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Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, Maryland 21250, USA
Reprint requests to: Michael F. Summers, Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA; e-mail: summers{at}hhmi.umbc.edu; fax: (410) 455-1174.
(RECEIVED January 7, 2004; FINAL REVISION April 27, 2004; ACCEPTED April 27, 2004)
| Abstract |
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-helical conformation. The presence of a transient coil-to-helix equilibrium may explain the unusual and necessarily slow proteolysis rate of the CA-p2 junction. CACTD-p2-NC forms dimers and self-associates with an equilibrium constant (Kd = 1.78 ± 0.5 µM) similar to that observed for the intact capsid protein (Kd = 2.94 ± 0.8 µM), suggesting that Gag self-association is not significantly influence by the P2 domain. Keywords: NMR; protein structure and dynamics; HIV-1; p2
Abbreviations: HIV-1, human immunodeficiency virus type-1 CACTD, capsid C-terminal domain protein CA p24, full-length capsid protein p2, 14-residue protein within Gag NC, nucleocapsid protein MA, matrix protein SE, sedimentation equilibrium Kd, equilibrium dissociation constant NMR, nuclear magnetic resonance HSQC, heteronuclear single quantum correlation HNCA, triple resonance experiment HN(CO)CA, triple resonance experiment 2D, two-dimensional 3D, three-dimensional NOESY, nuclear Overhauser effect spectroscopy R1 (T1), longitudinal relaxation rate (time) R2 (T2), transversal relaxation (time) XNOE, heteronuclear 15N{1H} nuclear Overhauser effect TFE, 2,2,2-trifluoroethanol CSI, chemical shift index
Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04614804.
| Introduction |
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Recent computational studies suggest that residues at the capsid-p2 junction should prefer an
-helical conformation (Accola et al. 1998; Liang et al. 2002). However, in the crystal structure of a polypeptide that contains the HIV-1 CACTD and p2, the CACTD is folded, as expected, but no electron density was observed for residues of p2 or the CACTD-p2 junction, indicating that these residues are disordered or undergoing large amplitude motions (Worthylake et al. 1999). Although it is possible that p2 is fully disordered in the crystals, it is equally possible that p2 adopts an independently folded substructure (such as an
-helix) that is itself disordered relative to the CACTD. Similar results were observed for the crystal structure of the intact HIV-1 capsid protein, in which electron density was observed for the N-terminal domain (CANTD), but not for the independently folded C-terminal domain (Momany et al. 1996). Proper folding of p2 could also depend on the presence of the NC domain of Gag. In an attempt to better understand the behavior of p2 in the context of the Gag precursor polyprotein, we subcloned, overexpressed, and purified a 156-residue polypeptide with sequence spanning the C-terminal dimerization domain of capsid through the nucleocapsid domain (CACTD-p2-NC, residues 276431; Fig. 1A
), for NMR-based structural and sedimentation equilibrium (SE) analyses.
| Results and Discussion |
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NMR signal assignment and secondary structure
A representative 1H-15N HSQC spectrum obtained for CACTD-p2-NC is shown in Figure 1B
. Although the quality of the spectrum is generally good, a subset of signals exhibits broad linewidths and relatively poor resolution, and this subset is similar in appearance to 1H-15N HSQC data obtained for the isolated CACTD domain (data not shown). This broadening is due to the presence of a weak monomer-dimer equilibrium (Kd of 10 ± 3 µM [Rosé et al. 1992]) and a heterogeneous dimer interface (Gamble et al. 1997). HNCA and HN(CO)CA experiments were utilized to assign a majority of the backbone atoms CACTD-p2-NC. Although rapid T2 relaxation resulting from exchange between monomer and dimer species, as well as exchange between multiple dimer conformations, hindered our efforts to assign residues near the dimer interface of the CACTD domain, 100% of the residues linking the folded portions of CACTD and NC (including all of p2) were readily assigned. Representative spectra showing sequential connectivities for residues K358N371 (which include the CACTD-p2 junction) are shown in Figure 1C
.
