Side chains amino acid interactions

It is the sequence and types of amino acids and the way that they are folded that provides protein molecules with specific structure, activity, and function. Ionic charge, hydrogen bonding capability, and hydrophobicity are the major determinants for the resultant three-dimensional structure of protein molecules. The a-chain is twisted, folded, and formed into globular structures, a-helicies, and P-sheets based upon the side-chain amino acid sequence and weak intramolecular interactions such as hydrogen bonding between different parts of the peptide... 

J. and Bernal, 1. (2004) A critical look on the nature of the intra-molecular iriterligarid Jt,Jt-stackrng interaction in mixed-ligand copper(II) complexes of aromatic side-chain amino acidates and a,a -diimines. Cryst Eng Comm, 6, 627. 

Comparison of the X-ray based cubic section model with the substrate surrogate derived cubic section model gave a view of the amino acid residues around the substrate binding domain (Figure 21). Forbidden and boundary regions defined by the substrate surrogate overlay method are near the side chains amino acid residues. Substrate interactions with surface of the amino acid residues could be estimated by molecular mechanics (MACROMODEL). 

Ye SJ, Clark AA, Armentrout PB. Experimental and theoretical investigation of alkali metal cation interactions with hydroxyl side-chain amino acids. J Phys Chem B. 2008 112 10291-302. 

A possible explanation for the failure of LI(12,6) is the following. The LJ(12,6) is describing successfriUy atomic interactions. The shape of atoms is much better defined than the shape of amino acid side chains. Amino acids may have flexible side chains and alternative conformations, making the range of acceptable distances significantly larger. To represent alternative configurations of the same type of side chains, potentials with wide minima are required. 

The possibility of interactions with the peptide backbone has also been considered. Interactions involving more than two side-chain amino acids can occur, the limiting case being the formation of an entire hydrophobic region. The thermodynamic parameters for the transfer of nonpolar groups from water to the inside of the protein considered to be a nonpolar region were calculated and are listed in Table 3.5. 

What about tertiary structure Why does any protein adopt the shape it does The forces that determine the tertiary structure of a protein are the same forces that act on ail molecules, regardless of size, to provide maximum stability. Particularly important are the hydrophilic (water-loving Section 2.13) interactions of the polar side chains on acidic or basic amino acids. Those acidic or basic amino acids with charged side chains tend to congregate on the exterior of the protein, where they can be solvated by water. Those amino acids with neutral, nonpolar side chains tend to congregate on the hydrocarbon-like interior of a protein molecule, away from the aqueous medium. 

The stability of secondary structure is also influenced by surrounding structures (Fig. 2-3). Secondary structure may be stabilized by interactions between the side chains and by interactions of the side chains with other structures in the protein. For example, it is possible to arrange the amino acid sequence of a protein or peptide into a helix that has one face that is hydrophobic and one that is hydrophilic. The helix wheel shown in Fig. 2-3 illustrates how this is possible. View the helix as a long cylinder. The peptide backbone spirals up and around the cylinder. The... 

Being highly hydrophobic but less lipophilic than their hydrocarbon analogs, fluoroalkyl amino acid side chains tend to interact with one another by fluorine-fluorine contacts. Therefore, even one single fluorinated amino acid can direct polypeptide folding due to strong character of fluorine-fluorine interactions (Section 3.3 and 3.4). 

From this point, the primary structure was fully determined. The primary structure of an enzyme, or other protein, is the number, length, and composition of the polypeptide chains, the linear arrangement of their amino acids, and the number and position of (he cross-links between chains. (The geometrical configuration of the molecule, which is usually a three-dimensional coiled and folded structure, and the side chains and their interactions were not determined.)... 

Small peptides in solution are generally random coils however, above a certain critical length, the peptides will be able to have secondary structures distinctly different from the random coil. Thus, the critical length for a-helix formation is 7-9 amino acid residues (22). It is not generally possible to predict at what chain length two hydrophobic side-chains are able to interact, whereby the peptide becomes U-shaped, because this must depend on the actual position and nature of the side-chains. This hydrophobic interaction masks the side-chains, resulting in a reduction of the bitter taste. 

It has been proposed that simple non-carbohydrate analogues containing the carboxylate and the acetylamino groups attached to a cyclic backbone spacer would be suflSdent to generate lead compoimds for further elaboration as NA inhibitors. The spacer would need to orient correctly these groups as found in bound DANA. It has been also required thad such compounds adopt a planar structure near the carboxylate to mimic the transition state and be able to present additional side-chain functionality for interaction with other conserved amino acid residues in the sialic acid binding site. 

Crosslinking of protein monolayers by mercuric ion (MacRitchie, 1970) and silicic acid (Minones et al., 1973) has been reported. These studies are relevant to poisoning by heavy-metal ions and to silicosis, effects that seem likely to result from attack on the cell membrane proteins. Crosslinking by mercuric ion was detected by a spectacular increase in surface viscosity and a decrease in compressibility when a number of proteins (BSA, insulin, ovalbumin, and hemoglobin) were spread on 0.001 M mercuric chloride solution. Poly-DL-alanine was unaffected whereas poly-L-lysine and poly-L-glutamic acid were affected in a similar manner to the proteins, indicating that mercuric ion interacts with the ionizable carboxyl and amino groups on the protein side—chains. Silicic acid similarly caused protein monolayers... 

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