Andrew Hung

Ordering surfaces on the nanoscale: implications for protein adsorption.

Monolayer-protected metal nanoparticles (MPMNs) are a newly discovered class of nanoparticles with an ordered, striped domain structure that can be readily manipulated by altering the ratio of the hydrophobic to hydrophilic ligands. This property makes them uniquely suited to systematic studies of the role of nanostructuring on biomolecule adsorption, a phenomenon of paramount importance in biomaterials design. In this work, we examine the interaction of the simple, globular protein cytochrome C (Cyt C) with MPMN surfaces using experimental protein assays and computational molecular dynamics simulations. Experimental assays revealed that adsorption of Cyt C generally increased with increasing surface polar ligand content, indicative of the dominance of hydrophilic interactions in Cyt C-MPMN binding. Protein-surface adsorption enthalpies calculated from computational simulations employing rigid-backbone coarse-grained Cyt C and MPMN models indicate a monotonic increase in adsorption enthalpy with respect to MPMN surface polarity. These results are in qualitative agreement with experimental results and suggest that Cyt C does not undergo significant structural disruption upon adsorption to MPMN surfaces. Coarse-grained and atomistic simulations furthermore elucidated the important role of lysine in facilitating Cyt C adsorption to MPMN surfaces. The amphipathic character of the lysine side chain enables it to form close contacts with both polar and nonpolar surface ligands simultaneously, rendering it especially important for interactions with surfaces composed of adjacent nanoscale chemical domains. The importance of these structural characteristics of lysine suggests that proteins may be engineered to specifically interact with nanomaterials by targeted incorporation of unnatural amino acids possessing dual affinity to differing chemical motifs.

Dicarba α-conotoxin Vc1.1 analogues with differential selectivity for nicotinic acetylcholine and GABAB receptors.

Conotoxins have emerged as useful leads for the development of novel therapeutic analgesics. These peptides, isolated from marine molluscs of the genus Conus, have evolved exquisite selectivity for receptors and ion channels of excitable tissue. One such peptide, α-conotoxin Vc1.1, is a 16-mer possessing an interlocked disulfide framework. Despite its emergence as a potent analgesic lead, the molecular target and mechanism of action of Vc1.1 have not been elucidated to date. In this paper we describe the regioselective synthesis of dicarba analogues of Vc1.1 using olefin metathesis. The ability of these peptides to inhibit acetylcholine-evoked current at rat α9α10 and α3β4 nicotinic acetylcholine receptors (nAChR) expressed in Xenopus oocytes has been assessed in addition to their ability to inhibit high voltage-activated (HVA) calcium channel current in isolated rat DRG neurons. Their solution structures were determined by NMR spectroscopy. Significantly, we have found that regioselective replacement of the native cystine framework with a dicarba bridge can be used to selectively tune the cyclic peptides innate biological activity for one receptor over another. The 2,8-dicarba Vc1.1 isomer retains activity at γ-aminobutyric acid (GABAB) G protein-coupled receptors, whereas the isomeric 3,16-dicarba Vc1.1 peptide retains activity at the α9α10 nAChR subtype. These singularly acting analogues will enable the elucidation of the biological target responsible for the peptides potent analgesic activity.

Sulfur adsorption on Fe(110): a DFT study

The adsorption of atomic S on the Fe(1 1 0) surface is examined using density functional theory (DFT). Three different adsorption sites are considered, including the atop, hollow and bridge sites and the S is adsorbed at a quarter monolayer coverage in a p(2 × 2) arrangement. The hollow site is found to be the most stable, followed by the bridge and atop sites. At all three sites, S adsorption results in relatively minor surface reconstruction, with the most significant being that for the hollow site, with lateral displacements of 0.09 A. Comparisons between S-adsorbed and pure Fe surfaces revealed reductions in the magnetic moments of surface-layer Fe atoms in the vicinity of the S. At the hollow site, the presence of S causes an increase in the surface Fe d-orbital density of states between 4 and 5 eV. However, S adsorption has no significant effect on the structure and magnetic properties of the lower substrate layers.

Dicarba Analogues of α-Conotoxin RgIA. Structure, Stability, and Activity at Potential Pain Targets

α-Conotoxin RgIA is both an antagonist of the α9α10 nicotinic acetylcholine receptor (nAChR) subtype and an inhibitor of high-voltage-activated N-type calcium channel currents. RgIA has therapeutic potential for the treatment of pain, but reduction of the disulfide bond framework under physiological conditions represents a potential liability for clinical applications. We synthesized four RgIA analogues that replaced native disulfide pairs with nonreducible dicarba bridges. Solution structures were determined by NMR, activity assessed against biological targets, and stability evaluated in human serum. [3,12]-Dicarba analogues retained inhibition of ACh-evoked currents at α9α10 nAChRs but not N-type calcium channel currents, whereas [2,8]-dicarba analogues displayed the opposite pattern of selectivity. The [2,8]-dicarba RgIA analogues were effective in HEK293 cells stably expressing human Cav2.2 channels and transfected with human GABAB receptors. The analogues also exhibited improved serum stability over the native peptide. These selectively acting dicarba analogues may represent mechanistic probes to explore analgesia-related biological receptors.

