Marie M. Phelan

Cooperative Catalysis through Noncovalent Interactions

Noncovalent interactions, such as hydrogen bonding, electrostatic, p–p, CH–p, and hydrophobic forces, play an essential role in the action of nature s catalysts, enzymes. In the last decade these interactions have been successfully exploited in organocatalysis with small organic molecules. In contrast, such interactions have rarely been studied in the wellestablished area of organometallic catalysis, where electronic interactions through covalent bonding and steric effects imposed by bound ligands dictate the activity and selectivity of a metal catalyst. An interesting question is: What happens when an organocatalyst meets an organometallic catalyst? This unification has already created an exciting new space for both fields: cooperative catalysis, where reactants are activated simultaneously by both types of catalyst, thereby enabling reactivity and selectivity patterns inaccessible within each field alone. However, the mechanisms by which the two catalysts cooperatively effect the catalysis remain to be delineated. We recently found that combining an achiral iridium catalyst with a chiral phosphoric acid allows for highly enantioselective hydrogenation of imines (Scheme 1). To gain insight into the mechanism of this metal–organo cooperative catalysis, we studied the catalytic system with a range of techniques, including high pressure 2D-NMR spectroscopy, diffusion measurements, and NOEconstrained computation. Herein we report our findings. To evaluate the mechanism, a simplified achiral complex C was used, which leads to [C][A ] upon mixing, in situ or ex situ, with the chiral phosphoric acid HA through protonation at the amido nitrogen (Scheme 1). In the asymmetric hydrogenation of the model ketimine 1a, [C][A ] afforded 95% ee and full conversion. On the basis of related studies, the hydrogenation can be broadly explained by the catalytic cycle shown in Scheme 1, that is, [C][A ] activates H2 to give the hydride D and protonated 1a, which forms an ion pair with the phosphate affording [1a][A ]; hydride transfer furnishes the amine product 2a while regenerating [C][A ]. Questions pertinent to possible iridium–phosphate cooperation then arise: 1) How does the chiral phosphoric acid induce asymmetry in the hydrogenation? and 2) Does the enantioselectivity result from D being formed enantioselectively from [C][A ], from the phosphate salt [1a][A ], or from interactions involving all three components? We looked first at how the formation of hydride D and its transfer into the substrate are influenced by the chiral acid HA. The studies were carried out in CH2Cl2 or CD2Cl2 owing to the low solubility of the various metal complexes in toluene. The catalytic hydrogenation is feasible in both solvents, giving a 95% ee in toluene and 85 % ee in CH2Cl2 in the case of hydrogenation of 1a with C and HA under the conditions given in Scheme 1. The solution NMR studies show that the ionic complex [C][A ] is formed instantly on protonation of C (0.05 mmol) with one equivalent HA in CD2Cl2 (0.5 mL). Under H2 pressure (> 1 bar), proton transfer from a [C]–H2 dihydrogen intermediate (not observed) to 1a converts [C] into the hydride D and affords the salt [1a] [A ]. Formation of D took place instantly even at 78 8C, and it is observed during catalytic turnover, thus indicating that the hydrogenation is rate-limited by the hydride transfer step. Scheme 1. Hydrogenation of imine with achiral C and chiral acid HA (PMP = p-methoxyphenyl, Ar= 2,4,6-triisopropylphenyl, Ts = tosyl, Bn = benzyl).

Structure and Assembly of a Trans-Periplasmic Channel for Type IV Pili in Neisseria meningitidis

Type IV pili are polymeric fibers which protrude from the cell surface and play a critical role in adhesion and invasion by pathogenic bacteria. The secretion of pili across the periplasm and outer membrane is mediated by a specialized secretin protein, PilQ, but the way in which this large channel is formed is unknown. Using NMR, we derived the structures of the periplasmic domains from N. meningitidis PilQ: the N-terminus is shown to consist of two β-domains, which are unique to the type IV pilus-dependent secretins. The structure of the second β-domain revealed an eight-stranded β-sandwich structure which is a novel variant of the HSP20-like fold. The central part of PilQ consists of two α/β fold domains: the structure of the first of these is similar to domains from other secretins, but with an additional α-helix which links it to the second α/β domain. We also determined the structure of the entire PilQ dodecamer by cryoelectron microscopy: it forms a cage-like structure, enclosing a cavity which is approximately 55 Å in internal diameter at its largest extent. Specific regions were identified in the density map which corresponded to the individual PilQ domains: this allowed us to dock them into the cryoelectron microscopy density map, and hence reconstruct the entire PilQ assembly which spans the periplasm. We also show that the C-terminal domain from the lipoprotein PilP, which is essential for pilus assembly, binds specifically to the first α/β domain in PilQ and use NMR chemical shift mapping to generate a model for the PilP:PilQ complex. We conclude that passage of the pilus fiber requires disassembly of both the membrane-spanning and the β-domain regions in PilQ, and that PilP plays an important role in stabilising the PilQ assembly during secretion, through its anchorage in the inner membrane.

