Discovery and Characterization of Potential Prognostic Biomarkers for Dengue Hemorrhagic Fever

Half a million patients are hospitalized with severe dengue every year, many of whom would die without timely, appropriate clinical intervention. The majority of dengue cases are uncomplicated; however, 2–5% progress to severe dengue. Severe dengue cases have been reported with increasing frequency over the last 30 years. To discover biomarkers for severe dengue, we used surface-enhanced laser desorption/ionization time-of-flight mass spectrometry to analyze dengue virus positive serum samples from the acute phase of infection. Using this method, 16 proteins were identified as candidate biomarkers for severe dengue. From these 16 biomarkers, three candidates were selected for confirmation by enzyme-linked immunosorbent assay and Western blot: vitronectin (Vtn, 55.1 kDa), hemopexin (Hx, 52.4 kDa), and serotransferrin (Tf, 79.2 kDa). Vitronectin, Hx, and Tf best differentiated between dengue and severe dengue.     

Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury

Neuronal calcium (Ca²⁺)-binding proteins 1 and 2 (NECAB1/2) are members of the phylogenetically conserved EF-hand Ca²⁺-binding protein superfamily. To date, NECABs have been explored only to a limited extent and, so far, not at all at the spinal level. Here, we describe the distribution, phenotype, and nerve injury-induced regulation of NECAB1/NECAB2 in mouse dorsal root ganglia (DRGs) and spinal cord. In DRGs, NECAB1/2 are expressed in around 70% of mainly small- and medium-sized neurons. Many colocalize with calcitonin gene-related peptide and isolectin B4, and thus represent nociceptors. NECAB1/2 neurons are much more abundant in DRGs than the Ca²⁺-binding proteins (parvalbumin, calbindin, calretinin, and secretagogin) studied to date. In the spinal cord, the NECAB1/2 distribution is mainly complementary. NECAB1 labels interneurons and a plexus of processes in superficial layers of the dorsal horn, commissural neurons in the intermediate area, and motor neurons in the ventral horn. Using CLARITY, a novel, bilaterally connected neuronal system with dendrites that embrace the dorsal columns like palisades is observed. NECAB2 is present in cell bodies and presynaptic boutons across the spinal cord. In the dorsal horn, most NECAB1/2 neurons are glutamatergic. Both NECAB1/2 are transported into dorsal roots and peripheral nerves. Peripheral nerve injury reduces NECAB2, but not NECAB1, expression in DRG neurons. Our study identifies NECAB1/2 as abundant Ca²⁺-binding proteins in pain-related DRG neurons and a variety of spinal systems, providing molecular markers for known and unknown neuron populations of mechanosensory and pain circuits in the spinal cord.Calcium (Ca²⁺) plays a crucial role in many and diverse cellular processes, including neurotransmission (1). Glutamate and neuropeptides are neurotransmitters released from the central terminals of dorsal root ganglion (DRG) neurons in the spinal dorsal horn, where signals for different sensory modalities, including pain, are conveyed to higher centers (2–12). Neurotransmitter release is tightly regulated by Ca²⁺-dependent SNARE proteins whose activity is regulated by Ca²⁺-binding proteins (CaBPs) (1, 7, 13).Parvalbumin (PV), calbindin D-28K (CB), calretinin (CR), and secretagogin (Scgn) are extensively studied EF-hand CaBPs, and they have also emerged as valuable anatomical markers for morphologically and functionally distinct neuronal subpopulations (14–17). The expression of CaBPs in DRG neurons has been thoroughly studied (18). Moreover, neuronal Ca²⁺ sensor 1 and downstream regulatory element-antagonist modulator (DREAM) are also EF-hand Ca²⁺-binding proteins in DRGs and the spinal cord (19, 20). Despite these advances, a CaBP has so far not been characterized in the majority of small- and medium-sized DRG neurons, many of which represent nociceptors.The subfamily of neuronal Ca²⁺-binding proteins (NECABs) consists of three members (NECAB1–NECAB3), probably as a result of gene duplication (21). NECABs are also EF-hand proteins, with one pair of EF-hand motifs in the N terminus and a putative antibiotic biosynthesis monooxygenase domain in the C terminus, which are linked by a NECAB homogeneous region (22). NECAB1/2 are restricted to the nervous system, whereas NECAB3 is also expressed in the heart and skeletal muscle (21).NECAB1 was first identified as the target protein of synaptotagmin I C2A-domain by affinity chromatography, with its expression restricted to layer 4 cortical pyramidal neurons, inhibitory interneurons, and hippocampal CA2 pyramidal cells in mouse brain (21, 23). The gene of the second member was cloned from mouse and initially named Necab. It encodes a 389-aa (NECAB2) (24). NECAB2 was identified as a downstream target of Pax6 in mouse retina, which is involved in retinal development (24, 25), as well as being a binding partner for the adenosine A_2A receptor (22). Furthermore, an interaction between NECAB2 and metabotropic glutamate receptor 5 (mGluR5) was demonstrated in rat hippocampal pyramidal cells, possibly regulating mGluR5’s coupling to its signaling machinery (26). Finally, NECAB3, also known as XB51, was isolated as an interacting target for the neuron-specific X11-like protein and is possibly involved in the pathogenesis of Alzheimer’s disease (27, 28).Very recently, NECAB1/2 were shown to have complementary expression patterns in mouse hippocampus at the mRNA and protein levels, whereas NECAB3 is broadly distributed in the hippocampus (29). NECAB1-expressing cells were seen throughout the cell-sparse layers of Ammon’s horn and the hilus of the dentate gyrus. In contrast, NECAB2 is enriched in pyramidal cells of the CA2 region. A minority of NECAB1⁺ neurons were GABAergic yet did not coexpress PV, CB, or CR (29).Here, we investigated the expression of NECAB1/2 in mouse DRGs and spinal cord using quantitative PCR (qPCR), immunohistochemistry (also combined with CLARITY) (30), and Western blotting. We compared the distribution of NECABs with that of the four CaBPs restricted to neurons, PV, CB, CR, or Scgn. NECAB⁺ neurons in the spinal dorsal horn were phenotyped using transgenic mice harboring genetic markers for excitatory [vesicular glutamate transporter 2 (VGLUT2)] (31) or inhibitory [glutamate decarboxylase 67 (GAD67)] (32) cell identities. Finally, the effect of peripheral nerve injury was analyzed.     

