The Three-Fold Axis of the HIV-1 Capsid Lattice Is the Species-Specific Binding Interface for TRIM5alpha

Rhesus TRIM5alpha (rhTRIM5alpha) potently restricts replication of human immunodeficiency virus type 1 (HIV-1). Restriction is mediated through direct binding of the C-terminal B30.2 domain of TRIM5alpha to the assembled HIV-1 capsid core. This host-pathogen interaction involves multiple capsid molecules within the hexagonal HIV-1 capsid lattice. However, the molecular details of this interaction and the precise site at which the B30.2 domain binds remain largely unknown. The human orthologue of TRIM5alpha (hsTRIM5alpha) fails to block infection by HIV-1 both in vivo and in vitro This is thought to be due to differences in binding to the capsid lattice. To map the species-specific binding surface on the HIV-1 capsid lattice, we used microscale thermophoresis and dual-focus fluorescence correlation spectroscopy to measure binding affinity of rhesus and human TRIM5alpha B30.2 domains to a series of HIV-1 capsid variants that mimic distinct capsid arrangements at each of the symmetry axes of the HIV-1 capsid lattice. These surrogates include previously characterized capsid oligomers, as well as a novel chemically cross-linked capsid trimer that contains cysteine substitutions near the 3-fold axis of symmetry. The results demonstrate that TRIM5alpha binding involves multiple capsid molecules along the 2-fold and 3-fold interfaces between hexamers and indicate that the binding interface at the 3-fold axis contributes to the well-established differences in restriction potency between TRIM5alpha orthologues. IMPORTANCE TRIM5alpha is a cellular protein that fends off infection by retroviruses through binding to the viruses\u27 protein shell surrounding its genetic material. This shell is composed of several hundred capsid proteins arranged in a honeycomb-like hexagonal pattern that is conserved across retroviruses. By binding to the complex lattice formed by multiple capsid proteins, rather than to a single capsid monomer, TRIM5alpha restriction activity persists despite the high mutation rate in retroviruses such as HIV-1. In rhesus monkeys, but not in humans, TRIM5alpha confers resistance to HIV-1. By measuring the binding of human and rhesus TRIM5alpha to a series of engineered HIV-1 capsid mimics of distinct capsid lattice interfaces, we reveal the HIV-1 capsid surface critical for species-specific binding by TRIM5alpha

Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein

Intrinsically disordered proteins (IDPs) are increasingly recognized as a class of molecules that can exert essential biological functions even in the absence of a well-defined three-dimensional structure. Understanding the conformational distributions and dynamics of these highly flexible proteins is thus essential for explaining the molecular mechanisms underlying their function. Single-molecule fluorescence spectroscopy in combination with Förster resonance energy transfer (FRET) is a powerful tool for probing intramolecular distances and the rapid long-range distance dynamics in IDPs. To complement the information from FRET, we combine it with photoinduced electron transfer (PET) quenching to monitor local loop-closure kinetics at the same time and in the same molecule. Here we employed this combination to investigate the intrinsically disordered N-terminal domain of HIV-1 integrase. The results show that both long-range dynamics and loop closure kinetics on the sub-microsecond time scale can be obtained reliably from a single set of measurements by the analysis with a comprehensive model of the underlying photon statistics including both FRET and PET. A more detailed molecular interpretation of the results is enabled by direct comparison with a recent extensive atomistic molecular dynamics simulation of integrase. The simulations are in good agreement with experiment and can explain the deviation from simple models of chain dynamics by the formation of persistent local secondary structure. The results illustrate the power of a close combination of single-molecule spectroscopy and simulations for advancing our understanding of the dynamics and detailed mechanisms in unfolded and intrinsically disordered proteins

Ejaculate for Microbiological Culture: To Wash or Not To Wash?

Bacteria can be associated with male infertility. Antibacterial substances (e.g., zinc-containing proteins, antimicrobial peptides) in ejaculates might impair the growth of bacteria in culture. We therefore wanted to test if removing antibacterial substances by washing the ejaculate could improve the detection of bacteria in culture. All ejaculates from patients ≥18 years old, which were obtained for routine diagnostics to assess male infertility were included in this study (no exclusion criteria were applied). Test samples were diluted with 2 mL sterile 0.45% saline, vortexed, and centrifuged (5 min; 7.5 × g). After the removal of 2 mL of the supernatant and resuspension, 10 μL of the pellet was used for aerobic and anaerobic culture. Control samples were cultured identically but without washing. Species identification was done with matrix-assisted laser desorption ionization-time of flight mass spectrometry. A total of 186 samples were included. The data set was stratified into five groups (Gram-negative rods [GNR], anaerobes [AN], Enterococcus spp. [EC], coagulase-negative staphylococci [CNS], and viridans streptococci [VS]). Compared to the control arm, the test arm revealed significant lower proportions for CNS (59.1% versus 44.6%, P < 0.01) and VS (53.8% versus 41.9%, P = 0.03). Similarly, slightly lower proportions of GNR (16.1% versus 15.1%, P = 0.89), AN (19.9% versus 17.2%, P = 0.5), and EC (25.3% versus 23.1%, P = 0.63) were observed. The medians of CFU were lower in test samples compared to the control samples (6.5 × 103 versus 2.5 × 103, P < 0.01) for any bacterial growth. Lower colony counts were also observed for individual bacterial groups. In conclusion, preculture washing of ejaculates results in a decrease in total bacteria count and culture-positive samples. IMPORTANCE This study compares two methods for processing ejaculate samples from men undergoing investigations for infertility. The method of sample washing and centrifugation was compared to the standard method of direct inoculation and culture. The study hypothesis was that preprocessing of samples may increase bacterial yield by removing bactericidal substances from semen. However, we found that washing ejaculate samples before microbiological culture did not improve the detection of bacteria and led to a reduction in colony counts

