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Binyong Liang

Publications and source records attributed to Binyong Liang.

12 recordsLinked to original sources
PubMed2006

Increasing the accuracy of solution NMR structures of membrane proteins by application of residual dipolar couplings. High-resolution structure of outer membrane protein A.

The structure determination of membrane proteins is one of the most challenging applications of solution NMR spectroscopy. The paucity of distance information available from the highly deuterated proteins employed requires new approaches in structure determination. Here we demonstrate that significant improvement in the structure accuracy of the membrane protein OmpA can be achieved by refinement with residual dipolar couplings (RDCs). The application of charged polyacrylamide gels allowed us to obtain two alignments and accurately measure numerous heteronuclear dipolar couplings. Furthermore, we have demonstrated that using a large set of RDCs in the refinement can yield a structure with 1 A rms deviation to the backbone of the high-resolution crystal structure. Our simulations with various data sets indicate that dipolar couplings will be critical for obtaining accurate structures of membrane proteins.

Bacterial Outer Membrane Proteins↗
PubMed2006

Site-directed parallel spin-labeling and paramagnetic relaxation enhancement in structure determination of membrane proteins by solution NMR spectroscopy.

A major challenge for the structure determination of integral membrane proteins by solution NMR spectroscopy is the limited number of NOE restraints in these systems stemming from extensive deuteration. Paramagnetic relaxation enhancement (PRE) by means of nitroxide spin-labels can provide valuable long-range distance information but, in practice, has limits in its application to membrane proteins because spin-labels are often incompletely reduced in highly apolar environments. Using the integral membrane protein OmpA as a model system, we introduce a method of parallel spin-labeling with paramagnetic and diamagnetic labels and show that distances in the range 15-24 Angstroms can be readily determined. The protein was labeled at 11 water-exposed and lipid-covered sites, and 320 PRE distance restraints were measured. The addition of these restraints resulted in significant improvement of the calculated backbone structure of OmpA. Structures of reasonable quality can even be calculated with PRE distance restraints only, i.e., in the absence of NOE distance restraints.

Bacterial Outer Membrane Proteins↗
PubMed2005

Reactions of laser-ablated uranium atoms with H2O in excess argon: a matrix infrared and relativistic DFT investigation of uranium oxyhydrides.

Laser-ablated U atoms react with H2O during condensation in excess argon. Infrared absorptions at 1416.3, 1377.1, and 859.4 cm(-1) are assigned to symmetric H-U-H, antisymmetric H-U-H, and U=O stretching vibrations of the primary reaction product H(2)UO. Uranium monoxide, UO, also formed in the reaction, inserts into H2O to produce HUO(OH), which absorbs at 1370.5, 834.3, and 575.7 cm(-1). The HUO(OH) uranium(IV) product undergoes ultraviolet photoisomerization to a more stable H2UO2 uranium(VI) molecule, which absorbs at 1406.4 and 885.9 cm(-1). Several of these species, particularly H2UO2, appear to form weak Ar-coordinated complexes. The predicted vibrational frequencies, relative absorption intensities, and isotopic shifts from relativistic DFT calculations are in good agreement with observed spectra, which further supports the identification of novel uranium oxyhydrides from matrix infrared spectra.

Journal Article↗
PubMed2004

Folding and assembly of beta-barrel membrane proteins.

Beta-barrel membrane proteins occur in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. The membrane-spanning sequences of beta-barrel membrane proteins are less hydrophobic than those of alpha-helical membrane proteins, which is probably the main reason why completely different folding and membrane assembly pathways have evolved for these two classes of membrane proteins. Some beta-barrel membrane proteins can be spontaneously refolded into lipid bilayer model membranes in vitro. They may also have this ability in vivo although lipid and protein chaperones likely assist with their assembly in appropriate target membranes. This review summarizes recent work on the thermodynamic stability and the mechanism of membrane insertion of beta-barrel membrane proteins in lipid model and biological membranes. How lipid compositions affect folding and assembly of beta-barrel membrane proteins is also reviewed. The stability of these proteins in membranes is not as large as previously thought (<10 kcal/mol) and is modulated by elastic forces of the lipid bilayer. Detailed kinetic studies indicate that beta-barrel membrane proteins fold in distinct steps with several intermediates that can be characterized in vitro. Formation of the barrel is synchronized with membrane insertion and all beta-hairpins insert simultaneously in a concerted pathway.

