Protein amino acids properties

Water-in-oil microemulsions (w/o-MEs), also known as reverse micelles, provide what appears to be a very unique and well-suited medium for solubilizing proteins, amino acids, and other biological molecules in a nonpolar medium. The medium consists of small aqueous-polar nanodroplets dispersed in an apolar bulk phase by surfactants (Fig. 1). Moreover, the droplet size is on the same order of magnitude as the encapsulated enzyme molecules. Typically, the medium is quite dynamic, with droplets spontaneously coalescing, exchanging materials, and reforming on the order of microseconds. Such small droplets yield a large amount of interfacial area. For many surfactants, the size of the dispersed aqueous nanodroplets is directly proportional to the water-surfactant mole ratio, also known as w. Several reviews have been written which provide more detailed discussion of the physical properties of microemulsions [1-3]. 

As with any metalloprotein, the chemical and physical properties of the metal ion in cytochromes are determined by the both the primary and secondary coordination spheres (58-60). The primary coordination sphere has two components, the heme macrocycle and the axial ligands, which directly affect the bound metal ion. The pyrrole nitrogen donors of the heme macrocycle that are influenced by the substitutents on the heme periphery establish the base heme properties. These properties are directly modulated by the number and type of axial ligands derived from the protein amino acids. Typical heme proteins utilize histidine, methionine, tyrosinate, and cysteinate ligands to affect five or six coordination at the metal center. 

This unnatural acid is used as a chiral intermediate for the synthesis of a number of products. Chemical asymmetric synthesis was very difficult and so the stereoselective synthetic properties of enzymes were exploited to carry out a selective reduction reaction. The stereoselective hydrolysis of protein amino acid esters had already been commercialised by Tanabe in Japan using immobilised aminoacylase, and selective reduction reactions using whole yeast cells are already used in a number of processes, such as the selective reduction of the anti-cancer drag Coriolin. 

L-Canavanine and L-canaline are non-protein amino acids of certain leguminous plants, that function as protective allelochemicals. L-Canavanine is incorporated into de novo synthesized proteins in place of arginTne there is suggestive evidence that formation of such anomalous proteins figures significantly in canavanine s adverse biological effects. Canavanine, however, does not appear to inhibit overall protein synthesis. Thus, an important basis for canavanine s antimetabolic properties resides in the sustained production of biologically aberrant proteins. 

Part 2, Protein Structure and Function, contains four chapters that relate to the structures and functions of proteins. In chapter 3, The Building Blocks of Proteins Amino Acids, Peptides, and Polypeptides, we discuss basic structural and chemical properties of amino acids, peptides and polypeptides. In chapter 4, The Three-Dimensional Structures of Proteins, we describe how and why polypeptide chains fold into long fibrous molecules in some cases, or into compact globular molecules in other cases. In chapter... 

The whey produced during cheese and casein manufacturing contains approximately 20% of all milk proteins. It represents a rich and varied mixture of secreted proteins with wide-ranging chemical, physical and functional properties (Smithers et al., 1996). Due to their beneficial functional properties, whey proteins are used as ingredients in many industrial food products (Cheftel and Lorient, 1982). According to Kinsella and Whitehead (1989), functional properties of foods can be explained by the relation of the intrinsic properties of the proteins (amino acid composition and disposition, flexibility, net charge, molecular size, conformation, hydrophobicity, etc.), and various extrinsic factors (method of preparation and storage, temperature, pH, modification process, etc.). 

A large number of chemical and physical properties, manifest in the amino acid side chains, have been thoroughly examined by many investigators. Attempts have been made to correlate these properties with their relatedness among protein sequences. What is most relevant is how these side chains interact with the backbone and with one another and what roles they each play within particular types of secondary and tertiary structure. The parametric description of residue environments with the help of solvent accessibility, secondary structure, backbone torsion angles, pairwise residue-residue distances, or Ca positions is the comparison between amino acid types at protein sequence positions and residue locations in structural templates. A recent review has evaluated and quantified the extent to which the amino acid type-specific distributions of commonly used environment parameters discriminate with respect to the 20 amino acid types (Sunyaev et al., 1998). Some of the important amino acid properties and residue environments are discussed below. 

Jones DD. Amino acid properties and side-chain orientation in proteins a cross correlation approach. J. Theor. Biol. 1975 50 167-183. 

Chemical Modification of Proteins Amino Acids, Chemical Properties of Enzyme Catalysis, Chemical Strategies for Proteins, In Vivo Chemical Modifications of Peptides, Chemistry of... 

