Molecular dynamics simulations of membranes

II. MOLECULAR DYNAMICS SIMULATIONS OF MEMBRANES A. System Size and Construction... 

Grossfield, A., Feller, S.E., Pitman, M.C. Convergence of molecular dynamics simulations of membrane proteins. Proteins Struct. Funct. Bioinformatics 2007, 67, 31 10. 

R104 A. R. Braun and J. N. Sachs, Extracting Experimental Measurables from Molecular Dynamics Simulations of Membranes , in Annual Reports in Computational Chemistry, ed. R. Wheeler, Elsevier B. V. 2011, Vol. 7, p. 125. 

Marrink, S.J., Berkowitz, M., and Berendsen, H.J.C. 1993. Molecular dynamic simulation of membrane/water interface The ordering of water and its relation to the hydration forces. Langmuir 9 3122-3131. 

Jorgensen, W.L. Rives, T. (1988). The OPLS Potential Functions For Proteins - Energy Minimizations For Crystals Of Cydic-Peptides And Crambin. Journal of the American Chemical Society, Vol.llO, No.6, pp. 1657-1666 Kandt, C., Ash, W. Tieleman, D.P. (July 2009). InflateGRO, Available from http // www.csb.bit.uni-bonn.de/inflategro.html Kandt, C., Ash, W.L. Tieleman, D.P. (2007). Setting up and running molecular dynamics simulations of membrane proteins. Methods, Vol.41, No.4, pp. 475-488 Kanner, B.l. Zomot, E. (2008). Sodium-coupled neurotransmitter transporters. Chem Rev, Vol.108, No.5, pp. 1654-68... 

Khalili-Araghi, R, Gumbart, J., Wen, R C., Sotomayor, M., Tajkhorshid, E., 8c Schulten, K. (2009). Molecular dynamics simulations of membrane channels and transporters. Current Opinion in Structural Biology, 19,128. 

Molecular dynamics simulations of membrane protein systems are currently in progress in several laboratories, e.g., bacteriorhodopsin, Pfl phage coat protein, an ampipathic helix, and a polyalanine alpha helix. In addition, continued efforts are directed at investigating the properties of pure lipid bilayers (for a review, see Refs. 14 and 15). Those... 

The size-selectivity factor, which depends on the permeant s volume and the lateral pressure exerted by the membrane, is formulated as the reverse work done required to accommodate the permeant in the membrane. In this sense, it is analogous to the cavitation term in models of water solvation. Based on molecular dynamic simulations of membrane diffusion of small molecules, the calculated diffusion coefficients display small deviations across the membrane barrier. Assuming that the rates of diffusion in the membrane barrier are similar to those of bulk solvent with similar viscosity, or at least that they correlate strongly, the barrier diffusion coefficient is estimated using the size-dependent Stokes-Einstein relation, where kg is the Boltzmann constant, T is temperature, is membrane viscosity and is the radius of the permeant. 

H. Kovacs, A.E. Mark, J. Johansson, and W.F. van Gunsteren. The effect of environment on the stability of an integral membrane helix Molecular dynamics simulations of surfactant protein C in chloroform, methanol and water. J. Mol. Biol, 247 808-822, 1995. 

Has D ], K Tu and M L Klein 1997. Atomic-scale Molecular Dynamics Simulations of Lipid Membranes. Current Opinion in Colloid and Interfaee Seienee 2 15-26. 

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. 

Zubrzycki, I. Z., Xu, Y., Madrid, M. and Tang, P. (2000). Molecular dynamics simulations of a fully hydrated dimyristoylphosphatidylcholine membrane in liquid-crystalline phase, J. Chem. Phys., 112, 3437-3441. 

Tobias, D. J., Tu, K. and Klein, M. L. (1997). Atomic-scale molecular dynamics simulations of lipid membranes, Curr. Opin. Colloid Interf. Sci., 2, 15-26. 

Chiu, S. W., Clark, M., Balaji, V., Subramaniam, S., Scott, H. L. and Jakobsson, E. (1995). Incorporation of surface tension into molecular dynamics simulation of an interface a fluid phase lipid bilayer membrane, Biophys. J., 69,1230-1245. 

Berkowitz, M.L. Detailed molecular dynamics simulations of model biological membranes containing cholesterol. Biochim. Biophys. Acta 2009, 1788, 86-96. 

Smondyrev AM, Berkowitz ML (2000) Molecular dynamics simulation of dipalmitoylphos-phatidylcholine membrane with cholesterol sulphate, Biophys J, 78 1672-1680... 

Johnson RG Jr. (1988) Accumulation of biological amines into chromaffin granules a model for hormone and neurotransmitter transport. Physiol Rev 68 232-307 Jorgensen AM, Tagmose L, Jorgensen AM, Bogeso KP, Peters GH (2007a) Molecular dynamics simulations of Na-l-/Q(-)-dependent neurotransmitter transporters in a membrane-aqueous system. ChemMedChem 2 827- 40... 

To date, our reactive molecular dynamics simulations of proton transport have been limited to bulk water. However, the extension of Ae RMD algorithm to proton transport in PFSA membranes is analogous to what has been done in bulk water and simi-... 

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.)... 

In a somewhat similar paper, diffusion through a 2D porous solid modeled by a regular array of hard disks was evaluated [65] using non-equilibrium molecular dynamics. It was found that Pick s law is not obeyed in this system unless one takes different diffusion constants for different regions in the flow system. Other non-equilibrium molecular dynamics simulations of diffusion for gases within a membrane have been presented [66]. The membrane was modeled as a randomly... 

J. M. D. MacElroy, Nonequilibrium Molecular Dynamics Simulation of Diffusion and Flow in Thin Microporous Membranes, J. Chem. Phys. 101... 

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... 

Kovacs H, Mark AE, Johansson J, and van Gunsteren WF. The Effect of Environment on Stability of an Integral Membrane Helix Molecular Dynamics Simulations of Surfactant Protein C in Chloroform, Methanol and Water. JMol Biol 1995 247 808-822. 

Schlegel, B., Sippl, W., Holtje, H.-D. Molecular dynamics simulations of bovine rhodopsin influence of protonation states and different membrane-mimicking environments. J. Mol. Model. 2005,12, 49-64. 

DeMarco ML, Daggett V (2009) Characterization of cell-surface prion protein relative to its recombinant analogue insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein. J Neurochem 109 60... 

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

Tang, P., Xu, Y. (2002). From the Cover Large-scale molecular dynamics simulations of general anesthetic effects on the ion channel in the fully hydrated membrane The implication of molecular mechanisms of general anesthesia. Proceedings of the National Academy of Sciences of the United States of America, 99(25), 16035-16040. 

De Loof H, S C Harvey, J P Segrest and R W Pastor 1991. Mean Field Stochastic Botmdary Molecular Dynamics Simulation of a Phospholipid in a Membrane Biochemistry 30 2099-2113... 

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