Peptides three-dimensional structures

All protein molecules are polymers built up from 20 different amino acids linked end-to-end by peptide bonds. The function of every protein molecule depends on its three-dimensional structure, which in turn is determined by its amino acid sequence, which in turn is determined by the nucleotide sequence of the structural gene. 

Serine proteinases such as chymotrypsin and subtilisin catalyze the cleavage of peptide bonds. Four features essential for catalysis are present in the three-dimensional structures of all serine proteinases a catalytic triad, an oxyanion binding site, a substrate specificity pocket, and a nonspecific binding site for polypeptide substrates. These four features, in a very similar arrangement, are present in both chymotrypsin and subtilisin even though they are achieved in the two enzymes in completely different ways by quite different three-dimensional structures. Chymotrypsin is built up from two p-barrel domains, whereas the subtilisin structure is of the a/p type. These two enzymes provide an example of convergent evolution where completely different loop regions, attached to different framework structures, form similar active sites. 

The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC. Cell 70 1035-1048, 1992. 

There is great interest in the ability to reliably predict three-dimensional structures for peptides (11,21) or for portions of... 

A small number of proteins, and again insulin is an example, are synthesized as pro-proteins with an additional amino acid sequence which dictates the final three-dimensional structure. In the case of proinsulin, proteolytic attack cleaves out a stretch of 35 amino acids in the middle of the molecule to generate insulin. The peptide that is removed is known as the C chain. The other chains, A and B, remain crosslinked and thus locked in a stable tertiary stiucture by the disulphide bridges formed when the molecule originally folded as proinsulin. Bacteria have no mechanism for specifically cutting out the folding sequences from pro-hormones and the way of solving this problem is described in a later section. 

With this information in hand, we may now consider how the -ATPase polypeptide chain might fold into its functional three-dimensional structure. First, regarding the actual number of membrane-spanning stretches, the available experimental data indicate only that each of the three membrane-embedded peptides must have an even number of and a minimum of two such stretches. However, hydropathy analysis by the method of Mohana Rao and Argos [48] suggests that the second mem-... 

PROTEIN STRUCTURE OF PEPTIDE DEFORMYLASES Three-dimensional Structure Metal-binding Site... 

Figure 7.2 Schematic showing the relationship of the native antigen to the peptide mimic. The native antigen (a protein) is shown as a winding, twisted line, so as to represent a hypothetical three-dimensional structure. The peptide represents the antibody-binding epitope (shown in dotted lines) of the native antigen. The epitope can represent a linear sequence of the native protein. Alternatively, the epitope can be formed by amino acids that are not immediately adjacent to each other in the primary sequence but brought together by the three-dimensional folding of the protein. Adapted with permission from Sompuram et al.6...

Proteins are built up by aminoacids linked by peptide bonds into a polypeptide chain (Figure 2). The sequence of the aminoacids in the chain is known as the primary structure of the protein. The primary structure of the protein gives rise to the corresponding three-dimensional structure, and the spatial relationships of the constituents are the key for the peptide function. 

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... 

This technique has been described as a general method of studying protein-protein interactions as well as a method for investigating the three-dimensional structure of individual proteins (Muller et al., 2001 Back et al., 2003 Dihazi and Sinz, 2003 Sinz, 2003 Sinz, 2006). It also has been used for the study of the interactions of cytochrome C and ribonuclease A (Pearson et al., 2002), to investigate the interaction of calmodulin with a specific peptide binder (Kalkhof et al., 2005a Schmidt et al., 2005), and for probing laminin self-interaction (Kalkhof et al., 2005b). 

Langs, D. A. (1988). Three-dimensional structure at 0.86 A of the uncomplexed form of the transmembrane ion channel peptide gramicidin A. Science 241, 188-191. 

The peptide chain in globular proteins is folded into fairly compact conformations. Water-soluble enzymes are typical globular proteins which have most of the hydrophobic amino acid residues located in the interior and the hydrophilic residues located mainly at the surface in contact with solvent water. The average radii are 20-40 A (Boyer, 1970). It is clear that there are common morphological features between surfactant micelles and enzyme molecules. This fact has prompted many chemists to use micelles as enzyme models. However, it must be emphasized that micelles exist in dynamic equilibria with monomeric surfactant and their hydrophobic core is quite fluid, whereas enzyme molecules have precisely fixed three-dimensional structures. 

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