Biopolymer modeling

IS Lm, CE Lawrence. Bayesian inference on biopolymer models. Biomformatics 15 38-52, 1999. 

The biopolymer modeling of HyperChem includes Building polynucleotides, polypeptides and polysaccharides, Amino acid sequence (fasta format) editing, Mutations, Overlapping by RMS fit, and Merging structures. To facilitate manipulation of protein structures, there is often a need to display the protein backbone only as follows. 

For a long time, magic-angle spinning (MAS A has helped biomolecular NMR applications in cases where slow molecular tumbling or susceptibility effects prohibit high-resolution spectroscopy under static conditions. For example, the benehcial effect of MAS has been observed for structural studies on biopolymers, model membranes,... 

Enhanced catalytic activity of polymeric bound.imidazole has been investigated by numerous researchers who have used various types of macromolecular backbones and imidazole derivatives as biopolymer models. A summary of our work in the area of polymer containing imidazole has been presented in several review articles (6-8). In polymer catalysts containing imidazole there has been defined three important factors which contribute to the overall enhancement of the catalyst s efficiency cooperative interactions, electrostatic interactions and hydrophobic or apolar interactions. 

Mechanical Properties. Although wool has a compHcated hierarchical stmcture (see Fig. 1), the mechanical properties of the fiber are largely understood in terms of a two-phase composite model (27—29). In these models, water-impenetrable crystalline regions (generally associated with the intermediate filaments) oriented parallel to the fiber axis are embedded in a water-sensitive matrix to form a semicrystalline biopolymer. The parallel arrangement of these filaments produces a fiber that is highly anisotropic. Whereas the longitudinal modulus of the fiber decreases by a factor of 3 from dry to wet, the torsional modulus, a measure of the matrix stiffness, decreases by a factor of 10 (30). 

Figure 11.15 Cation-exchange mia O-LC analysis of a mixture of model proteins (a) the original sample consisting of myoglobin (M), cytochrome C (C) and lysozyme (L) (b) and (c) proteins adsorbed on to and then released from the polyaaylic acid coated fibre with exti ac-tion times of 5 and 240 s, respectively. Reprinted from Journal of Microcolumn Separations, 8, J.-L. Liao et al., Solid phase mia O exti action of biopolymers, exemplified with adsorption of basic proteins onto a fiber coated with polyaaylic acid, pp. 1-4, 1996, with permission from Jolm Wiley Sons, New York.

Klosinski, P., Penczek, S. Teichoic Acids and Their Models Membrane Biopolymers withPolphosphate Backbones. Synthesis, Structure and Properties. Vol. 79, pp. 139—157. 

Partially deacetylated chitin, a cellulose-like biopolymer consisting predominantly of N-acetyl-D-glucosamine chains, in the form of films or crosslinked hydrogels has been used for the delivery of drugs (28,29). The suitability of chitin as a vehicle for the sustained release of drugs was examined using indomethacin and papaverine hydrochloride as model drugs (30). In vitro studies showed that over 80% of the indomethacin was released within 7 hr, whereas papaverine hydrochloride dissolved almost immediately. 

Vibrational spectroscopy has played a very important role in the development of potential functions for molecular mechanics studies of proteins. Force constants which appear in the energy expressions are heavily parameterized from infrared and Raman studies of small model compounds. One approach to the interpretation of vibrational spectra for biopolymers has been a harmonic analysis whereby spectra are fit by geometry and/or force constant changes. There are a number of reasons for developing other approaches. The consistent force field (CFF) type potentials used in computer simulations are meant to model the motions of the atoms over a large ranee of conformations and, implicitly temperatures, without reparameterization. It is also desirable to develop a formalism for interpreting vibrational spectra which takes into account the variation in the conformations of the chromophore and surroundings which occur due to thermal motions. 

Kricheldorf H (1990) Polypeptides. In Pencze S (ed) Models of biopolymers by ring opening polymerization. CRC, Boca Raton, pp 1-132... 

Branco M, Wagner N, Pochan D et al (2009) Release of model macromolecules from selfassembling peptide hydrogels for injectable delivery. Biopolymers 92 318-318... 

Koltun WL. Precision space-filling atomic models. Biopolymers 1965 3 665-79. 

Here, an attempt to classify different strategies to generate 3D molecular models is undertaken with the aim to specify the remit of methods which will be covered under the term automatic 3D structure generators . The focus will be on methods designed for small, dmg-like molecules. The prediction of the geometry of polymers, in parhcular of biopolymers, is a task of its own and not even attempted by the approaches discussed here. 

Wilkes BC, Schiller, PW. Comparative analysis of various proposed models of the receptor-bound conformation of TIP(P)-related opioid antagonists. Biopolymers (Peptide Sci) 1995 37 391-400. 

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