Membrane Lipids↗
PubMed2004

On the noble-gas-induced intersystem crossing for the CUO molecule: experimental and theoretical investigations of CUO(Ng)n (Ng = Ar, Kr, Xe; n = 1, 2, 3, 4) complexes in solid neon.

Uranium atoms excited by laser ablation react with CO in excess neon to produce the novel CUO molecule, which forms distinct Ng complexes (Ng = Ar, Kr, Xe) when the heavier noble gases are added. The CUO(Ng) complexes are identified through CO isotopic and Ng substitution on the neon matrix infrared spectra and by comparison to DFT frequency calculations. The U-C and U-O stretching frequencies of CUO(Ng) complexes are slightly red-shifted from frequencies for the (1)Sigma(+) CUO ground state, which identifies singlet ground state CUO(Ng) complexes. In solid neon the CUO molecule is also a complex CUO(Ne)(n), and the CUO(Ne)(n-1)(Ng) complexes are likewise specified. The next singlet CUO(Ne)(x)(Ng)(2) complexes in excess neon follow in like manner. However, the higher CUO(Ne)(x)(Ng)(n) complex (n = 3, 4) stretching modes approach pure argon matrix CUO(Ar)(n) values and isotopic behavior, which are characterized as triplet ground state complexes by DFT frequency calculations. This work suggests that the singlet-triplet crossing occurs with 3 Ar, 3 Kr, or 4 Xe and a balance of Ne atoms coordinated to CUO in the neon matrix host.

Journal Article↗
PubMed2003

Bonding of multiple noble-gas atoms to CUO in solid neon: CUO(Ng)n (Ng=Ar, Kr, Xe; n=1, 2, 3, 4) complexes and the singlet-triplet crossover point.

Laser-ablated U atoms co-deposited with CO in excess neon produce the novel CUO molecule, which forms distinct Ng complexes (Ng=Ar, Kr, Xe) with the heavier noble gases. The CUO(Ng) complexes are identified through CO isotopic and Ng reagent substitution and comparison to results of DFT frequency calculations. The U[bond]C and U[bond]O stretching frequencies of CUO(Ng) complexes are slightly red-shifted from neon matrix (1)Sigma(+) CUO values, which indicates a (1)A' ground state for the CUO(Ng) complexes. The CUO(Ng)(2) complexes in excess neon are likewise singlet molecules. However, the CUO(Ng)(3) and CUO(Ng)(4) complexes exhibit very different stretching frequencies and isotopic behaviors that are similar to those of CUO(Ar)(n) in a pure argon matrix, which has a (3)A" ground state based on DFT vibrational frequency calculations. This work suggests a coordination sphere model in which CUO in solid neon is initially solvated by four or more Ne atoms. Up to four heavier Ng atoms successively displace the Ne atoms leading ultimately to CUO(Ng)(4) complexes. The major changes in the CUO stretching frequencies from CUO(Ng)(2) to CUO(Ng)(3) provides evidence for the crossover from a singlet ground state to a triplet ground state.

Journal Article↗
PubMed2003

Noble gas-actinide complexes of the CUO molecule with multiple Ar, Kr, and Xe atoms in noble-gas matrices.

Laser-ablated U atoms react with CO in excess argon to produce CUO, which is trapped in a triplet state in solid argon at 7 K, based on agreement between observed and relativistic density functional theory (DFT) calculated isotopic frequencies ((12)C(16)O, (13)C(16)O, (12)C(18)O). This observation contrasts a recent neon matrix investigation, which trapped CUO in a linear singlet state calculated to be about 1 kcal/mol lower in energy. Experiments with krypton and xenon give results analogous to those with argon. Similar work with dilute Kr and Xe in argon finds small frequency shifts in new four-band progressions for CUO in the same triplet states trapped in solid argon and provides evidence for four distinct CUO(Ar)(4-n)(Ng)(n) (Ng = Kr, Xe, n = 1, 2, 3, 4) complexes for each Ng. DFT calculations show that successively higher Ng complexes are responsible for the observed frequency progressions. This work provides the first evidence for noble gas-actinide complexes, and the first example of neutral complexes with four noble gas atoms bonded to one metal center.

