Traceability to units

On the grounds that clear and direct communication is required of us today, it is proposed that traceability be regarded as the ability to demonstrate that measurements are what they are purported to be and that traceability is thus to measurement units rather than reference values per se. It is suggested that such an approach may give greater flexibility in the establishment, maintenance and propagation of traceability, and that accreditation practices are becoming central to the practical establishment of traceability for chemical and biological measurement.     

稀土化合物增强ZA—27合金耐磨性的研究

对稀土化合物增强ＺＡ－２７合金的组织及耐磨性做了研究。试验发现,由于在ＺＡ－２７合金中加入一定量的ＥＲ和Ｓｉ元素,组织中出现一些颗粒状第二相;这些物相分布在晶界及枝晶间,阻止了晶粒长大。通过航向电镜能谱分析发现,该物相是一种含有Ｚｎ、Ａｌ、Ｓｉ及ＲＥ元素的复杂化合物。经测试,这种物相的显微硬度要比基体高得多。耐磨性等性能试验结果表明,这种合金的耐磨性要比ＺＡ－２７合金高４倍,比Ｓｉ相增强合金也高,     

Simulation studies of protein folding/unfolding equilibrium under polar and nonpolar confinement

We study the equilibrium folding/unfolding thermodynamics of a small globular miniprotein, the Trp cage, that is confined to the interior of a 2 nm radius fullerene ball. The interactions of the fullerene surface are changed from nonpolar to polar to mimic the interior of the GroEL/ES chaperonin that assists proteins to fold in vivo. We find that nonpolar confinement stabilizes the folded state of the protein due to the effects of volume reduction that destabilize the unfolded state and also due to interactions with the fullerene surface. For the Trp cage, polar confinement has a net destabilizing effect that results from the stabilizing confinement and the competitive exclusion effect that keeps the protein away from the surface hydration shell and stronger interactions between charged side chains in the protein and the polar surface that compete against the formation of an ion pair that stabilizes the protein folded state. We show that confinement effects due to volume reduction can be overcome by sequence-specific interactions of the protein side chains with the encapsulating surface. This study shows that there is a complex balance among many competing effects that determine the mechanism of GroEL chaperonin in enhancing the folding rate of polypeptide inside its cavity.     

A new turn structure for the formation of beta-hairpins in peptides

Previous studies by Gellman and co-workers have elegantly shown that mirror-image beta-turns based upon d-Pro-Gly are especially good at stabilizing beta-hairpins and have demonstrated that peptide 1 [Arg-Trp-Gln-Tyr-Val-d-Pro-Gly-Lys-Phe-Thr-Val-Gln-NH2] folds into a well-defined beta-hairpin [Espinosa, J. F.; Gellman, S. H. Angew. Chem., Int. Ed. 2000, 39, 2330-2333]. The present study establishes that the amino acid ornithine (Orn) also forms a turn structure that is excellent at stabilizing beta-hairpins when linked through the delta-amino group and that this turn is comparable to d-Pro-Gly in ability to induce beta-hairpin formation. Thus, 1H NMR chemical shift and NOE studies establish that Orn-containing analogue 2 [Arg-Trp-Gln-Tyr-Val-deltaOrn-Lys-Phe-Thr-Val-Gln-NH2] is comparable in structure to peptide 1. The present study also establishes that the Orn turn is superior to Asn-Gly turns and that replacement of the deltaOrn with epsilonLys or d-deltaOrn generates structures that do not fold significantly.     

On the reality of residual entropies of glasses and disordered crystals

We show that the hypothesis that the configurational entropy of a liquid disappears when it is kinetically frozen into a single glass state implies a spontaneous decrease of entropy. We show further that this is not an innocuous exception to the second law that requires a slight modification of that law, but rather implies directly the possibility of an uncompensated conversion of heat to work. We also note that the number of microstates visited in the course of a measurement does not determine the entropy, but rather that this number is always an inconceivably small fraction of the accessible microstates. Various experimental and computational tests of the possible vanishing of configurational entropy on kinetic arrest (e.g., from studies of glass vapor pressure and solubilities, and the coexistence curve between a disordered crystal and the liquid), with the exception of one questionable case, are consistent with the view that it does not vanish. We then show that this result is actually required by the second law. These considerations apply equally to the residual entropy of disordered crystals.     

