Reorientational Motions of the D96N and T46V/D96N Mutants of Bacteriorhodopsin in the Purple Membrane

Abstract— The reorientational motions of the D96N and T46V/D96N mutants of bacteriorhodopsin in purple membrane have been investigated by time-resolved linear dichroism measurements. The reorientations in the early stages of the photocycle are identical to those observed in wild-type bacteriorhodopsin: anisotropics of photocycle intermediates in both D96N and T46V/D96N are r_K= 0.38±0.01, r_L= 0.35±0.01, r_M= 0.35±0.01. The anisotropy of the initial state, r_BR, exhibits decays to zero in D96N and to negative values in T46V/D96N on the time scale of tens of milliseconds. This anisotropy decay can be explained by a model that involves the motion of unexcited or spectator proteins adjacent to a photocycling protein. The amplitude and time constants of spectator reorientational motion are similar to those that have been observed in the wild type. Contributions from the anisotropy of the N-state were detected in measurements of the T46V/D96N mutant, in which a large N-state population accumulates. The value of r_N is estimated to be 0.30±0.05 in T46V/D96N.     

The role of acidic residues and of sodium ion adduction on the gas-phase H/D exchange of peptides and peptide dimers

Gas-phase H/D exchange is widely used for characterizing the structure of ions. However, many structural parameters that affect the rate of H/D exchange are poorly understood, which complicates the interpretation of experimental data. Here, the effects of sodium ion adduction on the rate of H/D exchange with D₂O for a series of peptides and peptide dimers with varying numbers of acidic residues are described. The maximum number of sodium ion adducts that can be accommodated by the peptides and peptide dimers in this study is N + 1, where N is the number of free carboxylic acid groups. The formation of methyl-esters at all carboxylic acid groups, or the replacement of all the acidic hydrogens with sodium ions, effectively shuts down H/D exchange with D₂O. In contrast, both the rate and the extent of H/D exchange with D₂O are increased for most of the peptides and peptide dimers by the adduction of an intermediate number of sodium ions. These results are consistent with the H/D exchange occurring via a salt-bridge mechanism and show that the presence of two carboxylic acid groups is much better than one. The results with peptide dimers also indicate that surface accessibility may not be a dominant factor in the extent of H/D exchange for these ions.     

CE hydrogen deuterium exchange-MS in peptide analysis

CE and hydrogen-deuterium (H/D) exchange MS are useful tools in the analysis and characterisation of peptides. This study reports the facile coupling of these tools in the H/D exchange CE-MS analysis of model and pharmaceutically important peptides, using a sheath flow interface. The peptides varied in mass from 556 (leucine enkephalin) to 1620 Da (bombesin), and in charge state from 0.33 (leucine enkephalin) to 3.0 (substance P). The application of a BGE composed of ammonium formate buffer (25 mM, pD 3.5 in D(2)O (>98% D atom)), a sheath liquid composed of formic acid (0.25% v/v in D(2)O) and ACN (30:70 v/v), and dissolving the samples in a mixture of ACN/D(2)O (50:50 v/v) facilitates complete H/D exchange. Because of complete H/D exchange the ESI mass spectra produced are easy to interpret and comparable to those obtained from LC-MS analysis. The CE-H/D-MS approach has the advantage of requiring lower volumes of deuterated solvents. The b- and y-series fragments produced by using in-source decomposition correspond to those predicted. With the peptides studied, the complete exchange H/D exchange observed with both the molecular and fragment ions helps to confirm both amino acid composition and sequence.     

Micro‐Engineered 3D Scaffolds for Cell Culture Studies

Cells in physiological 3D environments differ considerably in morphology and differentiation from those in 2D tissue culture. Naturally derived polymer systems are frequently used to study cells in 3D. These 3D matrices are complex with respect to their chemical composition, mechanical properties, and geometry. Therefore, there is a demand for well‐defined 3D scaffolds to systematically investigate cell behavior in 3D. Here, fabrication techniques, materials, architectures, biochemical functionalizations, and mechanical properties of 3D scaffolds are discussed. In particular, work focusing on single cells and small cell assemblies grown in tailored synthetic 3D scaffolds fabricated by computer‐based techniques are reviewed and the influence of these environments on cell behavior is evaluated.

