Influence of Precipitants on Molecular Arrangements and Space Groups of Protein Crystals

In protein crystallization, precipitants are used to control the final protein concentration in the solution and/or to decrease the protein solubility for nucleation and growth. In this study, we obtained three crystal structures for the same kind of protein with three different crystallizing agents, in which one of the three different chemicals, ammonium sulfate, potassium sodium tartrate, and polyethylene glycol (PEG), was contained as a main precipitant. The space group of the protein crystal obtained by PEG was different from those obtained by the other two precipitants. Molecular dynamics simulations were carried out for the protein in the presence of each of the three precipitants at a concentration equivalent to the crystallizing condition or without any precipitant. The simulations showed that all of the three precipitants enhanced protein stability by decreasing the conformational fluctuation. The distribution of precipitant molecules was found to be not isotropic around the protein in every case. In the simulations with ammonium sulfate and potassium sodium tartrate, high-concentration areas of precipitants on the protein surface coincided with noncontact sites with other protein molecules in the crystals. In the simulations with PEG, low-concentration areas coincided with noncontact sites with other protein molecules in the crystal. The results suggest that precipitants play multiple roles not only of decreasing the protein solubility but also in restricting contact sites on the protein surface. This restriction is reflected in the molecular arrangement in protein crystals, thereby resulting in crystal growth with a specific space group

Theoretical Studies on the Unimolecular Decomposition of Ethylene Glycol

The unimolecular decomposition processes of ethylene glycol have been investigated with the QCISD(T) method with geometries optimized at the B3LYP/6-311++G(d,p) level. Among the decomposition channels identified, the H₂O-elimination channels have the lowest barriers, and the C–C bond dissociation is the lowest-energy dissociation channel among the barrierless reactions (the direct bond cleavage reactions). The temperature and pressure dependent rate constant calculations show that the H₂O-elimination reactions are predominant at low temperature, whereas at high temperature, the direct C–C bond dissociation reaction is dominant. At 1 atm, in the temperature range 500–2000 K, the calculated rate constant is expressed to be 7.63 × 10⁴⁷<i>T</i>^–10.38 exp(−42262/<i>T</i>) for the channel CH₂OHCH₂OH → CH₂CHOH + H₂O, and 2.48 × 10⁵¹<i>T</i>^–11.58 exp(−43593/<i>T</i>) for the channel CH₂OHCH₂OH → CH₃CHO + H₂O, whereas for the direct bond dissociation reaction CH₂OHCH₂OH → CH₂OH + CH₂OH the rate constant expression is 1.04 × 10⁷¹<i>T</i>^–16.16 exp(−52414/<i>T</i>)

A Dominant Factor for Structural Classification of Protein Crystals

With the increasing number of solved protein crystal structures, much information on protein shape and atom geometry has become available. It is of great interest to know the structural diversity for a single kind of protein. Our preliminary study suggested that multiple crystal structures of a single kind of protein can be classified into several groups from the viewpoint of structural similarity. In order to broadly examine this finding, cluster analysis was applied to the crystal structures of hemoglobin (Hb), myoglobin (Mb), human serum albumin (HSA), hen egg-white lysozyme (HEWL), and human immunodeficiency virus type 1 protease (HIV-1 PR), downloaded from the Protein Data Bank (PDB). As a result of classification by cluster analysis, 146 crystal structures of Hb were separated into five groups. The crystal structures of Mb (<i>n</i> = 284), HEWL (<i>n</i> = 336), HSA (<i>n</i> = 63), and HIV-1 PR (<i>n</i> = 488) were separated into six, five, three, and six groups, respectively. It was found that a major factor causing these structural separations is the space group of crystals and that crystallizing agents have an influence on the crystal structures. Amino acid mutation is a minor factor for the separation because no obvious point mutation making a specific cluster group was observed for the five kinds of proteins. In the classification of Hb and Mb, the species of protein source such as humans, rabbits, and mice is another significant factor. When the difference in amino sequence is large among species, the species of protein source is the primary factor causing cluster separation in the classification of crystal structures

Theoretical Studies on the Unimolecular Decomposition of Propanediols and Glycerol