Evidence for metabolic cleavage of a PEGylated protein in vivo using multiple analytical methodologies

PEGylation of therapeutic proteins is commonly used to extend half-lives and to reduce immunogenicity. However, reports of antibodies toward PEGylated proteins and of poly(ethylene glycol) (PEG) accumulation suggest that efficacy and safety concerns may arise. To understand the relationship among the pharmacology, immunogenicity, and toxicology of PEGylated proteins, we require knowledge of the disposition and metabolic fate of both the drug and the polymer moieties. The analysis of PEG by standard spectrophotometric or mass spectrometric techniques is problematic. Consequently, we have examined and compared two independent analytical approaches, based on gel electrophoresis and nuclear magnetic resonance (NMR) spectroscopy, to determine the biological fate of a model PEGylated protein, (40K)PEG-insulin, within a rat model. Both immunoblotting with an antibody to PEG and NMR analyses (LOD 0.5 μg/mL for both assays) indicated that the PEG moiety remained detectable for several weeks in both serum and urine following intravenous administration of (40K)PEG-insulin (4 mg/kg). In contrast, Western blotting with anti-insulin IgG indicated that the terminal half-life of the insulin moiety was far shorter than that of the PEG, providing clear evidence of conjugate cleavage. The application of combined analytical techniques in this way thus allows simultaneous independent monitoring of both protein and polymer elements of a PEGylated molecule. These methodologies also provide direct evidence for cleavage and definition of the chemical species present in biological fluids which may have toxicological consequences due to unconjugated PEG accumulation or immunogenic recognition of the uncoupled protein.

The Structure, Stability and Pheromone Binding of the Male Mouse Protein Sex Pheromone Darcin

Mouse urine contains highly polymorphic major urinary proteins that have multiple functions in scent communication through their abilities to bind, transport and release hydrophobic volatile pheromones. The mouse genome encodes for about 20 of these proteins and are classified, based on amino acid sequence similarity and tissue expression patterns, as either central or peripheral major urinary proteins. Darcin is a male specific peripheral major urinary protein and is distinctive in its role in inherent female attraction. A comparison of the structure and biophysical properties of darcin with MUP11, which belongs to the central class, highlights similarity in the overall structure between the two proteins. The thermodynamic stability, however, differs between the two proteins, with darcin being much more stable. Furthermore, the affinity of a small pheromone mimetic is higher for darcin, although darcin is more discriminatory, being unable to bind bulkier ligands. These attributes are due to the hydrophobic ligand binding cavity of darcin being smaller, caused by the presence of larger amino acid side chains. Thus, the physical and chemical characteristics of the binding cavity, together with its extreme stability, are consistent with darcin being able to exert its function after release into the environment.

NMR Structure of Hsp12, a Protein Induced by and Required for Dietary Restriction-Induced Lifespan Extension in Yeast

Dietary restriction (DR) extends lifespan in yeast, worms, flies and mammals, suggesting that it may act via conserved processes. However, the downstream mechanisms by which DR increases lifespan remain unclear. We used a gel based proteomic strategy to identify proteins whose expression was induced by DR in yeast and thus may correlate with longevity. One protein up-regulated by DR was Hsp12, a small heat shock protein induced by various manipulations known to retard ageing. Lifespan extension by growth on 0.5% glucose (DR) was abolished in an hsp12Δ strain, indicating that Hsp12 is essential for the longevity effect of DR. In contrast, deletion of HSP12 had no effect on growth under DR conditions or a variety of environmental stresses, indicating that the effect of Hsp12 on lifespan is not due to increased general stress resistance. Unlike other small heat shock proteins, recombinant Hsp12 displayed negligible in vitro molecular chaperone activity, suggesting that its cellular function does not involve preventing protein aggregation. NMR analysis indicated that Hsp12 is monomeric and intrinsically unfolded in solution, but switches to a 4-helical conformation upon binding to membrane-mimetic SDS micelles. The structure of micelle-bound Hsp12 reported here is consistent with its recently proposed function as a membrane-stabilising ‘lipid chaperone’. Taken together, our data suggest that DR-induced Hsp12 expression contributes to lifespan extension, possibly via membrane alterations.

In silico analysis of a novel MKRN3 missense mutation in familial central precocious puberty

The onset of puberty is influenced by the interplay of stimulating and restraining factors, many of which have a genetic origin. Premature activation of the GnRH secretion in central precocious puberty (CPP) may arise either from gain‐of‐function mutations of the KISS1 and KISS1R genes or from loss‐of‐function manner mutations of the MKRN3 gene leading to MKRN3 deficiency.