Tethered dimer inhibitors of NAD synthetase: parallel synthesis of an aryl-substituted SAR library

We previously reported that tethered dimers containing indoles on one end and a permanent positive charge on the other, using a 6-9 carbon polymethylene tether, provided NAD synthetase inhibitors with impressive antibacterial activities against Gram-positives. Here, we report that the phenyl ring is a good substitute for indole, and we utilize solution-phase parallel synthesis to explore structure-activity relationships for substituents on that ring. General conclusions are that nonpolar substituents are more effective than polar ones and that different positional isomers often have very different enzyme inhibition activities. This latter observation reveals that enzyme activity is sensitive to minor structural changes and suggests that nonspecific detergent actions are not important for the observed effects.     

五彩湾煤镜质组与惰质组在热解中的相互作用

以五彩湾煤镜质组、惰质组为研究对象,建立两种不同的体系,镜质组与惰质组无相互作用体系(A)和相互作用体系(B)。利用热重技术(TG)和傅里叶变换红外技术(FT-IR),将两体系的热解固体产物进行红外分析。结果表明,在300~450℃,体系B的脂肪氢含量高于体系A,表明镜质组与惰质组之间发生了烷基自由基转移反应,芳氢的含量也是体系B多于体系A,这说明镜质组与惰质组之间同时发生了芳构化作用,随温度升高,镜质组生成少量氢自由基与惰质组发生侧链取代反应;在500~700℃,体系B的脂肪氢含量和芳氢含量均低于体系A,表明此时镜质组与惰质组之间发生缩聚反应及缩合反应;750~800℃时,脂肪氢和芳香氢含量均为体系B大于体系A,说明体系B中,镜质组产生较多的氢自由基与惰质组大分子芳香结构发生氢化反应,同时与惰质组发生侧链取代反应;850~900℃时,镜质组与惰质组之间进一步发生多环芳香缩合反应。     

Molecular dynamics of apo-adenylate kinase: a principal component analysis

Adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes large-scale motions of its Lid and AMP-binding domains when its open form closes over its substrates, AMP and Mg2+-ATP. The third domain, the Core, is relatively stable during closing. The resulting trajectory is analyzed with a principal component analysis method that decomposes the atom motions into modes ordered by their decreasing contributions to the total protein fluctuation. Simulations at 303 K (normal T) and 500 K (high T) reveal that at both temperatures the first three modes account for 70% of the total fluctuation. The residues that contribute the most to these three modes are concentrated in the Lid and AMP-binding domains. Analysis of the normal T modes indicates that the Lid and AMP-binding domains sample a broad distribution of conformations indicating that AKE is designed to provide its substrates with a large set of conformations. The high T results show that the Lid initially closes toward the Core. Subsequently, the Lid rotates to a new stable conformation that is different from what is observed in the substrate-bound AKE. These results are discussed in the context of experimental data that indicate that adenylate kinases do sample more than one conformational state in solution and that each of these conformational states undergoes substantial fluctuations. A pair of residues is suggested for labeling that would be useful for monitoring distance fluctuations by energy transfer experiments.     

Impact of multiple re-use of anion-exchange chromatography media on virus removal

We evaluated viral clearance in multiply-cycled anion-exchange media run in flow-through mode. We found that anion-exchange columns do not lose viral clearance capacity after extensive re-use, if they are cleaned with recommended buffers that do not chemically degrade the media. In contrast, anion-exchange (AEX) columns that are not cleaned or are cleaned with buffers that chemically degrade the media lost viral clearance capacity after extended use. In these cases, other performance attributes that changed at the same time were increased band spreading, decreased DNA clearance and accumulating backpressure that prevented re-use past 80-120 cycles. Thus, our data suggests that flow through mode anion-exchange columns that are cleaned with recommended cleaning buffers, and periodically monitored for band spreading, DNA clearance and/or backpressure need not be re-evaluated for viral clearance at the end of the validated media lifetime.     

Peptide‐Guided Assembly of Repeat Protein Fragments

Herein, we present the peptide‐guided assembly of complementary fragments of designed armadillo repeat proteins (dArmRPs) to create proteins that bind peptides not only with high affinity but also with good selectivity. We recently demonstrated that complementary N‐ and C‐terminal fragments of dArmRPs form high‐affinity complexes that resemble the structure of the full‐length protein, and that these complexes bind their target peptides. We now demonstrate that dArmRPs can be split such that the fragments assemble only in the presence of a templating peptide, and that fragment mixtures enrich the combination with the highest affinity for this peptide. The enriched fragment combination discriminates single amino acid variations in the target peptide with high specificity. Our results suggest novel opportunities for the generation of new peptide binders by selection from dArmRP fragment mixtures.     

