Model building amino acid sequences

Further improvement of the map with these phases may reveal side chains more clearly. Now the trick is to identify some specific side chains so that the known amino-acid sequence of the protein can be aligned with visible features in the map. As mentioned earlier, chain termini are often ill-defined, so we need a foothold for alignment of sequence with map where the map is sharp. Many times the key is a short stretch of sequence containing several bulky hydrophobic residues, like Trp, Phe, and Tyr. Because they are hydro-phobic, they are likely to be in the interior where the map is clearer. Because they are bulky, their side-chain density is more likely to be identifiable. From such a foothold, the detailed model building can begin. 

The biopolymer modeling of HyperChem includes Building polynucleotides, polypeptides and polysaccharides, Amino acid sequence (fasta format) editing, Mutations, Overlapping by RMS fit, and Merging structures. To facilitate manipulation of protein structures, there is often a need to display the protein backbone only as follows. 

Go to the SWISS-MODEL Web site (http //www.swissmodel. expasy.org), select Automated Mode, input the e-mail address and the amino acid sequence of the protein retrieved from the Protein Information table, and click Submit Modeling Request to build target protein structure. (See the crystal structure of SpoVT AbrB (pdb code 2W1T) for Bacillus subtilis in Fig. 1.)... 

The amino acid sequence of the enzyme is homologous with those of the pancreatic enzymes and has been shown by model building to be compatible with a chymotrypsin-like three-dimensional structure and catalytic site (36). The homology in sequence is particularly well marked around His-57. The enzyme s catalytic properties are virtually indistinguishable from those of pancreatic elastase. 

The isoenzymes of phosphoglycerate kinase (PGK, EC 2.7.2.3) from barley leaves have been purified in this laboratory and used to raise antisera (1). These antisera were used to isolate the wheat cDNAs, specific for each isoenzyme, which have since been sequenced (2 ). The derived amino acid sequences have been used to build models for the structures of both isoenzymes on an Evans and Sutherland graphics station. The co-ordinates obtained from the x-ray crystallographic studies of the yeast structure, which have been deposited in the Brookhaven protein data bank, have been used as a template (3). 

Our research group also fabricated a pecuUar a-helix-based nanofiber by the precise design of heUx-helix interaction. Figure 30 shows the amino acid sequence and structural model of the amphiphiUc a-hehcal 18-mers peptide used as a building imit for self-assembly. The designed peptide contains the following sequence AEAQAQAEAARAQAQARA. Due to the high Ala content, the peptide is hehcal, and provides hydrophobic and hydrophiUc... 

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

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. 

Carell has recently presented the study of a flavin amino acid chimera to model riboflavin in DNA photolyases [68]. This amino acid LI (Fig. 20) was synthesized in an enantiopure fashion by building the alloxazine ring onto the epsilon amine of lysine. This coenzyme chimera was applied to the problem of repairing DNA damage caused by UV irradiation. LI was incorporated into an 21-residue peptide, P-1, possessing the sequence of the DNA-binding domain of the helix-loop-helix transcription factor MyoD. 

Regions that cannot be aligned with sequence are often built with polyala-nine, reflecting our knowledge that all amino acids contain the same backbone atoms, and all but one, glycine, have at least a beta carbon (Plate 11). In this manner, we build as many atoms into the model as possible in the face of our ignorance about how to align the sequence with the map in certain areas. 

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