Protein-based machines consilient mechanisms

Urry DW (2005) What sustains life Consilient mechanisms for protein-based machines and materials. Springer, Berlin Heidelberg New York... 

Urry, D.W. (2006) What Sustains Life Consilient Mechanisms for Protein-based Machines and Materials, Springer, New York, N.Y. 

The consilient mechanisms in relation to protein-based machines of biology are introduced. Before the four major assertions that... 

By the Consilient Mechanism Protein-based Machines Require Water to Function... 

A protein-based machine without water as an integral part of its structure could not function by the consilient mechanism. In other words, water is required in at least one of the two states in order to have a movable cusp of insolubility, and in order for competition for hydration to be relevant there must be adequate water present. The first prerequisite, therefore, in addressing the biological relevance of the consilient mechanism is to assess whether or not water exists within or between the changing structural elements of a protein motor during function. 

B A space-filling view of all water molecules detected by X-ray diffraction demonstrates the internal waters of ITiales available to function by the consilient mechanism for protein-based machines. (Figure preparation was based on the crystallographic data of Abrahams et al. obtained from the Protein Data Bank, Structure File IBMF.)... 

In Chapter 8, more structural background and molecular details of contraction exhibited by the linear myosin II motor are considered after, in Chapter 5, the physical basis for the apolar (oil-like)-polar (vinegar-like) repulsive energy that controls hydrophobic association is experimentally and analytically developed. The crystal structures of the cross-bridge of scallop muscle provide remarkable examples of the consilient mechanism functioning in this protein-based machine ... 

In this chapter we briefly note the improbability of a protein comprised of 20 different amino acids in specified sequence. Then we step through the details whereby a protein of specified sequence comes into being, and, like the accountant, sum up the cost in terms of the biological energy currency, adenosine triphosphate (ATP), that is, in terms of the number of ATP molecules consumed in the production of a protein of unique sequence. Such an essentially ordinary exercise requires inclusion in this book in order to remove unnecessary mystery of protein production, to provide an example whereby molecular machines utilize energy to produce biological structure, and to place in perspective the ease with which new protein-based machines evolve when functioning by the consilient mechanism. 

Consilient Mechanisms for Diverse Protein-based Machines The Efficient Comprehensive Hydrophobic Effect... 

Because hydrophobic association does not occur until the temperatiu e is above T, for the phosphorylated state, the phosphate cannot be folded into a low dielectric constant site, but instead would be fully exposed to the solvent. It is fundamental to the consilient mechanism of protein-based machines to understand how this can be As discussed in section 5.7, the high-energy state of the phosphate is due to competition for hydration between the phosphate and the hydrophobic groups, as reflected in the large change in Tt. 

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