Assembly of antibodies in lipid membranes for biosensor development

An investigation of the incorporation of antibody in lipid films of a composition that has been used for biosensor preparation is reported. IgG that is incorporated into lipid monolayers prepared from 7:3 mixtures of dipalmitoyl phosphatidylcholine and dipalmitoyl phosphatidic acid is edge-active, and enters and penetrates the fluid region of the mixed-phase system when monolayers are held at low pressure (< 20 mN/m). It was found that there is an “exclusion pressure” observed in pressure-area (π-A) curves that are collected for monolayers that contain antibody. This term refers to a specific threshold of lateral pressure (which is reached by monolayer compression) that can cause explusion of antibody from the interior of a membrane. Microscopic images of monolayers containing the fluorescent phospholipid nitrobenzoxadiazole dipalmitoyl phosphatidylethanolamine (NBD-PE), or antibody labeled with tetramethylrhodamine isothiocyanate (TRITC), were used to determine the structure of membranes, and the location of effects on structure caused by IgG. Ellipsometric measurements of lipid monolayers that were cast onto silicon wafers by the LangmuirBlodgett method were used to study the thickness of monolayers and to investigate the structural changes that occurred at the “exclusion pressure.” Both the use of fluorescent antigen and ellipsometry indicated that antibody binding activity was present and was dependent on compression pressure. The effects of pH and ionic strength of subphase, antibody concentration, incubation time, and lateral pressure have been examined. The results may indicate the conditions that can be used to improve the incorporation of active IgG for preparation of biosensors that are based on lipid membranes.     

REGULATION OF NITRATE REDUCTASE ACTIVITY IN RICE

The properties of NR from rice varieties Yuanfengzao and Jingyin 127 are the same in molecular weight of native enzyme and subunit, optimum pH, K_m value for substrates NO_3~- and NADH, stability in vitro and immunological characteristics. The decay rate in vitro of the activity of the partially purified NR from Yuanfengzao is 20％ lower than that from Jingyin 127. The results from antiserum titration and rocket immunoelectrophoresis indicated that the amount of NR in Yuanfengzao is about 1.5 times more than that in Jingyin 127. Further study on in vivo incorporation of ~3H-labeled amino acids into NR revealed that the rate of NR synthesis in Yuanfengzao is obviously higher than that in Jingyin 127. In vitro translation of mRNA showed that the products of NR-mRNA per unit of total mRNA of Yuanfengzao is much more than that of Jingyin 127. It is concluded that, therefore, NR activity in rice is regulated through NR synthesis and NR-inhibitory protein(s) system, the former is further controlled at the lev     

Measurement of water by oven evaporation using a novel oven design. 2. Water in motor oils and motor oil additives

The measurement of water in lubricating oils is important because water accelerates the corrosion of metal parts and bearings in motors. Some of the additives added to lubricating oils to improve their performance react with the Karl Fischer reagent (KFR) causing a positive bias in the water measurement. A new oven evaporation technique for measuring water in oils has been developed that is automated, requires less sample handling, is easily calibrated, and is capable of measuring relatively small mass fractions of water (50 mg/kg sample). A series of motor oils was analyzed with the standard KFR, a reagent that detects interfering substances that reduce iodine, and the aldehyde–ketone reagent that does not detect substances that react with methanol and form water. The oil samples were heated to 107°C and then reheated to 160°C. At both temperatures, material was measured by both KFRs, but only zinc dithiophosphate released sulfur compounds that would react with the reagent that detects interfering substances. Mass fractions of between 20 and 70% of the volatile material released at either temperature were measured with the standard KFR but not with the aldehyde–ketone reagent. These results demonstrate that there are a number of sources of positive bias in the measurement of water in motor oils and that the standard KFR cannot be used to measure water in motor oils and motor oil additives. These results also indicate that some of the material reacts with methanol to form water. Finally, these results suggest that some of the material that is volatile at 160°C and not at 107°C may be water that is physically occluded or may be substances that react with diethyleneglycol monomethylether to produce water.     