Solution Structure of Factor I-like Modules from Complement C7 Reveals a Pair of Follistatin Domains in Compact Pseudosymmetric Arrangement

Factor I-like modules (FIMs) of complement proteins C6, C7, and factor I participate in protein-protein interactions critical to the progress of a complement-mediated immune response to infections and other trauma. For instance, the carboxyl-terminal FIM pair of C7 (C7-FIMs) binds to the C345C domain of C5 and its activated product, C5b, during self-assembly of the cytolytic membrane-attack complex. FIMs share sequence similarity with follistatin domains (FDs) of known three-dimensional structure, suggesting that FIM structures could be reliably modeled. However, conflicting disulfide maps, inconsistent orientations of subdomains within FDs, and the presence of binding partners in all FD structures led us to determine the three-dimensional structure of C7-FIMs by NMR spectroscopy. The solution structure reveals that each FIM within C7 contains a small amino-terminal FOLN subdomain connected to a larger carboxyl-terminal KAZAL domain. The open arrangement of the subdomains within FIMs resembles that of first FDs within structures of tandem FDs but differs from the more compact subdomain arrangement of second or third FDs. Unexpectedly, the two C7-FIMs pack closely together with an approximate 2-fold rotational symmetry that is rarely seen in module pairs and has not been observed in FD-containing proteins. Interfaces between subdomains and between modules include numerous hydrophobic and electrostatic contributions, suggesting that this is a physiologically relevant conformation that persists in the context of the parent protein. Similar interfaces were predicted in a homology-based model of the C6-FIM pair. The C7-FIM structures also facilitated construction of a model of the single FIM of factor I.

The structure and selectivity of the SR protein SRSF2 RRM domain with RNA

SRSF2 is a prototypical SR protein which plays important roles in the alternative splicing of pre-mRNA. It has been shown to be involved in regulatory pathways for maintaining genomic stability and play important roles in regulating key receptors in the heart. We report here the solution structure of the RNA recognition motifs (RRM) domain of free human SRSF2 (residues 9–101). Compared with other members of the SR protein family, SRSF2 structure has a longer L3 loop region. The conserved aromatic residue in the RNP2 motif is absent in SRSF2. Calorimetric titration shows that the RNA sequence 5′AGCAGAGUA3′ binds SRSF2 with a Kd of 61 ± 1 nM and a 1:1 stoichiometry. NMR and mutagenesis experiments reveal that for SFSF2, the canonical β1 and β3 interactions are themselves not sufficient for effective RNA binding; the additional loop L3 is crucial for RNA complex formation. A comparison is made between the structures of SRSF2–RNA complex with other known RNA complexes of SR proteins. We conclude that interactions involving the L3 loop, N- and C-termini of the RRM domain are collectively important for determining selectivity between the protein and RNA.

Oxidative Stress Alters the Morphology and Toxicity of Aortic Medial Amyloid

The aggregation and fibril deposition of amyloid proteins have been implicated in a range of neurodegenerative and vascular diseases, and yet the underlying molecular mechanisms are poorly understood. Here, we use a combination of cell-based assays, biophysical analysis, and atomic force microscopy to investigate the potential involvement of oxidative stress in aortic medial amyloid (AMA) pathogenesis and deposition. We show that medin, the main constituent of AMA, can induce an environment rich in oxidative species, increasing superoxide and reducing bioavailable nitric oxide in human cells. We investigate the role that this oxidative environment may play in altering the aggregation process of medin and identify potential posttranslational modification sites where site-specific modification and interaction can be unambiguously demonstrated. In an oxidizing environment, medin is nitrated at tyrosine and tryptophan residues, with resultant effects on morphology that lead to longer fibrils with increased toxicity. This provides further motivation to investigate the role of oxidative stress in AMA pathogenicity.

Conformational characterization of synapse-associated protein 97 by nuclear magnetic resonance and small-angle X-ray scattering shows compact and elongated forms.

Synapse-associated protein 97 (SAP97) is a membrane-associated guanylate kinase protein that interacts with other proteins such as ion channels, subunits of glutamate receptors, and other cytoskeletal proteins and molecular scaffolds. The molecular diversity of SAP97 results from alternative splicing at the N-terminus, and in the U1 and U5 regions. There are two main N-terminal isoforms: the β-isoform has an L27 domain, whereas in the α-isoform, this is replaced by a palmitoylation motif. We have used multiangle light scattering, nuclear magnetic resonance, and small-angle X-ray scattering studies to characterize the conformation of a truncated form of the β-isoform, hence mimicking the α-isoform. This paper provides a comprehensive view of the small-angle X-ray scattering data, and the resulting data show that the scattering data are consistent with the presence of an ensemble of forms in dynamic equilibrium, with two prominent populations of compact and extended forms, with R(g) values of 38 ± 7 Å (52%) and 70 ± 10 Å (37%), respectively. The data show that without the L27 domain, the conformation of SAP97 is biased toward the compact form. We propose a hypothesis in which the overall conformation of SAP97 is determined by the nature of the N-terminus, which may, in turn, influence the specific role of a particular splice variant.