Gramicidin simulation

A good understanding of the properties of water is thus essential as we move to more complicated systems. We have been involving in the study of aqueous solution of many important biological molecules, such as acetylcholine, Gramicidin, deoxydinucleoside phosphate and proflavin, and DNA, etc., first at the Monte Carlo level and slowly moving to the molecular dynamics simulations. We will discuss some of the new results on the hydration structure and the dynamics of B- and Z-DNA in the presence of counterions in the following. 

Fig. 8 Proposed model for gramicidin S in a membrane according to the orientational constraints obtained from and N-NMR. The upright backbone alignment (r 80°) and slant of the /3-sheets (p -45°) are compatible with the formation of an oligomeric /3-barrel that is stabilized by hydrogen bonds (dotted lines). A The oligomer is depicted sideways from within the lipid bilayer interior (showing only backbone atoms for clarity, but with hydrophobic side chains added to one of the monomers). Atomic coordinates of GS were taken from a monomeric structure [4], and the two DMPC lipid molecules are drawn to scale (from a molecular dynamics simulation coordinate file). The bilayer cross-section is coloured yellow in its hydrophobic core, red in the amphiphilic regions, and light blue near the aqueous surface. B Illustrates a top view of the putative pore, although the number of monomers remains speculative...

Benoit Roux s group is using molecular dynamics (MD) simulations to elucidate the fundamental principles governing the transport of ions with a special interest in constructing detailed atomic models of the gramicidin channel.29 They also use MD simulations and free energy methodologies to study... 

B. Roux and M. Karplus, Annu. Rev. Biomol. Struct. Dyn., 23, 731 (1994). Molecular Dynamics Simulations of the Gramicidin Channel. 

In the second study, the proton diffusion through a polyglycine analog of the gramicidin channel was analyzed [27]. These simulations showed that the diffusion process is very rapid and furthermore, is assisted by the polypeptide backbone. Thus, the latter emerges cis a key factor for rapid proton transfer through the channel. 

Fig. 6.4.3. chemical shift powder pattern spectra of labeled gramicidin A. (A) Trpn gramicidin A—experimental data obtained with cross-polarization and H dipolar decoupling at 20.3 MHz for N. (B) spectral simulation with o-n = 36, saturated solution of NH4N03. (C) [ C,]Leuio-[ N ]Trpn gramicidin A—experiment as in (A) displaying a combination of N chemical shift anisotropy and the — " C dipolar interaction. (D) spectral simulation with the same an values as in (B) and with = 0° and Pu = 106°. 

MD simulations of ionophore/channel molecules intercalated into a lipid bilayer would require a large number of lipid molecules to ensure that the ionophore/channel molecule does not interact with its periodic images. Still, comparisons between boundary and bulk lipids may have to be done from independent simulations to get an accurate view of how these molecules affea bilayer dynamics. Typical channels like gramicidin show ion transport times of —10 s, which is a time scale that is presently unattainable in typical MD simulations. However, one can obtain insights into the molecular aspects of the energy barriers involved in the translocation of small molecules and ions from PMF calculations, particularly when there is no ambiguity about the path of the solute movement. Moreover, short time scale (10 s) simulations can... 

Time Correlation Analysis of Simulated Water Motion in Flexible and Rigid Gramicidin Channels. 

We summarise recent work on computer modelling and simulation of proteins involved in bioenergetic processes and in peptide-membrane interactions. Homology modelling, electrostatic calculations and conformational analysis of a photosynthetic reaction centre protein are described. Bacteriorhodopsin, a light-driven proton pump protein is examined from several aspects, including its hydration and conformational thermodynamics. Finally, we present results on lipid perturbation on interaction with a cyclic decapeptide antibiotic, gramicidin S. 

Liu, Z., Xu, Y, Tang, P. (2005). Molecular dynamics simulations of C2F6 effects on gramicidin A Implications of the mechanisms of general anesthesia. Biophysical Journal, 55(6), 3784—3791. 

In a subsequent work72 they studied the, 5N chemical shifts for a biologically relevant system, the gramicidin channel. In particular they also explored how these change when the conformation of the system is changing, whereby they used molecular-dynamics simulation to follow the structural changes. Due to... 

The structure of gramicidin A in a lipid bilayer environment has been determined using molecular dynamics simulations and solid state NMR. The obtained results underscore the utility of molecular dynamics simulations in the analysis and interpretation of structural information from solid state NMR. 

U. Hollerbach, D. P. Chen, and R. S. Eisenberg. Two- and three-dimensional Poisson-Nernst-Planck simulations of current flow through gramicidin A.J. Sci. Comput, 16(4) 373-409,2001. 

Figure 24.3 The simulation is based on the coordinates of H. Heller, M. Schaefer, and K. Schulten, Molecular Dynamics Simulation of a Bilayer of 200 Lipids inm the Gel and in the Liquid-Crystal Phases, Journal of Physical Chemistry, 97, 8343-8360 (1993) and taken from an interactive animated tutorial by E. Martz and A. Herraez, Lipid Bilayers and the Gramicidin Channel (http //molvis. sds.edu/bilayers/index.htm (2001) by courtesy of Professor Martz.

Gramicidin A. Gramicidin A (gA) is a small 15-residue antibiotic peptide formed as a dimer in a head-to-head (HH) or a double-helical (DH) conformation. " Because of its simplicity and reduced dimensions, the gA structure has been studied extensively and simulated as a model for ion channels,and has emerged as a benchmark for simulation approaches. " The structure exposes its hydrophobic sidechains to the lipid membrane that embeds the protein. The molecular structure of gA has been known for three decades,and has been recently resolved with NMR spectroscopyThe relation of the structure seen spectroscopically to that... 

Three-Dimensional Poisson-Nernst-Plank Simulations of Current Flow Through Gramicidin A. 

Huang P, Loew GH (1995) Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study. J Biomol Struct Dyn 12(5) 937-956 Bemeche S, Nina M, Roux B (1998) Molecular dynamics simulations of melittin in a dimy-ristoylphosphatidylcholine bilayer membrane. Biophys J 75(4) 1603 1618 Woolf TB, Roux B (1994) Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. PNAS 91(24) 11631 11635... 

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