Chemical shift deviations from random coil values for assigned 13C
atoms are plotted in Figure 2
. Consecutive positive deviations indicate the presence of
-helical secondary structure (Wishart et al. 1991). The helical boundaries identified from the 13C
(Fig. 2
) and 1HN (data not shown) chemical shift indices are consistent with those observed in the crystal structure of the isolated CACTD (Worthylake et al. 1999), as expected. The isolated CACTD is a globular four-helix protein that forms a weak, disordered dimer promoted mainly by the intermolecular packing of helix 3 (Worthylake et al. 1999), and the isolated NC protein consists of two zinc knuckle domains connected by a flexible linker and flanked by flexible N- and C-terminal tails (Summers et al. 1992). Our NMR data are consistent with these structures. The CSI values for the zinc knuckles of NC do not exhibit regular patterns commonly observed for folded proteins, because these domains lack substantial
-helical or
-sheet structural elements. Most important, small positive chemical shift deviations are observed for residues G351R386, which includes the p2 segment (Fig. 2
). An internal chemical shift reference (DSS) was used to ensure accuracy in referencing chemical shifts relative to established random-coil values. Although the chemical shift indices are not as large as those observed for the well defined
-helices, they exhibit uniform, positive deviations relative to random coil shifts and are not scattered randomly about zero, as is typically observed in random coil structures.1H-1H NOE data were also obtained for CACTD-p2-NC using 3D 15N-edited and 4D 13C,15N-edited NOESY experiments. The NOE cross-peak patterns and intensities observed for assigned residues of the CACTD and NC domains are consistent with previously reported X-ray (Gamble et al. 1997; Worthylake et al. 1999) and NMR (Summers et al. 1992; De Guzman et al. 1998; Amarasinghe et al. 2000) structures, respectively. Significantly, residues G351V389, which include the p2 segment, exhibit both strong dNN(i,i+1) and d
N(i,i+1) NOEs and no long-range NOEs. These results are typical of unfolded polypeptides (Wüthrich 1986), and support conclusions from the CSI analysis that residues G351V389 exist predominantly in a dynamic, random coil conformation.
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-helix (Accola et al. 1998; Liang et al. 2002, 2003). The NMR relaxation and NOE data indicate that residues G351V389 of CACTD-p2-NC are flexible, which explains the lack of observed electron density for the p2 residues in the CACTD-p2 crystal structure (Worthylake et al. 1999). However, NMR chemical shift indices indicate that these residues do not adopt a fully random coil conformation. The small positive deviations in the 13C
chemical shift indices of residues K358V369 suggest the presence of an
-helical conformation that is in equilibrium with a random coil conformation. CSI values have been shown to correlate with changes in CD spectra of
-helix forming peptides upon addition of TFE, reflecting the percentage of helix formation (Reily et al. 1992). Assuming CSI values of ~3.0 for a full populated
-helix and 0 for a random coil, the average value of 0.476 observed for residues K358V369 suggests the presence of only a minor helical population. The fact that only a single set of NMR signals are observed for these residues indicates that this equilibrium occurs rapidly on the NMR chemical shift timescale (sub-millisecond), consistent with the 15N relaxation and XNOE results. In addition, the SE experiments indicate that CACTD-p2-NC forms dimers with affinity that is essentially identical to that of the intact capsid protein. This indicates that the transiently formed helix does not promote self-association via, for example, formation of an intermolecular coiled-coil. In view of these findings, it is not clear how the p2 domain facilitates HIV-1 assembly and morphogenesis. One possibility is that p2 might form a stable helix and make intermolecular contacts in the context of the intact, native Gag polyprotein. In this regard, the native HIV-1 Gag polyprotein is posttranslationally myristoylated, and recent NMR and SE studies indicate that myristoylation induces trimerization of both the myristoylated matrix protein (myr-MA) and myr-MA-CA (Tang et al. 2004). It is thus likely that the intermolecular capsid interface is different in the context of a trimeric Gag structure, which could potentially promote the formation of a p2 coiled-coil structure. In addition, previous studies have shown that the N terminus of NC exists in a random coil conformation in the absence of RNA, but forms a helix when the protein binds to RNA stem loop recognition elements (De Guzman et al. 1998; Amarasinghe et al. 2000). It is thus possible that the helical structure could propagate to p2 when the intact Gag binds to RNA. Unfortunately, we have thus far been unable to obtain NMR data for CACTD-p2-NC:RNA complexes of suitable quality to directly address this possibility. Of course, p2 might remain flexible under all conditions, which would presumably be necessary in order for the protease to access the CA-p2 cleavage site during viral maturation. Finally, a transient helix could play a role in regulating the rate of proteolysis of the CA-p2 cleavage site. In general, the presence of bulky aromatic residues at positions directly N-terminal to the cleavage site facilitates cleavage, whereas bulky aromatic residues directly C-terminal to the cleavage site inhibits cleavage (Pettit et al. 2002). The p2-NC site, which is rapidly cleaved, and the CA-p2 cleavage site do not contain aromatic residues at either the N-terminal or C-terminal positions, suggesting that cleavage rates are regulated by a different mechanism. Interestingly, when the p2 domain was deleted, or the p2-NC cleavage site removed, cleavage at the C terminus of CA increased by 20-fold (Pettit et al. 1994). This suggests that there is a structural component to the relative proteolysis rate at the CA-p2 junction. The presence of a transient helix might inhibit processing, as the helical structures would have to be unwound when bound to the protease.