Überfachliche Kompetenzen stärken: Anregungen für die Planung, Förderung und Einschätzung überfachlicher Kompetenzen

Das vorliegende Dossier liefert Impulse für die Planung, Förderung und Einschätzung der überfachlichen Kompetenzen. Anhand eines theoretischen Überblicks, einer Checkliste für die Planung, detailliert ausgearbeiteter Praxisbeispiele, mehrerer Berichte von Lehrpersonen aus dem Schulalltag sowie eines Katalogs mit Anregungen zur Förderung in den drei Zyklen werden verschiedene Vorgehens- und Umsetzungsweisen dargestellt

Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes

Highly charged intrinsically disordered proteins can form complexes with very high affinity in which both binding partners fully retain their disorder and dynamics, exemplified by the positively charged linker histone H1.0 and its chaperone, the negatively charged prothymosin α. Their interaction exhibits another surprising feature: The association/dissociation kinetics switch from slow two-state-like exchange at low protein concentrations to fast exchange at higher, physiologically relevant concentrations. Here we show that this change in mechanism can be explained by the formation of transient ternary complexes favored at high protein concentrations that accelerate the exchange between bound and unbound populations by orders of magnitude. Molecular simulations show how the extreme disorder in such polyelectrolyte complexes facilitates (i) diffusion-limited binding, (ii) transient ternary complex formation, and (iii) fast exchange of monomers by competitive substitution, which together enable rapid kinetics. Biological polyelectrolytes thus have the potential to keep regulatory networks highly responsive even for interactions with extremely high affinities

Crossed cerebellar diaschisis in acute ischemic stroke: Impact on morphologic and functional outcome

Crossed cerebellar diaschisis (CCD) is the phenomenon of hypoperfusion and hypometabolism of the contralateral cerebellar hemisphere caused by dysfunction of the related supratentorial region. Our aim was to analyze its influence on morphologic and functional outcome in acute ischemic stroke. Subjects with stroke caused by a large vessel occlusion of the anterior circulation were selected from an initial cohort of 1644 consecutive patients who underwent multiparametric CT including whole-brain CT perfusion. Two experienced readers evaluated the posterior fossa in terms of CCD absence (CCD-) or presence (CCD+). A total of 156 patients formed the study cohort with 102 patients (65.4%) categorized as CCD- and 54 (34.6%) as CCD+. In linear and logistic regression analyses, no significant association between CCD and final infarction volume (beta = -0.440, p = 0.972), discharge mRS2 (OR = 1.897, p = 0.320), or 90-day mRS <= 2 (OR = 0.531, p = 0.492) was detected. CCD+ patients had larger supratentorial cerebral blood flow deficits (median: 164 ml vs. 115 ml;p = 0.001) compared to CCD-patients. Regarding complications, CCD was associated with a higher rate of parenchymal hematomas (OR = 4.793, p = 0.035). In conclusion, CCD is frequently encountered in acute ischemic stroke caused by large vessel occlusion of the anterior circulation. CCD was associated with the occurrence of parenchymal hematoma in the ipsilateral cerebral infarction but did not prove to significantly influence patient outcome

Depletion interactions modulate the binding between disordered proteins in crowded environments

Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of macromolecular crowding on the interactions of IDPs with their cellular targets. Here, we investigate the influence of crowding on the interaction between two IDPs that fold upon binding, with polyethylene glycol as a crowding agent. Single-molecule spectroscopy allows us to quantify the effects of crowding on a comprehensive set of observables simultaneously: the equilibrium stability of the complex, the association and dissociation kinetics, and the microviscosity, which governs translational diffusion. We show that a quantitative and coherent explanation of all observables is possible within the framework of depletion interactions if the polymeric nature of IDPs and crowders is incorporated based on recent theoretical developments. The resulting integrated framework can also rationalize important functional consequences, for example, that the interaction between the two IDPs is less enhanced by crowding than expected for folded proteins of the same size