Folding mechanism

C2.5.3.4 EXPLORING THE PROTEIN FOLDING MECHANISM USING THE LATTICE MODEL... 

The various folding mechanisms expected in foldable sequences may be classified in tenns of the (Sj,. We have already shown that sequences that fold extremely rapidly have very small values of Gj,. Based on our study of several model proteins as well as analysis of real proteins we classify the folding kinetics of proteins in the following [7]. 

Quahtative simulation is a specific KBS model of physical processes that are not understood well enough to develop a physics-based numeric model. Corrosion, folding, mechanical wear, equipment failure, and fatigue are not easily modeled, but decisions about them can be based on qualitative reasoning. See Refs. 178 and 292. 

ND Socci, IN Onuchic, PC Wolynes. Protein folding mechanisms and the multi-dimensional folding funnel. Protein Eng 32 136-158, 1998. 

Bachinger, H.P., Bruckner, P., Timpl, R., Prockop, D.J. and Engel, J. (1980) Folding mechanism of the triple helix in type-III collagen and type-III pN-collagen role of disulfide bridges and peptide bond isomerisation. European Journal of... 

A comparable folding mechanism was found in silks. A seminal study by Li et al. (2001) found that in vitro formation of silk fibrils is conformation dependent and occurred via a nucleation mechanism. Although now established as amyloidogenic (Kenney et al., 2002), the nature of the silk fibril assembly remains unclear. Noteworthy is the evidence for a cross-nucleation ability of silk proteins, supporting the amyloidogenicity of silk (Lundmark et al., 2005). 

Junker, M., Schuster, C. C., McDonnell, A. V., Sorg, K. A., Finn, M. C., Berger, B., and Clark, P. L. (2006). Pertactin beta-helix folding mechanism suggests common themes for the secretion and folding of autotransporter proteins. Proc. Natl. Acad. Sci. USA 103, 4918-4923. 

Voids often look similar to air bubbles. The appearance of voids in filaments or films, however, results for different reasons. Voids can be produced during stretching in the area of necking by a kind of folding mechanism. The formation of voids may also depend on the generation of a radial gradient structure during solidification of the threads. 

Infrared spectroscopy has been an important part of peptide structural analysis for 50 years now. From a rather basic beginning, applications have blossomed to encompass secondary structure analysis, polarization phenomena, membrane conformation, and orientation, and have extended to time-dependent conformational folding mechanisms. Questions have evolved from basic polymer chemistry to issues centered on peptides involved in socially... 

Cellular DNA, as we have seen, is extremely compacted, implying a high degree of structural organization. The folding mechanism must not only pack the DNA but also permit access to the information in the DNA. Before considering how this is accomplished in processes such as replication and transcription, we need to examine an important property of DNA structure known as super-coiling. 

Figure 19.4 A folding mechanism that proceeds along two parallel pathways.

The value of ( used here corresponds to 10 3 of its value in room temperature aqueous solutions. [80] On the one hand, using such weak friction improves the sampling efficiency in the simulations and does not affect equilibrium structural properties. On the other hand, the dynamical properties that we observe may be different from those probed by SM-FRET techniques, which would not be able to resolve conformational dynamics on such fast time scales. Thus, the relevance of the following analysis of dynamical properties relies on the assumption that increasing the friction will not significantly alter our main conclusions. It is interesting to note in this context that the folding mechanism in similar models has been observed to be relatively insensitive to the value of the friction coefficient. [81]... 

Typically, proteins fold to organize a very specific globular conformation, known as the protein s native state, which is in general reasonably stable and unique. It is this well-defined three-dimensional conformation of a polypeptide chain that determines the macroscopic properties and function of a protein. The folding mechanism and biological functionality are directly related to the polypeptide sequence a completely random amino acid sequence is unlikely to form a functional structure. In this view, polypeptide sequence... 

In principle, the ends of an RNA molecule can be moved by making circular permutations (Pan, 2000). As it is known that circular permutations can strongly affect folding mechanisms of RNA (Lease et al., 2007 Pan et al., 1999), this approach may be mosdy useful for studying structure and local dynamics of RNA. Also, after a circular permutation the ends of the molecule are expected to be right next to each other, so that the second dye has to be placed at some internal position. 

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