Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation

The CA (capsid) domain of immature HIV-1 Gag and the adjacent spacer peptide 1 (SP1) play a key role in viral assembly by forming a lattice of CA hexamers, which adapts to viral envelope curvature by incorporating small lattice defects and a large gap at the site of budding. This lattice is stabilized by intrahexameric and interhexameric CA-CA interactions, which are important in regulating viral assembly and maturation. We applied subtomogram averaging and classification to determine the oligomerization state of CA at lattice edges and found that CA forms partial hexamers. These structures reveal the network of interactions formed by CA-SP1 at the lattice edge. We also performed atomistic molecular dynamics simulations of CA-CA interactions stabilizing the immature lattice and partial CA-SP1 helical bundles. Free energy calculations reveal increased propensity for helix-to-coil transitions in partial hexamers compared to complete six-helix bundles. Taken together, these results suggest that the CA dimer is the basic unit of lattice assembly, partial hexamers exist at lattice edges, these are in a helix-coil dynamic equilibrium, and partial helical bundles are more likely to unfold, representing potential sites for HIV-1 maturation initiation.

The polyprotein Gag is the main structural component of HIV-1, consisting of the MA (matrix), CA (capsid), NC (nucleocapsid), and p6 domains as well as the spacer peptides SP1 and SP2 (1). Gag is produced in infected host cells and trafficked to the plasma membrane, where it assembles into a hexagonal lattice via its CA domain and recruits other viral proteins and the viral RNA genome (1, 2). Assembly of the curved Gag lattice is commensurate with membrane bending at the site of assembly, after which recruitment of Endosomal Sorting Complex Required for Transport III (ESCRT-III) components by the p6 domain of Gag induces membrane scission and release of the immature virus particle (2). The hexagonal Gag lattice accommodates curvature in the growing bud by incorporating vacancy defects (3). The activity of ESCRT-III is timed such that the final immature lattice is incomplete, giving rise to an additional large gap in the lattice, resulting in a truncated spherical shape (4–6).During or after budding, the viral protease is activated and cleaves this immature Gag lattice into its component domains, which leads to structural rearrangement within the virus particle (2). The released CA domains assemble to form a closed, conical capsid around the condensed ribonucleoprotein (RNP) complex of the mature virus (1, 7). Maturation is required for the virion to become infectious (1).Within the immature virus particle, the N-terminal domain of CA (CA_NTD) forms trimeric interactions linking three Gag hexamers while the C-terminal domain of CA (CA_CTD) forms dimeric interactions mediated by helix 9 of CA, linking two Gag hexamers together (8). The CA_CTD additionally forms intrahexamer interactions around the sixfold axis of the hexamer (8, 9). Amphipathic helices formed by the C-terminal residues of CA_CTD and the N-terminal residues of SP1 junction assemble into a six-helix bundle (6HB), thereby imposing hexagonal order on the CA domains, via classical knobs-in-holes packing mediated by exposed hydrophobic side chains, as also seen in coiled coils (9, 10). In combination, these relatively weak interactions give rise to a very dynamic, reversible assembly process that prevents the assembling lattice from becoming trapped in kinetically unfavorable states (11). This robust assembly behavior is consistent with icosahedral viruses (12–15). It is not surprising, therefore, that the energetics of Gag assembly are tightly controlled and highly dependent on scaffolding effects from the viral RNA and the membrane-interacting MA domain of Gag in order to ensure productive viral assembly (11, 16). Analysis of the diffusion pattern of fluorescently labeled Gag supports the notion that Gag is trafficked to the site of assembly as low-order multimers, although it is still unclear whether these are Gag dimers, trimers, or other multimeric forms of Gag (16, 17).The primary assembly unit of the Gag lattice remains largely unknown. We can identify two hypothetical ways in which the lattice could assemble. First, the lattice could grow by addition of Gag hexamers (or sets of six component monomers), such that the CA-SP1 junction is assembled within a hexameric 6HB at all positions in the lattice. In this case, interfaces between hexamers would be unoccupied at the edge of the lattice. From a purely energetic perspective, this appears most reasonable. Second, the lattice could form via addition of Gag dimers or Gag trimers (or equivalently from sets of either two or three component monomers). This would maintain, for example, the dimeric CA-CA interhexamer interactions but leave incomplete hexamers at the lattice edges, including unoccupied hexamer-forming interfaces along the CA-SP1 bundle. It additionally remains unclear whether the unoccupied Gag-Gag interfaces at the lattice edges are simply exposed, or whether they are stabilized by alternative conformations of individual domains or proteins, or by other binding partners. Understanding the structure of the edge of the immature Gag lattice therefore has implications for understanding the mechanism of virus assembly.Viral assembly, budding, and maturation are tightly linked, and disrupting the kinetics of any of these processes can give rise to defects in maturation and formation of noninfectious viral particles (1, 18, 19). The rate-limiting proteolytic cleavage site in the maturation process resides within the CA-SP1 6HB (20). Unfolding of the helical bundle is required to allow proteolytic cleavage to proceed (21–23), but the exact mechanism for protease access to this site is not known. The spatial localization of proteolytic processing within the context of the immature Gag lattice is relevant: Does the protease act on Gag within the lattice, or does it act on the edges of the Gag lattice, causing a cascade of lattice disruption? At the lattice edge, is the substrate for the protease with a 6HB or within an incomplete hexamer? Understanding the structure of the edge of the immature Gag lattice therefore has implications for understanding the mechanism of virus maturation.High-resolution immature Gag structures have previously been determined directly from purified viruses by cryo-electron tomography (cryo-ET) and subtomogram averaging (10). These structures represent an average hexamer within the immature lattice, with a full complement of six Gag hexamer neighbors. Here, we have applied subtomogram classification and averaging approaches to an existing immature virus dataset (10) in order to determine the structures of Gag assemblies at lattice edges. We also applied atomistic molecular dynamics simulations to assess the roles of the different CA-CA interactions in immature lattice stabilization and predict the properties of the structures we observe at lattice edges. Together, our results suggest that the basic unit of immature HIV-1 assembly is a Gag dimer and partial CA-SP1 helical bundles are present at the edges of the assembled lattice and may be substrates for initiation of maturation.     

