Macromolecular structures representation

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,... 

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. 

The aim of this chapter is to introduce and summarize the work on polymer nomenclature which has emanated, firstly, from the Commission on Macromolecular Nomenclature of the lUPAC Macromolecular Division and, latterly, from the Sub-Committee on Polymer Terminology of the lUPAC Macromolecular (now Polymer) Division, jointly with the lUPAC Chemical Nomenclature and Structure Representation Division. The Commission on Macromolecular Nomenclature is henceforth denoted as the Commission . 

Macromolecular structures such as star copolymers have been synthesized in the search for polymers with new mechanical and thermal properties and new degradation profiles. Fig. 7 shows a schematic representation of four-armed homo- and block copolymers. 

All representations of proteins are models of the actual structures themselves. These models can be built for different purposes, thus may or may not contain information about specific aspects of interest.3 The most common representations of proteins are based on 3D atomic coordinates, constituting the basis of the Protein Data Bank (PDB) format used to store as many as 63,000 macromolecular structures in the PDB4 as of February, 2010. These models, the majority of them determined by X-ray crystallography, are generally static in nature and give the impression that proteins adopt a single or just a few well-defined conformations... 

CML is the best known of the XML notations for capture of structural data, but several other formats use XML-based syntax. The Protein Data Bank (PDB) (http // www.wwpdb.org/) is the single worldwide repository for macromolecular structure data. A representation of the Brookhaven PDB is available in an XML format called PDBML (Westbrook et al. 2005). PDBML provides a way to export structures and information about them from a relational database. Another database that offers... 

The analysis of the resonant solution scattering data demands a different representation of the Debye Equation (30). If the macromolecular structure would have a spherical appearance, then the formalism of isomorphous replacement in single crystal diffraction outlined in the preceding section would apply. This is not surprising as the rotation of a spherical structure could not be noticed anyhow. In more complicated, asymmetric macromolecular structures it is the spherical average of the structure which can be subjected to the phase analysis described above. As this state-... 

Representation of the Macromolecu-lar Receptor. The most straightforward approach for representing the macromolecular structure in a docking application would be by atomic coordinates of the entire protein. A full atomic representation, however, is generally impractical because of the size and complexity of protein structures. The structural information therefore needs to be reduced to a manageable yet representative size and form. 

As biochemistry has advanced, more attention has been focused on the structures of biological macromolecules and their complexes. These structures comprise thousands or even tens of thousands of atoms. Although these structures can be depicted at the atomic level, it is difficult to discern the relevant structural features because of the large number of atoms. Thus, more schematic representations—ribbon diagrams and surface representations—have been developed for the depiction of macromolecular structures in which atoms are not shown explicitly (Figure 1.18). 

Structural representations of humic and fulvic acids are purely hypothetical and should just be considered as an attempt to rationalize chemical behavior. Several structural models have been proposed based on data gathered from degradative and nondegradative models. The different proposed models should be considered as complementary since each emphasizes certain particular properties. Briefly, humic acids are macromolecular and complex, and composed of substituted aromatic and aliphatic hydrocarbon core materials. It is probable that some aliphatic and aromatic ring compounds are heterocyclic with N, O, or S as the heteroatom. Segments or some side-chain components in the structures are substantially hydrophobic. In general, however, the... 

The architecture of complex polymers can be represented by simplified models consisting of beads connected by nonbreakable bonds in a way that corresponds to backbone contours of the macromolecules. Sueh molecules consist usually of a large number of beads assuming specific positions within a complex bond skeleton characteristic for each type of macromolecule. In this simplified representation of macromolecular structures, sizes of monomers are not distinguishable. With this approximation, the macromolecules can, however, be represented on lattices. The lattice plays the role of a topological skeleton of space and allows fast identification of neighbors. An example of such a representation of a linear macromolecule on the face-centered cubic (fee) lattice is shown in Fig. 9a. 

Macromolecules, including biopolymers, represent a challenge in generating meaningful structure representations and corresponding names, because frequently complete structural information is not known. Illustrations are shown from existing recommendations of the International Union of Pure and Applied Chemistry (lUPAC), and the International Union of Biochemistry (lUB). Examples from drafts under consideration by the lUPAC Commission on Macromolecular Nomenclature are also presented. Current handling of macromolecules by Chemical Abstracts Service (CAS) as well as some enhancements under development are illustrated. 

In this article the use of formula 3 will always refer to rotated Fischer projections. In any case, the formulas must represent a section of chain long enough to illustrate the structural features excluding, unless explicitly required, the terminal groups. This representation corresponds to the use of a macromolecular model with an infinite chain length. 

Fig. 13. Schematic representation of macromolecular liquid crystals. A smectic structure is assumed for all cases...

The linear size dependence of the AFDF family of methods is an advantage that can be exploited in the rapid generation of macromolecular electron density representations which are of better quality than those obtained by locally spherical distributions in the usual structure refinement process. The proposed approach, a quantum crystallographic application of the AFDF method (QCR-AFDF) is outlined below. 

Figure 1.89 Structure of dipalmitoyl L-a-phosphatidylcholine (DPPC) to illustrate the main molecular parameters and structural features that dictate the formation of crystalline lamellar phases of macromolecular lipid assemblies. Schematic representation of a phospholipid molecule is also show (inset).

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