Model proteins transitions

O Toole, E.M., Panagiotopoulos, A.Z. Monte Carlo simulation of folding transitions of simple model proteins using a chain growth algorithm. J. Chem. Phys. 1992, 97, 8644-52. 

Deng et al. (1993,1998) and Ray et al. (1993) have used V " as an analogue of in an attempt to model the transition state of the hydrolysis of phospho-diesters by ribonuclease A since is assumed to adopt the expected five coordination more readily than Examination of the vibrational spectrum of the vanadate analogue indicates that the terminal V-O bonds are only slightly weakened when bonded to the protein. A quantitative bond valence analysis effectively rules out two proposed mechanisms that involve the protonation of the terminal O atoms. 

In sharp contrast to the large number of experimental and computer simulation studies reported in literature, there have been relatively few analytical or model dependent studies on the dynamics of protein hydration layer. A simple phenomenological model, proposed earlier by Nandi and Bagchi [4] explains the observed slow relaxation in the hydration layer in terms of a dynamic equilibrium between the bound and the free states of water molecules within the layer. The slow time scale is the inverse of the rate of bound to free transition. In this model, the transition between the free and bound states occurs by rotation. Recently Mukherjee and Bagchi [14] have numerically solved the space dependent reaction-diffusion model to obtain the probability distribution and the time dependent mean-square displacement (MSD). The model predicts a transition from sub-diffusive to super-diffusive translational behaviour, before it attains a diffusive nature in the long time. However, a microscopic theory of hydration layer dynamics is yet to be fully developed. 

Optimal rates of folding occur when there is not an initial collapse of structure, hydrophobic or otherwise, but when there is a specific and extended nucleus in the transition state model proteins evolve toward nucleation mechanisms with extended nuclei.45,47... 

Fig. 5. Free energy landscape of a lattice model protein (see Sect. 2.2), as a function of two order parameters, the number of contacts C and the number of native contacts Qo (see Sect. 2.3). Unlike the energy landscape funnel picture, the free energy shows two stable states separated by a barrier (the transition state). Extended unfolded conformers quickly collapse to the molten globule, and have to overcome a barrier to folding to the native state. The funnel picture is thus reconciled with the two-state concept of a free energy barrier. Reprinted from Dinner et ah. Trends Biochem. Sci. 25, 331, (2000) with permission from Elsevier...

In order to understand the effect of temperature on the water dynamics and how it leads to the glass transition of the protein, we have performed a study of a model protein-water system. The model is quite similar to the DEM, which deals with the collective dynamics within and outside the hydration layer. However, since we want to calculate the mean square displacement and diffusion coefficients, we are primarily interested in the single particle properties. The single particle dynamics is essentially the motion of a particle in an effective potential described by its neighbors and thus coupled to the collective dynamics. A schematic representation of the d)mamics of a water molecule within the hydration layer can be given by ... 

Moreover, to model proteins and peptides, MARCH-INSIDE biodescriptors were derived from the kth powers of an electron-transition stochastic matrix based on the —> Electronic Charge Index used in place of the electronegativity [Ramos de Armas, Gonzalez Diaz et al., 2005]. 

The NMR signal-to-noise ratio is directly proportional to the square root of the number of transitions and the total experimental time is mainly determined by the repetition time between two successive transitions, that is about five times of the spin longimdinal relaxation time Tj. Therefore, NMR sensitivity enhancement can be achieved by shortening the spin longitudinal relaxation time T. Ishii and colleagues have demonstrated that H Tj values of the two model proteins. 

Figure 19. Bacterial representatives of active ion-transport through membranes, modeling phase-transition strategies of protein information function lines stereo-presentation of a CPK-valinomycin movie , mediating by highly sophisticated biomesogenic interplays a K -ion membrane passage [7 a, 33 p, q, 35].

Quite the inverse occurs for water-dissolved protein of interest here that is, by the consilient mechanism, heating from below to above the folding transition increases the order of the model protein. Because heating increases protein order, the transition is called an inverse temperature transition. 

Figure 2.7. These crystals of cyclo(GVGVAPGVG-VAP) form when the temperature of aqueous solutions is raised and dissolve when the temperature is lowered. This finding represents an unambiguous demonstration that the model protein component of the aqueous solution becomes more ordered on higher temperature and is one of the reasons that the transition is called an inverse temperature transition. (Adapted with permission from Urry et al. )...

The above equations for photosynthesis and respiration, exactly balanced with respect to CO2, H2O, [C(H20)]6, and O2, mask an extraordinarily intricate set of reactions where balance tends to be masked by blurring detail. The objective here, however, is to dissect out sufficient detail to expose the primary energyconverting steps common to both processes and to demonstrate that model proteins, utilizing inverse temperature transitions, emulate key elements of those energy-converting steps. ... 

What can be demonstrated with model proteins functioning as contractile molecular machines is that two of the most effective means of lowering the temperature of an inverse temperatine transition to drive contraction are positively charged calcium ions (Ca ) binding at paired negatively charged carboxylates (COO ) to decrease net charge... 

The essential aspect of the capacity of the inverse temperature transition to achieve diverse energy conversions resides within large chain molecules, which were just becoming known when the first edition of Schrodinger s book appeared. As we have sketched above, the functional properties of the model protein-... 

Figure 2.18. Energies are shown that can be inter-converted by means of elastic-contractile model proteins capable of exhibiting inverse temperature transitions functioning by means of the competition for hydration between oil-like and charged groups called an apolar-polar repulsive free energy of hydration. See Chapter 5 for a more complete development of the phenomenology and physical basis and Chapter 8 for details of the molecular process.

A smart plastic would harmlessly disintegrate once its useful Life were completed. Plastics made of plastic-contractile model proteins with controllable inverse temperature transitions can be designed as smart plastics. A smart protein-based plastic, having fulfilled its role, would swell and become a fragile, edible gelatin-like substance. Rather than foretell death for the fishes, a smart protein-based plastic could provide food for the fishes, once its useful Life as a plastic were complete. 

D-amino acid residue on the right (an optical isomer that does occur in biology, but in those peptides not encoded for by the genetic code). C The effect of insertion of a D-amino acid residue in an otherwise L-amino acid residue protein in the P-spiral structure of the elastic-contractile model protein of our focus would be to disrupt the regular structure. This is difficult to avoid completely in chemical synthesis, and it increases the temperature at which occurs the inverse temperature transition and decreases the heat of the transition due to less optimal association of oil-like groupings. 

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