Decoys

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... 

Park B and M Levitt 1996. Energy Functions that Discriminate X-ray and Near-native Folds from V constructed Decoys, journal of Molecular Biology 258 367-392. 

Another contribution of Picatinny s pyrotechnics engineers was the development of the infrared decoy, used by planes to divert enemy missiles which are attracted to the plane s infrared exhaust emanations. These decoys consist of high-efficiency infrared flares which are ejected by the plane at the appropriate time, attracting the missiles to the decoys and away from the plane... 

A special type of a flare is a thermal decoy which has a strong emission in the infrared. Decays may utilize the Mg-fluorocarbon reaction which form hot carbon particles as the source of radiant energy (see sample equil calcn, Section 4 of the article) (Ref 59)... 

Polymerization Binder for M48 Decoy Flares , NAD-RDTR No 232 (1973) 60) R.C. Harris,... 

Li MJ, Kim J, Li S, Zaia J, Yee JK, Anderson J, Akkina R, Rossi JJ (2005b) Long-term inhibition of HlV-1 infection in primary hematopoietic cells by lentiviral vector delivery of a triple combination of anti-HIV shRNA, anti-CCR5 ribozyme, and a nucleolar-localizing TAR decoy. Mol Ther 12 900-909... 

RNA decoys from HCV stem-loop structures in NS5B coding region sequester replication complexes HCV (Zhang et al. 2005)... 

Tat-transactivation Anti-hCyclinTl intrabodies tdTat Transdominant HIV Tat protein scFV to Tat Tar decoy HIV-1 Bahner et al. 1996 Bevec et al. 1996 Duan et al. 1994 Malim et al. 1989 Malim et al. 1988 Reddy et al. 1999... 

Nuclear export of unspliced RNA RevMlO Transdominant HIV Rev protein Dominant negative Sam68, a Rev homolog scFv to Rev RRE decoy HIV-1 Habu et al. 2005 Hotchkiss et al. 2004 Li et al. 1998a, b Yamada et al. 1994... 

Antisense RNAs, RNA decoys, ribozymes, small interfering RNAs, and RNA ap-tamers are potential tools in antiviral gene therapy. The application of the antiviral RNAs is described in detail in Chap. 9 of this volnme by J. Haasnoot and B. Berkhont. 

RRE decoy CD34+ bone marrow cells Traps Rev and thus inhibits transactivation of HIV-1 gene expression Kohn et al. 1999... 

Borgatti M., Romanelli A., Saviano M., Pedone C., Lampronti 1., Breda L., Nastruzzi C., Bianchi N., Mischiati C., Gambari R. Resistance of decoy PNA-DNA chimeras to enzymatic degradation in cellular extracts and serum. Oncol. Res. 2003 13 279-287. 

A step closer toward realism is taken by off-lattice models in which the backbone is specified in some detail, while side chains, if they are represented at all, are taken to be single, unified spheres [44-50]. One indication that this approach is too simplistic was given in [51], which proved that for a backbone representation in which only Ca carbons were modeled, no contact potential could stabilize the native conformation of a single protein against its nonnative ( decoy ) conformations. However, Irback and co-workers were able to fold real protein sequences, albeit short ones, using a detailed backbone representation, with coarse-grained side chains modeled as spheres [49, 52-54]. 

Vendruscolo M, Najmanovich R, Domany E. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading Proteins 2000 38 134-48. 

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