Macromolecular conformations

Grubmiiller, 1995] Grubmiiller, H. Predicting slow structural transitions in macromolecular systems Conformational Flooding. Phys. Rev. E. 52 (1995) 2893-2906... 

M. Levitt and Shneior Lifson. Refinement of protein conformation using a macromolecular energy minimization procedure. J. Mol. Biol., 46 269-279, 1969. 

The NAs such as DNA usually used in the experiments consist of 10" -1 o nucleotides. Thus, they should be considered as macrosystems. Moreover, in experiments with wet NA samples macroscopic quantities are measured, so averaging should also be performed over all nucleic acid molecules in the sample. These facts justify the usage of the macroscopic equations like (3) in our case and require the probabilities of finding macromolecular units in the certain conformational state as variables of the model. 

R and M M Hann 2000. The In Silico World of Virtual Libraries. Drug Discovery Today 5 326-336. R and I D Kuntz 1990. Conformational Analysis of Flexible Ligands in Macromolecular eptor Sites. Journal of Computational Chemistry 13 730-748. 

An understanding of a wide variety of phenomena concerning conformational stabilities and molecule-molecule association (protein-protein, protein-ligand, and protein-nucleic acid) requires consideration of solvation effects. In particular, a quantitative assessment of the relative contribution of hydrophobic and electrostatic interactions in macromolecular recognition is a problem of central importance in biology. 

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. 

MK Gilson, B Homg. Calculation of the total electrostatic energy of a macromolecular system Solution energies, binding energies, and conformational analysis. Proteins 4 7-18, 1988. 

On the basis of the above data it has been hypothesized that the conductivity of PFCM is due not to the contact between the filler particles but the current passes across the thin (less than 1 -2 microns) polymer interlayers. The conductivity arises when a spontaneous pressure exceeding the threshold value develops in the material. The overstresses apparently arise as a result of PP crystallization in the very narrow gaps between the filler particles [312], Since crystallization must strongly affect the macromolecular conformation whereas the narrowness of the gap and fixed position of molecules on the filler prevent it, the heat released in the process of crystallization must, in part, be spent to overcome this hindrance, whereby a local high pressure may arise in the gap. This effect is possible only where there are gaps of the size comparable with that of macromolecules. The small gap thickness will also hamper pressure relaxation, since the rate of flow from such a narrow clearance should be negligibly small. 

Alzheimer s Disease. Figure 1 A(3 monomers can self-associate to form dimers, trimers and higher oligomers. Globular structures of synthetic A(342 are known as A(3-derived diffusible ligands (ADDLs) (3-12-mers of A(3). These structures are similar to the smallest protofibrils and represent the earliest macromolecular assembly of synthetic A(3. The characteristic amyloid fiber exhibits a high beta-sheet content and is derived in vitro by a nucleation-dependent self-association and an associated conformational transition from random to beta-sheet conformation of the A(3 molecule. Intermediate protofibrils in turn self-associate to form mature fibers. 

Within the class of polymer crystals having, ideally, long-range positional order for all the atoms, different crystalline forms (polymorphs) may arise as a result of having different almost isoenergetic macromolecular conformations (of the main chain, in most known cases) or as a result of different, almost isoenergetic modes of packing of macromolecules with identical conformations [1-3]. 

Morris, G. A. Castile, J. Smith, A. Adams, G.G. Harding, S.E. 2009. Macromolecular conformation of chitosan in dilute solution A new global hydrodynamic approach. Carbohydrate Polymers 76, 616-621. 

Ortega, A. Garcia de la Torre, J. 2007. Equivalent Radii and Ratios of Radii from Solution Properties as Indicators of Macromolecular Conformation, Shape, and Flexibility. Biomacromolecules 8, 2464-2475. 

The solid state conformations of macromolecular phosphazene chains can be successfully modeled using short chain oligomers. 

Otting G, Wiithrich K. Heteronuclear filters in two-dimensional H H] NMR spectroscopy combined use with isotope labelling for studies of macromolecular conformation and intermolecular interactions. Q Rev Biophys 1990 23 39-96. 

Viscosimetric studies of organotin copolymer solutions allow the changes in the shape of the macromolecules to be followed as a function of the electrostatic charge. From the plot of the intrinsic viscosity of copolymers in DMFA solution against the degree of dilution it is seen that increasing dilution results in a rise of viscosity, probably due to an extension of macromolecular chains accompanied by conformational transformations. Naturally, this rise in viscosity with dilution cannot proceed infinitely since a coiled chain cannot be extended more than a completely extended chain conformation, due to intramolecular repulsion. 

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