Binyong Liang

Structure of outer membrane protein G by solution NMR spectroscopy

The bacterial outer membrane protein G (OmpG), a monomeric pH-gated porin, was overexpressed in Escherichia coli and refolded in β-octyl glucoside micelles. After transfer into dodecylphosphocholine micelles, the solution structure of OmpG was determined by solution NMR spectroscopy at pH 6.3. Complete backbone assignments were obtained for 234 of 280 residues based on CA, CB, and CO connection pathways determined from a series of TROSY-based 3D experiments at 800 MHz. The global fold of the 14-stranded β-barrel was determined based on 133 long-range NOEs observed between neighboring strands and local chemical shift and NOE information. The structure of the barrel is very similar to previous crystal structures, but the loops of the solution structure are quite flexible.

Dynamic structure of lipid-bound synaptobrevin suggests a nucleation-propagation mechanism for trans-SNARE complex formation.

The synaptic vesicle protein synaptobrevin engages with syntaxin and SNAP-25 to form the SNARE complex, which drives membrane fusion in neuronal exocytosis. In the SNARE complex, the SNARE motif of synaptobrevin forms a 55-residue helix, but it has been assumed to be mostly unstructured in its prefusion form. NMR data for full-length synaptobrevin in dodecylphosphocholine micelles reveals two transient helical segments flanked by natively disordered regions and a third more stable helix. Transient helix I comprises the most N-terminal part of the SNARE motif, transient helix II extends the SNARE motif into the juxtamembrane region, and the more stable helix III is the transmembrane domain. These helices may have important consequences for SNARE complex folding and fusion: helix I likely forms a nucleation site, the C-terminal disordered SNARE motif may act as a folding arrest signal, and helix II likely couples SNARE complex folding and fusion.

Structure and function of the complete internal fusion loop from Ebolavirus glycoprotein 2

Ebolavirus (Ebov), an enveloped virus of the family Filoviridae, causes hemorrhagic fever in humans and nonhuman primates. The viral glycoprotein (GP) is solely responsible for virus–host membrane fusion, but how it does so remains elusive. Fusion occurs after virions reach an endosomal compartment where GP is proteolytically primed by cathepsins. Fusion by primed GP is governed by an internal fusion loop found in GP2, the fusion subunit. This fusion loop contains a stretch of hydrophobic residues, some of which have been shown to be critical for GP-mediated infection. Here we present liposome fusion data and NMR structures for a complete (54-residue) disulfide-bonded internal fusion loop (Ebov FL) in a membrane mimetic. The Ebov FL induced rapid fusion of liposomes of varying compositions at pH values at or below 5.5. Consistently, circular dichroism experiments indicated that the α-helical content of the Ebov FL in the presence of either lipid-mimetic micelles or small liposomes increases in samples exposed to pH ≤5.5. NMR structures in dodecylphosphocholine micelles at pH 7.0 and 5.5 revealed a conformational change from a relatively flat extended loop structure at pH 7.0 to a structure with an ∼90° bend at pH 5.5. Induction of the bend at low pH reorients and compacts the hydrophobic patch at the tip of the FL. We propose that these changes facilitate disruption of lipids at the site of virus–host cell membrane contact and, hence, initiate Ebov fusion.

Prefusion structure of syntaxin-1A suggests pathway for folding into neuronal trans-SNARE complex fusion intermediate

