Proteins structure, nomenclature

In hPL there is a long surface loop between the disulfide-bridged cysteines 238 and 262 (Winkler et al., 1990). Positioned directly above the catalytic triad, this loop contains at its apex a short helix (residues 249 to 255), similar to the RmL lid, which is connected to the main body of the protein by two elongated stretches of the polypeptide chain. One of the central amino acids in this helix is a tryptophan (Trp-253), again reminiscent of the RmL structure. The second, smaller lid is made up of the loop that connects strand j85 of the central sheet with the helix a2 [secondary structure nomenclature follows that of Winkler et al. (1990)]... 

In a general case the second residue of the classic type IT turn (the position occupied in the lipase turn by the nucleophilic serine) adopts the so-called e conformation within the Ramachandran space [the nomenclature is again that of Efimov (1986), extended by Sibanda et al., (1989)]. This secondary structure of the nucleophile is preserved among all the structurally characterized members of the lipase-esterase suf>erfamily (see Section IV,B). Although unusual, it has been observed several times in other protein structures (for a discussion, see De-rewenda and Derewenda, 1991). In RmL the interatomic distances between C/8 of Ser-144 and other atoms of the turn are very short (N of Leu-145, 2.85 A C of His-143, 2.77 A O of His-143, 2.81 A). Similar... 

During the course of the structure validation project, we have discovered about one class of errors every 2 weeks. Most of these errors are fully unimportant to the average PDB-file user, but they are errors nonetheless. Consequently, it is impossible even to list all types of errors here. In this chapter, we have to limit ourselves to a discussion of a few classes of errors that, if not detected, could severely hamper the scientist who bases an experiment on a three-dimensional structure. We will discuss flipping of asparagine, histidine, and glutamine side-chains, administration of alternate atoms and residues, and the role of water molecules in protein structures. A large class of error types is formed by nomenclature errors. Table 3 lists some nomenclature errors we found in the PDB. 

The folding patterns of hexapeptide fragments have been determined from the atomic coordinates of the protein structures using the standard procedure of Kabsch and Sander [66]. Every residue is given a secondary structure descriptor. To reduce complexity, residues were classified as helical h (G, H or I in Kabsch-Sander nomenclature), extended strand s (E), P turn t (T) or remained unassigned n. With these four structural classes there are still 4096 possible folding patterns for hexapep-... 

Following the hierarchical nomenclature of protein structure, RNA tertiary structure represents a more global layout than secondary structure alone. The "kissing loops" motif is a prime example of an RNA tertiary structure contact not regularly seen in secondary structure [12]. In sequence and in secondary structure, the two loops of the motif may be distant. In the tertiary structure, the loops are seen to be close in space and form a hydrogen bond. Hence, the... 

This chapter will present the most fundamental concepts for structure, nomenclature, and chemical reactions of amines. Biological applications will focus on the characteristics, formation, and reactions of amino acids. The use of amino acids in proteins and relatively simple reactions that form peptides will be discussed. In addition, several chemical reactions that lead to controlled degradation of peptides and proteins will be introduced. 

Carbohydrates constitute one the of most complex structures occurring in nature (with nucleic acids and proteins) due to i) the monosaccharide diversity, ii) the type of linkage and iii) the nature of carbohydrate-linked molecules. As a result, GHs present a wide range of activities, which have necessitated the creation of a specific classification more explicit than the lUB Enzyme Nomenclature. In 1998, the Carbohydrate-Active Enzymes (CAZy) database was created, gathering glycosidases in famiUes based on amino-acid sequence and protein structures similarities. ... 

Nucleotide and protein sequences, protein structures, enzyme nomenclature and reactions... 

Portal to databases of chemical suppliers lUBMB nomenclature for enzymes Nucleotide and protein sequences, protein structures, enzyme nomenclature and reactions Infrared, Raman, and mass spectra Portal to Infotherm, Acronyms, thermophysical properties See B.6... 

Synthetically produced or modified carbohydrate-protein conjugates are sometimes referred to as neoglycoproteins. The nomenclature for the carbohydrate-containing substituents in such structures is analogous to sequential oligosaccharide nomenclature (2-Carb-37.2)... 

Figure 5.12 Structures and nomenclature of the ions formed in the mass spectral fragmentation of peptides which involve scission of the polypeptide backbone. From Chapman, J. R. (Ed.), Protein and Peptide Analysis by Mass Spectrometry, Methods in Molecular Biology, Vol. 61, 1996. Reproduced by permission of Humana Press, Inc.

This essay was written in an attempt to explain our overview of primary cell walls and to reach consensus on the nomenclature of primary cell wall polysaccharides. We present evidence supporting the hypothesis that cellulose, xyloglucan, arabinoxylan, homogalacturonan, RG-I, and RG-II are the six polysaccharides common to all primary cell walls of higher plants. In many cells, these six polysaccharides account for all or nearly all of the primary wall polysaccharides. Like the physically interacting proteins that constitute the electron transport machinery of mitochondria, the structures of the six patently ubiquitous polysaccharides of primary cell walls have been conserved during evolution. Indeed, we hypothesize that the common set of six structural polysaccharides of primary cell walls have been structurally... 

Fig. 7.14 Nomenclature for characteristic regions of peptide c >,t /-space taken from Karplus (1996). The frequencies of observed peptide conformations in protein crystal structures decrease from areas enclosed by a heavy solid line to regions enclosed by a plain solid line, to dashed outlines. Areas outside the dashed lines are disallowed in peptide conformational space. The lines are an approximate rendering of the exact contours given by Karplus (1996).

Myelin basic protein. In PNS myelin, MBP varies from approximately 5% to 18% of total protein, in contrast to the CNS, where it is close to 30% [ 1 ]. In rodents, the same four 21,18.5,17 and 14kDa MBPs found in the CNS are present in the PNS. In adult rodents, the 14kDa MBP is the most prominent component and is termed Pr in the PNS nomenclature. The 18.5 kDa component is present and is often referred to as the P, protein in the nomenclature of peripheral myelin proteins. Another species-specific variation in human PNS is that the major basic protein is not the 18.5 kDa isoform that is most prominent in the CNS but rather a form of about 17 kDa. It appears that MBP does not play as critical a role in myelin structure in the PNS as it does in the CNS. For example, the shiverer mutant mouse, which expresses no MBP (Table 4-2), has a greatly reduced amount of CNS myelin, with no compaction of the major dense line. By contrast, shiverer PNS has essentially normal myelin,both in amount and structure, despite the absence of MBP. This CNS/PNS difference in the role of MBP is probably because the cytoplasmic domain of P0 has an important role in stabilizing the major dense line of PNS myelin. Animals doubly deficient for P0 and MBP have a more severe defect in compaction of the PNS major dense line than P0-null mice, which indicates that both proteins contribute to compaction of the cytoplasmic surfaces in PNS myelin [23],... 

Merops (http //merops.sanger.ac.uk), database of peptidases and their proteinaceous inhibitors. Includes enzyme classification and nomenclature, external links to literature, and the structure of proteins of interest (if known). Enables one to find the gene coding for a given peptidase or to find the best enzyme to digest a chosen substrate. 

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