, full interpretation of ADC measures remains an elusive goal, due to a lack of detai...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.04.050
更新日期:2009-07-22 00:00:00
abstract::We investigate the permeability of lipid membranes for fluorescence dyes and ions. We find that permeability reaches a maximum close to the chain melting transition of the membranes. Close to transitions, fluctuations in area and compressibility are high, leading to an increased likelihood of spontaneous lipid pore fo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.01.062
更新日期:2009-06-03 00:00:00