Identifying Key Amino Acid Residues that Affect α-Conotoxin AuIB Inhibition of α3β4 Nicotinic Acetylcholine Receptors

Background: α-Conotoxin AuIB interacts with α3β4 nAChRs and GABAB receptors, but structural determinants of these interactions are unknown. Results: Using alanine scanning mutagenesis and molecular dynamics, we identified residues crucial for AuIB·α3β4 nAChR interaction. Conclusion: We identified the key residues that mediate AuIB·α3β4 nAChR interaction. Significance: Ability to direct α-conotoxin binding to nAChRs or GABAB receptors will improve analgesic conopeptides. α-Conotoxin AuIB is a selective α3β4 nicotinic acetylcholine receptor (nAChR) subtype inhibitor. Its analgesic properties are believed to result from it activating GABAB receptors and subsequently inhibiting CaV2.2 voltage-gated calcium channels. The structural determinants that mediate diverging AuIB activity at these targets are unknown. We performed alanine scanning mutagenesis of AuIB and α3β4 nAChR, homology modeling, and molecular dynamics simulations to identify the structural determinants of the AuIB·α3β4 nAChR interaction. Two alanine-substituted AuIB analogues, [P6A]AuIB and [F9A]AuIB, did not inhibit the α3β4 nAChR. NMR and CD spectroscopy studies demonstrated that [F9A]AuIB retains its native globular structure, so its activity loss is probably due to loss of specific toxin-receptor residue pairwise contacts. Compared with AuIB, the concentration-response curve for inhibition of α3β4 by [F9A]AuIB shifted rightward more than 10-fold, and its subtype selectivity profile changed. Homology modeling and molecular dynamics simulations suggest that Phe-9 of AuIB interacts with a two-residue binding pocket on the β4 nAChR subunit. This hypothesis was confirmed by site-directed mutagenesis of the β4-Trp-59 and β4-Lys-61 residues of loop D, which form a putative binding pocket. AuIB analogues with Phe-9 substitutions corroborated the finding of a binding pocket on the β4 subunit and gave further insight into how AuIB Phe-9 interacts with the β4 subunit. In summary, we identified critical residues that mediate interactions between AuIB and its cognate nAChR subtype. These findings might help improve the design of analgesic conopeptides that selectively “avoid” nAChR receptors while targeting receptors involved with nociception.

Density-functional theory studies of xanthate adsorption on the pyrite FeS2(110) and (111) surfaces

We have used the density functional theory (DFT) method with a plane wave-pseudopotential basis to compute the structure and properties of a model xanthate molecule (HOCS2−) and its adsorption characteristics on the pyrite FeS2(110) and (111) surfaces. Molecular calculations revealed that HOCS2− and CH3CH2OCS2− have similar head group electronic structure and, therefore, the use of the model xanthate is a justifiable approximation in simulations of xanthate head group attachment to FeS2 surfaces. Results from DFT calculations suggest that HOCS2− readily undergoes dissociation at the fourfold coordinated surface Fe on the (110) surface, and the bridging S of the (111) surface. These results suggest that xanthate may undergo chemisorption at defect sites on real FeS2 surfaces, which contain low-coordinate Fe sites and sites in proximity to cleaved S–S bonds.

Amphiphilic amino acids: a key to adsorbing proteins to nanopatterned surfaces?

It has been suggested that amphiphilic amino acids play an important role in the adsorption of proteins on nanostructured surfaces with an ordered, striped domain structure such as those presented by monolayer-protected metal nanoparticles (MPMNs). We have proposed and now further explore this hypothesis by studying the adsorption behaviour of proteins on MPMN surfaces by molecular dynamics (MD) simulations. Our atomistic MD simulations of lysozyme (Lyz) on nanostructured surfaces, including single component surfaces and several theoretical nanopatterns of different spacing, presented here confirm the special role of amino acids containing sidechain amines in facilitating direct protein adsorption to MPMN surfaces. While we have previously demonstrated that an amphiphilic amino acid lysine is responsible for selective adsorption behaviour of Cyt C on nanostructured surfaces, in the case of Lyz it is the amphipathic character of arginine that enables the protein to form close contacts with both polar and non-polar surface ligands simultaneously. This renders it especially important for interactions with surfaces composed of adjacent nano-scale chemical domains. Arg is also capable of forming close contacts with homogeneous hydrophobic and hydrophilic ligand surfaces. We have also found that other amphiphilic amino acids, such as tyrosine and tryptophan, interact with surfaces via water-mediated contacts. Bridging water molecules adopt orientations which differ from those of simple surface-adsorbed waters, with the specificity of their orientations facilitating the protein-surface contacts. Our findings suggest that not only nanopatterned surfaces can be designed to selectively interact with different proteins but proteins may be engineered to specifically interact with nanomaterials by targeted incorporation of synthetic amino acids which can mimic natural amphiphilic amino acids possessing multiple affinities to different chemical motifs.

