Protein primary structure, effect

Y. Bai, J.S. Milne, L. Mayne and S.W. Englander, Primary structure effects on peptide group hydrogen exchange, Proteins Struct. Function Genet., 17 (1993) 75-86. 

Primary structure effects on peptide group hydrogen exchange. Proteins, 17, 75-86. 

Hydrophobic interactions are the single most important stabilizing influence of protein native structure. The hydrophobic effect refers to the tendency of non-polar substances to minimize contact with a polar solvent such as water. Non-polar amino acid residues constitute a significant proportion of the primary sequence of virtually all polypeptides. These polypeptides will fold in such a way as to maximize the number of such non-polar residue side chains buried in the polypeptide s interior, i.e. away from the surrounding aqueous environment. This situation is most energetically favourable. 

Protein polymers based on Lys-25 were prepared by recombinant DNA (rDNA) technology and bacterial protein expression. The main advantage of this approach is the ability to directly produce high molecular weight polypeptides of exact amino acid sequence with high fidelity as required for this investigation. In contrast to conventional polymer synthesis, protein biosynthesis proceeds with near-absolute control of macromolecular architecture, i.e., size, composition, sequence, topology, and stereochemistry. Biosynthetic polyfa-amino acids) can be considered as model uniform polymers and may possess unique structures and, hence, materials properties, as a consequence of their sequence specificity [11]. Protein biosynthesis affords an opportunity to completely specify the primary structure of the polypeptide repeat and analyze the effect of sequence and structural uniformity on the properties of the protein network. 

Now we can ask what is likely to happen to the three-dimensional structure of a protein if we make a conservative replacement of one amino acid for another in the primary structnre. A conservative replacement involves, for example, substitution of one nonpolar amino acid for another, or replacement of one charged amino acid for another. Intnitively, one would expect that conservative replacements would have rather little effect on three-dimensional protein structure. If an isoleucine is replaced by a valine or leucine, the structnral modification is modest. The side chains of all of these amino acids are hydrophobic and will be content to sit in the molecnlar interior. This expectation is borne out in practice. We have noted earlier that there are many different molecnles of cytochrome c in nature, all of which serve the same basic function and all of which have similar three-dimensional structnres. We have also noted the species specificity of insulins among mammalian species. Here too we find a number of conservative changes in the primary structure of the hormone. Although there are exceptions, as a general rule conservative changes in the primary structnre of proteins are consistent with maintenance of the three-dimensional structures of proteins and the associated biological functions. 

Like all fats, milk fat provides lubrication. They impart a creamy-mouth feel as opposed to a dry texture. Fat globules produce a shortening effect in cheese by keeping the protein matrix extended to give a soft texture. Milk proteins are one of the most important constituents. The primary structure of proteins consists of... 

The size, shape, and configuration of the protein molecule are determined not only by its primary structure and composition but also by stearic effects and secondary binding forces such as electrostatic, hydrogen, and hydrophobic bonding. These forces are influenced by the environment of the protein molecule, including such factors as the temperature, pH, and composition of the dispersing medium. 

The biological function of peptides and proteins depends on their native conformation. The side-chain functionalities of the a-amino acids that comprise peptides and proteins have profound effects on their properties. These functionalities reside in the 20 naturally occurring a-amino acids, which have different propensities for formation of the three major secondary structural conformations. 1 In addition to these naturally occurring a-amino acids whose primary structure enables the polypeptide to fold into a predictable secondary and tertiary structure, the incorporation of unnatural amino acids has opened important areas of research. 

The amino-acids that make up the primary structure of proteins will change their charge when the pH of the solution is altered due to their acid-base properties (Section 5.3 and Appendix 5.1). The effects of pH on enzyme-catalysed reactions can be complex since both Km and may be affected. Here, only the effects on Kmax are considered, as this usually reflects a single constant rather than several that may be associated within the constant Km (see Section 5.4.4.). It is assumed that pH does not change the limiting step in a multi-step process and that the substrate is saturating at all times. 

Although similar in primary structure to proteins, endorphins are smaller, ranging from five to forty or more amino acids in length. Endorphins are not considered to be neurotransmitter molecules, but are instead classified as neuromodulatory, that is, they modify the action of neurotransmitters through a number of effects associated with pain or pleasure. 

The above discussions have shown how selected analytical techniques can be applied to vastly different proteins to solve a myriad of problems. These include routine assays amino acid and sequencing analyses specialized techniques FAB-MS and IEF conventional techniques refined to improve their utility reversed-phase HPLC using different pHs, organic modifiers, and temperatures and chemical and enzymatic modifications. The latter two procedures have been shown to be effective not only in elucidating primary structure but also in probing the conformation of proteins. 

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