Protein-based machines developing

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 ... 

Straightforward Development of Elastic Protein-based Machines for Pumping Iron... 

Accordingly, the perspectives in Chapter 5, developed on elastic-contractile protein-based polymers, introduce new concepts into the functional description of biology s protein-based machines. As with the introductory comments in Chapter 7, the footnote relevant to reactions toward new concepts in science is repeated here in footnote form. ... 

One of the more challenging locations, therefore, for consideration of the comprehensive hydrophobic effect in the panoply of biological energy conversions is the electron transport chain embedded within the inner mitochondrial membrane. Essential parts of these protein-based machines insert into and function in very hydrophobic lipid bilayers. Here the ingress and egress of protons for develop-... 

The second point addresses the nature of elastic force development in relation to imder-standing efficient energy conversion. If the energy required for chain deformation during elastic force development becomes lost to other parts of the protein and to the surrounding water, then so too is efficient energy conversion lost. In other words, elastomeric force development on deformation in a protein-based machine followed by marked hysteresis on relaxation necessarily denotes an inefficient protein-based machine. 

The development of force under conditions of fixed length, as in an isometric contraction, involves the elastic deformation of a chain or chains within the protein-based machine. On relaxation, ideal elastic elements return the total energy of deformation to the protein-based machine for the performance of mechanical work. Thus, the approach toward high efficiency for the function of a protein-based linear motor, or even for the RIP domain movement in Complex III, depends on how nearly the extension of an elastomeric chain segment approaches ideal elasticity. 

Even so, crystal structures provide the best snapshots of forces in action. Crystal structures provide an unparalleled opportunity to assess relevance to the major protein-based machines of biology of the free energy transduction so dominantly displayed by elastic-contractile model proteins (as developed in Chapter 5). If the apolar-polar repulsive free energy of hydration, AG.p, the operative component of the Gibbs free energy of hydrophobic association, AGha> is active in ATP synthase, then it should become apparent in these snapshots. 

E.3.2 Idols That Retard Utilization of the Elastic Consilient Mechanism in Understanding and Developing Protein-based Machines and Materials... 

This volume represents a sincere attempt, backed by extensive commitment and effort, to overcome some of the current idols which beset men s minds in the area of protein-based machines and materials. More broadly, it opens the door for a new look at the physical basis whereby amphiphilic polymers function in water and presents the basis with which to engineer protein-based polymers as has not previously been possible. TTie primary purpose is to extend knowledge of the forces that provide function for protein-based machines and materials and thereby to achieve a greater comprehension of living organisms and to develop new materials for the benefit of society. 

In Chapter 9, the capacity to design protein-based molecular machines and materials turns toward the development of useful applications for improving individual health and environmental health. With insight as to how the protein-based machines of biology work, and, because we know how they work, we can... 

B and W J Howe 1991. Computer Design of Bioactive Molecules - A Method for Receptor-Based Novo Ligand Design. Proteins Structure, Function and Genetics 11 314-328. i H L 1965. The Generation of a Unique Machine Description for Chemical Structures - A hnique Developed at Chemical Abstracts Service. Journal of Chemical Documentation 5 107-113. J 1995. Computer-aided Estimation of Symthetic Accessibility. PhD thesis. University of Leeds, itan R, N Bauman, J S Dixon and R Venkataraghavan 1987. Topological Torsion A New )lecular Descriptor for SAR Applications. Comparison with Other Descriptors. Journal of emical Information and Computer Science 27 82-85. 

In this study, a machine learning model system was developed to classify cell line chemosensitivity exclusively based on proteomic profiling. Using reverse-phase protein lysate microarrays, protein expression levels were measured by 52 antibodies in a panel of 60 human cancer cell (NCI-60) lines. The model system combined several well-known algorithms, including Random forests, Relief, and the nearest neighbor methods, to construct the protein expression-based chemosensitivity classifiers. 

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