Connective protein, determination

A role as a recognition surface in connecting proteins, similar to the role of SH2 and SH3 domains, has been postulated for PH domains. However, protein partners specifically recognizing PH domains are rare. Therefore, a role of PH domains in anchoring soluble proteins to membranes succeeded the original assumption that PH domains determine protein-protein interactions. In that case, PH domains would be like covalently attached fatty-acid residues, which also help to attach proteins to the membrane. The structural properties of PH domains support a role in bringing cytosolic proteins to the membrane. The structure of a PH domain is shown in Plate 4a. Structures of complexes of inositol phosphates with a PH domain were solved, both by X-ray crystallography and The structural feamres are shown in Plate 4b. 

Increasing reeling speed can produce stronger but less extensible fibers (Figure 6.7). As the crosslinks connecting protein chains in silk fibrils (see Figure 6.2), P-crystaUites play important roles in determining mechanical properties of silk. The size and orientation of the crystallites as well as the... 

The secondary structure elements, formed in this way and held together by the hydrophobic core, provide a rigid and stable framework. They exhibit relatively little flexibility with respect to each other, and they are the best-defined parts of protein structures determined by both x-ray and NMR techniques. Functional groups of the protein are attached to this framework, either directly by their side chains or, more frequently, in loop regions that connect sequentially adjacent secondary structure elements. We will now have a closer look at these structural elements. 

Figure 2.11 Beta sheets are usuaiiy represented simply by arrows in topology diagrams that show both the direction of each (3 strand and the way the strands are connected to each other along the polypeptide chain. Such topology diagrams are here compared with more elaborate schematic diagrams for different types of (3 sheets, (a) Four strands. Antiparallel (3 sheet in one domain of the enzyme aspartate transcarbamoylase. The structure of this enzyme has been determined to 2.8 A resolution in the laboratory of William Lipscomb, Harvard University, (b) Five strands. Parallel (3 sheet in the redox protein flavodoxin, the structure of which has been determined to 1.8 A resolution in the laboratory of Martha Ludwig, University of Michigan, (c) Eight strands. Antiparallel barrel in the electron carrier plastocyanln. This Is a closed barrel where the sheet is folded such that (3 strands 2 and 8 are adjacent. The structure has been determined to 1.6 A resolution in the laboratory of Hans Freeman in Sydney, Australia. (Adapted from J. Richardson.)...

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

This electron microscopy reconstruction has since been extended to high resolution (3 A) where the connections between the helices and the bound retinal molecule are visible together with the seven helices (Figure 12.3c). The helices are tilted by about 20° with respect to the plane of the membrane. This is the first example of a high-resolution three-dimensional protein structure determination using electron microscopy. The structure has subsequently been confirmed by x-ray crystallographic studies to 2 A resolution. 

The contractile apparatus may be thought of as the sum of those intracellular components which constitute the machinery of chemomechanical transduction. It is the set of proteins which convert the chemical energy of the terminal phosphate ester bond of ATP into mechanical work. The structure of the contractile apparatus is determined by the connections between the various protein molecules via specific binding sites or, in a minority of cases, via labile covalent linkages. The kinetics of the contractile machinery are determined by the regulation of changes in these connections. 

The polarity and thermal instability of biopolymers, together with the almost exclusive formation of singly charged ions renders APCl an inappropriate ionization technique for their study. Much of the early work involving electrospray ionization, on the other hand, was connected with the analysis of this type of molecule, in particular determining the molecular weight of proteins for which it is particularly effective. 

Collagen, the major component of most connective tissues, constimtes approximately 25% of the protein of mammals. It provides an extracellular framework for all metazoan animals and exists in virmally every animal tissue. At least 19 distinct types of collagen made up of 30 distinct polypeptide chains (each encoded by a separate gene) have been identified in human tissues. Although several of these are present only in small proportions, they may play important roles in determining the physical properties of specific tissues. In addition, a number of proteins (eg, the Clq component of the complement system, pulmonary surfactant proteins SP-A and SP-D) that are not classified as collagens have... 

Numerous organisms, both marine and terrestrial, produce protein toxins. These are typically relatively small, and rich in disulfide crosslinks. Since they are often difficult to crystallize, relatively few structures from this class of proteins are known. In the past five years two dimensional NMR methods have developed to the point where they can be used to determine the solution structures of small proteins and nucleic acids. We have analyzed the structures of toxins II and III of RadiarUhus paumotensis using this approach. We find that the dominant structure is )9-sheet, with the strands connected by loops of irregular structure. Most of the residues which have been determined to be important for toxicity are contained in one of the loops. The general methods used for structure analysis will be described, and the structures of the toxins RpII and RpIII will be discussed and compared with homologous toxins from other anemone species. 

Both enzymes belong to the family of a,p-hydrolases." The active site of MeHNL is located inside the protein and connected to the outside through a small channel, which is covered by the bulky amino acid tryptophane 128." It was possible to obtain the crystal structure of the complex with the natural substrate acetone cyanohydrin with the mutant SerSOAla of MeHNL. This complex allowed the determination of the mode of substrate binding in the active site." A summary of 3D structures of known HNLs was published recently." " ... 

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