Protein-based machines

Another feature of protein-based information processing is the relatively large number of moving parts in a molecular machine. Unlike a digital circuit with electrons and holes as moving parts, protein-based machines consist of electrons. 

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. 

Protein-based machines undergo a special kind of phase separation that converts energy from one form to another ... 

As is argued in Chapter 8, small, often reversible, energy excursions back and forth across the boundary between associated (water-insoluble) and dissociated (water-soluble) oil-like domains (clusters of oil-like groups) drive the protein-based machines of biology. Biology often achieves mobility by many linear motors comprised of protein, such... 

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

Elemental Contractile Event as One Aspect of Protein-based Machines... 

Energy inputs cause shape changes in protein-based machines because of changes in association of oil-like domains. 

Such shape changes cause contractile protein-based machines to perform mechanical work. 

By this means, contractile protein-based machines can lift or pull weights they can pump iron. 

Analogy Between Fully Charged Carboxylate (-COO ) State of Model Proteins and the ATP -bound State of Protein-based Machines... 

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. 

ATPase, Biology s Workhorse Protein-based Machine... 

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.)... 

Thereby, the objective of this book is to demonstrate the phase separation mechanism of oil-like domains separating from water and related controlling phenomena at the molecular level as relevant to specific biological protein-based machines. 

These results of 18 years ago, demonstrating the capacity of de wovo-designed model protein-based machines for the conversion of chemical energy into mechanical work, remain unex-... 

The protons, now at 1,000-fold higher concentration in the thylakoid lumen than in the surrounding stroma, return across the thylakoid membrane from lumen to stroma and produce the chemical energy ATP by means of the protein-based machine ATP synthase, briefly considered below and in some detail in Chapter 8. 

The 1,000-fold greater concentration of protons (acid) of the intermembrane space return across the inner mitochondrial membrane and produce chemical energy, in the form of ATP. As in photosynthesis, the ATP results from the protein-based machine ATP synthase. 

The families of proteins that consume ATP while functioning as protein-based machines are called ATPases. Muscle contraction, just noted above, is a member of the family of linear (contractile) protein motors that also includes ATPases that walk along protein tubules and transport elements from one part of the cell to another. Another class of protein motors that uses ATP rotary and nonrotary ion pumps transports ions from one side to the other of the... 

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 ... 

Now, because it can cost just as much energy to produce an inefficient and more limited protein-based machine as it can to produce a more efficient and/or a new machine that can access a new energy source, obviously with natural selection the arrow of time for biology is toward greater complexity and diversity function (see Chapter 6). 

Protein-based Machines as Catalysts for Energy Conversion... 

Due to the struggle to survive under circumstances of limited food supply, organisms evolve to use the most efficient mechanism available to their composition. The most efficient mechanism available to the proteins that sustain Life would seem to be the apolar-polar repulsive free energy of hydration as observed for the inverse temperature transitions for hydrophobic association. The efficiency of designed elastic-contractile protein-based machines and a number of additional properties make designed protein-based materials of substantial promise for the marketplace of the future. 

Protein-based Machines in the Thylakoid and Inner Mitochondrial Membranes... 

A flow of electrons in a series of cell membrane-associated oxidation and reduction cycles provides the energy source in the energyconverting thylakoid membranes of plants and inner mitochondrial membranes of plants and animals. In the process of this electron flow, membrane proteins pump protons across a cell membrane to increase the concentration of protons on one side of the membrane (to be considered in Chapter 8). Another protein-based machine uses the high concentration of protons on one side of a cell membrane to drive the formation of ATP as the protons pass to the low concentration side of the membrane (also to be considered in Chapter 8). 

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