Macromolecular structure, function

Ruan, K and Balny, C, 2002, High pressure static fluorescence to study macromolecular structure-function. Biochimica Biophysica Acta. Proteins and Proteomics. 1595, 94-102. 

The neuropharmacology of the ionenes is presumably not restricted to interactions with AcChR. Choline re-uptake, release of transmitter, and esterase activity may also be affected by this class of polymers, since in all cases recognition sites for quaternary nitrogen functions are involved. Thus the present paper is no more than a beginning in the application of ionenes to the pharmacological and biochemical study of the various macromolecular structures functioning in cholinergic transmission. 

It is possible to go beyond the SASA/PB approximation and develop better approximations to current implicit solvent representations with sophisticated statistical mechanical models based on distribution functions or integral equations (see Section V.A). An alternative intermediate approach consists in including a small number of explicit solvent molecules near the solute while the influence of the remain bulk solvent molecules is taken into account implicitly (see Section V.B). On the other hand, in some cases it is necessary to use a treatment that is markedly simpler than SASA/PB to carry out extensive conformational searches. In such situations, it possible to use empirical models that describe the entire solvation free energy on the basis of the SASA (see Section V.C). An even simpler class of approximations consists in using infonnation-based potentials constructed to mimic and reproduce the statistical trends observed in macromolecular structures (see Section V.D). Although the microscopic basis of these approximations is not yet formally linked to a statistical mechanical formulation of implicit solvent, full SASA models and empirical information-based potentials may be very effective for particular problems. 

Organization into macromolecular structures. There are no apparent templates necessary for the assembly of muscle filaments. The association of the component proteins in vitro is spontaneous, stable, and relatively quick. Filaments will form in vitro from the myosins or actins from all three kinds of muscle. Yet in vitro smooth muscle myosin filaments are found to be stable only in solutions somewhat different from in vivo conditions. The organizing principles which govern the assembly of myosin filaments in smooth muscle are not well understood. It is clear, however, a filament is a sturdy structure and that individual myosin molecules go in and out of filaments whose structure remains in a functional steady-state. As described above, the crossbridges sticking out of one side of a smooth muscle myosin filament are all oriented and presumably all pull on the actin filament in one direction along the filament axis, while on the other side the crossbridges all point and pull in the opposite direction. The complement of minor proteins involved in the structure of the smooth muscle myosin filament is unknown, albeit not the same as that of skeletal muscle since C-protein and M-protein are absent. 

This approximation has already proven very effective in the calculation of likelihood functions for maximum likelihood refinement of parameters of the heavy-atom model, when phasing macromolecular structure factor amplitudes with the computer program SHARP [53]. A similar approach was also used in computing the variances to be used in evaluation of a %2 criterion in [54]. 

Well-defined complicated macromolecular structures require complex synthetic procedures/techniques and characterization methods. Recently, several approaches leading to hyperbranched structures have been developed and will be the focus of this section. The preparation of hyperbranched poly(siloxysilane) has been reported [198] and is based on methylvinyl-bis(dimethyl siloxysilane), an A2B type monomer, and a progressive hydrosi-lylation reaction with platinum catalysts. An appropriate hydrosilylation reaction on the peripheral - SiH groups led to the introduction of polymeric chain (PIB, PEO) or functional groups (epoxy, - NH2) [199]. 

Protein Explorer, a free RasMol and Chime derivative with extended capabilities, is available at http //www.umass.edu/microbio/chime/explorer/. The program allows the user to visualize macromolecular structure in relation to function. 

Weak Interactions Are Crucial to Macromolecular Structure and Function... 

Short range order in liquid-like systems as well as long range order in crystalline domains are reflected in WAXS-patterns very dearly. Some examples of calculated X-ray patterns from PTFE (Phase I), a smectic LC-phase and even a PE melt, show that our model covers a wide range of macromolecular structures running the whole scale from crystalline systems over mesophases up to polymer melts. The range of intra- and intermolecular order can be estimated fairly well with the help of density correlation functions. 

Figure 5.3. A humic acid macromolecule interacting with a surface of a clay mineral. The proposed macromolecular structure of the soil humic acid (HA) is based on the following common average characteristics of humic acids MW 6386 Da elemental analysis (%) C, 53.9 N, 5.0 H, 5.8 0,35.1 S, 0.5 C/N, 10.7 NMR information (%) aliphatic C, 18.1 aromatic C, 20.9 carbohydrate C, 23.7 metoxy C, 4.9 carboxylic C, 8.4 ketone C, 4.5 phenolic C, 4.2 functional groups (cmol/g) carboxyl, 376 phenol, 188 total acidity, 564. The structure was created using the ACD/ChemSketch program. [HA-clay complex Chen s group, unpublished (2008). Individual HA molecule Grinhut et al., 2007.]...

Variables Influencing Tg. Since Tg is a function of macromolecular mobility, any changes to the macromolecular structure that increases or decreases this mobility will have an effect upon Tg. The following discussion highlights several variables that can impact the observed glass transition temperature. 

Covalent and metallosupramolecular block copolymers have been combined in a single macromolecular structure. In this respect a terpyridine-functionalized PS-P2 VP has been complexed with a terpyridine-functionalized PEO, leading to a PS32-P2VPi3-[Ru]-PE07o ABC triblock copolymer [330]. This copolymer was further used to prepare core-shell-corona micelles consisting of a PS core, a pH-responsive P2VP shell, and a PEO corona. 

Reactive polymer processing modifies or functionalizes the macromolecular structure of reactor polymers, via chemical reactions, which take place in polymer processing equipment after the polymer is brought to its molten state. The processing equipment then takes on an additional attribute, that of a reactor, which is natural since such equipment is uniquely able to rapidly and efficiently melt and distributively mix reactants into the very viscous molten polymers. The operation is shown schematically in Fig. 1.3. 

The viscoelastic response of polymer melts, that is, Eq. 3.1-19 or 3.1-20, become nonlinear beyond a level of strain y0, specific to their macromolecular structure and the temperature used. Beyond this strain limit of linear viscoelastic response, if, if, and rj become functions of the applied strain. In other words, although the applied deformations are cyclic, large amplitudes take the macromolecular, coiled, and entangled structure far away from equilibrium. In the linear viscoelastic range, on the other hand, the frequency (and temperature) dependence of if, rf, and rj is indicative of the specific macromolecular structure, responding to only small perturbations away from equilibrium. Thus, these dynamic rheological properties, as well as the commonly used dynamic moduli... 

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