     

Isomeric differentiation of green tea catechins using gas-phase hydrogen/deuterium exchange reactions

Hydrogen/deuterium exchange reactions in a quadrupole ion trap mass spectrometer are used to differentiate galloylated catechin stereoisomers (catechin gallate and epicatechin gallate; gallocatechin gallate and epigallocatechin gallate) and the nongalloylated analogs (catechin and epicatechin, gallocatechin and epigallocatechin). Significant differences in the hydrogen/deuterium exchange behavior of the four pairs of deprotonated catechin stereoisomers are observed upon reaction with D(2)O. Interestingly, the nongalloylated catechins undergo H/D exchange to a much greater extent than the galloylated species, incorporating deuterium at both aromatic/allylic and active phenolic sites. Nongalloylated catechin isomers are virtually indistinguishable by their H/D exchange kinetics over a wide range of reaction times (0.05 to 10 s). Our experimental results are explained using high-level ab initio calculations to elucidate the subtle structural variations in the catechin stereoisomers that lead to their differing H/D exchange kinetics.     

Mass spectrometric separation and quantitation of overlapping isotopologues. H2O/HOD/D2O and H2Se/HDSe/D2Se mixtures

Three conceptually different mathematical methods are presented for accurate mass spectrometric determination of H2O/HOD/D2O and H2Se/HDSe/D2Se concentrations from mixtures. These are alternating least-squares, weighted two-band target entropy minimization, and a statistical mass balance model. The otherwise nonmeasurable mass spectra of partially deuterated isotopologues (HOD and HDSe) are mathematically constructed. Any recorded isotopologue mixture mass spectra are then deconvoluted by least-squares into their components. This approach is used to study the H2O/D2O exchange reaction, and is externally validated gravimetrically. The H2O/D2O exchange equilibrium constant is also measured from the deconvoluted 70 eV electron impact GC/MS data (K = 3.85 +/- 0.03).     

Two-dimensional infrared correlation spectroscopic studies of polymer blends--specific interactions in polyethylene adipate/cholesteryl palmitate blends

Generalized two-dimensional infrared (2D IR) correlation spectroscopy has been applied to the study of the conformational changes and specific interactions in blends of polyethylene adipate (PEA) and cholesteryl palmitate (CP). IR spectra of CP, PEA, and their blends of different compositions: 10/90, 16/84, 32/68, 64/36, and 80/20 have been recorded. In order to apply 2D IR correlation analysis, the samples are divided into two sets: set A with high PEA content 0/100, 10/90, 16/84, 32/68 CP/PEA and set B with high CP content 64/36, 80/20 and 100/0 CP/PEA. The 2D IR synchronous correlation analysis separates the bands of PEA from those of CP. The cross-peaks in 2D IR asynchronous correlation analysis are indicative of the specific interaction or the conformational change in the blends. The bands of CO, OH and C-O vibrations of PEA, and CH(3) and C-O vibrations of CP that are very sensitive to the intermolecular hydrogen bonding effect and consequently the partial miscibility of components, have been assigned by 2D correlation analysis.     