From the Cover: Staphylococcus aureus secretes a unique class of neutrophil serine protease inhibitors

Neutrophils are indispensable for clearing infections with the prominent human pathogen Staphylococcus aureus. Here, we report that S. aureus secretes a family of proteins that potently inhibits the activity of neutrophil serine proteases (NSPs): neutrophil elastase (NE), proteinase 3, and cathepsin G. The NSPs, but not related serine proteases, are specifically blocked by the extracellular adherence protein (Eap) and the functionally orphan Eap homologs EapH1 and EapH2, with inhibitory-constant values in the low-nanomolar range. Eap proteins are together essential for NSP inhibition by S. aureus in vitro and promote staphylococcal infection in vivo. The crystal structure of the EapH1/NE complex showed that Eap molecules constitute a unique class of noncovalent protease inhibitors that occlude the catalytic cleft of NSPs. These findings increase our insights into the complex pathogenesis of S. aureus infections and create opportunities to design novel treatment strategies for inflammatory conditions related to excessive NSP activity.Infections with the human pathogen Staphylococcus aureus constitute a major risk to human health. Although this bacterium harmlessly colonizes more than 30% of the population via the nose or skin, it causes severe morbidity and mortality upon invasion of deeper tissues (1). To avert these serious infections, neutrophils play an indispensable role (2). Neutrophil serine proteases (NSPs), including neutrophil elastase (NE), proteinase 3 (PR3), and cathepsin G (CG), are important for various neutrophil functions. Active NSPs are stored within the azurophilic granules (3), but upon neutrophil activation, they either enter the nucleus to regulate extracellular trap (NET) formation (4) or they are released into the extracellular milieu to kill certain bacteria (5), cleave bacterial virulence factors (5, 6), or regulate immune responses by cleaving chemokines and receptors (7). Recently, a fourth neutrophil serine protease, denoted NSP4, was identified (8).Given the central role of NSPs in neutrophil function, we wondered whether S. aureus had evolved mechanisms to cope with NSPs. In this study, we discover that S. aureus secretes a family of proteins that specifically and potently block NSPs: extracellular adherence protein (Eap) and the hitherto functional orphans Eap-homologue (EapH) 1 and 2. Structural studies presented here show that Eap molecules represent a unique class of noncovalent NSP inhibitors that is distinct from the well-known chelonianin class of inhibitors. These mechanistic insights can initiate development of novel, broad-range NSP inhibitors to be used in various inflammatory conditions. Furthermore, these insights increase our understanding of the pathogenicity of S. aureus and underline the exceptional capability of this pathogen to adapt to its host by modulating the immune response.     

