Thermodynamic hypothesis modeling

The existence of clathrate-like water structure adjacent to the hydrophobic surfaces of macromolecules is an attractive hypothesis. Models have been proposed which have received some support from thermodynamical arguments [808]. However, this concept has proved ineffective as a basis for the interpretation of the structure associated with the many electron density solvent peaks, separated by 2.8 A to 3.0 A, which are frequently observed on the Fourier X-ray maps close to the surface of a protein [809, 810], Recently, however, some local clathrate-like water has been observed in special cases in the high-resolution studies of the small plant protein, crambin [811], in a hydrated deoxydinucleoside-phosphate drug complex [812], in (Phe4Val6) antamanide hydrate [8131 and in an oligodeoxy-nucleotide duplex [814],... 

A somewhat simpler, but by no means trivial, task is to find the lowest energy state of the model polypeptide. Due to the thermodynamic hypothesis [158], which postulates that native proteins are in the global minimum of the conformational energy, the minimum energy state of a properly designed protein... 

The main point of this exercise and considerations is that you can easily examine the feasibility of the desolvation hypothesis by using well-defined thermodynamic cycles. The only nontrivial numbers are the solvation energies, which can however be estimated reliably by the LD model. Thus for example, if you like to examine whether or not an enzymatic reaction resembles the corresponding gas-phase reaction or the solution reaction you may use the relationship... 

A simple model of the chemical processes governing the rate of heat release during methane oxidation will be presented below. There are simple models for the induction period of methane oxidation (1,2.>.3) and the partial equilibrium hypothesis (4) is applicable as the reaction approaches thermodynamic equilibrium. However, there are apparently no previous successful models for the portion of the reaction where fuel is consumed rapidly and heat is released. There are empirical rate constants which, due to experimental limitations, are generally determined in a range of pressures or concentrations which are far removed from those of practical combustion devices. To calculate a practical device these must be recalibrated to experiments at the appropriate conditions, so they have little predictive value and give little insight into the controlling physical and chemical processes. 

Although the thermodynamic only hypothesis has not yet been extended to the whole spectrum of secretory proteins, it remains an alternative of choice to the quality control model. However, an integrated mechanism combining both hypotheses may represent a third option, then most likely applicable to all secretory proteins. 

Analysis of these new data have led to intensive development of a version of the hypothesis of formation of the BIF which can be called the biogeo-chemical accumulation version. In the U.S.S.R., besides in the works by Khodyush (1969) and Kaukin (1969), this hypothesis has been developed in recent years by Mel nik (1973, 1975) and Belevtsev and Mel nik (1976) on the basis of geologic, geochemical, and physicochemical investigations, including thermodynamic calculations and experimental modeling. The factual data, their interpretation, and possible models of deposition of the BIF will be examined in more detail in this book. 

The theoretical calculation of the thermodynamic properties of condensed phases is still in an early stage of development and only the simplest models can be treated quantitatively. For solids the simplest useful theory, that of Debye, assumes that the distribution of vibration frequencies among the atoms in the solid is the same as that of the frequencies of vibration of a continuous medium. The errors introduced by this hypothesis are difficult to estimate. Some progress has, however, been made recently in the direct evaluation of the thermodynamic properties of crystal lattices without having to liken them to continuous media.f... 

All in all, the conclusions of this stage of the analysis are that even quite simple physical models can account for many of the properties of the coexistence of solidlike and liquidlike clusters. But let us recall that all this was carried out assuming that the two forms could exist in thermodynamic equilibrium. The question was posed by Natanson et al. ° of what would be the necessary and sufficient conditions for that hypothesis to be valid. Answering that question and pursuing its immediate consequences, even at a qualitative or semiquantitative level, constituted the second stage of the analytic study. 

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