Similar with different amino acid

A similar scaffold for the preparation of peptidomimetics was prepared by Mitsunobu cyclization of the molecule coming from the coupling of 4-benzylprolinol and iV-nosyl(o-nitrobenzensulfonyl) tryptophan 316 (Scheme 41). A Mitsunobu cyclization occurred easily due to the acidity of the NH of the nosyl group that could be further selectively deprotected under very mild conditions. The so-formed bicyclic amine 317 can be further coupled with different amino acids to give compounds 318, employed in the search of a new somatostatin pharmacophore <2005BML4033>. 

Many enzymes exist within a cell as two or more isoenzymes, enzymes that catalyze the same chemical reaction and have similar substrate specificities. They are not isomers but are distinctly different proteins which are usually encoded by different genes.22 23 An example is provided by aspartate aminotransferase (Fig. 2-6) which occurs in eukaryotes as a pair of cytosolic and mitochondrial isoenzymes with different amino acid sequences and different isoelectric points. Although these isoenzymes share less than 50% sequence identity, their internal structures are nearly identical.24-27 The two isoenzymes, which also share structural homology with that of E. coli,28 may have evolved separately in the cytosol and mitochondria, respectively, from an ancient common precursor. Tire differences between them are concentrated on the external surface and may be important to as yet unknown interactions with other protein molecules. 

Transfer RNA molecules are the adaptors that associate an amino acid with its correct base sequence. Transfer RNA molecules are structurally similar to one another each adopts a three-dimensional cloverleaf pattern of base-paired groups (Figure 2,10). Subtle differences in structure enable the protein-synthesis machinery to distinguish transfer RNA molecules with different amino acid specificities. 

The differences in fluctuations of I24, A24, V24 and L24 are presented on Fig. 8.6, where root mean square fluctuations (SviSF) of C C> and C atoms are compared. The fluctuation depends also on temperature and position of C atom in side chain. Because of temperature dependence it is possible only to compare fluctuations from simulations made by same conditions of atoms with same parameters. The Leu side chains are most stable, while the He side chains are the most fluctuating. The fluctuation of Val side chains are between that of Leu and He. This instabihty of amino acids side chains affect also surrounding lipids (see below). The fluctuations are affected also by distortions in helical stmcture—for example C in DPPC/gel. In this case in C end of the peptide the fluctuations are similar in Leu and He. But the L24 peptide formed a kink at this position (aprox. one turn from C end). The stability of side chains has been studied also by Pace et al. [87] and Johanson and Lindahl [54] (determined enthalpy and entropy of exchanging Ala with different amino acids in poly-Ala transmembrane chain) and Barlow et al. [86] (studied entropy of % angles). 

Domains are formed by different combinations of secondary structure elements and motifs. The a helices and p strands of the motifs are adjacent to each other in the three-dimensional structure and connected by loop regions. Sequentially adjacent motifs, or motifs that are formed from consecutive regions of the primary structure of a polypeptide chain, are usually close together in the three-dimensional structure (Figure 2.20). Thus to a first approximation a polypeptide chain can be considered as a sequential arrangement of these simple motifs. The number of such combinations found in proteins is limited, and some combinations seem to be structurally favored. Thus similar domain structures frequently occur in different proteins with different functions and with completely different amino acid sequences. 

We have described a general relationship between structure and function for the a/p-barrel structures. They all have the active site at the same position with respect to their common structure in spite of having different functions as well as different amino acid sequences. We can now ask if similar relationships also occur for the open a/p-sheet structures in spite of their much greater variation in structure. Can the position of the active sites be predicted from the structures of many open-sheet a/p proteins ... 

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

If the sequence of a protein has more than 90% identity to a protein with known experimental 3D-stmcture, then it is an optimal case to build a homologous structural model based on that structural template. The margins of error for the model and for the experimental method are in similar ranges. The different amino acids have to be mutated virtually. The conformations of the new side chains can be derived either from residues of structurally characterized amino acids in a similar spatial environment or from side chain rotamer libraries for each amino acid type which are stored for different structural environments like beta-strands or alpha-helices. 

Normal hemoglobin molecules are complex, three-dimensional structures consisting of four chains of amino acids known as polypeptide chains. Two of these chains are known as alpha subunits with 141 amino acid residues each, and the remaining polypeptide chains are the beta subunits with 146 amino acid residues each. The sequences of amino acids in the alpha and beta subunits are different, but fold up via noncovalent interactions to form similar three-dimensional structures. When a polypeptide chain arranges itself in space, i.e., when it folds, amino acids that were far apart in the chain are brought closer in proximity. The final overall shape of the protein molecule is influenced by (1) the amino acids in the chain, and (2) the interactions that are possible between distant amino acids. 

A similar study has been performed on silk [Howell et al. 2007]. The ToF-SIMS fingerprint of silk exhibits the presence of different amino acid fragments (positive ion mode). In contrast to wool, the effect of artificial ageing is not obvious and no modification appears in the ToF-SIMS spectra. Nevertheless, the study of the cleaning procedures leads to the same conclusion as that in the case of wool. The amount of remaining surfactant increases with artificial ageing. 

All amino acids except glycine exist in these two different isomeric forms but only the L isomers of the a-amino acids are found in proteins, although many D amino acids do occur naturally, for example in certain bacterial cell walls and polypeptide antibiotics. It is difficult to differentiate between the D and the L isomers by chemical methods and when it is necessary to resolve a racemic mixture, an isomer-specific enzyme provides a convenient way to degrade the unwanted isomer, leaving the other isomer intact. Similarly in a particular sample, one isomer may be determined in the presence of the other using an enzyme with a specificity for the isomer under investigation. The other isomer present will not act as a substrate for the enzyme and no enzymic activity will be demonstrated. The enzyme L-amino acid oxidase (EC 1.4.3.2), for example, is an enzyme that shows activity only with L amino acids and will not react with the D amino acids. 

How does one go about finding all of the relevant proteins in a database once it has been decided to carry out an analysis of an entire protein family The simplest approach is to use similarity search software such as SSEARCH or FASTA (Smith and Waterman, 1981 Pearson and Lipman, 1988) or BLAST (Altschul et al, 1997) with the amino acid sequences of one or two well-known members of the family as queries. The problem is initially the same as that of identifying all proteins that are homologous to a family of proteins, although with some important practical differ-... 

---