Pseudo-elastic PP and PSSP modeling in stratified media

Many modeling techniques have been developed to find the acoustic and elastic responses of a stack of plane layers to a plane spectral wave. For an elastic medium bounded above by an acoustic half-space, the acoustic wave propagator matrix modeling method can be modified to model pseudoelastic PP arrivals and PSSP arrivals. PP arrivals propagate as pure longitudinal (P) waves in the layers, whereas PSSP arrivals propagate as shear (S) waves in the elastic part of the model. A simple modification of the pseudoelastic PP response modeling scheme allows modeling of primary P reflections. A primary reflection event involves just one reflection in the plane stratified model and thus excludes internal multiples. The propagator modeling scheme is formulated in the frequency-horizontal slowness domain. By applying inverse Fourier transforms over the frequency and horizontal wavenumbers, where the wavenumber is the horizontal slowness divided by the frequency, modeled seismograms are computed and displayed in the time-space domain. By applying an inverse Fourier transform over the frequency for selected horizontal slowness components, the computed seismograms can be shown in the intercept time-horizontal slowness ( τ- p) domain. When the source wavelet is unity for frequencies of interest, the τ- p domain seismograms become plane-wave Green’s function seismograms. The p-traces of the Green’s function primary P-wave seismograms accumulate with increasing time band-limited step functions weighted by reflection strengths.

Multiple signals in the gut contract the mouse norovirus capsid to block antibody binding while enhancing receptor affinity.

Human norovirus is the leading cause of gastroenteritis world-wide, with no approved vaccine or antiviral treatment to mitigate infection. These plus-strand RNA viruses have T=3 icosahedral protein capsids with 90 pronounced protruding (P) domain dimers to which antibodies and cellular receptors bind. We previously demonstrated that bile binding to the capsid of mouse norovirus (MNV) causes several major conformational changes; the entire P domain rotates by ∼90° and contracts onto the shell, the P domain dimers rotate about each other, and the structural equilibrium of the epitopes at the top of the P domain shift towards the ‘closed’ conformation that favors receptor binding while blocking antibody binding. Here we demonstrate that MNV undergoes reversible conformational changes at pH 5.0 nearly identical to when bile binds. Notably, at low pH or when metals bind, a cluster of acidic resides in the G’H’ loop interact, distort the G’H’ loop, and this may drive C’D’ loop movement towards the closed conformation. ELISA assays with infectious virus particles at low pH or in the presence of metals demonstrated that all tested antibodies do not bind to this contracted form, akin to what was observed with the MNV/bile complex. Therefore, low pH, cationic metals, and bile salts are physiological ‘triggers’ in the gut for P domain contraction and structural rearrangement that synergistically prime the virus for receptor binding while blocking antibody binding. Importance The protruding domains on the Calicivirus capsids are recognized by cell receptor(s) and antibodies. We demonstrated that mouse norovirus (MNV) P domains are highly mobile and bile causes contraction onto the shell surface while allosterically blocking antibody binding. We present the near atomic cryo-EM structures of infectious MNV at pH 5.0 and 7.5. Surprisingly, low pH is sufficient to cause the same conformational changes as when bile binds. A cluster of acidic residues on the G’H’ loop was the most likely involved with the pH effects. These residues also bind divalent cations and had the same conformation as observed here at pH 5. Binding assays demonstrate that low pH and metals block antibody binding and therefore the G’H’ loop might be driving the conformational changes. Therefore, low pH, cationic metals, and bile salts in the gut synergistically prime the virus for receptor binding while blocking antibody binding.

Broadly cross-reactive human antibodies that inhibit genogroup I and II noroviruses

The rational development of norovirus vaccine candidates requires a deep understanding of the antigenic diversity and mechanisms of neutralization of the virus. Here, we isolate and characterize a panel of broadly cross-reactive naturally occurring human monoclonal IgMs, IgAs and IgGs reactive with human norovirus (HuNoV) genogroup I or II (GI or GII). We note three binding patterns and identify monoclonal antibodies (mAbs) that neutralize at least one GI or GII HuNoV strain when using a histo-blood group antigen (HBGA) blocking assay. The HBGA blocking assay and a virus neutralization assay using human intestinal enteroids reveal that the GII-specific mAb NORO-320, mediates HBGA blocking and neutralization of multiple GII genotypes. The Fab form of NORO-320 neutralizes GII.4 infection more potently than the mAb, however, does not block HBGA binding. The crystal structure of NORO-320 Fab in complex with GII.4 P-domain shows that the antibody recognizes a highly conserved region in the P-domain distant from the HBGA binding site. Dynamic light scattering analysis of GII.4 virus-like particles with mAb NORO-320 shows severe aggregation, suggesting neutralization is by steric hindrance caused by multivalent cross-linking. Aggregation was not observed with the Fab form of NORO-320, suggesting that this clone also has additional inhibitory features.

Two P domain potassium channels in GtoPdb v.2021.2

The 4TM family of K channels mediate many of the background potassium currents observed in native cells. They are open across the physiological voltage-range and are regulated by a wide array of neurotransmitters and biochemical mediators. The pore-forming α-subunit contains two pore loop (P) domains and two subunits assemble to form one ion conduction pathway lined by four P domains. It is important to note that single channels do not have two pores but that each subunit has two P domains in its primary sequence; hence the name two P domain, or K2P channels (and not two-pore channels). Some of the K2P subunits can form heterodimers across subfamilies (e.g. K2P3.1 with K2P9.1). The nomenclature of 4TM K channels in the literature is still a mixture of IUPHAR and common names. The suggested division into subfamilies, described in the More detailed introduction, is based on similarities in both structural and functional properties within subfamilies and this explains the "common abbreviation" nomenclature in the tables below.

