Elastic-contractile model proteins structure

Based on a series of designed elastic-contractile model proteins. Figure 1.2 exhibits a family of curves whereby stepwise linear increases in oil-like character give rise to supra-linear increases in curve steepness, that is, in positive cooperativity. More oil-like phenylalanine (Phe, F) residues with the side chain -CH2-C6H5 replace less oil-like valine (Val, V) residues with the side chain -CH-(CH3)2. Here the structural symmetry is translational with as many as 42 repeats (Model protein v) of the basic 30-residue sequence, and the structure is designed beginning with a repeating five-residue sequence of a fibrous protein, the mam-mahan elastic fiber. 

Most significantly, however, the molecular basis for positive cooperativity and the result of increased functional efficiency in designed elastic-contractile model proteins has been experimentally determined to be the competition for water that occurs between oil-like domains and charged groups constrained to coexist within a protein structure (see immediately below and Chapter 5, section 5.1.7.4). This represents the principal statement of the Mechanistic Assertion. 

Ec(uivalence of Energy Conversion to Biology s Proteins yet Structural Limitations of Elastic-contractile Model Proteins... 

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. 

The family of dynamic elastic-contractile model proteins that form the basis for the assertions of the central message of this volume do not lend themselves to the precise spatial descriptions of proteins that form crystals. Nonetheless, important structural description is possible for the poly(GVGVP) family. Indeed, the experimental and computational elucidation of... 

Figure 3.12. Molecular structure of the parent elastic-contractile model protein as described in the text. See Chapter 5 for discussion of experimental basis of the structure. (Parts A, B, C, D, E, and F reproduced with permission from Urry et al., ° Cook et al., Urry, Urry, and Urry et al., respectively.)...

Several points require consideration on identification of AH,(CH2) - T,(GVGIP)AS,(CH2) as -AGha(CH2). The points include the separability assumption of Equations (5.3) and (5.4), the relevance of the model protein to such identification, and the choice of reference state in order that the nonlinearity of hydrophobic-induced pKa shifts be included. From the data of Butler, the separability is reasonable for a simple CH group, but examination of the calculated result is required to be satisfied whether or not extension to more complex substituents is warranted. As the inverse temperature transition of (GVGVP) has been experimentally shown to involve no Raman detectable changes in secondary structure, the elastic-contractile model proteins of focus here reasonably represent the best known model available for such an effort. It should be noted, however, that NMR studies on the temperature and solvent dependence of peptide NH and... 

The following consideration of cytochrome c oxidase reviews (1) composition, (2) structure, (3) overall reaction, (4) the electron transfer steps of cytochrome c oxidase, (5) status of proton translocation and proposed aqueous D- and K-channels for proton ingress, (6) the redox Bohr effect and its correlation with electrochemical transduction in elastic-contractile model proteins, and (7) possible molecular sources of protons for translocation with an abundant and uniquely positioned functional side chain that exhibits interesting parallels to the states of QH2 with, however, single rather than double proton changes and coordination to a metal ion required for electron transfer capability. 

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. 

Furthermore, yet to be computed by any program is the fundamental thermo-mechanical transduction wherein the cross-linked elastic-contractile model proteins contract and perform mechanical work on raising the temperature through their respective inverse temperature transitions. These results first appeared in the literature in 1986 and have repeatedly appeared since that time with different preparations, compositions, and experimental characterizations. Additionally, the set of energies converted by moving the temperature of the inverse temperature transition (as the result of input energies for which the elastic-contractile model protein has been designed to be responsive) have yet to be described by computations routinely used to explain protein structure and function. 

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