AEG3482 is an antiapoptotic compound that inhibits Jun kinase activity and cell death through induced expression of heat shock protein 70

We describe a group of small-molecule inhibitors of Jun kinase (JNK)-dependent apoptosis. AEG3482, the parental compound, was identified in a screening effort designed to detect compounds that reduce apoptosis of neonatal sympathetic neurons after NGF withdrawal. We show that AEG3482 blocks apoptosis induced by the p75 neurotrophin receptor (p75NTR) or its cytosolic interactor, NRAGE, and demonstrate that AEG3482 blocks proapoptotic JNK activity. We show that AEG3482 induces production of heat shock protein 70 (HSP70), an endogenous inhibitor of JNK, and establish that HSP70 accumulation is required for the AEG3482-induced JNK blockade. We show that AEG3482 binds HSP90 and induces HSF1-dependent HSP70 mRNA expression and find that AEG3482 facilitates HSP70 production while retaining HSP90 chaperone activity. These studies establish that AEG3482 inhibits JNK activation and apoptosis by a mechanism involving induced expression of HSP proteins.     

Mass spectrometric characteristics and kinetics of iron release in visceral mass of Saccostrea cucullata

Ferritins with electrophoretic homogeneity were prepared from the visceral mass of Saccostrea cucullata in batch. The native PAGE approach showed similar electrophoretic mobility among pig pancreatic ferritin, liver ferritin of Dasyatis akajei, and visceral mass ferritin of Saccostrea cucullata. SDS-PAGE indicated that the Saccostrea cucullata visceral ferritin (SCVF) consisted of a single subunit type and had a molecular weight (MW) of approximately 20 kDa, suggesting that the protein shell in SCVF was composed of a single subunit. In addition, peptide mass fingerprinting and transmission electron microscopy were used to identify SCVF further, and to observe its molecular structure. We found that the molecular structure in SCVF was similar to that of most mammalian ferritins, which are composed of a protein shell and an iron core. The results of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry under the assistance of an acidic matrix, sinapic acid, also showed that SCVF was composed of a single subunit type and its subunit MW was calculated to be 19871.042 Da in the absence of heme. Kinetics analysis revealed that the complete process of iron release fitted the law of a first-order reaction, which is similar to that of most ferritins in mammals. Similar to bacterial ferritin, studies indicated that the shell consisted of a single subunit type and showed similar kinetics of iron release, suggesting that this subunit plays two important roles in iron release and storage, and that it shows different stability and intensity of interaction in carrying out its physiological functions in SCVF.     

Do commercially available metal salts mediate calixarene formation via hydrogen-bonded dimers?

In this article we report the first example of a Lewis acid promoted, one-pot, Br?nsted acid free, high-yielding synthesis of the calixarene macrocycle from the "monomer" p-tert-butylphenol. We report that when a commercially available metal salt (Lewis acid) is incorporated within the calixarene-forming reaction, a certain amount of control over the size of the calixarenes produced can be gained. Although a detailed mechanistic rationale on how the macrocycle is assembled is unclear, what is evident from this work is that the metal cation, the counteranion, and the oxidation state of the salt employed are all important contributors to the outcome of the reaction process. Indeed, evidence to date suggests that a subtle "symbiotic" relationship exists between the metal cation, its oxidation state, and the anion that allows the efficient transformation of the "monomeric" p-tert-butylphenol into linear oligomers and, ultimately, into macrocyclic calixarenes. Athough the metal salt mediated process described herein is efficient and high-yielding, what is also fundamentally important is that a comprehensive mechanistic understanding of how the calixarenes are assembled be accrued. Searching for possible indicators or clues, we propose that oligomeric methylene-linked phenolic entities are initially formed and that these, we tentatively suggest, generate metal and/or anion hydrogen-bonded supramolecular intermediates. It is possible that the preorganization of the linear polyphenolic oligomers allows the formation of hydrogen-bonded structures which, critically, result in the formation of supramolecular assemblies that are subsequently "stitched" together, generating the p-tert-butylcalix[n]arenes (n = 4-9) in excellent yields. Substantiating the possibility that hydrogen-bonded entities are generated (and that these subsequently afford metal-templated assemblies), we make reference to a seldom cited 1962 Nature publication that reported the propensity of polyphenolic linear oligomers to form "well-defined intramolecularly hydrogen-bonded conformations".     

