Solution structure and backbone dynamics of Mason‐Pfizer monkey virus (MPMV) nucleocapsid protein

Abstract

Retroviral nucleocapsid proteins (NCPs) are CCHC-type zinc finger proteins that mediate virion RNA binding activities associated with retrovirus assembly and genomic RNA encapsidation. Mason-Pfizer monkey virus (MPMV), a type D retrovirus, encodes a 96-amino acid nucleocapsid protein, which contains two Cys-X2-Cys-X4-His-X4-Cys (CCHC) zinc fingers connected by an unusually long 15-amino acid linker. Homonuclear, two-dimensional sensitivity-enhanced l5N-'H. three-dimensional "N-IH, and triple resonance NMR spectroscopy have been used to determine the solution structure and residue-specific backbone dynamics of the structured core domain of MPMV NCP containing residues 2 1-80. Structure calculations and spectral density mapping of N-H bond vector mobility reveal that MPMV NCP 2 1-80 is best described as two independently folded, rotationally uncorrelated globular domains connected by a seven-residue flexible linker consisting of residues 42-48. The N-terminal CCHC zinc finger domain (residues 24-37) appears to adopt a fold like that described previously for HIV-1 NCP; however, residues within this domain and the immediately adjacent linker region (residues 38-41) are characterized by extensive conformational averaging on the ps-ms time scale at 25 "C. In contrast to other NCPs, residues 49-77, which includes the C-terminal CCHC zinc-finger (residues 53-66). comprise a well-folded globular domain with the Val49-Pro-Gly-Leu52 sequence and C-terminal tail residues 67-77 characterized by amide proton exchange properties and "N RI, R2, and {'H-I'NN) NOE values indistinguishable to residues in the core C-terminal finger. Twelve refined structural models of MPMV NCP residues 49-80 (pairwise backbone RMSD of 0.77 A) reveal that the side chains of the conserved Pro50 and Trp62 are in van der Waals contact with one another. Residues 70-73 in the C-terminal tail adopt a reverse turn-like structure. Ile77 is involved in extensive van der Waals contact with the core finger domain, while the side chains of Ser68 and Am75 appear to form hydrogen bonds that stabilize the overall fold of this domain. These residues outside of the core finger structure are conserved in D-type and related retroviral NCPs, e.g., MMTV NCP, suggesting that the structure of MPMV NCP may be representative of this subclass of retroviral NCPs. Keywords:Mason-Pfizer monkey virus (MPMV) is the prototypical member of the primate D-type retroviruses that include simian AIDS retrovirus type 1 (SRV-I) and SRV-2, the causative agents of simian AIDS in captive macaque populations (Power et al., 1986). Mouse mammary tumor virus (MMTV) is a type B retrovirus most closely

Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins

“…The shape of the free NC displays an extended configuration compatible with an unfolded protein. In contrast, NC in complex with oligonucleotide has a much bulkier appearance, larger excluded volume and is well superimposed with the relatively compact atomic model of this complex obtained by NMR (1A1T, 1AAF) (30). …”

Two Basic Regions of NCp7 Are Sufficient for Conformational Conversion of HIV-1 Dimerization Initiation Site from Kissing-loop Dimer to Extended-duplex Dimer

“…The NC proteins of all retroviruses except those of spumaviruses have one or two zinc fingers of CX 2 CX 4 HX 4 C motif surrounded by basic amino acid sequences. Three-dimensional structures of NC proteins in several retroviruses are known (3)(4)(5)(6)(7)(8)(9)(10). The crystal structure of complex of the NC protein and packaging signal of the genomic RNA in the human immunodeficiency virus type 1 (HIV-1) demonstrated two zinc finger knuckles bind to G-rich loop of the RNA in a stem-loop structure and N-terminal basic sequence forms a 3 10 -helix and binds to major groove of stem (5).…”

Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

“…As a result it is common practice to use experimentally derived distance and angle restraints with approximate force constants to constrain metal ions in place, as in the case when using modified amino acids with “dummy” coordination-covalent bonds to the metal with other coordination bonds constrained to X-ray absorption spectroscopy (XAS)-derived distances, or alternatively, to not include metal ions at all during the structure determination process (Banci et al 2007; Arunkumar et al 2009; Eustermann et al 2010; Brockmann et al 2012; Gao et al 1998). The use of such approaches introduces possible errors in describing the metal-binding site as either excessively rigid or too flexible.…”