Structure control within poly(amidoamine) dendrimers: size, shape and regio-chemical mimicry of globular proteins

This work describes the syntheses of a new poly(amidoamine) (PAMAM) dendrimer family possessing a disulfide function (cystamine) in its core. Traditional redox-chemistry associated with the disulfide core in these dendrimer structures, provides a versatile strategy for designing unique sizes, shapes and controlling the regio-disposition of chemical groups on the surface of these dendrimers. Various single site, sulfhydryl functionalized dendron reactants may be generated in situ, under standard reducing conditions (i.e. dithiothreitol (DTT)). Facile control of size, shape and chemical functionality placement involves covalent hybridization of these single point, sulfhydryl reactive dendron components. This is accomplished by re-oxidation in the presence of air, to yield generation/surface chemistry differentiated cross-over products which may be isolated by preparative thin layer or column chromatography. Differentiated cystamine core dendrimers derived from combination and permutation of lower generation (i.e. Gen.=0-3) sulfhydryl functionalized dendrons possessing amino, hydroxyl, acetamido or dansyl surface groups, were synthesized and isolated. They were characterized by a variety of methods including; ¹³C NMR, capillary electrophoresis (CE), gel electrophoresis (PAGE), thin layer chromatography (TLC) and electrospray (ES) or matrix assisted laser desorption ionization (MALDI-TOF) mass spectrometry. This general strategy has broad implications for the systematic size, shape and regio-chemical control of a wide range of dendritic nanostructures, many of which may be designed to mimic the sizes, shapes and regio specific chemo-domains observed for globular proteins.     

Rapid Protein Hydrolysis by Microwave Irradiation Using Heat-Resistant Teflon-Pyrex Tubes

A rapid peptide-bond hydrolysis by means of microwave irradiation is introduced for the facile preparation of protein hydrolysates used for amino acid analysis. The optimal hydrolysis condition has been determined using several enzymes with known amino acid compositions. The effects of hydrolysis time on the recovery of various labile and hydrophobic amino acids are also exemplified in the microwave heating of standard amino acids. The method has been applied to the complete amino acid analysis with a single nonvolatile solvent of methanesulfonic acid with good recovery of tryptophan and half-cystine. It provides a radical expedition of protein and peptide hydrolysis via commercial microwave ovens and specially-designed Teflon-Pyrex tubes, circumventing the tedious procedures using vacuum-sealed pyrex lubes heating at 110°C for more than 24 h. This novel type of microwave chemistry associated with rapid peptide-bond cleavage is of great potential in the automation of the complete process of amino acid analysis starting from the preparation of protein hydrolysates.     

New methods for data analysis of isothermal titration calorimetry

Heat divided by ligand concentration vs. heat, similar to the Scatchard plot, was introduced to obtain the equilibrium constant (K) and the enthalpy of binding (DH) using isothermal titration calorimetry data. Values of K and DH obtained by this linear pseudo-Scatchard plot for a system with a set of independent binding sites (such as binding fluoride ions on urease and monosaccharide methyl a-D-mannopyranoside on concavalin A) were remarkably like that obtained from a normal fitting Wiseman method and other our technical methods. On applying this graphical method to study the binding of copper ion on myelin basic protein (MBP), a concave downward curve obtained was consistent with the positive cooperativity in the binding. A graphical fitting by simple method for determination of thermodynamic parameters was also introduced. This method is general, without any assumption and restriction made in previous method. This general method was applied to the product inhibition study of adenosine deaminase. This revised version was published online in July 2006 with corrections to the Cover Date.     

Concerning the Thermal Diastereomerization of the Green Fluorescent Protein Chromophore

Summary. Two model compounds for the green fluorescent protein chromophore were prepared. One of them incorporates the natural 4-hydroxybenzylidene group of the natural tyrosin derived chromophore, the other one bears a methyl group instead of the hydroxy group. Whereas the photochemically prepared (E)-diastereomer of the first compound very effectively reverted thermally (room temperature) to the thermodynamically stable (Z)-diastereomer, the (E)-diastereomer of the second derivative proved to be stable even at elevated temperatures for more than a day. This finding can be rationalized by constructing the appropriate resonance structures showing that only in the first case an effective delocalization enables partial single bond character of the benzylidene double bond. From the standpoint of chemical etiology, only Nature’s choice of the tyrosin derived chromophore of the green fluorescent protein provides an efficient radiationless thermal relaxation channel for the unwanted photo-diastereomerization product formed after excitation besides the dominating fluorescence channel of its chromophore.     