Strategies adopted to manage physical and psychosocial challenges after returning home among people with stroke: A qualitative study

Stroke survivors encounter various physical and psychosocial challenges after hospital discharge. Systematic reviews consistently suggest the importance of self-management in promoting post-stroke recovery. However, stroke survivors’ performance of self-management behaviors after returning home is poorly understood. This study was conducted to explore how stroke survivors manage their life after returning home from the hospital. This was a qualitative study with individual, semi-structured interviews. We recruited a purposive sample of adults who had a first or recurrent ischemic or hemorrhagic stroke and currently lived at home. Participants were asked about their post-stroke experiences, challenges encountered, and strategies adopted for managing post-stroke conditions. Data were transcribed verbatim and analyzed using thematic analysis. A total of 30 stroke survivors (mean age = 61.97 years, SD = 10.20) were interviewed. Most were men (n = 18), married (n = 25), and retired (n = 21). Two-thirds had experienced an ischemic stroke. Five key themes emerged: pursuing lifelong learning to live well after a stroke; reinterpreting unpleasant experiences as new learning opportunities; engaging in life activities to better adapt to post-stroke challenges; being confident in oneself to persevere in self-management behaviors; and continuing to accept the current self and explore the new self. Participants regarded learning as a prerequisite for improving their affected functions and managing uncertainties in recovery. Learning requires self-participation, building self-efficacy and positive outcome expectations, testing and adapting strategies to one''s own health conditions, and engaging in leisure or social activities. These findings will guide future development of interventions for enhancing stroke survivors’ recovery outcomes.     