In summary, our findings indicate that the p2 segment of CACTD-p2-NC does not adopt a stable secondary structure, but instead exists as a dynamic equilibrium of predominantly random coil and, to a smaller extent, helical states. The presence of a dynamic coil-helix equilibrium provides an explanation for the reduced proteolysis rate of the CA-p2 junction, which is important for ordered assembly of the capsid core particle during viral maturation. The p2 domain does not significantly affect the oligomerization properties of the CA or the isolated CACTD domain. Although our findings do not support suggestions that p2 promotes Gag assembly by forming an intramolecular coiled-coil, they do not rule out the possibility that such interactions might occur in the context of the intact, myristoylated, and possibly RNA-associated Gag polyprotein.
| Materials and methods |
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Purification was similar to that of HIV-1 NC (De Guzman et al. 1998), still using a combination of anion (SP) and cation (CM) exchange chromatography, where the anion exchange column was removed after protein loading and protein was eluted from the cation exchange column using buffer B (identical to buffer A, except for 1 M NaCl). The CACTD-p2-NC purification scheme involved, however, higher resolution gel filtration (Superdex 75, Amersham), with 500 mM NaCl in buffer A and a 0.1 mL/min flow rate. Fractions containing pure protein after gel filtration were pooled, concentrated, and passed through a 1-mL benzamidine column to remove proteases. The protein was then exchanged into acetate buffer, 25 mM (CD3COO), 3 mM DTT, 3 mM TCEP, 25 mM NaCl, by membrane ultrafiltration (Centricon) and concentrated to ~600 µL. NMR samples were 5% D2O/95% H2O and ~1.4 mM in concentration.
NMR data collection
All NMR spectra were collected at 30°C with a Bruker AVANCE 600 MHz spectrometer equipped with a broadband 5-mm probe-head and shielded Z-axis-gradient coil. 2D 15N HSQC (15N-labeled sample), 3D HNCA (13C15N-labeled sample), and 3D HN(CO)CA (13C15N-labeled sample) data sets were collected to facilitate assignment of backbone 15N, 1HN, 1H
, and 13C
resonances (Grzesiek and Bax 1992). 3D 15N-edited NOESY (Kay et al. 1989) and 4D 15N/13C edited NOESY experiments (Kay et al. 1990;
m = 100 ms) were collected to make intraresidue side-chain assignments and identify NOEs between backbone 1HN amide protons and side-chain 1HC protons.
Longitudinal (R1), transversal (R2), and 15N{1H} heteronuclear NOE (XNOE) data for the backbone 15N nuclei of CACTD-p2-NC protein were collected in interleave mode as 1024*(HN) x 96*(N) data sets with 16 scans per point, 4-sec interscan delay for T1 and T2, and 2 x 1024*(HN) x 128*(N) points, 64 scans, and an inter-scan delay of 4 sec for the XNOE experiment. The XNOE experiment consisted of a reference experiment with a recovery delay of 8 sec, and the second experiment (NOE experiment) applied proton saturation during the last 3 sec of the 8-sec recovery delay. 15N T1 (=1/R1) and T2 (=1/R2) experiments employed delays of 10.1, 128.6, 514.6, 643.3, 1286.6, 2058.6, and 2573.2 msec for T1, and 0, 15.9, 31.9, 47.9, 63.8, 79.8, 95.7, and 111.6 msec for T2. The R1, R2, and XNOE experiments were collected in 1.5, 1.5, and 3 d, respectively.
NMR data processing and analysis
All NMR data were processed using NMRPipe (Delaglio et al. 1995) and analyzed using NMRView (Johnson and Blevins 1994). Heteronuclear dimensions were extended via linear prediction and zero-filled prior to Fourier transform. XNOE values were calculated as (I/Io), where I and Io represent the intensity ratio of the 15N-H correlation peak in the presence and absence of 3-sec proton saturation, respectively.
Sedimentation equilibrium
Sedimentation equilibrium (SE) data for CACTD-p2-NC and CA p24 were collected at speeds of 20,000 and 24,000 rpm at 20°C on a Beckman Optima XL-A analytical ultracentrifuge. All data were collected in absorbance mode at 280 nm. Sample conditions were 25 mM NaPO4, 100 mM NaCl, 2 mM TCEP, Calbiochem protease inhibitor cocktail set V (pH 6.5). CACTD-p2-NC initial concentrations were 10, 20, and 35 µM. Best global fits to a monomer-dimer equilibrium model were obtained for both CA p24 and CACTD-p2-NC using winNONLIN (Johnson and Faunt 1992), resulting in a Kd value of 1.78 ± 0.5 µM for CACTD-p2-NC and 2.94 ± 0.8 for CA p24.
| Acknowledgments |
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The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.
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