Significance Soluble N-ethylmaleimide-sensitive factor attachment protein (SNAP) receptors (SNAREs) are the key molecules that control fusion in intracellular vesicle traffic. A special case of vesicle-to-plasma membrane fusion is exocytosis of synaptic vesicles at the presynaptic membrane to release neurotransmitters into the synaptic cleft. Structures are known of postfusion SNARE complexes, including a famous four-helix bundle with parallel C-terminal transmembrane domains. However, prefusion structures and the structures of intermediate trans-SNARE complexes remain much more elusive. Using nuclear magnetic resonance, we have determined the prefusion structure of the lipid-bound t-SNARE syntaxin-1A, with its transmembrane domain, and confirmed its lipid interactions and conformational transitions on co-t-SNARE SNAP-25 binding by high-resolution interference contrast microscopy in lipid bilayers. We discuss how these structures and their folding into later SNARE complexes might drive membrane fusion. The assembly of the three neuronal soluble N-ethylmaleimide-sensitive factor attachment protein (SNAP) receptor (SNARE) proteins synaptobrevin 2, syntaxin-1A, and SNAP-25 is the key step that leads to exocytotic fusion of synaptic vesicles. In the fully assembled SNARE complex, these three proteins form a coiled-coil four-helix bundle structure by interaction of their respective SNARE motifs. Although biochemical and mutational analyses strongly suggest that the heptad-repeat SNARE motifs zipper into the final structure, little is known about the prefusion state of individual membrane-bound SNAREs and how they change conformation from the unzippered prefusion to the zippered postfusion state in a membrane environment. We have solved the solution NMR structure of micelle-bound syntaxin-1A in its prefusion conformation. In addition to the transmembrane helix, the SNARE motif consists of two well-ordered, membrane-bound helices separated by the “0-layer” residue Gln226. This unexpected structural order of the N- and C-terminal halves of the uncomplexed SNARE motif suggests the formation of partially zippered SNARE complex intermediates, with the 0-layer serving as a proofreading site for correct SNARE assembly. Interferometric fluorescence measurements in lipid bilayers confirm that the open SNARE motif helices of syntaxin interact with lipid bilayers and that association with the other target-membrane SNARE SNAP-25 lifts the SNARE motif off the membrane as a critical prerequisite for SNARE complex assembly and membrane fusion.

Matrix Infrared Spectra and Theoretical Studies of Thorium Oxide Species: ThOx and Th2Oy

Infrared spectra of three new thorium oxide species have been obtained in argon and neon matrixes. All of the products are experimentally characterized using isotopic oxygen samples with the aid of electronic structure calculations. Ground state thorium atoms react with O(2) to form the ThO(2) molecules, which can dimerize to give Th(2)O(4) products. Th(2)O(4) is predicted to have nonplanar C(2h) symmetry for its closed shell singlet ground state. The rhombus-shaped Th(2)O(2) molecule in the (1)A(g) (D(2h)) ground state is also observed and its formation is proposed via the reaction of Th(2) with O(2). In addition, electron capture of neutral thorium dioxide results in the formation of the ThO(2)(-) anion. It is predicted to have a doublet ground state with a geometry similar to that of the neutral ThO(2) molecule. Electronic structure calculations on the unobserved Th(2)O and Th(2)O(3) molecules are also provided.

Infrared Spectra and Density Functional Theory Calculations of Group 8 Transition Metal Sulfide Molecules

Laser-ablated titanium, zirconium, and hafnium atoms react with discharged sulfur vapor during co-condensation in excess argon. The primary reaction product MS2 molecules are identified for the first time, and evidence for metal monosulfides is also presented. The ν1 and ν3 modes for TiS2, ZrS2, and HfS2 absorb at 533.5 and 577.8 cm-1, 502.9 and 504.6 cm-1, and 492.2 and 483.2 cm-1, respectively, in solid argon. On the basis of the isotopic frequencies for the ν3 modes, the bond angles of TiS2, ZrS2, and HfS2 are determined as 113 ± 4°, 107 ± 4°, and 108 ± 4°. DFT/B3LYP calculations predict 1A1 ground states and bond angles of 113.3°, 108.5°, and 109.5°, for the MS2 molecules, M = Ti, Zr, and Hf, respectively, and frequencies in excellent agreement with the observed values. The same calculation also predicts 3Δ ground states for TiS and ZrS, the 1Σ+ ground state for HfS, and frequencies in agreement with the observed values.