Effects of Substitutions D73E, D73N, D103N and V106M on Signaling and pH Titration of Sensory Rhodopsin II

Abstract— Several mutations in the repellent phototaxis receptor sensory rhodopsin II (SRII), in residues homologous to residues important in the related proton pump bacteriorhodopsin, were expressed in Pho81Wr^–, a Halobacterium salinarum strain deficient in production of SRII and its transducer protein HtrII. The lack of production of SRII and HtrII is shown to be due to insertion of an ISH2 transposon into the promoter region upstream of the htrII - sopH gene pair. Near wild-type phototaxis responses are rescued in Pho81Wr^– by expression of HtrII with D73E, D103N or V106M receptors. Partial responses are restored by the HtrII-D73N pair. From absorption spectroscopy of his-tag-purified receptor protein from mutants D73N and D73E we conclude that Asp73 is the primary counterion to the protonated Schiff base in SRII, like the corresponding Asp85 in bacteriorhodopsin. The absorption maximum of SRII (487 nm) is shifted to 514 nm in mutant D73N, a 1080 cm⁻¹ shift identical to that caused by D85N in bacteriorhodopsin. Acid titration of SRII also induces the red shift with a pK of 3.0 in wild type. The absorption shift and the pK are nearly the same in V106M and D103N, but the pK is raised to 5.1 in D73E, confirming that Asp73 is the residue responsible for this spectral transition.     

Ab initio and DFT studies of the spin-orbit and spin-spin contributions to the zero-field splitting tensors of triplet nitrenes with aryl scaffolds

Spin-orbit and spin-spin contributions to the zero-field splitting (ZFS) tensors (D tensors) of spin-triplet phenyl-, naphthyl-, and anthryl-nitrenes in their ground state are investigated by quantum chemical calculations, focusing on the effects of the ring size and substituted position of nitrene on the D tensor. A hybrid CASSCF/MRMP2 approach to the spin-orbit term of the D tensor (D(SO) tensor), which was recently proposed by us, has shown that the spin-orbit contribution to the entire D value, termed the ZFS parameter or fine-structure constant, is about 10% in all the arylnitrenes under study and less depends on the size and connectivity of the aryl groups. Order of the absolute values for D(SO) can be explained by the perturbation on the energy level and spatial distributions of π-SOMO through the orbital interaction between SOMO of the nitrene moiety and frontier orbitals of the aryl scaffolds. Spin-spin contribution to the D tensor (D(SS) tensor) has been calculated in terms of the McWeeny-Mizuno equation with the DFT/EPR-II spin densities. The D(SS) value calculated with the RO-B3LYP spin density agrees well with the D(Exptl) -D(SO) reference value in phenylnitrene, but agreement with the reference value gradually becomes worse as the D value decreases. Exchange-correlation functional dependence on the D(SS) tensor has been explored with standard 23 exchange-correlation functionals in both RO- and U-DFT methodologies, and the RO-HCTH/407 method gives the best agreement with the D(Exptl) -D(SO) reference value. Significant exchange-correlation functional dependence is observed in spin-delocalized systems such as 9-anthrylnitrene (6). By employing the hybrid CASSCF/MRMP2 approach and the McWeeny-Mizuno equation combined with the RO-HCTH/407/EPR-II//U-HCTH/407/6-31G* spin densities for D(SO) and D(SS), respectively, a quantitative agreement with the experiment is achieved with errors less than 10% in all the arylnitrenes under study. Guidelines to the putative approaches to D(SS) tensor calculations are given.     

Selectable one-dimensional or two-dimensional gas chromatography-olfactometry/mass spectrometry with preparative fraction collection for analysis of ultra-trace amounts of odor compounds

