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Samples of papers artificially (2 to 60 days) and naturally (10, 45, and 56 years) aged were studied by the Py-GC/MS method to identify decomposition products. Possible reaction scenarios for cellulose degradation were developed. One of the degradation products is acetic acid, which can (auto)catalyze the cleavage of cellulose β(1→4)-glycosidic bonds of cellulose polymer chains. However, during 20 s of Py-GC/MS analysis, temperatures of up to 300 °C did not significantly increase or modify the formation of decomposition products of paper components. At 300 °C, the amount of several cellulose decomposition products increased regularly depending on the number of days of artificial aging and natural aging, demonstrated mainly by the generation of 2-furancarboxaldehyde, 5-hydroxymethylfurfural, and levoglucosan and its consecutive dehydration products. No correlation between the amount of lignin decomposition products and the time of aging was found when the pyrolysis was performed at 300 °C and 500 °C. Compounds present in the products of decomposition at 500 °C bear the imprint of the chemical composition of the sampled paper. Pyrograms taken at 300 °C using the Py-GC/MS method can give additional information on the changes in the chemical structure of paper during natural or artificial aging, mainly about the cleavage of β(1→4)-glycosidic bonds during aging.

In Europe, the use of aluminium(III) compounds, namely AlK(SO 4 ) 2 ·12H 2 O and later on Al 2 (SO 4 ) 3 ·18H 2 O for hardening gelatin sizes was recorded as early as the 16th century. This review is focused on the critical assessment of published data concerning the following chemical aspects of paper degradation: direct influence of H 3 O + ions formed during hydrolysis of aluminium(III) species; influence of low-molecular organic acids formed within degradation processes; influence of pH variation on the redox potential of reactive oxygen species acting as oxidizing agent; consequences of the absorption of gaseous NO 2 and SO 2 present in the air for paper degradation; involvement of aluminium species in redox radical oxidation catalytic processes; possible effect of the coordination of Al(III) with small radius and high charge on oxygen atoms of cellulose carboxyl or hydroxyl groups. It is indicated how the understanding of the above mentioned effects can help slow down paper degradation., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Online vendors are offering a new legal high, 4-methylpentedrone (4-MPD). Information for potential users provided by internet vendors of 4-MPD includes incorrect structures and nonexistent CAS numbers. A sample of 4-MPD was obtained and analyzed using GC-MS, NMR, and LC-EIS. The fragmentation data from the GC-MS and LC-EIS produced an M-1 ion that suggested the molecular mass was 219 amu, rather than 205 amu as calculated for 4-methylpentedrone. The difference in molecular mass corresponded to the addition of a methyl group. Based on the mass and fragmentation pattern, two standards were synthesized, 2-(ethylamino)-1-(4-methylphenyl)-1-pentanone and 1-(4-methylphenyl)-2-(propylamino)-1-butanone. The synthesis involved bromination of the appropriate ketone followed by the reaction with ethylamine or propylamine. Based on the NMR data and unique fragmentation patterns produced by these molecules, the sample was identified as 2-(ethylamino)-1-(4-methylphenyl)-1-pentanone, not 4-methylpentedrone., (© 2015 American Academy of Forensic Sciences.)

In this study, we developed a novel synthesis method to create a complex collagen-based biopolymer that promises to possess the necessary material properties for a bone graft substitute. The synthesis was carried out in several steps. In the first step, a ring-opening polymerization reaction initiated by hydroxyapatite nanoparticles was used to polymerize d,l-lactide and glycolide monomers to form poly(lactide-co-glycolide) co-polymer. In the second step, the polymerization product was coupled with succinic anhydride, and subsequently was reacted with N-hydroxysuccinimide in the presence of dicyclohexylcarbodiimide as the cross-linking agent, in order to activate the co-polymer for collagen attachment. In the third and final step, the activated co-polymer was attached to calf skin collagen type I, in hydrochloric acid/phosphate buffer solution and the precipitated co-polymer with attached collagen was isolated. The synthesis was monitored by proton nuclear magnetic resonance, infrared and Raman spectroscopies, and the products after each step were characterized by thermal and mechanical analysis. Calculations of the relative amounts of the various components, coupled with initial dynamic mechanical analysis testing of the resulting biopolymer, afforded a preliminary assessment of the structure of the complex biomaterial formed by this novel polymerization process., (Copyright © 2015. Published by Elsevier Ltd.)