Polyols, a typical type of alcohol containing multiple hydroxyl groups, are being regarded as a new generation of a green energy platform. In this paper, the decomposition mechanisms for three polyol molecules, i.e., 1,2-propanediol, 1,3-propanediol, and glycerol, have been investigated by quantum chemistry calculations. The potential energy surfaces of propanediols and glycerol have been built by the QCISD­(T) and CBS-QB3 methods, respectively. For the three molecules studied, the H₂O-elimination and C–C bond dissociation reactions show great importance among all of the unimolecular decomposition channels. Rate constant calculations further demonstrate that the H₂O-elimination reactions are predominant at low temperature and pressure, whereas the direct C–C bond dissociation reactions prevail at high temperature and pressure. The temperature and pressure dependence of calculated rate constants was demonstrated by the fitted Arrhenius equations. This work aims to better understand the thermal decomposition process of polyols and provide useful thermochemical and kinetic data for kinetic modeling of polyols-derived fuel combustion

Experimental and Modeling Investigation of <i>n</i>‑Decane Pyrolysis at Supercritical Pressures

The pyrolysis mechanism of fuel under supercritical conditions is an important concern for developing regenerative cooling technology of advanced aircraft using hydrocarbon fuel as the primary coolant. <i>n</i>-Decane as a component of some jet fuels was studied at the temperature range from 773 to 943 K in a flow reactor under the pressure of 3, 4, and 5 MPa. Gas chromatograph/mass spectrometry was used to analyze the pyrolysis products, which were mainly alkanes from C₁–C₉ and alkenes from C₂–C₉. A kinetic model containing 164 species and 842 reactions has been developed and validated by the experimental results including the distributions of products and the chemical heat sink of fuel. The decomposition pathways of <i>n</i>-decane were illustrated through the reaction flux analysis. It is concluded that the C₄–C₉ alkanes are mainly generated by the recombinations of alkyls, while the small alkanes (C₁–C₃) are formed by H-abstraction reactions by C₁–C₃ alkyl radicals. The applicability at supercritical pressure and high fuel concentration condition of previous models was discussed, and the performance of the present model in reproducing the experimental data is reasonably good

Functional role of polyproline motifs.

<p>(A) Occurrence of polyproline motifs in the first 50 residues is higher than elsewhere in the protein sequence (Mann-Whitney-Wilcoxon test, <i>p</i>-value < 2.2e-16; fold change 0.94 vs 0.78). Error bars indicate the standard deviation. (B) Occurrence of polyproline motifs is associated with domain boundaries. Regions with relatively high motif occurrence are marked red. Data are smoothed over a three-residue window. Left: frequency of motifs relative to domain start (dashed line). Right: frequency of motifs relative to domain end (dashed line). The enrichment of motifs in these two regions is significant (<i>p</i>-values < 0.05; fold changes 1.19 and 1.23). (C) Frequency of polyproline motifs relative to the start position of TMH. TMH is marked green (assuming the typical length of 21 residues). Regions with high motif frequency are marked red. Data are smoothed over a three-residue window. (D) Schematic illustration of the site III location relative to TMH and the non-transmembrane region. In protein A site III of TMH1 locates in the TMH2 while in protein B site III of TMH1 is in the non-transmembrane region.</p

Distribution and conservation of polyproline motifs.

<p>(A) Occurrence of polyproline motifs in <i>E</i>. <i>coli</i> K-12 MG1655 is lower than the random level (fold change 0.80). The histogram shows the numbers of motifs found in 1,000 sets of random sequences, and the blue line shows the number of motifs found in real sequences. (B) Numbers of polyproline motifs negatively correlate with the strength of the ribosome stalling effect in <i>E</i>. <i>coli</i> K-12 MG1655. The differences are significant according to Mann-Whitney-Wilcoxon test. (C) Occurrence of polyproline motifs in the core proteome of <i>E</i>. <i>coli</i> K-12 MG1655 is lower than that in the accessory proteome. The differences are significant according to Mann-Whitney-Wilcoxon test. (D) In the core proteome more aligned regions have a negative PSEC (chi-squared test) while in the accessory proteome PSEC values display no strong preference.</p

Evaluation of the Cross Section of Elongated Micelles by Static and Dynamic Light Scattering