A novel selectable one-dimensional ((1)D) or two-dimensional ((2)D) gas chromatography-olfactometry/mass spectrometry with preparative fraction collection (selectable (1)D/(2)D GC-O/MS with PFC) system was developed. The main advantages of this system are the simple and fast selection of (1)D GC-O/MS or (2)D GC-O/MS or (1)D GC-PFC or (2)D GC-PFC operation with a mouse click (without any instrumental set-up change), and total transfer of enriched compounds with thermal desorption (TD) on the same system for identification with (2)D GC-O/MS analysis. Recovery of PFC enrichment with 20 injection cycles of 15 model compounds at 500pg each (e.g. alcohol, aldehyde, ester, lactone, and phenol) was very good with recoveries in the range of 98-116%. The feasibility and benefit of the proposed system was demonstrated with an identification of off-flavor compounds (e.g. 2,4,6-trichloroanisole (TCA), 2-isobutyl-3-methoxypyrazine (IBMP), and geosmin) in spiked wine at odor perception threshold level (5-50ngL(-1)). After parallel stir bar sorptive extraction (SBSE) for 20 aliquots of a sample and subsequent PFC enrichment for the odor-active fractions from the 20 stir bars, three off-flavor compounds were clearly resolved and detected with TD-(2)D GC-O/MS in scan mode. The good efficiency of SBSE-PFC enrichment in the range of 71-78% shows that all analytical steps, e.g. SBSE, TD, (1)D/(2)D GC-O/MS, and PFC, are quantitative and identification of off-flavor compounds at ngL(-1) level in wine is possible.     

PEEM/LEEM技术在两维原子晶体表面物理化学研究中的应用

光发射电子显微镜(PEEM)/低能电子显微镜(LEEM)技术能够原位实时对表面结构、表面电子态和表面化学进行动态成像研究,在催化、能源、纳米、材料等领域有着重要的应用。本文着重介绍这两种技术的新进展,以及该技术在两维原子晶体的表面物理化学研究中的应用;包括原位研究两维原子晶体(石墨烯、氮化硼等)的生长、异质结构的形成、两维原子晶体表面下的插层反应和限域催化反应;将表面原位成像、微区低能电子衍射(μ-LEED)、图像亮度随电子束能量变化(I－V)曲线研究与其它表面表征技术相结合,能够有效理解两维层状材料表面以及层状材料与衬底界面上的动态过程。     

Determination of Anafranil in Pharmaceuticals by Difference and Difference-Derivative Spectrophotometry

Abstract

Difference (ΔA) and difference first- (ΔD1) and second- (ΔD2) derivative spectrophotometric methods are described for the assay and quality control of anafranil, a powerful antidepressant, in pharmaceutical formulations.

The procedures are based upon the measurement of ΔA, ΔD1 and ΔD2 of anafranil in alkaline solutions against their acidic solutions as blanks.

Interferences of the excipients and diluents or irrelevant absorptions are nullified. Calibration graphs of ΔA, ΔD1 and ΔD2 versus the concentration of the drug showed linear relationships up to 10 μg/ml, with correlation coefficients ranging from 0.9998 to 0.9999.

Detection limits at p = 0.01 level of significance were calculated to be 0.060 (ΔA), 0.056 (ΔD1) and 0.063 (ΔD2) μg/ml. The limits of quantification were 0.45 (ΔA), 0.36 (ΔD1) and 0.81 (ΔD2) μg/ml.

The procedures have been successfully applied to the determination of anafranil in synthetic samples and in commercial pills and injections for this drug with high reliability and repeatability.     

Polymer brushes in cylindrical pores: simulation versus scaling theory

The structure of flexible polymers endgrafted in cylindrical pores of diameter D is studied as a function of chain length N and grafting density sigma, assuming good solvent conditions. A phenomenological scaling theory, describing the variation of the linear dimensions of the chains with sigma, is developed and tested by molecular dynamics simulations of a bead-spring model. Different regimes are identified, depending on the ratio of D to the size of a free polymer N(3/5). For D>N(3/5) a crossover occurs for sigma=sigma*=N(-6/5) from the "mushroom" behavior (R(gx)=R(gy)=R(gz)=N(35)) to the behavior of a flat brush (R(gz)=sigma(1/3)N,R(gx)=R(gy)=sigma(-1/12)N(1/2)), until at sigma**=(D/N)3 a crossover to a compressed state of the brush, [R(gz)=D,R(gx)=R(gy)=(N(3)D/4sigma)(1/8)相似文献   

Distribution of the cationic state over the chlorophyll pair of the photosystem II reaction center