Analysis of the relationship between amino acid properties and protein stability showed that hydrophobicity is the major factor for the stability of proteins during substitution of amino acids in the interior of the protein. The stability of protein mutants is attributed to the number of carbon atoms, which shows the direct relationship between hydrophobicity and stability. 

For the mutations on the surface of the protein, the classifications based on the chemical nature of amino acids, such as hydrophobic amino acids (Ala, Cys, Phe, Gly, He, Leu, Met, Val, Trp, and Tyr), amino acid side chains that can form hydrogen bonds (Asp, Cys, Glu, His, Lys, Met, Asn, Gin, Arg, Ser, Thr, Trp, and Tyr), and so forth, improved the correlation between amino acid properties and protein mutant stability. Furthermore, the inclusion of neighboring and surrounding residues remarkably improved the correlation in all the subgroups of mutations. This result indicates that the information from nearby polar/charged amino acid residues and/or the aliphatic and aromatic residues that are close in space is important for the stability of exposed mutations. 

Gromiha MM, Oobatake M, Sarai A. Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys. Chem. 1999 82 51-67. 

The 2-D TLC was successfully applied to the separation of amino acids as early as the beginning of thin-layer chromatography. Separation efficiency is, by far, best with chloroform-methanol-17% ammonium hydroxide (40 40 20, v/v), n-butanol-glacial acetic acid-water (80 20 20, v/v) in combination with phenol-water (75 25, g/g). A novel 2-D TLC method has been elaborated and found suitable for the chromatographic identification of 52 amino acids. This method is based on three 2-D TLC developments on cellulose (CMN 300 50 p) using the same solvent system 1 for the first dimension and three different systems (11-IV) of suitable properties for the second dimension. System 1 n-butanol-acetone -diethylamine-water (10 10 2 5, v/v) system 11 2-propanol-formic acid-water (40 2 10, v/v) system 111 iec-butanol-methyl ethyl ketone-dicyclohexylamine-water (10 10 2 5, v/v) and system IV phenol-water (75 25, g/g) (h- 7.5 mg Na-cyanide) with 3% ammonia. With this technique, all amino acids can be differentiated and characterized by their fixed positions and also by some color reactions. Moreover, the relative merits of cellulose and silica gel are discussed in relation to separation efficiency, reproducibility, and detection sensitivity. Two-dimensional TLC separation of a performic acid oxidized mixture of 20 protein amino acids plus p-alanine and y-amino-n-butyric acid was performed in the first direction with chloroform-methanol-ammonia (17%) (40 40 20, v/v) and in the second direction with phenol-water (75 25, g/g). Detection was performed via ninhydrin reagent spray. 

Side chains of amino acids are responsible for the packing of the regular elements of secondary structure and then for the tertiary structure of a protein. As a consequence, the structure of a protein can be expressed quantitatively by means of side chain amino acid properties. Several —> amino acid descriptors have been proposed, which contain information about properties of side chains of amino acids. 

A simple approach to protein description consists of representing a protein by a sequence of properties of its constituent amino acids. Each amino acid is described by one ore more properties and therefore the total number of protein descriptors is given by the product of the number of amino acids in the protein and the number of selected amino acid properties. As this number of descriptors increases very fast with the size of proteins, this approach is usually applied to small- and medium-size peptides. Moreover, in QSAR studies that require uniform-length descriptors, it can be used only to describe a series of peptide analogues, vhich are peptide sequences with the same length. To enable QSAR studies of peptide sequences with different length, some method is required that is able to translate the peptide sequences into vectorial descriptors with the same number of variables. For example, ACC transforms were applied to compress information about principal properties of amino acids into peptide sequences with different length. 

For instance, several protein descriptors both topological and geometric were calculated by weighting amino acids with the WHIM descriptors related to size (Am), shape (Km), and atom distribution density (Dm) of the single amino acids [Mauri, Ballabio et al, 2008]. These amino acid properties were calculated on the isolated 3D structure of amino acids and are... 

Jones, D. D. (1975) Amino-Acid Properties and Side-Chain Orientation in Proteins - Cross-Correlation Approach, J. 

DNA BASE SEQUENCE = RNA BASE SEQUENCE = PROTEIN AMINO-ACID SEQUENCE The biopolymers provide striking evidence that the same atomic properties that give rise to covalent bonds, molecular shape, and intermolecular forces provide the means for all life forms to flourish. 

---