Loop modelling

There are two main classes of loop modeling methods (1) the database search approaches, where a segment that fits on the anchor core regions is found in a database of all known protein structures [62,94], and (2) the conformational search approaches [95-97]. There are also methods that combine these two approaches [92,98,99]. 

Q Zheng, R Rosenfeld, C DeLisi, DJ Kyle. Multiple copy sampling in protein loop modeling Computational efficiency and sensitivity to dihedral angle perturbations. Protein Sci 3 493-506, 1994. 

Fig. 3. Classification of single-spanning membrane proteins based on topology, (a) The loop model for explaining the biogenesis of type I topology in the translocon. The stop-transfer signal stops the integration, (b) Type I protein and a cleaved signal peptide, (c) Type II (NcytCexo) is made by a type II signal-anchor, (d) Type III (Nexo-Ccyto often called type I) is made by a type I signal-anchor, (e) Type IV (C-tail) is made independently from the translocon.

Note that this classification does not cover all the theoretical possibilities. For example, a cleavable signal peptide cannot direct the creation of a topology opposite to a type I (according to the loop model). Why other types are not observed must be explained from their insertion mechanisms. This classification can be naturally expanded into multi-spanning proteins (polytopic proteins) based on the location of their N terminus (therefore, type IV cannot be defined). 

Figure 2.9 The chronically isolated intestinal loop model. Key (B) blood catheter (C) head-to-tail connection of the intestine (IL) internal loop with intact blood supply and innervation and (P) perfusion tubes (Adapted from Poelma and Tukker [130]).

Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA (2002) Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J Cell Biol 157 579-589 Mangenot S, Leforestier A, Vachette P, Durand D, Livolant F (2002) Salt-induced conformation and interaction changes of nucleosome core particles. Biophys J 82 345-356 Marsden MP, Laeimnh UK (1979) Metaphase chromosome structure evidence for a radial loop model. Cell 17 849-858... 

Attempts were also made to estimate the rate of turnover of the mucus gel. Telnet al. [14] measured the amount of mucus produced per time imit, using an in situ perfused intestinal loop model in the rat. They foimd that this turnover time is varying between 0.8 and 4.5 hr. 

R. K. Sachs, G. van den Engh, B. Trask, H. Yokota, and J. E. Hearst, A random-walk/giant-loop model for interphase chromosomes. Proc. Natl. Acad. Sci. USA 92, 2710-2714 (1995). 

Qualitatively all of the observed GPC degradation characteristics can be rationalized by the above loop model. Reasonable estimates of the onset of degradation in GPC can be made, and estimates of the percent degradation can be made cautiously. 

Gupta, S., J. N. S. Yadava, and J. S. Tandon. Antisecretory (antidiarrheal) activity of Indian medicinal plants against Escherichia coli enterotoxin-in-duced secretion in rabbit and Guinea pig ileal loop models. Int J Pharmacog 1993 31(3) 198-204-... 

The enhancement of insulin absorption by sodium caprate (Ci0) in a closed loop model in rats showed the following rank of efficiency colon > ileum > jejunum > duodenum. On the other hand, sodium glycocholate affected the intestinal permeability in a different way. With this surfactant, the order of permeation enhancement was colon > jejunum > duodenum > ileum [95], These results show that the absorption site in the GI tract may strongly affect the effectiveness of permeation enhancer. 

Reactor and Gas Loop Model The number of lumps used is determined by comparing the rigorous steady-state results with models using different numbers of lumps. The rigorous steady-state reactor exit temperature is 500 K with a 460 K inlet reactor temperature. When a 10-lump model is used with the same amount of catalyst, the steady-state exit temperature is 505 K. This occurs because of the numerical diffusion or effective back-mixing that is inherent with a lumped model. A 50-lump reactor model is used in all the simulations. It gives a steady-state reactor exit temperature of 501 K. The differences between the dynamic responses of the 10-lump and 50-lump reactors are shown in the next section. 

Several techniques have been used to estimate the rate of mucus secretion, but their accuracy seems to be doubtful. Nevertheless, it has been concluded that a slow baseline secretion of mucus is maintained by exocytosis from goblet cells in the gastrointestinal tract, which appears to be under cholinergic control. Rubinstein and Tirosh used carbachol (cholinergic agonist) at different doses to increase the mucus thickness in different parts of the gastrointestinal tract. Attempts were also made to estimate the rate of turnover of the mucus gel. Lehr et al. measured the amount of mucus produced per time unit, using an in situ perfused intestinal loop model in the rat. They found that this turnover time varies between... 

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