Mechanism of protein remodeling by ClpA chaperone

ClpA, a newly discovered ATP-dependent molecular chaperone, remodels bacteriophage P1 RepA dimers into monomers, thereby activating the latent specific DNA binding activity of RepA. We investigated the mechanism of the chaperone activity of ClpA by dissociating the reaction into several steps and determining the role of nucleotide in each step. In the presence of ATP or a nonhydrolyzable ATP analog, the initial step is the self-assembly of ClpA and its association with inactive RepA dimers. ClpA-RepA complexes form rapidly and at 0°C but are relatively unstable. The next step is the conversion of unstable ClpA-RepA complexes into stable complexes in a time- and temperature-dependent reaction. The transition to stable ClpA-RepA complexes requires binding of ATP, but not ATP hydrolysis, because nonhydrolyzable ATP analogs satisfy the nucleotide requirement. The stable complexes contain approximately 1 mol of RepA dimer per mol of ClpA hexamer and are committed to activating RepA. In the last step of the reaction, active RepA is released upon exchange of ATP with the nonhydrolyzable ATP analog and ATP hydrolysis. Importantly, we discovered that one cycle of RepA binding to ClpA followed by ATP-dependent release is sufficient to convert inactive RepA to its active form.     

Approach to the patient with recurrent neprolithiasis

Although recurring nephrolithiasis may not be as common as single-episode disease, it poses greater problems to the patient's daily lifestyle and general future health status. The general need for an adequate history, examination, and radiological assessment is acknowledged, but a more intensive investigative and management approach is required. Investigations for secondary causes are paramount and may lead to identification of unusual metabolic abnormalities and specific therapies. Such medical approaches entail consideration of dietary adjustments to lower the urinary excretion of components of the renal stones, pharmacological therapies to modulate urinary constituents and limit renal stone risk, and monitoring efficacy of the therapy over time. This approach will prevent significant deterioration of renal function and other serious metabolic consequences.     

Mycoplasma pneumoniae and Chlamydia pneumoniae in asthma: effect of clarithromycin

STUDY OBJECTIVES: To determine the effect of clarithromycin therapy in patients with asthma. DESIGN: Randomized, double blind, placebo-controlled trial. SETTING: A tertiary referral center. PATIENTS OR PARTICIPANTS: Fifty-five subjects with chronic, stable asthma recruited from the general Denver, CO, community. INTERVENTIONS: Patients underwent airway evaluation for Mycoplasma pneumoniae and Chlamydia pneumoniae by polymerase chain reaction (PCR) and culture, followed by treatment with clarithromycin, 500 bid, or placebo for 6 weeks. MEASUREMENTS AND RESULTS: Outcome variables were lung function, sinusitis as measured by CT, and the inflammatory mediators tumor necrosis factor (TNF)-alpha, interleukin (IL)-2, IL-4, IL-5, and IL-12 messenger RNA (mRNA) measured via in situ hybridization, in airway biopsies, and BAL. Mycoplasma or chlamydia were detected by PCR in 31 of 55 asthmatics. Treatment resulted in a significant improvement in the FEV(1), but only in the PCR-positive subjects (2.50 +/- 0.16 to 2.69 +/- 0.19 L, mean +/- SEM; p = 0.05). This was not appreciated in the PCR-negative subjects (2.59 +/- 0.24 to 2.54 +/- 0.18 L, p = 0.85) or the PCR-positive or PCR-negative subjects who received placebo. Sinus CTs revealed no change in sinusitis with clarithromycin treatment. In situ hybridization revealed no significant difference in baseline airway tissue or BAL-mediator expression between the PCR-positive and PCR-negative subjects. However, the PCR-positive subjects who received clarithromycin demonstrated a reduction in TNF-alpha (p = 0.006), IL-5 (p = 0.007), and IL-12 (p = 0.004) mRNA in BAL and TNF-alpha mRNA in airway tissue (p = 0.0009). The PCR-negative subjects who received clarithromycin only demonstrated a reduction in TNF-alpha (p = 0.01) and IL-12 (p = 0.002) mRNA in BAL and TNF-alpha mRNA in airway tissue (p = 0.004). There were no significant differences in cytokine expression in those subjects who received placebo. CONCLUSIONS: These observations support the hypothesis that clarithromycin therapy improves lung function, but only in those subjects with positive PCR findings for M pneumoniae or C pneumoniae.     