We describe simultaneous static (SLS) and dynamic light scattering (DLS) measurements on dilute solutions of a series of poly­(ferrocenyldimethylsilane-<i>b</i>-isoprene) (PFS₅₀–PI₁₀₀₀) block copolymer micelles of uniform length in <i>tert</i>-butyl acetate (<i>t</i>BA) and in decane. The subscripts in the term PFS₅₀–PI₁₀₀₀ refer to the mean degree of polymerization of each block. The SLS experiments show that in both solvents the micelles formed are elongated and rigid. We also observed that the large length of the PI block (1000 units) contributes to the SLS signal. From the SLS data, we calculated the mass per unit length (linear aggregation number), as well as the cross section of the micelles in both solvents. Interestingly, the linear aggregation number and the micelle cross sections, as deduced by SLS, were the same in decane and in <i>t</i>BA. However, the fitting of DLS data indicates that the hydrodynamic cross section of the micelles in <i>t</i>BA is much larger than that in decane, and both values are larger than the values determined by SLS. We hypothesize that the difference between cross sections deduced from SLS and DLS data fitting is related to the shape of the segment density profile of the corona. In <i>t</i>BA, the PI chains are more stretched than in decane, increasing the hydrodynamic radius of the micelle cross section

Online Study on the Pyrolysis of Polypropylene over the HZSM‑5 Zeolite with Photoionization Time-of-Flight Mass Spectrometry

The production of hydrocarbons through the pyrolysis of polyolefins is a promising way of fuel recycling. In this work, online single-photon ionization time-of-flight mass spectrometry (SPI–TOFMS) was used to study both thermal and catalytic decompositions of polypropylene (PP) in a tubular furnace. SPI produces few or no fragments of molecular ions, making the identification and interpretation of complex pyrolysis products in real time possible. The mass spectra at different reaction temperatures and time-evolved profiles of selected species during the pyrolysis processes were measured. The pyrolysis products can be classified into three groups: alkenes, dienes, and aromatics. As the coke precursors, aromatics mainly composed of benzene, toluene, and xylene (BTX) were observed at a very low temperature of 300 °C with the presence of HZSM-5, which cannot be detected for pure PP until 700 °C, indicating that HZSM-5 can accelerate the coke formation. Because of the secondary reactions, different tendencies of product intensities were exhibited as the reaction temperature increased. In addition, in comparison of the time-evolved profiles of the alkenes and BTX under high temperatures, a two-stage catalytic degradation process taking place on the external surface and the micropores of HZSM-5 was verified. A degradation mechanism was also proposed for the pyrolysis of PP with a low HZSM-5 content based on the time-evolved profiles performed at a low temperature. This work demonstrates the good performance of SPI–TOFMS for the online study of the polymer pyrolysis as well as the evaluation of the catalyst

Experimental Study of a Fuel-Rich Premixed Toluene Flame at Low Pressure

A low-pressure premixed toluene/O₂/Ar flame with the equivalence ratio of 1.90 was investigated using tunable synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry. Combustion intermediates up to C₁₉H₁₂ were identified by the measurements of the photoionization mass spectrum and photoionization efficiency spectrum. Mole fraction profiles of flame species were evaluated from the scan of burner position at photon energies near ionization thresholds. Furthermore, flame temperature was recorded by a Pt/Pt-13%Rh thermocouple. The comprehensive experimental data concerning the flame structure facilitate the discussion about the flame chemistry of toluene and other monocyclic aromatic fuels. Benzyl and benzene were found to be major primary intermediates of toluene degradation; and benzene is suggested to originate mainly from fuel degradation instead of radical recombination channels in fuel-rich monocyclic aromatic hydrocarbon flames. On the basis of the intermediate identification, comparison is made among the current mechanisms relevant to the formation of polycyclic aromatic hydrocarbons (PAHs). It is concluded that the molecular growth process in this flame is consistent with the synergy of the hydrogen-abstraction-carbon-addition (HACA) mechanism and the resonantly stabilized radical addition mechanism. In particular, the HACA mechanism can connect a great deal of aromatic intermediates observed in the present work and consequently explain the regular ring enlargement by consecutive addition of 2 or 4 carbon atoms, while the resonantly stabilized radical addition mechanism may have marked and sometimes predominant influences on the formation of many typical PAHs