A norovirus uses bile salts to escape antibody recognition while enhancing receptor binding.

Noroviruses, members of the Calicivirus family, are the major cause of epidemic gastroenteritis in humans, causing ∼20 million cases annually. These plus-strand RNA viruses have T=3 icosahedral protein capsids with 90 pronounced protruding (P) domain dimers to which antibodies and cellular receptors bind. In the case of mouse norovirus (MNV), bile salts have been shown to enhance receptor (CD300lf) binding to the P domain. We previously demonstrated that the P domains of several genotypes are markedly flexible and ‘float’ over the shell, but the role of this flexibility was unclear. Recently, we demonstrated that bile causes a 90° rotation and collapse of the P domain on to the shell surface. Since bile binds distal to the P/shell interface, it was not at all clear how it could cause such dramatic changes. Here we present the near-atomic resolution cryo-EM structure of the protruding MNV complexed with a neutralizing Fab. Combined with previous results, we show here that bile salts cause allosteric conformational changes in the P domain that block antibody recognition to the top of the P domain. In addition, bile also causes a major rearrangement of the P domain dimers that are likely responsible for the bile-induced collapse of the P domain onto the shell. In the contracted shell conformation, antibodies to the P1 and shell domains are not expected to bind. Therefore, at the site of infection in the gut, the host’s own bile allows the virus to escape antibody-mediated neutralization while enhancing cell attachment. Importance: The major feature of the Calicivirus capsids are the 90 protruding domains (P domains) that are the site of cell receptor(s) attachment and antibody epitopes. We previously demonstrated that these P domains are highly mobile and that bile causes these ‘floating’ P domains in mouse norovirus (MNV) to contract onto the shell surface. Here, we present the near atomic cryo-EM structure of the isolated MNV P domain complexed with a neutralizing Fab fragment. Together, the data shows that bile causes two sets of changes. First, bile causes allosteric conformational changes in the epitopes at the top of the P domain that block antibody binding. Second, bile causes the P domain dimer subunits to rotate relative to each other, causing contraction of the P domain that buries epitopes at the base of the P and shell domains. Collectively, MNV uses the host’s own metabolites to enhance cell receptor binding while simultaneously blocking antibody recognition.

Murine norovirus capsid plasticity – Glycochenodeoxycholic acid stabilizes P-domain dimers and triggers escape from antibody recognition

The murine norovirus (MNV) capsid protein is the target for various neutralizing antibodies binding to distal tips of its protruding (P)-domain. The bile acid glycochenodeoxycholic acid (GCDCA), an important co-factor for murine norovirus (MNV) infection, has recently been shown to induce conformational changes in surface-loops and a contraction of the virion. Here, we employ protein NMR experiments using stable isotope labeled MNV P-domains to shed light on underlying molecular mechanisms. We observe two separate sets of NMR resonance signals for P-domain monomers and dimers, permitting analysis of the corresponding exchange kinetics. Unlike human norovirus GII.4 P-dimers, which exhibit a half-life in the range of several days, MNV P-dimers are very short lived with a half-life of about 17 s. Addition of GCDCA shifts the equilibrium towards the dimeric form by tightly binding to the P-dimers. In MNV virions GCDCA-mediated stabilization of the dimeric arrangement of P-domains generates a more ordered state, which in turn may entropically assist capsid contraction. Numerous long-range chemical shift perturbations (CSPs) upon addition of GCDCA reflect allosteric conformational changes as a feature accompanying dimer stabilization. In particular, CSPs indicate rearrangement of the E’F’ loop, a target for various neutralizing antibodies. Indeed, treating MNV virions with GCDCA prior to neutralizing antibody exposure abolishes neutralization. These findings advance our understanding of GCDCA-induced structural changes of MNV capsids and experimentally support an intriguing viral immune escape mechanism relying on GCDCA-triggered conformational changes of the P-dimer.Significance StatementThis study sheds light on the role of glycochenodeoxycholic acid (GCDCA) in promoting murine norovirus (MNV) infection and immune escape. Binding of GCDCA to the dimeric P-domain has been well characterized by crystallography and cryo EM studies, showing that upon GCDCA binding, a 90° rotation of the P-domain occurs, which results in its collapse onto the underlying shell of the virus. Our NMR experiments now reveal P-dimer stability as a new dimension of plasticity of MNV capsids and suggest that capsid contraction is entropically assisted. Conformational changes as a feature of P-dimer stabilization eliminate recognition by neutralizing antibodies, no longer being able to prevent infection. These findings highlight key differences between human and MNV capsid structures, promote our understanding of MNV infection on a molecular level, and reveal a novel immune escape mechanism.

Same Degree of Intensification with Different Degrees of Sentential Projections

In Chengdu Chinese, degree intensifiers for APs/VPs are attested to pair with three different types of sentence-final particles (SFPs), i.e., the FinP-level, the FocP-level and the ExclP-level SFPs, which function to complete a sentence, encode a focus and express exclamation. In our analysis, a degree intensifier projects a DegP, which pairs with one of the three sentential projections, viz., FinP, FocP and ExclP. This pairing is motivated by feature checking, as intensifiers contain the uninterpretable semantic features of [+Fin], [+Foc] or [+Excl], which need to be checked by sentential projections. Due to the inalienable sentential functions, intensifiers are barred from occurring in any kind of non-finite contexts. Furthermore, FinP and FocP are within the vP-domain, whereas ExclP is in the CP domain. Thus, ExclP-type intensifiers, unlike FinP-type and FocP-type intensifiers, defy relativization. This study of associating degree intensification with sentential functions not only explains the syntactic behaviors of Chengdu intensifiers but also sheds new light on the well-known Mandarin hen puzzle.