NORMAL GENOMIC

• Seigneuret M
• Complete predicted three-dimensional structure of the facilitatortransmembrane protein and hepatitis C virus receptor CD81: conserved andvariable structural domains in the tetraspanin superfamily.
• Biophys J. 2006; 90: 212-27
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• Tetraspanins are a superfamily of transmembrane proteins implicated incellular development, motility, and activation through their interactionswith a large range of proteins and with specific membrane microdomains.The complete three-dimensional structure of the tetraspanin CD81 has beenpredicted by molecular modeling and from the crystallographic structure ofthe EC2 large extracellular domain. Periodicity of sequence conservation,homology modeling, secondary structure prediction, and protein dockingwere used. The transmembrane domain appears organized as a four-strandedleft-handed coiled coil directly connecting to two helices of the EC2. Asmaller extracellular loop EC1 contains a small largely hydrophobicbeta-strand that packs in a conserved hydrophobic groove of the EC2. Thepalmitoylable intracellular N-terminal segment forms an amphipathicmembrane-parallel helix. Structural variability occurs mainly in anhypervariable subdomain of the EC2 and in intracellular regions.Therefore, the variable interaction selectivity of tetraspanins originatesboth from sequence variability within structurally conserved domains andfrom the occurrence of small structurally variable domains. In CD81 andother tetraspanins, the numerous membrane-exposed aromatic residues areasymmetrically clustered and protrude on one side of the transmembranedomain. This may represent a functional specialization of these two sidesfor interactions with cholesterol, proteins, or membrane microdomains.

• Liepinsh E, Baryshev M, Sharipo A, Ingelman-Sundberg M, Otting G, Mkrtchian S
• Thioredoxin fold as homodimerization module in the putative chaperoneERp29: NMR structures of the domains and experimental model of the 51 kDadimer.
• Structure. 2001; 9: 457-71
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• BACKGROUND: ERp29 is a ubiquitously expressed rat endoplasmic reticulum(ER) protein conserved in mammalian species. Fold predictions suggest thepresence of a thioredoxin-like domain homologous to the a domain of humanprotein disulfide isomerase (PDI) and a helical domain similar to theC-terminal domain of P5-like PDIs. As ERp29 lacks the double-cysteinemotif essential for PDI redox activity, it is suggested to play a role inprotein maturation and/or secretion related to the chaperone function ofPDI. ERp29 self-associates into 51 kDa dimers and also higher oligomers.RESULTS: 3D structures of the N- and C-terminal domains determined by NMRspectroscopy confirmed the thioredoxin fold for the N-terminal domain andyielded a novel all-helical fold for the C-terminal domain. Studies of thefull-length protein revealed a short, flexible linker between the twodomains, homodimerization by the N-terminal domain, and the presence ofinteraction sites for the formation of higher molecular weight oligomers.A gadolinium-based relaxation agent is shown to present a sensitive toolfor the identification of macromolecular interfaces by NMR. CONCLUSIONS:ERp29 is the first eukaryotic PDI-related protein for which the structuresof all domains have been determined. Furthermore, an experimental model ofthe full-length protein and its association states was established. It isthe first example of a protein where the thioredoxin fold was found to actas a specific homodimerization module, without covalent linkages orsupporting interactions by further domains. A homodimerization modulesimilar as in ERp29 may also be present in homodimeric human PDI.

• Kister AE, Roytberg MA, Chothia C, Vasiliev JM, Gelfand IM
• The sequence determinants of cadherin molecules.
• Protein Sci. 2001; 10: 1801-10
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• The sequence and structural analysis of cadherins allow us to find sequence determinants-a few positions in sequences whose residues are characteristic and specific for the structures of a given family. Comparison of the five extracellular domains of classic cadherins showed that they share the same sequence determinants despite only a nonsignificant sequence similarity between the N-terminal domain and other extracellular domains. This allowed us to predict secondary structures and propose three-dimensional structures for these domains that have not been structurally analyzed previously. A new method of assigning a sequence to its proper protein family is suggested: analysis of sequence determinants. The main advantage of this method is that it is not necessary to know all or almost all residues in a sequence as required for other traditional classification tools such as BLAST, FASTA, and HMM. Using the key positions only, that is, residues that serve as the sequence determinants, we found that all members of the classic cadherin family were unequivocally selected from among 80,000 examined proteins. In addition, we proposed a model for the secondary structure of the cytoplasmic domain of cadherins based on the principal relations between sequences and secondary structure multialignments. The patterns of the secondary structure of this domain can serve as the distinguishing characteristics of cadherins.