Article

Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl.

Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
Biophysical Journal (impact factor: 3.65). 04/2004; 86(3):1601-9. DOI:10.1016/S0006-3495(04)74227-7 pp.1601-9
Source: PubMed

ABSTRACT Two 40 ns molecular dynamics simulations of a palmitoyl-oleoyl phosphatidylserine (POPS) lipid bilayer in the liquid crystalline phase with Na(+) counterions and NaCl were carried out to investigate the structure of the negatively charged lipid bilayer and the effect of salt (NaCl) on the lipid bilayer structure. Na(+) ions were found to penetrate deep into the ester region of the water/lipid interface of the bilayer. Interaction of the Na(+) ions with the lipid bilayer is accompanied by a loss of water molecules around the ion and a simultaneous increase in the number of ester carbonyl oxygen atoms binding the ion, which define an octahedral and square pyramidal geometry. The amine group of the lipid molecule is involved in the formation of inter- and intramolecular hydrogen bonds with the carboxylate and the phosphodiester groups of the lipid molecule. The area per lipid of the POPS bilayer is unaffected by the presence of 0.15M NaCl. There is a small increase in the order parameter of carbon atoms in the beginning of the alkyl chain in the presence of NaCl. This is due to a greater number of Na(+) ions being coordinated by the ester carbonyl oxygen atoms in the water/lipid interface region of the POPS bilayer.

0 0
 · 
0 Bookmarks
 · 
23 Views
  • Source
    Article: Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel.
    David L Bostick, Charles L Brooks
    [show abstract] [hide abstract]
    ABSTRACT: The AmtB channel passively allows the transport of NH4(+) across the membranes of bacteria via a "gas" NH3 intermediate and is related by homology (sequentially, structurally, and functionally) to many forms of Rh protein (both erythroid and nonerythroid) found in animals and humans. New structural information on this channel has inspired computational studies aimed at clarifying various aspects of NH4(+) recruitment and binding in the periplasm, as well as its deprotonation. However, precise mechanisms for these events are still unknown, and, so far, explanations for subsequent NH3 translocation and reprotonation at the cytoplasmic end of the channel have not been rigorously addressed. We employ molecular dynamics simulations and free energy methods on a full AmtB trimer system in membrane and bathed in electrolyte. Combining the potential of mean force for NH4(+)/NH3 translocation with data from thermodynamic integration calculations allows us to find the apparent pKa of NH4(+) as a function of the transport axis. Our calculations reveal the specific sites at which its deprotonation (at the periplasmic end) and reprotonation (at the cytoplasmic end) occurs. Contrary to most hypotheses, which ascribe a proton-accepting role to various periplasmic or luminal residues of the channel, our results suggest that the most plausible proton donor/acceptor at either of these sites is water. Free-energetic analysis not only verifies crystallographically determined binding sites for NH4(+) and NH3 along the transport axis, but also reveals a previously undetermined binding site for NH4(+) at the cytoplasmic end of the channel. Analysis of dynamics and the free energies of all possible loading states for NH3 inside the channel also reveal that hydrophobic pressure and the free-energetic profile provided by the pore lumen drives this species toward the cytoplasm for protonation just before reaching the newly discovered site.
    PLoS Computational Biology 03/2007; 3(2):e22. · 5.22 Impact Factor
  • Source
    Article: Understanding the molecular conformations of Na-dimyristoylphosphatidylglycerol (DMPG) using DFT-based method
    D. Mishra, S. Krishnamurty, S. Pal
    Molecular Simulation 09/2011; 37(11):953. · 1.33 Impact Factor
  • Source
    Article: Thermodynamics of monolayers formed by mixtures of phosphatidylcholine/phosphatidylserine.
    Carlos Luna, Kimberly M Stroka, Harry Bermudez, Helim Aranda-Espinoza
    [show abstract] [hide abstract]
    ABSTRACT: In this work we obtain the thermodynamic properties of mixed (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) PC and (1-stearoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (sodium salt)) PS monolayers. Measurements of compressibility (isotherms, bulk modulus, and excess area per molecule) and surface potential show that the properties of monolayers at the air-water interface depend on the concentration of ions (Na(+) and K(+)) and the proportion of PS in the mixture. The dependence on PS arises because the molecule is originally bound to a Na(+) counterion; by increasing the concentration of ions the entropy changes, creating a favorable system for the bound counterions of PS to join the bulk, leaving a negatively charged molecule. This change leads to an increase in electrostatic repulsions which is reflected by the increase in area per molecule versus surface pressure and a higher surface potential. The results lead to the conclusion that this mixture of phospholipids follows a non ideal behavior and can help to understand the thermodynamic behavior of membranes made of binary mixtures of a zwitterionic and an anionic phospholipid with a bound counterion.
    Colloids and surfaces. B, Biointerfaces 03/2011; 85(2):293-300. · 2.60 Impact Factor

Show more

Data provided are for informational purposes only. Although carefully collected, accuracy cannot be guaranteed. The impact factor represents a rough estimation of the journal's impact factor and does not reflect the actual current impact factor. Publisher conditions are provided by RoMEO. Differing provisions from the publisher's actual policy or licence agreement may be applicable.

Keywords

amine group
 
carbon atoms
 
ester carbonyl oxygen atoms
 
ester carbonyl oxygen atoms binding
 
ester region
 
greater number
 
intramolecular hydrogen bonds
 
lipid bilayer
 
lipid bilayer structure
 
lipid molecule
 
liquid crystalline phase
 
negatively charged lipid bilayer
 
order parameter
 
palmitoyl-oleoyl phosphatidylserine
 
phosphodiester groups
 
small increase
 
square pyramidal geometry
 
water molecules
 
water/lipid interface
 
water/lipid interface region