Safety of sputum induction in moderate-to-severe chronic obstructive pulmonary disease

This retrospective study was designed to evaluate the safety and efficacy of a bronchoprotective sputum induction protocol in moderate to severe chronic obstructive pulmonary disease (COPD). Forty-two adults with COPD (FEV1 = 51.7 +/- 3.2% predicted (mean +/- SEM)) under went sputum induction using a protocol designed to minimize hypertonic saline-induced bronchoconstriction. Hypertonic (3%) saline was used for subjects with FEV1 > or = 50%, and normal (0.9%) saline was used for subjects with FEV1 < 50%. Primary outcomes were change in peak flow, FEV1 and oxygen saturation. Mean decline in peak flow during sputum induction was 13.2 +/- 2.1%. FEV1 fell by 11.4 +/- 2.3%, an absolute fall of 0.14 +/- 0.031. Oxygen saturation did not change. A fall in peak flow of > or = 20% reliably predicted a fall in FEV1 of > or = 20%. Thirty-five of 42 subjects (83.3%) produced an acceptable sputum sample. Sputum eosinophil and neutrophil percentages were 2.8 +/- 0.9 and 73.0 +/- 3.0%, respectively, and were not correlated with changes in peak flow, FEV1 or oxygen saturation. A protocol for sputum induction which restricts the use of hypertonic saline based on lung function is both safe and effective in subjects with moderate to severe COPD.     

Exaggerated natriuretic and calciuric responses to hydrochlorothiazide in renal hypercalciuria but not in absorptive hypercalciuria

Patients with hypercalciuria have been reported to have an exaggerated response to hydrochlorothiazide (HCTZ), implying a renal tubular defect in solute reabsorption. To determine whether this disturbance is generalized or unique to a particular pathogenetic type of hypercalciuria, we measured the increments in urinary sodium (delta Na), calcium (delta Ca), and magnesium after a 100-mg dose of oral HCTZ in 10 normal subjects and 31 patients with different types of hypercalciuric nephrolithiasis. Eleven patients with renal hypercalciuria had significantly greater delta Na (P less than 0.005) and delta Ca (P less than 0.005) than the normal subjects. Ten patients with absorptive hypercalciuria and 10 patients with fasting hypercalciuria without parathyroid stimulation had delta Na and delta Ca indistinguishable from those of normal subjects. In all groups, urinary HCTZ and basal 24-h urinary Na did not differ. The results suggest that the unique natriuretic and calciuric responses to HCTZ occur only in renal hypercalciuric patients with secondary hyperparathyroidism. The data support a renal tubular defect in renal hypercalciuric in contrast to other diagnostic categories of hypercalciuric nephrolithiasis.     

Elevated levels of transforming growth factor-beta(1) in serum of patients with stable bronchiectasis

Bronchiectasis is a chronic inflammatory and infective airway disease characterized by irreversible dilatation of the bronchi and persistent purulent sputum. Transforming growth factor-beta(1) (TGF-beta(1)) has been found to be increased in the lungs or bronchoalveolar lavage fluid of patients with inflammatory lung diseases. However, little is known on the serum TGF-beta(1) levels in patients with bronchiectasis. We aimed to determine the serum TGF-beta(1) concentrations in 95 patients with stable bronchiectasis (63 women; mean+/-sd age, 58.9+/-14.1 years) and 68 control subjects (23 women; 48.9+/-12.8 years) by ELISA, and to correlate with clinical parameters. The serum TGF-beta(1) levels were significantly higher in bronchiectatic patients compared with control subjects (median [range], 1812.5 pg/ml [1226.4-4114.5 pg/ml] vs. 1342.4 pg/ml [940.3-2371.7 pg/ml]; P<0.001). There was, however, no correlation between serum TGF-beta(1) levels with FEV(1) (% predicted), FVC (% predicted), 24h sputum volume, the number of bronchiectatic lung lobes or total white blood cell count (P>0.05). Our findings support previous indications that TGF-beta(1) may contribute to bronchiectatic airway inflammation. Further studies on the potential mechanisms and pathogenesis implications of this elevation should also be pursued in future.