Role of cavities and hydration in the pressure unfolding of T4 lysozyme

It is well known that high hydrostatic pressures can induce the unfolding of proteins. The physical underpinnings of this phenomenon have been investigated extensively but remain controversial. Changes in solvation energetics have been commonly proposed as a driving force for pressure-induced unfolding. Recently, the elimination of void volumes in the native folded state has been argued to be the principal determinant. Here we use the cavity-containing L99A mutant of T₄ lysozyme to examine the pressure-induced destabilization of this multidomain protein by using solution NMR spectroscopy. The cavity-containing C-terminal domain completely unfolds at moderate pressures, whereas the N-terminal domain remains largely structured to pressures as high as 2.5 kbar. The sensitivity to pressure is suppressed by the binding of benzene to the hydrophobic cavity. These results contrast to the pseudo-WT protein, which has a residual cavity volume very similar to that of the L99A–benzene complex but shows extensive subglobal reorganizations with pressure. Encapsulation of the L99A mutant in the aqueous nanoscale core of a reverse micelle is used to examine the hydration of the hydrophobic cavity. The confined space effect of encapsulation suppresses the pressure-induced unfolding transition and allows observation of the filling of the cavity with water at elevated pressures. This indicates that hydration of the hydrophobic cavity is more energetically unfavorable than global unfolding. Overall, these observations point to a range of cooperativity and energetics within the T₄ lysozyme molecule and illuminate the fact that small changes in physical parameters can significantly alter the pressure sensitivity of proteins.The destabilization of proteins by pressure is a fundamental and highly informative probe of their structural free energy landscape but remains inadequately understood (1). The underlying determinants of pressure-induced unfolding have recently been a subject of several detailed investigations (2–10). Fundamentally, pressure-induced unfolding of proteins results from the population of nonnative conformations having a lower total system volume than the native structure seen at ambient pressure. Various mechanisms for pressure-induced unfolding have been proposed including changes in water structure that weaken the hydrophobic effect at high pressure (11, 12), increases in solvent density at the protein surface that contribute to a reduction in the total volume of the protein–water system (13, 14), and the elimination of cavities in the protein interior through exposure to solvent (3). With the development of high-pressure sample cells compatible with modern solution NMR probes (15), detailed measurements of proteins unfolding under pressure with atomic resolution have now become possible (5, 16–18). Recent studies of staphylococcal nuclease (SNase) compellingly argue that the filling of void volumes present in the native state is the primary determinant of pressure-induced unfolding (4–6). A critical aspect of a “destruction of voids” mechanism for pressure-induced unfolding of proteins is whether the voids or cavities are occupied with water in the folded state. Early investigations of buried hydrophobic pockets indicated that even large cavities are typically not hydrated, whereas hydrophilic cavities generally are occupied by water (19, 20). Many of the key studies impacting this question used the L99A single-point mutant of the model enzyme T₄ lysozyme (20).The L99A mutation creates an internal cavity with an estimated volume of ∼150–160 ų, large enough to accommodate three or four water molecules (21) (Fig. 1). Crystallographic investigation found no electron density within this pocket at ambient pressure (22, 23). In contrast, solution NMR and molecular-dynamics simulations suggest that the region of the protein around the hydrophobic pocket is highly dynamic, possibly to the extent that the pocket may be transiently accessible to solvent (22, 24–27). Crystallographic studies conducted at high pressure conversely suggested that the region around the pocket is rigid and exhibits increasing rigidity with increased pressure (23). Electron density also increased within the cavity as the hydrostatic pressure was increased (22), consistent with a pressure-induced filling of the hydrophobic cavity with water molecules. In contrast, fluorescence and small-angle X-ray scattering studies in bulk solution demonstrated that the protein is unfolded at these elevated pressures (2), suggesting that the crystal packing effects stabilize the protein. The hydrophobic cavity also provides a general, moderate-affinity binding site for small, relatively nonpolar ligands (28).Open in a separate windowFig. 