Protein structure types

Protein Structural type Number of Number of solvent Resolution R factor a (bonds) Refinement method Reference... 

To note, intermediate filaments are cytoskeletal structures that are formed by different members of a family of related, highly conserved proteins (Godsel et al. 2008). Most types of intermediate filaments are located in the cytoplasm. The nuclearly localized intermediate filaments are called lamins. Categorization of intermediate filaments into six groups has been done on the basis of similarities in amino acid sequence and protein structure. Types I and II intermediate filaments are acidic and basic keratins, namely epithelial keratins and trichocytic keratins (e.g., in hair and horns). Type III intermediate filaments are, e.g., vimentin (widely expressed in fibroblasts), Type IV intermediate filaments are, e.g., neurofilaments, type V intermediate filaments are nuclear lamins, type VI intermediate filaments are nestin. A well-known disease resulting from... 

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

Lipids differ from the other classes of naturally occurring biomolecules (carbohy drates proteins and nucleic acids) in that they are more soluble m nonpolar to weakly polar solvents (diethyl ether hexane dichloromethane) than they are m water They include a variety of structural types a collection of which is introduced m this chapter... 

Eortunately, a 3D model does not have to be absolutely perfect to be helpful in biology, as demonstrated by the applications listed above. However, the type of question that can be addressed with a particular model does depend on the model s accuracy. At the low end of the accuracy spectrum, there are models that are based on less than 25% sequence identity and have sometimes less than 50% of their atoms within 3.5 A of their correct positions. However, such models still have the correct fold, and even knowing only the fold of a protein is frequently sufficient to predict its approximate biochemical function. More specifically, only nine out of 80 fold families known in 1994 contained proteins (domains) that were not in the same functional class, although 32% of all protein structures belonged to one of the nine superfolds [229]. Models in this low range of accuracy combined with model evaluation can be used for confirming or rejecting a match between remotely related proteins [9,58]. 

All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves. These are difficult to illustrate. Therefore we use different types of simplified representations, including space-filling models ball-and-stick models, where atoms are spheres and bonds are sticks and models that illustrate surface properties. The most detailed representation is the ball-and-stick model. However, a model of a protein structure where all atoms are displayed is confusing because of the sheer amount of information present (Figure 2.9a). 

Figure 2.10 Examples of schematic diagrams of the type pioneered by Jane Richardson. Diagram (a) illustrates the structure of myoglobin in the same orientation as the computer-drawn diagrams of Figures 2.9b-d. Diagram (b), which is adapted from J. Richardson, illustrates the structure of the enzyme triosephosphate isomerase, determined to 2.5 A resolution in the laboratory of David Phillips, Oxford University. Such diagrams can easily be obtained from databases of protein structures, such as PDB, SCOP or CATH, available on the World Wide Web.

The way that Pn peptides self-assemble is important for polypeptides and proteins amyloid-type structures are believed to have the same core stmcture, and in fact the propensity to self-assemble in this manner is hypothesized to be a general property of polypeptides [52]. It is therefore unsurprising that systems featuring this motif are common. In recent years, a push towards the use of peptide-based self-assembled materials has led to increasing interest in extending their functionality by derivatising them. 

NMR Experiments and the Types of Labeling Suited for Protein Structure Determination ... 

The plant cell wall contains different types of polysaccharides, proteins (structural glycoproteins and enzymes), lignin and water, as well as some inorganic components (1, 14-16). The plant cell suspensions, however, grow as a population of cells with a primary cell wall(17). The main components of these walls are cellulose-free polysaccharides and pectic polysaccharides in particular, which constitute 1/3 of their dry weight. (18). Some fragments, e g. methanol, acetic, ferulic and p-cumaric acids, are connected with the pectic polysaccharides by ester bonds with the carboxylic and hydroxylic groups. 

Taylor JS et al (2003) Structure of mammalian protein geranylgeranyltransferase type-I. EMBO J 22(22) 5963—5974... 

Because protein ROA spectra contain bands characteristic of loops and turns in addition to bands characteristic of secondary structure, they should provide information on the overall three-dimensional solution structure. We are developing a pattern recognition program, based on principal component analysis (PCA), to identify protein folds from ROA spectral band patterns (Blanch etal., 2002b). The method is similar to one developed for the determination of the structure of proteins from VCD (Pancoska etal., 1991) and UVCD (Venyaminov and Yang, 1996) spectra, but is expected to provide enhanced discrimination between different structural types since protein ROA spectra contain many more structure-sensitive bands than do either VCD or UVCD. From the ROA spectral data, the PCA program calculates a set of subspectra that serve as basis functions, the algebraic combination of which with appropriate expansion coefficients can be used to reconstruct any member of the... 

---