Molecular dynamics phospholipids

M2irrink et al., 1998] Marrink, S.-J., Berger, O., Tieleman, R, and Jahnig, F. Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics dimulations. Biophys. J. 74 (1998) 931-943... 

Stepaniants et al., 1997] Stepaniants, S., Izrailev, S., and Schulten, K. Extraction of lipids from phospholipid membranes by steered molecular dynamics. J. Mol. Model. 3 (1997) 473-475... 

This chapter has given an overview of the structure and dynamics of lipid and water molecules in membrane systems, viewed with atomic resolution by molecular dynamics simulations of fully hydrated phospholipid bilayers. The calculations have permitted a detailed picture of the solvation of the lipid polar groups to be developed, and this picture has been used to elucidate the molecular origins of the dipole potential. The solvation structure has been discussed in terms of a somewhat arbitrary, but useful, definition of bound and bulk water molecules. 

B Roux, TB Woolf. Molecular dynamics of Pfl coat protein in a phospholipid bilayer. In KM Merz Ir, B Roux, eds. Biological Membranes A Molecular Perspective from Computation and Experiment. Boston Birkhauser, 1996, pp 555-587. 

Zahn, D. and Brickmann, R. (2002). Molecular dynamics study of water pores in a phospholipid bilayer, Chem. Phys. Lett., 352, 441-446. 

Membrane-Interaction (MI)-QSAR approach developed by Iyer et al. was used to develop predictive models of some organic compounds through BBB, and to simulate the interaction of a solute with the phospholipide-rich regions of cellular membranes surrounded by a layer of water. Molecular dynamics simulations were used to determine the explicit interaction of each test compound with the DMPC-water model (a model of dimyristoylphosphatidylcholine membrane monolayer, constructed using the software Material Studio according to the work done by van der Ploeg and Berendsen). Six MI-QSAR equations were constructed (Eqs. 74-79) ... 

Hofsass, C., Lindahl, E., Edholm, O. Molecular dynamics simulations of phospholipid bilayers with cholesterol. Biophys. J. 2003, 84, 2192-206. 

In the study of the dynamic properties of phospholipids, two main levels of detail are used mean field and all-atom representation of the system. Likewise, there are two main simulation techniques Monte Carlo (MC) and molecular dynamics (MD) simulations. 

In an attempt to find a better way of considering the interfacial region, molecular dynamics simulations of different helices were performed in phospholipid environ-... 

We enhanced the model by addition of phospholipids and performed molecular dynamics in periodic box. Three types of phospholipids were used with... 

The whole system was soaked in water, counterions were added and molecular dynamics was conducted in periodic box. The final model of rhodopsin oligomer is shown on Figure 11-3. Phospholipids flow on the left and right side of the central double row in channels two phospholipids wide. Thinner channels one phospholipid wide, hidden below the extended cytoplasmic loops of TMH-V and TMH-VI, flow perpendicularly to the wider channels. 

Smondyrev, A.M., Berkowit, M.L. 2001. Effects of oxygenated sterol on phospholipids bilayer properties a molecular dynamics simulation. Chem. Phys. Lipids 112, 31-39. 

Lai, C. S., Joseph, J., and Shih, C. C. (1989), Molecular dynamics of antitumor ether-linked phospholipids in model membranes A spin-label study,Biochem. Biophys. Res. Commun., 160,1189-1195. 

Griac, P., and Henry, S.A., 1996, Phosphatidylcholine biosynthesis in Saccharomyces cerevisiae Effects on regulation of phospholipid synthesis and respiratory competence. In Op den Kamp, J.A.F. (ed.), NATO ASI Series Molecular Dynamics of Biological Membranes. Springer, Verlag, pp. 339-346. 

The exact dimensions of a phospholipid bilayer membrane in terms of the in-plane area and the height of the lipid molecules as well as the thickness of the water layer that is associated with them is dependent on the chemical identity of the phospholipid head group, the length and the degree of saturation of the acyl chains, and the degree of hydration. This information may be obtained from a combination of small-angle X-ray diffraction by MLV or oriented multi-bilayer samples of phospholipids in excess water, electron and/or neutron density profiles across lipid bilayers, and atomic level molecular dynamics simulations of hydrated lipid bilayers. H-NMR studies on selectively deuter-ated phospholipids have also been important in elucidating acyl... 

FIGURE 14.2 Molecular dynamics simulation of the diffusion of benzene within a hydrated lipid bilayer membrane. Benzene molecules are shown as Corey-Pauling-Koltun (CPK) models atoms in the phospholipid head groups are shown as ball and stick models and hydrocarbon chains and water molecules as dark and light stick models, respectively. (Reproduced with permission from Bassolino-Klinaas D, Alper HE, Stouch TR. Biochemistry 1993 32 12624-37.)... 

Molecular dynamics is one of the most powerful computational methods for investigating the behavior of assemblies of atoms or molecules. One of the advantages of this technique is that it permits the determination, both as a function of time and as an average, of properties that cannot be measured experimentally. Molecular dynamics has been applied successfully to such systems as neat water [1-5], proteins in vacuum [6] and in solution [7,8], nucleic acids [9], phospholipid membranes [10-13], polymers [14], and metals [15]. 

Smondyrev, A.M. and Voth, G.A. (2002). Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane. Biophys. J. 82, 1460-1468... 

Masetti M, Cavalli A, Recanatini M (2008) Modeling the hERG potassium channel in a phospholipid bilayer molecular dynamics and drug docking studies. J Comput Chem 29(5) 795-808... 

Although the first section of this chapter was concerned with structural and dynamic information on monolayers of lipopolymers, before investigating lipopolymer-phospholipid mixtures, it is reasonable to consider the structural information that exists concerning pure phospholipid monolayers at the air-water interface. Film balance experiments, X-ray and neutron reflectometry, and molecular dynamics simulations have provided insight into the structural properties of these biologically... 

A FIGURE 5-7 Gel and fluid forms of the phospholipid bilayer. (Top) Depiction of gel-to-fluid transition. Phospholipids with long saturated fatty acyl chains tend to assemble into a highly ordered, gel-like bilayer in which there is little overlap of the nonpolar tails in the two leaflets. Heat disorders the nonpolar tails and induces a transition from a gel to a fluid within a temperature range of only a few degrees. As the chains become disordered, the bilayer also decreases in thickness. Bottom) Molecular models of phospholipid monolayers in gel and fluid states, as determined by molecular dynamics calculations. 

Recently, a molecular dynamics study of the phospholipid DLPE was reported by Damodaran et al. using a united atom model. The model was built from the crystal structure of DLPE reported by Elder et al. The fully hydrated DLPE bilayer has an interlamellar water layer of 5 A. The bilayer was solvated by 553 SPCE waters ( 11 water molecules/lipid) in the head group region. This lipid has a gel-to-liquid-crystalline transition temperature of... 

Field Stochastic Boundary Molecular Dynamics Simulation of a Phospholipid in a Membrane. 

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