Folding model

J Novotny, AA Rashm, RE Bruccoleri. Criteria that discriminate between native proteins and mcoiTectly folded models. Proteins 4 19-30, 1988. 

Abstract—Experimental and theoretical studies of the vibrational modes of carbon nanotubes are reviewed. The closing of a 2D graphene sheet into a tubule is found to lead to several new infrared (IR)- and Raman-active modes. The number of these modes is found to depend on the tubule symmetry and not on the diameter. Their diameter-dependent frequencies are calculated using a zone-folding model. Results of Raman scattering studies on arc-derived carbons containing nested or single-wall nanotubes are discussed. They are compared to theory and to that observed for other sp carbons also present in the sample. 

Ejtehadi MR, Avail SP, Plotkin SS. Three-body interactions improve the prediction of rate and mechanism in protein folding models. Proc Natl Acad Sci USA 2004 101 15088-93. 

Cox, G.A. and Johnston, R.L., Analyzing energy landscapes for folding model proteins, /. Chem. Phys., 124,204714,2006. 

For the model in Figure 1, y = 1/2, f 1/2, and = 1/3. We can imagine more highly folded models. For example, if half the crystalline chains fold twice and the other half three times, the value of t, is 1/7. The greater the number of folds, the smaller the value of . Since the force at equilibrium is... 

C. L. Woodcock, S. A. Grigoryev, R. A. Horowitz, and N. Whitaker, A chromatin folding model that incorporates linker variabihly generates fibers resembling the native structures. Prvc. Natl. 

Woodcock, C.L., Grigoryev, S.A., Horowitz, R.A., and Whitaker, N. (1993) A chromatin folding model that incorporates linker variability generates fiber resembling the native structures. Proc. Natl. Acad. Sci. 1 90(19), 9021-9025. 

Horton et al. analyzed the Mn -binding properties of hammerhead ribozyme-substrate complexes by EPR [81]. The results are consistent with the two-phase folding model. They found two classes of metal-binding sites with higher affinity and lower affinity, by monitoring the number of bound Mn + ions per hammerhead ribozyme-substrate complex at various concentrations of NaCl. They observed, in the presence of a constant concentration of Mn + ions, a sudden decrease in the number of bound low-affinity Mn ions at a lower concentration of NaCl, followed by a slow decrease or a plateau value of the number of bound high-affinity Mn ions at a higher concentration of NaCl. For example, in the absence of NaCl and in the presence of either 0.3 mmol/1 or 1 mmol/1 Mn + ions, the number of bound Mn ions per hammerhead ribozyme-substrate complex was approximately 14. Addition... 

In chemistry, one area that has received outstanding attention is that of RNA folding, shape, and evolution. Peter Schuster, Walter Fontana, Peter Stadler and their colleagues have made major contributions. Among the concepts here are energy landscapes for computer-folded models of RNA molecules, the evolution of model RNA sequences over these landscapes in sequence space, the folded shapes of model RNA sequences, and the existence of connected neutral pathways across sequence space among model RNA molecules that fold to the same shape. 

A functional map of the Na+ channel a subunits. The transmembrane folding model of the a subunit is depicted with experimentally demonstrated sites of cAMP-dependent phosphorylation (P), interaction of site-directed antibodies that define transmembrane orientation covalent attachment... 

Fibrillin-rich microfibrils have endowed tissues with elasticity throughout multicellular evolution. X-ray studies and mechanical testing of microfibril bundles showed that bound calcium influences load deformation, but is not necessary for high extensibility and elasticity (Eriksen et al, 2001 Wess et al, 1997, 1998a,b). Thus, tissue microfibril elasticity is modified by, but not dependent on, calcium-induced beaded periodic changes. This is consistent with the molecular folding model. 

Fig. 13 The super-folding model according to Sadler and Keller [85] showing the conformation of a single molecule in a solution-grown single crystal...

Figure 1. The diatom Aulonia hexagona is an almost perfect 100000-fold model of a giant fullerene with about 1200 carbon atoms. (From On growth and form, by W. D Arey Thompson. Courtesy of Cambridge University Press.)...

Norlen, L., Skin barrier formation the membrane folding model, J. Invest. Dermatol., 117, 823, 2001. 

Electron diffraction assessments of single crystals from inulin fractions indicate two antiparallel six-fold helices (Andre et al., 1996) a five-fold model has also been proposed (Marchessault et al., 1980). The hemihydrate molecule contains one water molecule for each two fructosyl units, while the monohydrate has one water molecule per fructosyl unit. When intermolecular hydrogen bonds are present, however, there is no evidence of intramolecular hydrogen bonding in the crystals. Crystal structures of 1-kestose (GF2) (Jeffrey and Park, 1972), nystose (GF3) (Jeffrey and Huang, 1993), and cycloinulohexaose (cF6) (Sawada et al., 1990) have been reported. 

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