1.Hydration of T₄ lysozyme L99A at ambient pressure (∼1 bar). A backbone ribbon representation of L99A [Protein Data Bank (PDB) ID code 1L90 (63)] is shown with the N-terminal domain (residues 13–65) illustrated in blue, and the C-terminal domain (residues 1–12 and 66–164) is colored green. The hydrophobic pocket created by the L99A mutation is shown as orange mesh, and the three tryptophan side chains are shown as stick representations. The helices are numbered as a reference for discussion in the text. Cyan spheres are shown at the positions of amide hydrogens where an NOE to the water resonance was detected. Yellow spheres indicate the positions of amide hydrogens within NOE distance (5 Å) of the interior of the hydrophobic pocket, but outside NOE distance to the protein surface. These are the sites where detection of NOEs to the water resonance would indicate hydration of the pocket. No NOE cross-peaks from these sites to the water resonance were observed, suggesting that the pocket is not hydrated at ambient pressure.T₄ lysozyme is one of the smallest known proteins to contain more than one cooperative folding unit. The folding of WT T₄ lysozyme has been examined in detail by using hydrogen–deuterium exchange approaches and has been shown to contain two domains that fold cooperatively and with distinct free energy profiles (29–32). The N-terminal domain is ∼6 kcal/mol less stable than the C-terminal domain. The cavity created by the L99A mutation is in the center of the C-terminal domain. The thermal stability of the L99A mutant is reduced compared with the WT protein by 16 °C (5 kcal/mol) (33), an effect that is partially abrogated by binding hydrophobic ligands to the cavity (28, 34).The L99A mutant of T₄ lysozyme provides a unique system to examine the hydration of internal pockets and the details of pressure-induced unfolding. In principle, protein–water interactions can be characterized by solution NMR methods (35), but severe artifacts often render the approach quite limited (36). Recently, it has been shown that various advantageous properties of proteins and water encapsulated within reverse micelles largely overcome these artifacts (37, 38). Here, we use this approach to directly measure the hydration of the internal cavity. High-pressure NMR is used to examine the pressure-induced response of the protein in bulk solution and under confinement by the reverse micelle. We demonstrate that the hydrophobic pocket appears to be essentially dehydrated at ambient pressure (∼1 bar) and that the pressure response of the protein is an unfolding of the C-terminal domain only, representing an inversion of the relative stability of the domains as a result of the cavity-creating mutation. This result is in contrast to the unfolding of the cysteine-free WT (WT*) protein, which shows only the earliest stages of pressure-induced subglobal unfolding. Furthermore, the L99A mutant with benzene occupying the cavity shows no evidence of pressure unfolding. Nanoscale confinement of the protein also suppresses the L99A pressure-induced unfolding transition (P_u) as a result of the restriction of conformational space imposed by the reverse micelle. In lieu of the pressure unfolding transition, the volume reduction imposed by increasing pressure is compensated for in the reverse micelle by progressively increasing incorporation of water into the cavity interior, essentially recapitulating the observations from high-pressure crystallography in a solution measurement. These findings have important implications with respect to the nature of pressure-induced unfolding, the roles of cavities in protein structural stability, and the effects of confinement, a critical parameter when considering the intracellular milieu, in which proteins must fold and carry out their functions.