The reaction center chlorophylls a (Chla) of photosystem II (PSII) are composed of six Chla molecules including the special pair Chla P(D1)/P(D2) harbored by the D1/D2 heterodimer. They serve as the ultimate electron abstractors for water oxidation in the oxygen-evolving Mn(4)CaO(5) cluster. Using the PSII crystal structure analyzed at 1.9 ? resolution, the redox potentials of P(D1)/P(D2) for one-electron oxidation (E(m)) were calculated by considering all PSII subunits and the protonation pattern of all titratable residues. The E(m)(Chla) values were calculated to be 1015-1132 mV for P(D1) and 1141-1201 mV for P(D2), depending on the protonation state of the Mn(4)CaO(5) cluster. The results showed that E(m)(P(D1)) was lower than E(m)(P(D2)), favoring localization of the charge of the cationic state more on P(D1). The P(D1)(?+)/P(D2)(?+) charge ratio determined by the large-scale QM/MM calculations with the explicit PSII protein environment yielded a P(D1)(?+)/P(D2)(?+) ratio of ~80/~20, which was found to be due to the asymmetry in electrostatic characters of several conserved D1/D2 residue pairs that cause the E(m)(P(D1))/E(m)(P(D2)) difference, e.g., D1-Asn181/D2-Arg180, D1-Asn298/D2-Arg294, D1-Asp61/D2-His61, D1-Glu189/D2-Phe188, and D1-Asp170/D2-Phe169. The larger P(D1)(?+) population than P(D2)(?+) appears to be an inevitable fate of the intact PSII that possesses water oxidation activity.     

Purification and Analytical Application of <Emphasis Type="Italic">Vigna mungo</Emphasis> Chitinase for Determination of Total Fungal Load of Stored Cereals

Chitinases are glycosyl hydrolases that catalyze the hydrolysis of β-(1,4)-glycosidic bonds in chitin, the major structural polysaccharide presented in the cuticle and gut peritrophic matrix of insects. Two aspartate residues (D143, D145) and one tryptophan (W146) in the Lymantria dispar chitinase are highly conserved residues observed within the second conserved motif of the family 18 chitinase catalytic region. In this study, a chitinase cDNA, LdCht5, was cloned from L. dispar, and the roles of the three residues were investigated using site-directed mutagenesis and substituting them with three other amino acids. Seven mutant proteins, D143E, D145E, W146G, D143E/D145E, D143E/W146G, D145E/W146G, and D143E/D145E/W146G, as well as the wild-type enzyme, were produced using the baculovirus-insect cell line expression system. The enzymatic and kinetic properties of these mutant enzymes were measured using the oligosaccharide substrate MU-(GlcNAc)₃. Among the seven mutants, the D145E, D143E/D145E, and D145E/W146G mutations kept some extant catalytic activity toward MU-(GlcNAc)₃, while the D143E, W146G, D143E/W146G, and D143E/D145E/W146G mutant enzymes were inactivated. Compared with the mutant enzymes, the wild-type enzyme had higher values of k _cat and k _cat / K _m . A study of the multiple point mutations in the second conserved catalytic region would help to elucidate the role of the critical residues and their relationships.     

Chitosan and Whey Protein Bio-Inks for 3D and 4D Printing Applications with Particular Focus on Food Industry

The application of chitosan (CS) and whey protein (WP) alone or in combination in 3D/4D printing has been well considered in previous studies. Although several excellent reviews on additive manufacturing discussed the properties and biomedical applications of CS and WP, there is a lack of a systemic review about CS and WP bio-inks for 3D/4D printing applications. Easily modified bio-ink with optimal printability is a key for additive manufacturing. CS, WP, and WP–CS complex hydrogel possess great potential in making bio-ink that can be broadly used for future 3D/4D printing, because CS is a functional polysaccharide with good biodegradability, biocompatibility, non-immunogenicity, and non-carcinogenicity, while CS–WP complex hydrogel has better printability and drug-delivery effectivity than WP hydrogel. The review summarizes the current advances of bio-ink preparation employing CS and/or WP to satisfy the requirements of 3D/4D printing and post-treatment of materials. The applications of CS/WP bio-ink mainly focus on 3D food printing with a few applications in cosmetics. The review also highlights the trends of CS/WP bio-inks as potential candidates in 4D printing. Some promising strategies for developing novel bio-inks based on CS and/or WP are introduced, aiming to provide new insights into the value-added development and commercial CS and WP utilization.     

