Structure macromolecular

In this section I have chosen not to describe solution structures of free proteins, as such publications have increasingly modest impact. Structures of macro-molecular complexes are considerably more informative from a biological perspective and this year has seen further impressive studies. 

Dipolar waves describe the structure and topology of helices in membrane proteins. The fit of sinusoids with the 3.6 residues per turn period of ideal 

Recent applications of solid state NMR to membrane protein characterisation also include the light-harvesting complex II of Rhodopseudomonas acidophila , glycinated mastoparan-X , diacylglyerol kinase from E. coli phospholamban , Rv2433c from Mycobacterium tuberculosis and the ABC transporter LmrA from Lactococcus lactis .  

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Flendrickson W A 1991 Determination of macromolecular structures from anomalous diffraction of synchrotron radiation Soienoe 254 51-8... 

F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E. Meyer, M.D. Bryce, J.R. Rogers, O. Kennard, T. Shikanouchi and M. Tasumi, The protein data bank A computer-based archival file for macromolecular structures, J. Mol. Biol. 112 (1977), 535-542. 

An alternative and much more flexible approach is represented hy the STAR file format [L48, 149, which can be used for building self-describing data files. Additionally, special dictionaries can be constructed, which specify more precisely the contents of the eorresponding data files. The two most widely used such dictionaries (and file formats) arc the CIF (Crystallographic Information File) file format [150] - the International Union of Crystallography s standard for representation of small molecules - and mmCIF [151], which is intended as a replacement for the PDB format for the representation of macromolecular structures,... 

Bernstein F C, T F Koetzle, G J B Williams, E Meyer, M D Bryce, J R Rogers, O Kennard, T Shikanouchi and M Tasumi 1977. The Protein Data Bank A Computer-Based Archival File for Macromolecular Structures. Journal of Molecular Biology 112 535-542. 

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. 

Molecular modeling is an indispensable tool in the determination of macromolecular structures from NMR data and in the interpretation of the data. Thus, state-of-the-art molecular dynamics simulations can reproduce relaxation data well [9,96] and supply a model of the motion in atomic detail. Qualitative aspects of correlated backbone motions can be understood from NMR structure ensembles [63]. Additional data, in particular residual dipolar couplings, improve the precision and accuracy of NMR structures qualitatively [12]. 

PC Bernstein, TP Koetzle, GIB Williams, EE Meyer, MD Brice, JR Rodgers, O Kennard, T Shimanouchi, M Tasumi. Protein Data Bank Computer based archival file for macromolecular structure. J Mol Biol 112 535-542, 1977. 

Bernstein, F.C., et al. The protein data bank a computer-based archival file for macromolecular structures. 

Walter, R.L., et al. High resolution macromolecular structure determination using CCD detectors and synchrotron radiation. Structure 3 835-844, 1995. 

Stuhrmann, H. Resoance Scattering in Macromolecular Structure Research. Vol. 67, pp. 123-164. 

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. 

The structural investigations have been extended to potassium derivatives of the "super" formamidine HC(NC6H3Pr2-2,6)(NHC6H3Pr2-2,6) ( = HDippForm). Treatment of the free formamidine with KN(SiMe3)2 yielded the formamidinate species [K(DippForm)2K(THF)2l (THF) , which exhibits a macromolecular structure of alternating fj -arene f/ -amidinate bound potassium di-amidinate and potassium di-THF units in a one-dimensional polymeric array (Figure 5). Addition of a further equivalent of HDippForm afforded hydrogen-bonded [K(DippForm)(THF)3](HDippForm). ... 

The concept of silicates as inorganic polymers was implicit in the ideas developed by W. H. Zacheriasen in the early 1930s. He conceived of silicates as consisting of macromolecular structures held together by covalent bonds but including network-dwelling cations. These cations were not assumed to have a structural role but merely to be present in order to balance the charges on the anionic polymer network. 

Advances in the study of macromolecular structures, e.g., complex and supramolecu-lar fluids, and the synthesis of new materials, e.g., nanostructured media, which may lead to the design of optimal materials for given separations or other applications... 

Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr., Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank A computer-based archival file for macromolecular structures. J Mol Biol 1977 112 535-42. 

Murshudov GN, Vagin AA, Oodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst 1997 053 240-55. 

Hendrickson WA. Stereochemically restrained refinement of macromolecular structures. Methods Enzymol 1985 115 252-70. 

A worldwide repository for the processing and distribution of three-dimensional biologic macromolecular structure data.) The Protein Kinase Resource http //pkr.sdsc.edu/html/index. shtml... 

The implications of the foregoing concept have profoundly influenced modern trends in polymer research. If polymers owe their differences from other compounds to the extent and arrangement of their primary valence structures, the problem of understanding them is twofold. It is necessary in the first place to provide appropriate means, both experimental and theoretical, for elucidating their macromolecular structures a[Pg.3]

Thaler, H., Macromolecular structures in coffee, Coll. Int. Chlm. Cafe, 7, 175, 1975. 

M. B. Mathews, Connective Tissue Macromolecular Structure and Evolution, Springer-Verlag, New York, 1975. 

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]. 

Hauptman, H. (in press) The phase problem of X-ray crystallography. In Direct Methods for Solving Macromolecular Structures, Fortier, S. (Ed.), Kluwer, Dordrecht. 

Pullman, A., and B. Pullman. 1980. Electrostatic Effect of Macromolecular Structure on the Biochemical Reactivity of the Nucleic Acids. Significance for Chemical Carcinogenesis. Int. I. Quant. Chem., Quant. Biol. Symp. 7, 245. 

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