Nucleocapsid protein

Since our original aPNA publication, there have been other reports of the incorporation of nucleobases into a-helical peptides. Mihara and coworkers reported that a-hehcal coiled-coiled peptides could be stabilized by base pairs between complementary y-nucleobase-a-aminobutanoic acids [78] They have also reported that the incorporation of such nucleoamino acids into a-hehcal segments of HIV-1 Rev and HIV-1 nucleocapsid protein can result in increased binding affinity and specificity to HIV-1 RRE RNA and SL3 RNA respectively [79, 80]. 

Alee TM, Popik W (2004) APOBEC3G is incorporated into virus-hke particles by a direct interaction with HIV-1 Gag nucleocapsid protein. J Biol Chem 279(33) 34083-34086... 

Ramanathan, H.N., Chung, D.-H., Plane, S.J., Sztul, E., Chu, Y.-K., Gutderi, M.C., McDowell, M., Ali, G., and Jonsson, C.B. (2007) Dynein-dependent transport of the Hantaan virus nucleocapsid protein to the endoplasmic reticulum-golgi intermediate compartment./. Virol. 81, 8634-8647. 

Figure 6. Structure of a HIV vilion with envelope glycoproteins and nucleocapside proteins. Magnified wire structure of its glysoprotein gp120 shows V3 and V4 loops with S-S bonding sites.

Figure 8. Primary structure of the nucleocapsid protein p7 with the two zinc fingers.

Maynard, A. T., Huang, M., Rice, W. G., and Covell, D. G. 1998. Reactivity of the HIV-1 nucleocapsid protein p7 zinc finger domains from the perspective of density-functional theory. Proc. Natl. Acad. Sci. USA 95 11578-11583. 

Zinc-finger proteins are also possible targets for bicyclams. All nu-cleocapsid proteins of known strains of retroviruses contain one or two copies of an invariant sequence, Cys-X2-Cys-X4-His-X4-Cys. Proteins with this sequence bind zinc stoichiometrically with dissociation constants of ca. 10-12M (377). Under physiological conditions, a 10-fold excess of EDTA removes only 50% of zinc from the zinc finger domain of HIV-1 nucleocapsid protein (378). 

The mechanism of zinc deprivation by 3-nitrosobenzamide was elucidated most recently. When the reconstituted nucleocapsid protein p7 of HIV-1 (15 i-M) was incubated with 3-nitrosobenzamide (300 iM) at pH 7.5, three disulfide bonds per protein molecule were formed while 3-nitrosobenzamide was reduced to the hydroxylamine. Molecular masses of p7 adducts augmented by one or two 3-nitrosobenzamide residues were observed by electrospray ionization MS, consistent with covalent bond formation between cysteine sulfur and the nitroso nitrogen atom127. 

C2HC Zn finger (smart00343) KCYNCGKPGHIARDC PS Found in the Nucleocapsid protein of retrovirus. Also found in eukaryotic RNA-or ssDNA-binding proteins Human Rb-BP 6 (NP 008841)-retmoblatoma-binding protein 6 378, 379... 

Alfadhli, A., Steel, E., Finlay, L., Bachinger, H. P., and Barklis, E. (2002). Hantavirus nucleocapsid protein coiled-coil domains./. Biol. Chem. 277, 27103-27108. 

Bertrand, E.L. and Rossi, J.J. (1994) Facilitation of hammerhead ribozyme catalysis by the nucleocapsid protein of HIV-1 and the heterogeneous nuclear ribonucleoprotein Al. EMBO J., 13,2904-2912. 

Xi, X., et al (2008). HIV-1 nucleocapsid protein NCp7 and its RNA stem loop 3 partner Rotational dynamics of spin-labeled RNA stem loop. Biochemistry 47, 10099—10110. 

Zhang, Z., et al. (2008). Rotational dynamics of HIV-1 nucleocapsid protein NCp7 as probed by a spin label attached by peptide synthesis. Biopolymers 89, 1125—1135. 

Khandogin J, K Musier-Forsyth, DM York (2003) Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from hnear-scahng quantum methods. J. Mol. Biol. 330 (5) 993-1004... 

Kraeusslich, H. G. Paecke, M. Heuser, A. M. Konvalinka, J. Zentgraf, H. The spacer peptide between human immunodeficiency virus capsid and nucleocapsid proteins is essential for ordered assembly and viral infectivity. J. Virol., 1995, 69 3407-3419. 

Truncated versions of the nucleocapsid protein that lacked various portions of the N terminus revealed that deletion of the first 32 amino acids interfered with assembly, but this deletion did not eliminate interaction of the coat protein with nucleic acid. When present in small amounts, this mutant coat protein could be incorporated into capsids assembled from the wild-type protein. However, when present in large amounts, the mutant coat protein inhibited assembly of the wild-type protein. 

Further analysis of the cross-linked intermediate showed that lysine at position 250 of one capsid subunit was covalently linked to the identical amino acid on a second subunit. In a model of the nucleocapsid derived from both cryoelectron microscopy (cryo-EM) analysis and X-ray analysis of the nucleocapsid protein, the covalent bond connects a pentamer of coat proteins with a hexamer of coat proteins, that is, it is an intercapsomer contact rather than an intracapsomer contact. This finding was unexpected because a possible assembly model proposed preassembly of pentameric and hexameric units that would recruit RNA for assembly into the final structure. In light of the new data, however, this scenario is unlikely. Instead, the initial assembly intermediate appears to be a coat protein dimer bound to RNA and the dimer spans the intercapsomere space. 

Gag has three consituent proteins, linked by spacer peptides. These are the matrix protein associated with the membrane, the capsid protein forming the internal capsid of the virus, and the nucleocapsid protein binding the viral RNA. A classic electron microscopy study of the interaction of actin with HIV revealed the radial organization of the proteins in the immature capsid, where it binds the nucleocapsid domain of the Gag structural polyprotein (Wilk et al, 1999). A further... 

Fig. 20. Structurally characterized retroviral Gag proteins, (a) Capsid protein, N-terminal part (Gamble et al., 1996) (b) capsid protein, C-terminal oligomerization domain (Gamble et al, 1997) (c) matrix protein (Hill et al, 1996) (d) nucleocapsid protein (De Guzman et al, 1998).

The nucleocapsid protein (NC) has many nucleic acid-associated functions, such as packaging, transcription initiation, and stabilization of proviral DNA (Turner and Summers, 1999, and references therein). The parts that have been characterized structurally are the zinc fingers, which are common nucleic acid-binding motifs (Berg, 1986). Most retroviral NCs... 

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