Constructing protein models

Figure 18 MODELLER uses these files to construct protein models. The ClustalX alignment file (a) is imported into GeneDoc (and the alignment modified if needed) and exported as a PIR file for conversion into the MODELLER alignment file format. Beneath the aligned amino acid residues are or a blank indicating the...

The biological properties of dioxin include an ability to bind to a protein known as the AH (aromatic hydrocarbon) receptor Dioxin IS not a hydrocarbon but it shares a certain structural property with aromatic hydrocarbons Try constructing molecular models of dioxin and anthracene to see these similarities... 

If site-specific spin-labeled protein is available [20], quantification of quenching effects on both first-site and second-site ligands can additionally aid in constructing a model of the ternary complex. 

Lamzin, V. S., Perrakis, A. and Wilson, K. S. (2001). The ARP/wARP suite for automated construction and refinement of protein models. In International Tables for Crystallography. Volume F Crystallography of biological macromolecules, Rossmann, M. G. and Arnold, E. eds., pp. 720-722. Dordrecht, Kluwer Academic Publishers, The Netherlands. 

Crystal structure of a protein molecule can also be determined by x-ray crystallography. Purified protein is crystallized either by batch methods or vapor diffusion. X-rays are directed at a crystal of protein. The rays are scattered depending on the electron densities in different positions of a protein. Images are translated onto electron density maps and then analyzed computationally to construct a model of the protein. It is especially important for structure-based drug designs. 

Using the electron density map a three-dimensional model of the protein can be built. For years, the customary procedure was to construct a model at a scale of 2 cm = 0.1 ran using an optical comparator, but... 

The synthesis of peptidyl polymers has a long and elegant history, beginning with the construction of homopolypeptides and random copolypeptides. More recently, biomolecules that incorporate peptide entities into classic polymer structures have been created. Sequential peptide polymers have been constructed that model the three-dimensional structure of connective tissue proteins. This article describes methods for the assembly of a variety of peptidyl polymers. 

Figure 14.3. Display of 3D structure with Chem3D. Heptapeptide, STANLEY, is constructed by entering HSerThreAlaAsnLeuGluTyrOH into the replacement box (left side, under icons). Alternatively an ISIS Draw, stanldy.skc can be converted to stanley.cdx (ChemDraw) and then imported into Chem3D. The atomic coordinates file is saved as Stanley.pdb and can be edited for protein modeling. Note The file does not contain ATOM columns with residue ID.)...

M. J. SippL, M. Hendhch, and P. Lackner. Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments development of strategies and construction of models for myoglobin, lysozyme, and thymosin beta 4. Protein Set 7 625-640 (1992). 

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