Electric dipole moments of thietane in excited states of the ring puckering vibration: an experimental and ab initio study

The electric dipole moment in the ground state (v_p = 0) and the first five excited states (v_p = 1 … 5) of the ring puckering vibration of thietane have been determined from Stark shifts of rotational transitions. The results are: 0|μ_a|0 = 1.87583(16) D, 1|μ_a|1 = 1.87341(18) D, 2|μ_a|2 = 1.89759(28) D, 3|μ_a|3 = 1.88688(29) D, 4|μ_a|4 = 1.90036(18) D, 5|μ_a|5 = 1.88596(59) D. The dependence of these values on v_p shows the zig-zagging behaviour typical of modes with double minimum potentials. A combined analysis of the ground and first excited states yielded also a precise value for the transition moment, 0|μ_c|1 = 0.24023(49) D.

A potential and electric dipole moment function has been derived from ab initio calculations, using MP2 and the 6–31G** basis set. Expectation values of the dipole and transition moments were determined from these data. Absolute values are about 5% in error, but the variation with vibrational state is reproduced excellently by the theoretical values.     

铝粉粒度对高氯酸铵热分解动力学的影响

采用热重-差示扫描量热(TG-DSC)联合技术研究了10.7 μm, 2.6 μm和40 nm铝粉对高氯酸铵(AP)热分解的影响. 结果表明, 铝粉的加入对AP的低温放热峰有抑制作用, 对高温放热分解反应有促进作用, 并且随铝含量的增加和铝粒径的减小这种作用更强烈. 采用多元非线性拟合技术对不同升温速率下TG-DSC实验数据进行拟合, 结果表明, 质量分数为40%的不同粒径铝粉的加入对AP的热分解三阶段(A→B→C→D)反应模型无影响, 但反应机理函数发生了改变. 纯AP, AP/Al(10.7 μm), AP/Al(2.6 μm)及AP/Al(40 nm)的反应机理函数组合分别为C1/D1/D1, C1/D1/D3, C1/D1/D4和C1/D1/F2.     

Selective ion binding by protein probed with the statistical mechanical integral equation theory

Selective ion binding by human lysozyme and its mutants is probed with the three-dimensional interaction site model theory which is the statistical mechanical integral equation theory. Preliminary and partial results of the study have been already published (Yoshida, N. et al. J. Am. Chem. Soc. 2006, 128, 12042-12043). The calculation was carried out for aqueous solutions of three different electrolytes, CaCl2, NaCl, and KCl, and for four different mutants of the human lysozyme: wild type, Q86D, A92D, and Q86D/A92D, which have been studied experimentally. The discussion of this article focuses on the cleft that consists of amino acid residues from Q86 to A92. For the wild type of protein in the aqueous solutions of all the electrolytes studied, there are no distributions observed for the ions inside the cleft. The Q86D mutant shows essentially the same behavior with that of the wild type. The A92D mutant shows strong binding ability to Na+ in the recognition site, which is in accord with the experimental results. There are two isomers of the Q86D/A92D mutant, e.g., apo-Q86D/A92D and holo-Q86D/A92D. Although both isomers exhibit the binding ability to the Na+ and Ca2+ ions, the holo isomer shows much greater affinity compared with the apo isomer. Regarding the selective ion binding of the holo-Q86D/A92D mutant, it shows greater affinity to Ca2+ than to Na+, which is also consistent with the experimental observation.