Feature Based Retention Time Alignment for Improved HDX MS Analysis

An algorithm for retention time alignment of mass shifted hydrogen-deuterium exchange (HDX) data based on an iterative distance minimization procedure is described. The algorithm performs pairwise comparisons in an iterative fashion between a list of features from a reference file and a file to be time aligned to calculate a retention time mapping function. Features are characterized by their charge, retention time and mass of the monoisotopic peak. The algorithm is able to align datasets with mass shifted features, which is a prerequisite for aligning hydrogen-deuterium exchange mass spectrometry datasets. Confidence assignments from the fully automated processing of a commercial HDX software package are shown to benefit significantly from retention time alignment prior to extraction of deuterium incorporation values.      

CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations

CHARMM‐GUI Membrane Builder, http://www.charmm‐gui.org/input/membrane , is a web‐based user interface designed to interactively build all‐atom protein/membrane or membrane‐only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance‐based algorithm for faster initial ion displacement, (5) CHARMM inputs for P₂₁ image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM‐GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. © 2014 Wiley Periodicals, Inc.     

Ultrastructural description of spermiogenesis within the Mediterranean Gecko, Hemidactylus turcicus (Squamata: Gekkonidae)

We studied spermiogenesis in the Mediterranean Gecko, Hemidactylus turcicus, at the electron microscope level and compared to what is known within other Lepidosaurs. In H. turcicus germ cells are connected via cytoplasmic bridges where organelle and cytoplasm sharing is observed. The acrosome develops from merging transport vesicles that arise from the Golgi and subsequently partition into an acrosomal cap containing an acrosomal cortex, acrosomal medulla, perforatorium, and subacrosomal cone. Condensation of DNA occurs in a spiral fashion and elongation is aided by microtubules of the manchette. A nuclear rostrum extends into the subacrosomal cone and is capped by an epinuclear lucent zone. Mitochondria and rough endoplasmic reticulum migrate to the posterior portion of the developing germ cell during the cytoplasmic shift and the flagellum elongates. Mitochondria surround the midpiece as the anlage of the annulus forms. The fibrous sheath begins at mitochondrial tier 3 and continues into the principal piece. Peripheral fibers associated with microtubule doublets 3 and 8 are grossly enlarged. During the final stages of germ cell development spermatids are wrapped with a series of Sertoli cell processes, which exhibit ectoplasmic specializations and differing cytoplasmic consistencies. The results observed here corroborate previous studies, which show the conservative nature of sperm morphology. However, ultrastructural character combinations specific to sperm and spermiogenesis seem to differ among taxa. Further studies into sperm morphology are needed in order to judge the relevance of the ontogenic changes recorded here and to determine their role in future studies on amniote evolution.     

Synthesis of N-acyl-N,O-acetals from N-aryl amides and acetals in the presence of TMSOTf

Secondary amides undergo in situ silyl imidate formation mediated by TMSOTf and an amine base, followed by addition to acetal acceptors to provide N-acyl-N,O-acetals in good yields. An analogous, high-yielding reaction is observed with 2-mercaptothiazoline as the silyl imidate precursor. Competing reduction of the acetal to the corresponding methyl ether via transfer hydrogenation can be circumvented by the replacement of CY₂NMe with 2,6-lutidine under otherwise identical reaction conditions.     

Determination of thermodynamic parameters for the interaction of a lipid-binding peptide and insulin with a reversed-phase column

The effect of temperature was investigated on the reversed-phase chromatography of a synthetic lipid associating peptide (LAP), with the following sequence (LESFLKSWLSALEQALKA) and on insulin. The LAP was chromatographed on a muBondapak-alkylphenyl column with 1% aq. triethylammonium phosphate, pH 3.2-2-propanol (80:20) as the isocratic mobile phase. The insulin was separated on a Resolve-C18 column with a mobile phase that contained 0.1 M sodium phosphate, pH 2.0-acetonitrile (71.5:28.5). With the LAP the Van't Hoff plot (In k' vs. 1000/T) was linear and the value of enthalpy for association of the peptide with the reversed-phase column was large and negative. The phase ratio was estimated for the column used in the separation and then derivation of the corresponding entropic term demonstrated that the association was enthalpy and not entropy drive. By contrast the corresponding Van't Hoff plot derived or the insulin study was non-linear and with a positive slope. Further study indicated that the formation of the insulin-reversed phase complex could be attributed to a favorable entropy change. It is probable that the non-classical thermodynamics observed during the insulin chromatography could be related to conformational changes in the insulin structure during the chromatographic process.     

Separation and quantitation of insulins and related substances in bulk insulin crystals and in injectables by reversed-phase high performance liquid chromatography and the effect of temperature on the separation

The Food and Drug Administration performs potency assays of insulin products as part of the insulin certification program required by the Code of Federal Regulations. The official method specified in the United States Pharmacopeia (USP) is a bioassay measuring the depression of blood sugar concentrations in rabbits treated with the insulin under test and the official standard. The insulin products resulting from today's technology include highly purified isolates from bovine or porcine pancreas and insulin that is identical in structure to human insulin. A study of the effects of temperature on the separation of the components in insulin injectables led to the development of a reversed-phase high performance liquid chromatographic (HPLC) method that uses a sulfate buffer/acetonitrile mobile phase at 40 degrees C for the separation and quantitation of bovine, porcine, and human insulins and related substances. This HPLC method reduces analysis time to 1/60 of that required for the bioassay and yields more information about purity than the percent nitrogen determination that is one of the USP official procedures. The results of HPLC analyses were compared with those for the bioassay by means of a potency/area conversion factor computed on a species by species basis. Results for the bioassays and the HPLC determinations for 40 lots of bulk crystalline insulin were compared in this study; in general, the HPLC estimates fell within the 95% confidence interval for combined independent bioassays.     

Eine Neuberechnung der Atomgewichte

Ohne Zusammenfassung     

Single crystal electron paramagnetic resonance study of rubidium lead hexanitrocuprate (II) at 295 K

At 295 K g_| = 2.073 and g_⊥ = 2.155 for Rb₂PbCu(NO₂)₆. The minimum g tensor principal axis is aligned with the c axis of the unit cell which is along the short Cu-N bond in the compressed tetragonal CuN₆ environment.     

A MICROEMULSION COSURFACTANT WITH EXCELLENT WATER SOLUBILIZATION AT HIGH OIL CONTENT

Medium chain length alkyl amines were found to be more effective cosurfactants for microemulsion formation than are medium chain length alcohols at high hydrocarbon levels with sodium doecyl sulfate as the surfactant. Both aromatic and short chain aliphatic hydrocarbons were studied. By contrast, the amines were found virtually Ineffective with quaternary anmoniutn salts whereas the alcohols showed good performance. This suggests the possibility that complementarity of function between surfactant and cosurfactant may be a desirable feature of a microemulsion system at high hydrocarbon levels.