Amino acids solvent accessibility

Fig. 2.11. Correlation between accessible surface area and hydrophobicity expressed as free energy of transfer between organic solvent and water for various hydrocarbons (iunlabeled dots), and for amino acids. The accessible surface area is obtained by rolling a water molecule (sphere 1.4 A) around the solute molecule and calculating the contact surface. The slopes of the lines are 25 cal A-2 for hydrocarbons and polar amino acids and 22 cal A-2 for nonpolar amino acids [137]...

The second task, resolution of synthetic D,L-amino acids has been solved by conversion of the neutral amino acids into real carboxyUc acids by acylation of the amino group, either by the benzoyl or the formyl residue. The D,L-acyl amino acids then formed diastereomeric salts with optically active bases, mostly alkaloids, which differed in their solubihty in various solvents, and so could be separated by recrystallization. This method is still in use, although enzymatic procedures, specific oxidation of the D-antipode in the presence of D-amino acid oxidase or enzymatic, stereospecific removal of iV-acyl residues from d,l-AT-acetyl-amino acids by acylase, are more convenient. Certainly, L-amino acids became accessible from nature by the ester method, but without synthetic material, extended experiments of peptide couphng would have been impossible. 

Based on these preliminary findings, related couplings to pyruvates and iminoacetates were explored as a means of accessing a-hydroxy acids and a-amino acids, respectively. It was found that hydrogenation of 1,3-enynes in the presence of pyruvates using chirally modified cationic rhodium catalysts delivers optically enriched a-hydroxy esters [102]. However, chemical yields were found to improve upon aging of the solvent 1,2-dichloroethane (DCE), which led to the hypothesis that adventitious HC1 may promote re-... 

The crystal structure of the OCP from Arthrospira maxima has been solved to 2.1 A resolution (Kerfeld et al. 2003). It is composed of two domains and the carotenoid, 3 -hydroxyechinenone, spans both. The carotenoid is almost completely buried within the protein only 3.4% of the pigment surface is accessible to solvent (see Figure 1.3a). The OCP is a dimer in solution the intermolecular interactions are largely mediated by hydrogen bonding among the N-terminal 30 amino acids, as shown in Figure 1.3b... 

Proteins are highly complex, folded polypeptide chains consisting of at least 20 different amino acids that are strung together in unique sequences, which relate to structure and function. Particular amino acids in proteins may be further modified post-translationally to contain a wide variety of covalent modifications normally found in native proteins. The way in which a peptide chain is wrapped and folded governs each amino acid s relative exposure to the outside environment, but post-translational modifications also can obscure the protein surface from easy access to the solvent environment. 

However, just considering the individual properties of each amino acid type is not enough to determine its accessibility to the surrounding aqueous environment. There have been many attempts at developing analytical models with predictive value for determining buried or surface accessible amino acids in a folded polypeptide chain. These studies have concluded fractional assignments for each residue that relate to its accessible surface area (ASA) or its solvent exposed area (SEA). 

Three levels of SEA are presented in the graph for each amino acid, which corresponds to areas in A2 accessible to the solvent environment greater than 30 A2 for highly accessible amino acids, between 10 and 30A2 for medium accessibility, and less than 10 A2 for those residues that are relatively not accessible to the solvent. Only the SEA for each amino acid of >30A2 is shown in the plotted data. The graph shows that the polar amino acids such as serine, threonine,... 

Ahmad, S., Gromiha, M.M., and Sarai, A. (2003) Real value prediction of solvent accessibility from amino acid sequence. Proteins 50(4), 629-635. 

Since the primary structure of a peptide determines the global fold of any protein, the amino acid sequence of a heme protein not only provides the ligands, but also establishes the heme environmental factors such as solvent and ion accessibility and local dielectric. The prevalent secondary structure element found in heme protein architectures is the a-helix however, it should be noted that p-sheet heme proteins are also known, such as the nitrophorin from Rhodnius prolixus (71) and flavocytochrome cellobiose dehydrogenase from Phanerochaete chrys-osporium (72). However, for the purpose of this review, we focus on the structures of cytochromes 6562 (73) and c (74) shown in Fig. 2, which are four-a-helix bundle protein architectures and lend themselves as resource structures for the development of de novo designs. 

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