Lone pair-pi and pi-pi interactions play an important role in proton-coupled electron transfer reactions

Proton-coupled electron transfer (PCET), a class of formal hydrogen atom transfer (HAT) reactions, is of widespread interest because it is implicated in a broad range of chemical and biochemical processes. PCET is typically differentiated from HAT by the fact that it occurs when a proton and electron are transferred between different sets of molecular orbitals. Previous theoretical work predicted that hydrogen bonding between reactants is a necessary but not sufficient condition for H exchanges to take place by PCET. This implies that HAT is the only mechanism for H exchange between two carbon atoms. In this work, we present computational results that show that the H exchange in the tert-butylperoxyl/phenol couple, a prototypical antioxidant exchange reaction, occurs by PCET and that the transfer of the electron can occur via an oxygen lone pair-ring pi overlap. We then show that the H exchange in a model for the tyrosyl/tyrosine couple, which is implicated in ribonucleotide reductase chemistry, occurs via PCET and that one path for the electron transfer is provided by a strong pi-stacking interaction. Finally, we show that a pi-stacking interaction in the benzyl/toluene couple, a system in which there is no H-bonding, can result in this exchange occurring via PCET to some extent. Collectively, these results indicate that PCET reactions are not unique to systems that can engage in H-bonding and that lone pair-pi and pi-pi interactions in these systems may be more important than previously understood.     

Development of non-phospholipid liposomes containing a high cholesterol concentration

We present a novel formulation of non-phospholipid liposomes formed from cholesterol and palmitic acid. Despite the fact that these two lipidic species do not form individually fluid bilayers, we show that once mixed together, fluid bilayers can be obtained and, moreover, these can be extruded using classical extrusion processes to form liposomes. The chemical analysis indicates that these liposomes contain 70 mol % cholesterol, a content that is considerably higher that the saturation limit generally reported for phospholipid bilayers. These cholesterol-rich liposomes, formed with molecules that have low toxicity in vivo, display an improved impermeability relative to that of traditional phospholipid liposomes. In addition, because of the presence of palmitic acid, the stability of the liposomes is pH-dependent, and it is possible to trigger the release of encapsulated materials by pH stimuli.     

Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state

Solution NMR spin-relaxation experiments were used to compare mus-ms dynamics in RNase A in the apo form and as complexed to the substrate-mimic, pTppAp. The crystal structure of the RNase A/pTppAp complex was determined and demonstrates that this ligand binds at the active site and utilizes established substrate binding sites in its interaction with RNase A. Relaxation-compensated CPMG experiments identify flexible residues in and around the active site in both the apo and pTppAp-bound enzyme. Quantitative analysis of the NMR spin-relaxation dispersion curves show that the time scale of motion in RNase A is unchanged when pTppAp binds and is similar to the time scale for the rate-determining step of the catalytic reaction. Temperature-dependent measurements provide an activation barrier for motion of 5.2 +/- 1.0 kcal/mol and 4.5 +/- 1.2 kcal/mol for the apo and pTppAp forms of RNase A, respectively. These data indicate very similar motion exists in the free and bound enzyme. Additionally, chemical shift data suggests that the magnitude of motion is also similar for these two forms and that it is likely that apo enzyme interconverts to a structure that resembles a ligand-bound form. Likewise, it appears that the bound conformation samples the apo enzyme form even when ligand is present. Taken together the data imply that RNase A is in a preexisting dynamic equilibrium between two conformations that represent the open and closed enzyme forms. These data suggest that ligand binding stabilizes the bound conformer but does not induce it.     

The molecular underpinnings of a solute-pump/solvent-probe spectroscopy: the theory of polarizability response spectra and an application to preferential solvation

Recent ultrafast experiments on liquids have made clear that it is possible to go beyond light scattering techniques such as optical Kerr spectroscopy that look at the dynamics of a liquid as a whole. It is now possible to measure something far more conceptually manageable: how that liquid dynamics (and that light scattering) can be modified by electronically exciting a solute. Resonant-pump polarizability-response spectra (RP-PORS) in particular, seem to show that different solvents respond in noticeably distinct ways to such solute perturbations. This paper is a theoretical attempt at understanding the kinds of molecular information that can be revealed by experiments of this sort. After developing the general classical statistical mechanical linear response theory for these spectra, we show that the experimentally interesting limit of long solute-pump/solvent-probe delays corresponds to measuring the differences in 4-wave-mixing spectra between solutions with equilibrated ground- and excited-state solutes-meaning that the spectra are essentially probes of how changing liquid structure affects intermolecular liquid vibrations and librations. We examine the spectra in this limit for the special case of an atomic solute dissolved in an atomic-liquid mixture, a preferential solvation problem, and show that, as with the experimental spectra, different solvents can lead to spectra with different magnitudes and even different signs. Our molecular-level analysis of these results points out that solvents can also differ in how local a portion of the solvent dynamics is accessed by this spectroscopy.