Identification of the pathological prion protein allotypes in scrapie-infected heterozygous bank voles (Clethrionomys glareolus) by high-performance liquid chromatography-mass spectrometry

Cerebral formation of the pathological isoform of the prion protein (PrP) is a crucial molecular event in prion diseases. The bank vole (Clethrionomys glareolus) is a rodent species highly susceptible to natural scrapie. The PrP gene of bank vole is polymorphic (Met/Ile) at codon 109. Here we show that homozygous 109Met/Met voles have incubation times shorter than heterozygous 109Met/Ile voles after experimental challenge with three different scrapie isolates. An HPLC-MS/MS method was optimized and applied to investigate whether in heterozygous animals both PrP allotypes are able to undergo pathological conversion. The results demonstrate that both allotypes of the prion protein participate to pathological deposition.     

Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields

An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol.     

On the Temperature–Pressure Free‐Energy Landscape of Proteins

We studied the thermodynamic stability of a small monomeric protein, staphylococcal nuclease (Snase), as a function of both temperature and pressure, and expressed it as a 3D free‐energy surface on the p,T‐plane using a second‐order Taylor expansion of the Gibbs free‐energy change ΔG upon unfolding. We took advantage of a series of different techniques (small‐angle Xray scattering, Fourier‐transform infrared spectroscopy, differential thermal analysis, pressure perturbation calorimetry and densitometry) in the evaluation of the conformation of the protein and in evaluating the changes in the thermodynamic parameters upon unfolding, such as the heat capacity, enthalpy, entropy, volume, isothermal compressibility and expansivity. The calculated results of the free‐energy landscape of the protein are in good agreement with experimental data of the p,T‐stability diagram of the protein over a temperature range from 200 to 400 K and at pressures from ambient pressure to 4000 bar. The results demonstrate that combined temperature–pressure‐dependent studies can help delineate the free‐energy landscape of proteins and hence help elucidate which features and thermodynamic parameters are essential in determining the stability of the native conformational state of proteins. The approach presented may also be used for studying other systems with so‐called re‐entrant or Tamman loop‐shaped phase diagrams.     

Incorporation of FT-IR spectral data in a computer-assisted prediction of globular protein structure

Currently, much effort is being directed to the determination of the three-dimensional structure of proteins. Two classes of research are of interest; spectrometric techniques which include Fourier transform infrared (FT-IR) spectrometry, and non-spectrometric prediction schemes. The spectra obtained using FT-IR spectrometry, are analyzed to determine the percentages of alpha-helices, beta-pleated sheets, and non-structured coils in a protein. Unfortunately, FT-IR, as well as other spectrometric techniques, cannot be used to determine the exact secondary structure of a protein reliably. Non-spectrometric prediction methods yield information on the exact secondary structure, but are not always accurate. Most prediction methods relate the primary amino acid sequence to the secondary structure of a protein, allowing sequential secondary structure information for the protein examined to be obtained. The goal of this research is to incorporate FT-IR with a prediction method, resulting in an improvement in the accuracy of the prediction.     

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability.     

CaO和NaCl焙烧混合稀土精矿过程中的分解反应

用XRD和TG-DTA热分析技术, 研究了含独居石和氟碳铈镧矿的混合稀土精矿在100～1000 ℃焙烧过程中, 添加CaO, NaCl时, REPO4和REFCO3的分解反应. 研究结果表明: 不添加CaO和NaCl时, 仅在377～450 ℃范围内存在REFCO3的分解反应, 其产物是REOF, RE2O3, 以及Ce2O3进一步的氧化产物CeO2, 而REPO4不分解; 添加CaO后在660～750 ℃之间, CaO有3种分解作用: (1) CaO分解REPO4, 其产物是RE2O3和Ca3(PO4)2. (2) CaO分解REOF, 其产物是RE2O3和CaF2. (3) CaO和REOF的分解产物CaF2共同作用分解REPO4, 其分解产物为RE2O3, Ca5F(PO4)3; 添加CaO, NaCl后, 混合精矿的分解率明显提高, NaCl的作用是为反应体系提供了液相, 促进了固相反应物间的传质过程, 加快了反应速度. 与此同时NaCl还可能参加了CaO分解REPO4的反应.