Protein secondary structures entries

Figure 7-16. Superimpasition of the X-ray structure of the tetracycline repressor class D dimer (dark, protein database entry 2TRT) with the calculated geometrical average of a 3 ns MD simulation (light trace). Only the protein backbone C trace Is shown, The secondary structure elements and the tertiary structure are almost perfectly reproduced and maintained throughout the whole production phase of the calculation,...

Figure 7.4 A subset consisting of a total of 75000 amino acids in available 3D structures in the Brookhaven Protein Data Base has been screened for secondary structural preferences. Three categories has been classified , and turn. In (A) the total count has been given. Note the different total abundance of the amino acids. In (B) the percentages are given (number of a selected amino acid in a given secondary structural category divided with the total count of that amino acid). The third column in each entry gives the % abundance of an amino...

Each SWISS-PROT entry consists of general information about the entry (e.g., entry name and date, accession number), Name and origin of the protein (e.g., protein name, EC number and biological origin), References, Comments (e.g., catalytic activity, cofactor, subuit structure, subcellular location and family class, etc.), Cross-reference (EMBL, PIR, PDB, Pfam, ProSite, ProDom, ProtoMap, etc.), Keywords, Features (e.g., active site, binding site, modification, secondary structures, etc.), and Sequence information (amino acid sequence in Swiss-Prot format, Chapter 4). 

Fig. 12. a/fi barrel domain of MR (based on Protein Data Bank entry 1 mnr). Important active site residues and the associated secondary structure elements are labeled and designated with arrows. From Babbitt and Gerlt (1997, Figure 1, p. 30592). 

Viral and cellular lipid membranes must first fuse to allow entry of the viral core into a host cell. The primary receptor required for the entry of primate lentiviruses, HIV-1, HIV-2, and SIV, into cells is the CD4 molecule (1). The interaction of viral envelope protein with CD4 not only attaches virus particles to the cell surface but also induces conformational changes in the envelope protein. These structural alterations allow a secondary interaction with a coreceptor to occur which triggers the fusion process. 

RNA secondary structure plays a role in the regulation of iron metabolism in eukaryotes. Iron is an essential nutrient, required for the synthesis of hemoglobin, cytochromes, and many other proteins. However, excess iron can be quite harmful because, untamed by a suitable protein environment, iron can initiate a range of free-radical reactions that damage proteins, lipids, and nucleic acids. Animals have evolved sophisticated systems for the accumulation of iron in times of scarcity and for the safe storage of excess iron for later use. Key proteins include transferrin, a transport protein that carries iron in the serum, transferrin receptor, a membrane protein that binds iron-loaded transferrin and initiates its entry into cells, and ferritin, an impressively efficient iron-storage protein found primarily in the liver and kidneys. Twenty-four ferritin polypeptides form a nearly spherical shell that encloses as many as 2400 iron atoms, a ratio of one iron atom per amino acid (Figure 31.37). 

The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) [29]. The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does not predict protein structure [29]. 

FIGURE 12.11 Capsid-like pentameric assembly of recombinant JC virus protein VPl. The secondary structure of the pentamer (left panel) and the surface electropotential (right panel) have been obtained from PDB entry IVPN. ... 

The bacterial RNA viruses are all of quite small size, about 26 nm in size, and they are all icosahedral, with 180 copies of coat protein per virus particle. The complete nucleotide sequence of several RNA phages are known. In the RNA phage MS2, which infects Escherichia coli, the viral RNA is 3,569 nucleotides long. The virus RNA, although single stranded, has extensive regions of secondary and tertiary structure. The RNA strand in the virion has the plus (+) sense, acting directly as mRNA upon entry into the cell. 

---