Amino acids computer simulation

Fig. 9. — (a) H-N.m.r. Spectrum (270 MHz, Resolution-enhanced) of Beef-lung Heparin in D20 (40%, w/v) at 90° (b) Computer-simulated Spectrum, with Calculated, Interproton Coupling-Constants (/, at 35°) for the Amino Sugar (A) and L-Iduronic acid (I) Residues.84... 

Ladunga, I., Czako, F., Csabai, I., and Geszti, T. (1991). Improving signal peptide prediction accuracy by simulated neural network. Comput. Appl. Biosci. 7, 485-487. Landolt-Marticorena, C., Williams, K., Deber, C., and Reithmeier, R. (1993). Non-random distribution of amino acids in the ransmembrane segments of human type I single span membrane proteins. J. Mol. Biol. 229, 602-608. 

MacCallum, J.L., Bennett, W.F.D., Tieleman, D.P. Distribution of amino acids in a lipid bilayer from computer simulations. Biophys. J. 2008, 94, 3393 04. 

The computer program presented here can generate very different relative frequencies of occurrence of all amino acids (and stop codons) within a target set. One-pot, two-pot, and three-pot syntheses can be simulated. Optionally, correction factors can be included to compensate for the (possible) differences in chemical coupling efficiencies of the nucleotide synthons. Finally, the codon usage of three major expression microorganisms can be considered, treating rare codons as pseudo stop codons. 

This approach was later extended to off-lattice models and a more detailed description of the transfer energy of the different amino acid residues [77]. Magainin, melit-tin, and several other amphipathic peptides were simulated. In these simulations, differences in the interaction of the peptides with the lipid phase were observed. For example, magainin only showed adsorption onto the lipid and no crossing of the lipid occurred, whereas melittin crossed the lipid and formed a stable transmembrane helix. These results are in full agreement with later studies reported by other research groups presented below, involving more elaborate simulation protocols and representations of the peptides and the lipid. These examples show the potential of computer simulations even when some simplifications have to be made to make the system computationally tractable. 

In a study of chiral dipeptide [2]rotaxanes it was found that the presence of an intrinsically achiral benzylic amide macrocycle near to the chiral center could induce an asymmetric response in the aromatic ring absorption bands [62], This induced circular dichroism (ICD) effect was stronger in apolar solvents (Fig. 9), where intercomponent interactions are maximized, showing a direct relationship to the tightness with which the macrocycle binds the chiral thread. Computer simulations showed that chirality is transmitted from the amino acid asymmetric center on the thread via the achiral macrocycle to the aromatic rings of the achiral C-terminal stopper. 

The Monte Carlo method has been applied more extensively to the study of solvation phenomena. Clementi has looked at solvent distribution around a large variety of amino acids and nucleotides. This work is summarized by Clementi in detail in this volume[l7e]. It should be noted that all this work on solvent using these powerful simulation techniques has appeared within the last five years and most of it even more recently. This is a direct result of the advances in computer technology as well as the adaptation of the... 

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