Peptides acid-base properties

Individual ammo acids differ m their acid-base properties This is important m peptides and proteins where the properties of the substance depend on its ammo acid constituents especially on the nature of the side chains It is also important m analyses m which a complex mixture of ammo acids is separated into its components by taking advantage of the differences m their proton donating and accepting power... 

Electrophoresis is used primarily to analyze mix tures of peptides and proteins rather than individual ammo acids but analogous principles apply Because they incorporate different numbers of ammo acids and because their side chains are different two pep tides will have slightly different acid-base properties and slightly different net charges at a particular pH Thus their mobilities m an electric field will be differ ent and electrophoresis can be used to separate them The medium used to separate peptides and proteins is typically a polyacrylamide gel leading to the term gel electrophoresis for this technique... 

Noszal, B. Osztas, E., Acid-base properties for each protonation site of six corticotropin fragments, Int. J. Peptide Protein Res. 33, 162-166 (1988). 

In many problems of peptide sequencing and peptide synthesis it is necessary to be able to separate mixtures of peptides and proteins. The principal methods used for this purpose depend on acid-base properties or on molecular sizes and shapes. 

The acid-base properties, and hence ionic character, of peptides and proteins also can be used to achieve separations. Ion-exchange chromatography, similar to that described for amino acids (Section 25-4C), is an important separation method. Another method based on acid-base character and molecular size depends on differential rates of migration of the ionized forms of a protein in an electric field (electrophoresis). Proteins, like amino acids, have isoelectric points, which are the pH values at which the molecules have no net charge. At all other pH values there will be some degree of net ionic charge. Because different proteins have different ionic properties, they frequently can be separated by electrophoresis in buffered solutions. Another method, which is used for the separation and purification of enzymes, is affinity chromatography, which was described briefly in Section 9-2B. 

Stereochemistry of Amino Acids 339 Acid-Base Properties of Amino Acids 339 The Isoelectric Point 342 Electrophoresis 343 The Peptide Bond 343 Primary Structure of Proteins 344 Secondary Structure of Proteins 344 Tertiary Structure of Proteins 345 The Folding Problem 346 Denaturing Proteins 346 Enzymes 347... 

Separation of proteins based on differences in their electrical charge depends on their acid-base properties, which are mostly determined by the number and type of ionizable side groups in the peptide chain. Since proteins are different from each other with respect to their composition and amino acid sequence, they also have distinct acid-base properties. Information on these properties allows a prediction of the behavior of a given protein when exposed to an electrical field. 

The following two sections illustrate how a knowledge of the acid-base properties of amino acids and peptides can be used to advantage in designing separation procedures, or predicting separation patterns. 

The chemistry behind amino acid analysis is nothing more than acid-catalyzed hydrolysis of amide (peptide) bonds. The peptide is hydrolyzed by heating in 6 M hydrochloric acid for about 24 h to give a solution that contains all the amino acids. This mixture is then separated by ion-exchange chromatography, which separates the amino acids mainly according to their acid-base properties. As the amino acids leave the chromatography column, they are mixed with ninhydrin and the intensity of the ninhydrin... 

The influence of micelles on the acid-base properties of analytes can be significant and is reflected in changes in log Kh. A gocd example is the acid-base behavior of amino acids and peptides, which present the following equilibria [44,45] ... 

Another very important factor influencing the reactivity of both reaction partners is pH. Protonisation of the carbonyl group in acidic solutions increases the reactivity of nucleophOic reagents, while protonised amino groups are less reactive as the nitrogen atom does not have a free electron pair (Figure 4.74). Acid base properties of amino acids, peptides and proteins (formation of cations, amphions and anions) are described in Section 2.2.3.1. 

Based on our current understanding of ribosomal protein synthesis, several strategies have been developed to incorporate amino acids other than the 20 standard proteinogenic amino acids into a peptide using the ribosomal machinery . This allows for the design of peptides with novel properties. On the one hand, such a system can be used to synthesize nonstandard peptides that are important pharmaceuticals. In nature, such peptides are produced by nonribosomal peptide synthetases, which operate in complex pathways. On the other hand, non-natural residues are a useful tool in biochemistry and biophysics to study proteins. For example, incorporation of non-natural residues by the ribosome allows for site-specific labeling of proteins with spin labels for electron paramagnetic resonance spectroscopy, with... 

Varying the side groups X in 27b affects both the stability and selectivity of the complexes (lateral discrimination), and allows the receptor-substrate interactions in biological systems to be modelled, for instance, the interaction between nicotinamide and tryptophan [2.109b]. One may attach to 27b amino acid residues (leading to parallel peptides [2.109] as in 27c), nucleic acid bases or nucleosides, saccharides, etc. The structural features of 27 and its remarkable binding properties make it an attractive unit for the construction of macropolycyclic multisite receptors, molecular catalysts, and carriers for membrane transport. Such extensions require sepa-... 

Another use for combinatorial libraries has been the screening of peptides for antimicrobrial properties. In this case, the design of the library is based on antimicrobial peptides found in nature. A combinatorial synthesis is used to find alternative unnatural amino acids expected to mimic the antimicrobial properties.23 Peptide libraries also have been used to find compounds that could bind the lytic peptide mellitin.24 The library was synthesized in solution phase, purified, and evaluated using time-of-flight mass spectrometry (TOF-MS). The sequences determined to bind to mellitin contained hydrophobic pairs. By binding to mellitin, they were able to prevent the cell-surface mellitin interaction. This is an example of a peptide library able to afford compounds that interact with other small peptides without having to find an interacting protein first. 

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