Macro-molecular structures

Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, R, Grosse-Kunstleve, R. W., etal. (1998) Crystallography and NMR system Anew software suite for macro-molecular structure determination. Acta Crystallogr. D 54, 905-921. 

Hendrickson, W. A. (1991). Determination of macro-molecular structures from anomalous diffraction of synchrotron radiation. Science 254, 51-58. 

How are the mechanical properties related to the arrangement of macro-molecular structures and their functional significance ... 

In order to begin to understand and appreciate how a protein may interact with a surface, it is important to be able to see the protein in three dimensions. This usually requires the use of models which, in the case of proteins, are terribly cumbersome and expensive. In many institutions molecular models have been replaced by three-dimensional molecular computer graphics. There are some 70 major molecular graphics installations throughout the world which have the capabilities of imaging large macro-molecular structures in three dimensions. 

A]successful introduction for those who try to understand and explore biological macro-molecular structures...The text is loaded with many excellent didactic concepts and approaches."... 

Inkson et al. (61) and McLeish (62) in a recent review have proposed also a multimode pom-pom model in an attempt to account for the multiple levels of branching believed to be present in LDPE molecules. Because the precise structure and degree of branching of LDPE molecules are unknown, with no experimental techniques to determine them, the potential exists for these multimode models to characterize the LDPE macro-molecular structure through fitting with experimental rheological data. 

Despite the high turnover rates of Glaser-type couplings, their applicability to the synthesis of macro-molecular structures is limited by two points ... 

Unconjugated dienes can produce an even more complicated range of macro-molecular structures. Homopolymers of such monomers are not of current commercial importance but small proportions of monomers like 1,5-cyclooctadicne are copolymerized with ethylene and propylene to produce so-called EPDM rubbers. Only one of the diene double bonds is enchained when this terpolymeriza-tion is carried out with Ziegler-Natta catalysts (Section 9.5). The resulting small amount of unsaturation permits the use of sulfur vulcanization, as described in Section 1.3.3. 

Bmnger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice, LM, Simonson, T, and Warren, GL. Crystallography NMR system A new software suite for macro-molecular structure determination. Acta Cryst. D-Biol. Cryst. 1998 54 905-921. 

As has been discussed above, molecular clusters produced in a supersonic expansion are preferred model systems to study solvation-mediated photoreactions from a molecular point of view. Under such conditions, intramolecular electron transfer reactions in D-A molecules, traditionally observed in solutions, are amenable to a detailed spectroscopic study. One should note, however, the difference between the possible energy dissipation processes in jet-cooled clusters and in solution. Since molecular clusters are produced in the gas phase under collision-free conditions, they are free of perturbations from many-body interactions or macro-molecular structures inherent for molecules in the condensed phase. In addition, they are frozen out in their minimum energy conformations which may differ from those relevant at room temperature. Another important aspect of the condensed phase is its role as a heat bath. Thus, excess energy in a molecule may be dissipated to the bulk on a picosecond time-scale. On the other hand, in a cluster excess energy may only be dissipated to a restricted number of oscillators and the cluster may fragment by losing solvent molecules. 

Therapeutic proteins typically exist in a noncrystalline or amorphous form because their macro-molecular structures are not readily crystallized. These materials are commonly prepared in an amorphous dispersion with bulking and stabilizing excipients to ensure an adequate product shelf life and ease of administration. Examples of such therapeutic proteins include insulin and interferon. 

If the model derived from the diffraction data were correct in every way, and the measured data were perfect, then the agreement would be exact Fhkt-obs would always equal Fhki-caic and R = 0. But this is never the case. The data, of course, contain measurement errors, the atomic positions may be accurate and precise, but still not perfect, temperature factors and the ellipsoids of vibration may be only approximate, and so on. In general, even for a very well and correctly determined structure, R will commonly be in the range of 0.05 to 0.10 for a conventional crystal having an asymmetric unit of 50 or so atoms. For macro-molecular structure determinations, R is normally in the range of 0.15 to 0.25. The R factor is in most cases the ultimate criterion of model quality at the resolution it was determined. 

In order to exploit the heavy atom method with crystals of conventional molecules, or to utilize the isomorphous replacement method or anomalous dispersion technique for macro-molecular structure determination, it is necessary to identify the positions, the x, y, z coordinates of the heavy atoms, or anomalously scattering substituents in the crystallographic unit cell. Only in this way can their contribution to the diffraction pattern of the crystal be calculated and employed to generate phase information. Heavy atom coordinates cannot be obtained by biochemical or physical means, but they can be deduced by a rather enigmatic procedure from the observed structure amplitudes, from differences between native and derivative structure amplitudes, or in the case of anomalous scattering, from differences between Friedel mates. 

Fifty percent of the total energy needed to produce plastic materials is used in the polymerization process. Thus at first sight, it seems sensible to re-use plastic and rubber waste materials (8 ). But Re-use processes have a negative influence on the macro-molecular structure which is mainly a chain depolymerisation effect (9 ). Therefore Re-use by itself is not a satisfactory process. In addition,a large proportion of the plastic waste is polluted and mixed with other types of waste so that Re-use is impossible. 

The best extractants in the above list of salts form complexes with the polyvalent metals that neutralize charges on the humic substances and link them to the inorganic soil colloids. These polyvalent ions are replaced by sodium ions from the salts. The efficiency of each solvent system will depend on the extent to which the resident cations are exchanged and removed from humic structures. Diffusion of the salts to the interior of solid humic substances is slow. Some channeling can take place, but extensive penetration would probably require the opening up from the outside of the macro-molecular structures. It would be necessary for these structures to remain open to allow exchange from the interior to take place. 

Tailor-made materials require access to linear as well as to branched macro-molecular structures. FTIR spectra of the polymer and GC analysis of the oligomers in solution (if present) can be used for characterization and as a reference for structural changes. 

Chacon, P., and W. Wriggers. 2002. Multi-resolution contour-based fitting of macro-molecular structures. J Mol Biol 317 375-84. 

Molecular dynamics (MD), while computationally very expensive, is often used to relax structures, relieve local strain, and refine models of macro-molecular structures or complexes of these with ligands docked into the receptor site. Basically, MD consists of solving Newton s equations of motion for each atom in a system as a function of time and energy funaions describing interatomic forces. > While calculating the atomic trajeaories is slow, once calculated these can be stored and often played back in real time, thus creating a picture of the system as it evolves over time. 

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