Effects of oxidation, pH and lipids on amyloidogenic peptide structure: implications for fibril formation?

We have performed experimental and computational studies to investigate the influences of phospholipids, methionine oxidation and acidic pH on amyloid fibril formation by a peptide derived from human apolipoprotein C-II (apoC-II), a known component of proteinaceous atherosclerotic plaques. Fibril growth monitored by thioflavin T fluorescence revealed inhibition under lipid-rich and oxidising conditions. We subsequently performed fully-solvated atomistic molecular dynamics (MD) simulations of the peptide monomer to study its conformations under both fibril favouring (neutral and low pH) and inhibiting (lipid-rich and oxidising) conditions. Examination of the chain topology, backbone hydrogen-bonding patterns and aromatic sidechain orientations of the peptide under different conditions reveals that, while the peptide adopts similar structures under the fibril-favouring conditions, significantly different structures are obtained under fibril-disruptive conditions. Based on our results, we advance hypotheses for the roles of peptide conformation on aggregation and fibrillisation propensities.

Alanine Scan of α-Conotoxin RegIIA Reveals a Selective α3β4 Nicotinic Acetylcholine Receptor Antagonist

Background: The molecular mechanism by which α-conotoxin RegIIA inhibits α3β4, α3β2, and α7 nAChRs is unknown. Results: Alanine scanning mutagenesis and molecular dynamic simulations of RegIIA revealed Asn11 and Asn12 confer improved selectivity at α3β4 nAChR. Conclusion: We synthesized the [N11A,N12A]RegIIA analog that selectively inhibits α3β4. Significance: These findings could be used to develop α3β4-selective drugs to treat lung cancer. Activation of the α3β4 nicotinic acetylcholine receptor (nAChR) subtype has recently been implicated in the pathophysiology of various conditions, including development and progression of lung cancer and in nicotine addiction. As selective α3β4 nAChR antagonists, α-conotoxins are valuable tools to evaluate the functional roles of this receptor subtype. We previously reported the discovery of a new α4/7-conotoxin, RegIIA. RegIIA was isolated from Conus regius and inhibits acetylcholine (ACh)-evoked currents mediated by α3β4, α3β2, and α7 nAChR subtypes. The current study used alanine scanning mutagenesis to understand the selectivity profile of RegIIA at the α3β4 nAChR subtype. [N11A] and [N12A] RegIIA analogs exhibited 3-fold more selectivity for the α3β4 than the α3β2 nAChR subtype. We also report synthesis of [N11A,N12A]RegIIA, a selective α3β4 nAChR antagonist (IC50 of 370 nm) that could potentially be used in the treatment of lung cancer and nicotine addiction. Molecular dynamics simulations of RegIIA and [N11A,N12A]RegIIA bound to α3β4 and α3β2 suggest that destabilization of toxin contacts with residues at the principal and complementary faces of α3β2 (α3-Tyr92, Ser149, Tyr189, Cys192, and Tyr196; β2-Trp57, Arg81, and Phe119) may form the molecular basis for the selectivity shift.

Lipids enhance apolipoprotein C-II-derived amyloidogenic peptide oligomerization but inhibit fibril formation

We investigated the effect of submicellar lipids on amyloid fibril formation. Thioflavin T fluorescence studies showed that submicellar levels of the short-chain phospholipids, dipentanoylphosphatidylcholine and dihexanoylphosphatidylcholine, strongly inhibited amyloid fibril formation by an 11-residue peptide derived from human apolipoprotein C-II (apoC-II(60-70)). In contrast, sedimentation equilibrium analysis of these peptide-lipid mixtures indicated the presence of soluble oligomeric complexes. To acquire insight into the atomic level influences of these lipids on the initial stages of aggregation of the peptide, we performed molecular dynamics (MD) simulations coupled with umbrella sampling to determine dimerization free energies of a number of beta-stranded and random coil dimer complexes, both in the presence and absence of lipids. The simulations indicate that, in contrast to their inhibitory effects on fibril formation, short-chain phospholipids promote the formation and stabilization of dimers by enhancing intersubunit hydrophobic interactions. On the basis of these experimental and computational results, we propose that peptide-bound lipids can inhibit amyloid fibril formation by trapping of dimers and other oligomeric species in diverse nonfibril forming conformations, reducing their likelihood of acquiring subunit conformations prone to fibril nucleation and growth. In light of the demonstrated cytotoxicity of amyloid peptide oligomers, our results suggest that, by enhancing the stability of oligomeric peptide species, the presence of solvated lipids may contribute to the cytotoxicity of fibrillogenic proteins and peptides.