Journal Article↗
PubMed2002

Noble gas-actinide compounds: evidence for the formation of distinct CUO(Ar)(4-n)(Xe)(n) and CUO(Ar)(4-n)(Kr)(n) (n = 1, 2, 3, 4) complexes.

Laser-ablated U atoms react with CO in excess argon to produce CUO, which gives rise to 852.5 and 804.3 cm-1 infrared absorptions for the triplet state CUO(Ar)n complex in solid argon at 7 K. Relativistic density functional calculations show that the CUO(Ar) complex is stable and that up to four or five argon atoms can complex to CUO. When 1-3% Xe is added to the argon/CO reagent mixture, strong absorptions appear at 848.0 and 801.3 cm-1 and dominate new four-band progressions, which increase on annealing to 35-50 K as Xe replaces Ar in the intimate coordination sphere. Analogous spectra are obtained with 1-2% Kr added. This work provides evidence for eight distinct CUO(Ng)n(Ar)4-n (Ng = Kr, Xe, n = 1, 2, 3, 4) complexes and the first characterization of neutral complexes involving four noble-gas atoms on one metal center.

Journal Article↗
PubMed2002

Experimental and theoretical studies of the products of laser-ablated thorium atom reactions with H2O in excess argon.

Reactions of laser-ablated Th atoms with H2O during condensation in excess argon have formed a variety of intriguing new Th, H, O species. Infrared absorptions at 1406.0 and 842.6 cm-1 are assigned to the H-Th and Th=O stretching vibrations of HThO. Absorptions at 1397.2, 1352.4, and 822.8 cm-1 are assigned to symmetric H-Th-H, antisymmetric H-Th-H, and Th=O stretching vibrations of the major primary reaction product H2ThO. Thorium monoxide (ThO) produced in the reaction inserts into H2O to form HThO(OH), which absorbs at 1341.0, 804.0, and 542.6 cm-1. Both HThO(OH) and ThO2 add another H2O molecule to give HTh(OH)3 and OTh(OH)2, respectively. Weaker thorium hydride (ThH1(-4)) absorptions were also observed. Relativistic DFT and ab initio calculations were performed on all proposed molecules and other possible isomers. The good agreement between experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts provides support for these first identifications of Th, H, O molecular species.

Journal Article↗
PubMed2002

The First infrared spectra and quasirelativistic DFT studies of the US, US(2), and US(3) molecules.

Laser-ablated U atoms react with discharged sulfur vapor in excess argon to form the US, US(2), and US(3) molecules, which are identified from matrix infrared spectra using sulfur isotopic substitution. Vibrational frequencies from quasirelativistic DFT calculations support these assignments and provide an insight into the bonding and structure. Unlike linear UO(2), US(2) is bent because of more favorable U(6d)-S(3p) overlap, and US(2) has a 118 +/- 5 degrees (experimental based on isotopic shift) or 121 degrees (calculated (3)B(2) ground state, B3LYP) S-U-S bond angle.

Journal Article↗
PubMed2002

Noble gas-actinide compounds: complexation of the CUO molecule by Ar, Kr, and Xe atoms in noble gas matrices.

The CUO molecule, formed from the reaction of laser-ablated U atoms with CO in a noble gas, exhibits very different stretching frequencies in a solid argon matrix [804.3 and 852.5 wave numbers (cm(-1))] than in a solid neon matrix (872.2 and 1047.3 cm(-1)). Related experiments in a matrix consisting of 1% argon in neon suggest that the argon atoms are interacting directly with the CUO molecule. Relativistic density functional calculations predict that CUO can bind directly to one argon atom (U-Ar = 3.16 angstroms; binding energy = 3.2 kilocalories per mole), accompanied by a change in the ground state from a singlet to a triplet. Our experimental and theoretical results also suggest that multiple argon atoms can bind to a single CUO molecule.

Journal Article↗