Proteins hierarchical

SCOP Structural Classification of Proteins. Hierarchical protein structure database... 

Although the folding of short proteins has been simulated at the atomic level of detail [159,160], a simplified protein representation is often applied. Simplifications include using one or a few interaction centers per residue [161] as well as a lattice representation of a protein [162]. Some methods are hierarchical in that they begin with a simplified lattice representation and end up with an atomistic detailed molecular dynamics simulation [163]. 

CA Orengo, AD Michie, S Jones, DT Jones, MB Swindells, JM Thornton. CATH—A hierarchic classification of protein domain structures. Stnrcture 5 1093-1108, 1997. 

The first requirement for threading is to have a database of all the known different protein folds. Eisenberg has used his own library of about 800 folds, which represents a minimally redundant set of the more than 6000 structures deposited at the Protein Data Bank. Other groups use databases available on the World Wide Web, where the folds are hierarchically ordered according to structural and functional similarities, such as SCOP, designed by Alexey Murzin and Cyrus Chothia in Cambridge, UK. 

Srinivasan, R., and Rose, G. D., 1995. LINUS A hierarchic procedure to predict the fold of a protein. Proteins Structure, Function and Genetics 22 81-99. 

Uricanu, V. I., Duits, M. H. G., and Mellema, J. (2004). Hierarchical networks of casein proteins An elasticity study based on atomic force microscopy. Langmuir 20,5079-5090. 

Addition of third components to nanohybrids of proteins and mesoporous materials sometimes brings advantages in their functions. Kim, Hyeon, and coworkers immobilized enzyme molecules together with magnetite (Fe304) nanoparticles in hierarchically ordered, mesocellular, mesoporous silica (HMMS) (Figure 4.25)... 

Flies and worms. Expression of wild-type and mutant human tau proteins in nerve cells of D. melanogaster and C. elegans led to a reduced lifespan and the loss of nerve cells, in the apparent absence of tau filaments [40, 41]. Phosphorylation of tau was more extensive in the fly than in the worm. In Drosophila, phosphorylation of S262 and S356 in tau by PAR-1 kinase, the fly homologue of MARK, appeared to be necessary for the subsequent phosphorylation at other sites, indicating the existence of a hierarchical and temporally ordered phosphorylation process. 

In summary, the dynamics of the hierarchical interaction between silk proteins in solution suggest that spiders and insects are trading long range crystallinity for local conformational transitions, thus allowing the... 

In summary, the physiological control of silk protein conversion shows an ingenious balance of activating and inhibiting mechanisms that are dependent on composition and sequence arrangement (Krejchi et al., 1994). Denaturing effects observed in silks appear to be identical to those found in amyloid-forming proteins, and they principally alter the competitive outcome of the hydration of nonpolar and polar residues (Anfinsen, 1973 Dill, 1990 Dobson and Karplus, 1999 Kauzmann, 1959). The key differences to amyloids may lie in the hierarchical level of the structures (Muthukumar et al., 1997) involved in the assembly of silks compared to amyloids. 

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