Properties of proteins

Introduction. Proteins are substances produced by living matter which on enzymatic or acid hydrolysis yield amino acids. They are non-volatile and of high molecular weight, and form colloidal dispersions from which they may be precipitated by-heat, alcohol, various salts, and acids (tannic, picric, and phosphotungstic). Each protein has a minimum solubility at a characteristic pH which is called the iso-electric point. At this point the protein molecules exist as a regates and the solution has the maximum turbidity. The nature of the union of various amino acids in the protein molecule is not known. One theory assumes that the carboxyl of one amino acid unites with the amino group of another, thus  

This mode of union is called peptide linkage. The presence of the peptide linkage is thought to account for the development of a violet color when a protein comes in contact with an alkaline solution of cupric ion. The color is given by biuret, formed by urea on heating NH2CONHCONH2. The reaction is known as the biuret reacUon. It is not given by any amino acid. 

The protein molecule has free carboxyl and amino groups. Therefore it exhibits amphoteric properties. A number of color reactions have been developed for proteins to determine the presence of specific amino acids. The following are among the most important Millon s reaction. This reaction consists in the development of a red coloration when a substance containing a monohydroxyben-zene group is heated with a mixture of mercuric nitrate and nitrite (MUlon s reagent). Proteins giving this reaction contain tyrosine. 

Xanthroproteic reaction. This reaction is given by all proteins containing amino acids with phenyl radicals (tyrosine, tryptophane, phenylalanine). It consists in the development of a yellow color on heating with strong nitric acid. 

Tryptophane reactions. There are several tryptophane reactions one of these consists in the development of a violet color when a solution of protein which contains tryptophane is treated with glacial acetic acid and concentrated sulfuric acid. It is explained by the fact that the ordinary acetic acid contains glyoxylic acid, HOC—COOH, in small amounts, and this aldehyde-acid reacts with the indol group of tryptophane. The same color is given by glyoxylic acid. Proteins which do not yield tryptophane do not give this color. 

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Guemouri L, Ogier J and Ramsden J J 1998 Optical properties of protein monolayers during assembly J. Chem. 

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

Studies of electrical interactions in proteins, polypeptides, and amino acids started over 60 years ago [1]. To a large extent, electrostatic properties of proteins are determined by the ability of certain amino acids to exchange protons with their environment and the dependence of these processes on pH. The proton occupies a special position as a promoter and iiuxliator in... 

Focuses on force field calculations for understanding the dynamic properties of proteins and nucleic acids. Provides a useful introduction to several computational techniques, including molecular mechanics minimization and molecular dynamics. Includes discussions of research involving structural changes and short time scale dynamics of these biomolecules, and the influence of solvent in these processes. 

Biomechanical Machines. The mechanical properties of fibrous polypeptides could be put to use for the commercial production of fibers (qv) that are more elastic and resiUent than available synthetics (see Silk). The biochemical properties of proteins could also be harnessed for the conversion of mechanical energy to chemical energy (35). 

Figure 1.2 shows one way of dividing a polypeptide chain, the biochemist s way. There is, however, a different way to divide the main chain into repeating units that is preferable when we want to describe the structural properties of proteins. For this purpose it is more useful to divide the polypeptide chain into peptide units that go from one Ca atom to the next Ca atom (see Figure 1.5). Each C atom, except the first and the last, thus belongs to two such units. The reason for dividing the chain in this way is that all the atoms in such a unit are fixed in a plane with the bond lengths and bond angles very nearly the same in all units in all proteins. Note that the peptide units of the main chain do not involve the different side chains (Figure 1.5). We will use both of these alternative descriptions of polypeptide chains—the biochemical and the structural—and discuss proteins in terms of the sequence of different amino acids and the sequence of planar peptide units.

Iteration of the reaction shown in Figure 4.2 produces polypeptides and proteins. The remarkable properties of proteins, which we shall discover and come to appreciate in later chapters, all depend in one way or another on the unique properties and chemical diversity of the 20 common amino acids found in proteins. 

Salemme, F. R., 1983. Stnctnral properties of protein /3-sheets. Progress in Biophysics and Molecular Biology 42 95—loo. 

Just as individual amino acids have isoelectric points, proteins have an overall p/ because of the acidic or basic amino acids they may contain. The enzyme lysozyme, for instance, has a preponderance of basic amino acids and thus has a high isoelectric point (p/= 11.0). Pepsin, however, has a preponderance of acidic amino acids and a low- isoelectric point pi 1.0). Not surprisingly, the solubilities and properties of proteins with different pi s are strongly affected by the pH of the medium. Solubility- is usually lowest at the isoelectric point, where the protein has no net charge, and is higher both above and below the pi, where the protein is charged. 

Evolution has provided the cell with a repertoire of 20 amino acids to build proteins. The diversity of amino acid side chain properties is enormous, yet many additional functional groups have been selectively chosen to be covalently attached to side chains and this further increases the unique properties of proteins. Diese additional groups play a regulatory role allowing the cell to respond to changing cellular conditions and events. Known covalent modifications of proteins now include phosphorylation, methylation, acetylation, ubi-quitylation, hydroxylation, uridylylation and glycosyl-ation, among many others. Intense study in this field has shown the addition of a phosphate moiety to a protein... 

Summary of Predicted and Observed Ground-State Properties of Protein-Bound... 

Table 1. Physiochemical properties of proteins of the contact activation cascade... 

The phosphorylation and dephosphorylation of seryl, threonyl, and tyrosyl residues regulate the activity of certain enzymes of lipid and carbohydrate metabolism and the properties of proteins that participate in signal transduction cascades. 

Barron, E.S.G., Ambrose, J. and Johnson, P. (1955). Studies on the mechanisms of action of ionising radiations XIII. The effect of X-irradiation on some physiochemical properties of proteins. Radiat. Res. 2, 145-152. 

Rickard, E. C., Strohl, M. M., and Nielsen, R. G., Correlation of electrophoretic mobilities from capillary electrophoresis with physicochemical properties of proteins and peptides, Anal. Biochem., 197, 197, 1991. 

N. Katre, The conjugation of proteins with polyethylene glycol and other polymers. Altering properties of proteins to enhance their therapeutic potential. Advances Drug Del. Rev, 10, 91 (1993). 

Antosiewicz J, McCammon JA, Gilson MK (1994) Prediction of pH-dependent properties of proteins. JMol Biol 238 415 136. 

Koumanov A, Karshikoff A, Friis EP, Borchert TV (2001) Conformational averaging in pK calculations Improvement and limitations in prediction of ionization properties of proteins. J Phys Chem B 105 9339-9344. 

Although additional experiments and simulations are needed to determine how much of reality is captured in this model, it does explain one important property of proteins their rapid rate of refolding, which is independent of denaturation conditions. If the polypeptide chain is unable to escape from this steric trap and access conformations with the wrong topology, it could never wander far from the folded conformation and thereby avoid incorrect side chain/side chain interactions. 

Urquhart BL et al. Comparison of predicted and observed properties of proteins encoded in the genome of Mycobacterium tuberculosis H37Rv. Biochem Bio-phys Res Comm 1998 253 70-79. 

Buttkus H. On the nature of the chemical and physical bonds which contribute to some structural properties of protein foods a hypothesis. J. Food Sci. 1974 39 484 189. 

A general protocol that can serve as a guide for the use of heterobifunctional crosslinkers in the study of protein interactions is given below. Some optimization of concentrations may have to be done depending on the particular type and properties of proteins being studied. 

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