NMR as a tool to investigate the structure, dynamics and function of membrane proteins

Membrane-protein NMR occupies a unique niche for determining structures, assessing dynamics, examining folding, and studying the binding of lipids, ligands and drugs to membrane proteins. However, NMR analyses of membrane proteins also face special challenges that are not encountered with soluble proteins, including sample preparation, size limitation, spectral crowding and sparse data accumulation. This Perspective provides a snapshot of current achievements, future opportunities and possible limitations in this rapidly developing field.

Ground-State Reversal by Matrix Interaction: Electronic States and Vibrational Frequencies of CUO in Solid Argon and Neon

The reactions of laser-ablated metal atoms with small molecules during their condensation in frozen noble gas matrices have led to a remarkable number of fundamental small molecules that provide new insights into the structures of and bonding in metal complexes.

Optimizing nanodiscs and bicelles for solution NMR studies of two β-barrel membrane proteins

Solution NMR spectroscopy has become a robust method to determine structures and explore the dynamics of integral membrane proteins. The vast majority of previous studies on membrane proteins by solution NMR have been conducted in lipid micelles. Contrary to the lipids that form a lipid bilayer in biological membranes, micellar lipids typically contain only a single hydrocarbon chain or two chains that are too short to form a bilayer. Therefore, there is a need to explore alternative more bilayer-like media to mimic the natural environment of membrane proteins. Lipid bicelles and lipid nanodiscs have emerged as two alternative membrane mimetics that are compatible with solution NMR spectroscopy. Here, we have conducted a comprehensive comparison of the physical and spectroscopic behavior of two outer membrane proteins from Pseudomonas aeruginosa, OprG and OprH, in lipid micelles, bicelles, and nanodiscs of five different sizes. Bicelles stabilized with a fraction of negatively charged lipids yielded spectra of almost comparable quality as in the best micellar solutions and the secondary structures were found to be almost indistinguishable in the two environments. Of the five nanodiscs tested, nanodiscs assembled from MSP1D1ΔH5 performed the best with both proteins in terms of sample stability and spectral resolution. Even in these optimal nanodiscs some broad signals from the membrane embedded barrel were severely overlapped with sharp signals from the flexible loops making their assignments difficult. A mutant OprH that had two of the flexible loops truncated yielded very promising spectra for further structural and dynamical analysis in MSP1D1ΔH5 nanodiscs.

Infrared spectra and density functional theory calculations of group 10 transition metal sulfide molecules and complexes.

Laser-ablated Ni, Pd, and Pt atoms were reacted with sulfur molecules emerging from a microwave discharge in argon during condensation at 7 K. Reaction products were identified from matrix infrared spectra, sulfur isotopic shifts, spectra of sulfur isotopic mixtures, and frequencies from density functional calculations. The strongest absorptions are observed at 597.9, 596.1, and 583.6 cm(-1), respectively, for the group 10 metals. These absorptions show large sulfur-34 shifts and 32/34 isotopic frequency ratios (1.0282, 1.0285, 1.0298) that are appropriate for S-S stretching modes. Of most importance, mixed 32/34 isotopic 1/4/4/2/4/1 sextets identify this product with two equivalent S(2) molecules containing equivalent atomic positions as the bisdisulfur pi complexes M(S(2))(2). Our DFT calculations find stable D(2h) structures with B(1u) ground states and intense b(1u) infrared active modes a few wavenumbers higher than the observed values. A minor Ni product at 505.8, 502.7 cm(-1) shows the proper sulfur-34 shift for assignment to (58)NiS, (60)NiS. Another major product with Pt at 512.2 cm(-1) reveals an asymmetric triplet absorption with mixed sulfur 32/34, which is appropriate for assignment to the SPtS disulfide molecule. A weak 491.7 cm(-1) peak exhibits the sulfur-34 shift expected for PtS, and this assignment follows.