Native protein structures modeling techniques

Several steps were needed to determine the structure of the core particle to higher resolution (Fig. Id). The X-ray phases of the low-resolution models were insufficient to extend the structure to higher resolution, since the resolution of the early models of the NCP was severely limited by disorder in the crystals. The disorder was presumed to derive from both the random sequences of the DNA and from heterogeneity of the histone proteins caused by variability in post-translational modification of the native proteins. One strategy for developing an atomic position model of the NCP was to develop a high-resolution structure of the histone core. This structure could then be used with molecular replacement techniques to determine the histone core within the NCP and subsequently identify the DNA in difference Fourier electron density maps. 

In protein structure prediction, potentials are used to assign an energy-like quantity to a conformation of a protein molecule. If this quantity enables us to distinguish the native state of a protein, the potential is regarded as a reasonable model for a protein-solvent system. The rationale behind this relies on two assumptions (a) a solved protein in its native state can be described by an ensemble of closely related conformations, and (b) in this state the system is in the global minimum of free energy. Virtually all techniques designed for structure prediction are based on these principles [3,4]. 

Template-associated synthetic proteins (TASP), proteins that have been designed and synthesized de novo. Artificial tertiary structures can be constructed by covalent attachment of secondary structure building blocks, e.g., /3-sheets, a-helices, and turns, to a topological template. This results in a non-linear architecture of protein modules that is nevertheless able to mimic native proteins. The combination of different secondary structure motifs in TASP provides, e.g., /Sa/3-structures, helix-bundles, or /3-barrel tertiary structures. The design of TASP makes extensive use of molecular modeling techniques. Solid-phase synthesis and spot synthesis have been used to obtain TASP [G. Tuchscherer, M. Mutter,... 

Two additional decoy data sets of misfolded proteins [17] and of predicted protein structures from the Critical Assessment of Techniques for Protein Stmcture Prediction (CASP) [67] are also used to illustrate the method and its utility. Individual components of the energy perform worse than the total energy for example, for the bulk of the well-packed decoys, the van der Waals energy provides very little information about structural similarity between a well-packed non-native structure and the native state. It is also shown that some aspects of the SGB model results can be mimicked by a screened electrostatic energy, although the SGB approximation provides a better discriminatory measure between non-native and native states. 

This article describes the current state of the art and various applications of modeling techniques to the prediction of the native, biologically active conformation of a protein. This is a very active area of computational biology, and there are a number of excellent reviews of the field. " Here, we focus on the use of simplified or reduced protein models and the insights that they can provide into protein structure prediction and the nature of interactions in globular proteins. 

In addition to traditional X-ray techniques to study silk (Bram etal., 1997 Lotz and Cesari, 1979 Riekel et al., 1999a Warwicker, 1960), other structural tools have helped unravel various aspects of silk protein conformation. These include solid-state NMR (Asakura et al., 1983, 1988, 1994 Beek et al., 2000, 2002) studies of native and regenerated silk together with and studies of isotopically edited silks, which have dramatically improved the model of structure distribution within silk fibers (Beek et al., 2000, 2002). 

The determination of binding and conformational changes leaves the question of the detailed structure of complexes unanswered. At present there is no absolute method for structure determination of protein-surfactant complexes apart from x-ray diffraction, which has only been applied to lysozyme with three bound SDS molecules [49]. X-ray diffraction requires a crystal, so in the case of lysozyme cross-linked triclinic crystals of the protein were soaked in 1.1 M SDS and then transferred to water or a lower concentration (0.35 M) of SDS to allow the protein to refold. It was necessary to use cross-linked crystals to prevent them dissolving when exposed to a high SDS concentration. The resulting denatured-renatured crystals were found to have three SDS molecules within a structure that was similar but not identical to that of native lysosyme. Neutron scattering has been applied in a few cases (see Sec. IX), but this is a model-dependent technique. 

Infrared spectroscopy is largely unaJTected by the aforementioned problems. The technique can be used to study the secondary structure of proteins, both in their native environments, as well as after reconstitution into model membranes. In particular, infrared spectroscopy offers several advantages in studies of protein-lipid interactions. Information about lipid conformation and protein secondary structure can be obtained in a single experiment from the same sample. 

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