Recent advances in our understanding of translational dynamics indicate that codon usage and mRNA secondary structure influence translation and protein folding. The most frequent cause of cystic fibrosis (CF) is the deletion of three nucleotides (CTT) from the cystic fibrosis transmembrane conductance regulator (CFTR) gene that includes the last cytosine (C) of isoleucine 507 (Ile507ATC) and the two thymidines (T) of phenylalanine 508 (Phe508TTT) codons. The consequences of the deletion are the loss of phenylalanine at the 508 position of the CFTR protein (DeltaF508), a synonymous codon change for isoleucine 507 (Ile507ATT), and protein misfolding. Here we demonstrate that the DeltaF508 mutation alters the secondary structure of the CFTR mRNA. Molecular modeling predicts and RNase assays support the presence of two enlarged single stranded loops in the DeltaF508 CFTR mRNA in the vicinity of the mutation. The consequence of DeltaF508 CFTR mRNA "misfolding" is decreased translational rate. A synonymous single nucleotide variant of the DeltaF508 CFTR (Ile507ATC), that could exist naturally if Phe-508 was encoded by TTC, has wild type-like mRNA structure, and enhanced expression levels when compared with native DeltaF508 CFTR. Because CFTR folding is predominantly cotranslational, changes in translational dynamics may promote DeltaF508 CFTR misfolding. Therefore, we propose that mRNA "misfolding" contributes to DeltaF508 CFTR protein misfolding and consequently to the severity of the human DeltaF508 phenotype. Our studies suggest that in addition to modifier genes, SNPs may also contribute to the differences observed in the symptoms of various DeltaF508 homozygous CF patients.

Most cases of cystic fibrosis (CF) are caused by mutations that block the biosynthetic maturation of the CF gene product, the CF transmembrane conductance regulator (CFTR) chloride channel. CFTR-processing mutants fail to escape the endoplasmic reticulum and are rapidly degraded. Current efforts to induce the maturation of CFTR mutants target components of the biosynthetic pathway (e.g., chaperones) rather than CFTR per se. Such methods are inherently nonspecific. Here we show that the most common CF-causing mutant (DeltaF508-CFTR) can form mature, functional chloride channels that reach the cell surface when coexpressed with several other CFTR-processing mutants or with amino fragments of the wild-type CFTR protein. This transcomplementation effect required a specific match between the region flanking the disease-causing mutation and the complementing fragment; e.g., amino fragments complemented DeltaF508-CFTR but not H1085R (a carboxy-processing mutant), whereas a carboxy fragment complemented H1085R but not DeltaF508-CFTR. Transcomplementing fragments did not affect CFTR interactions with Hsc70, a chaperone previously implicated in CFTR biosynthesis. Instead, they may promote CFTR maturation by blocking nonproductive interactions between domains within the same or neighboring CFTR polypeptides that prevent normal processing. These findings indicate that it may be possible to develop CF therapies (e.g., mini-cDNA constructs for gene therapy) that are tailored to specific disease-causing mutants of CFTR.

Use of a room temperature ionic liquid as the medium for conventional free radical copolymerization of styrene and methyl methacrylate resulted in reactivity ratios that were significantly different from those obtained in conventional organic solvents or in bulk, demonstrating that polymerization in this alternative medium offers potential to create copolymers having new monomer sequences.

We report the high-resolution solution structure of the 6.3 kDa neurotoxic protein CsE-v5 from the scorpion Centruroides sculpturatus Ewing (CsE, range southwestern U.S.). This protein is the second example of an Old World-like neurotoxin isolated from the venom of this New World scorpion. However, unlike CsE-V, which is the first Old World-like toxin isolated and shows both anti-insect and anti-mammal activity, CsE-v5 shows high specificity for insect sodium channels. Sequence-specific proton NMR assignments and distance and angle constraints were obtained from 600 MHz 2D-NMR data. Distance geometry and dynamical simulated annealing refinements were performed to produce a final family of 20 structures without constraint violations, along with an energy-minimized average structure. The protein structure is well-defined (0.66 and 0.97 D rmsd for backbone and all heavy atoms, respectively) with a compact hydrophobic core and several extending loops. A large hydrophobic patch, containing four aromatic rings and other aliphatic residues, makes up a large area of one side of the protein. CsE-v5 shows secondary structural features characteristic of long-chain scorpion toxins: a two and a half-turn alpha-helix, a three-strand antiparallel beta-sheet, and four beta-turns. Among the proteins studied to date from the CsE venom, CsE-v5 is the most compact protein with nearly 50% of the amide protons having long exchange lifetimes, but CsE-v5 is unusual in that it has loop structures similar to both Old and New World toxins. Further, it also lacks prolines in its C-terminal 14 residues. It shows some important differences with respect to CsE-V not only in its primary sequence, but also in its electrostatic potential surface, especially around areas in register with residues 8, 9, 17, 18, 32, 43, and 57. The loss of anti-mammal activity in CsE-v5 and the differences in its anti-insect activity compared to that of other proteins such as CsE-V, v1, and v3 from this New World scorpion may be related to residue variations at these locations.

Alkaline hydrolysis of corneal proteins in the alkali-injured eye releases N-acetyl-proline-glycine-proline (Ac-Pro-Gly-Pro-OH) among other peptides. It has been shown that this tripeptide is a neutrophil chemoattractant. Existing data suggest that the release of this peptide is the catalytic event for early neutrophil invasion of the cornea leading to corneal ulcers. In order to design inhibitors of this tripeptide chemoattractant that would block neutrophil invasion and diminish corneal ulcers, we studied the solution properties of this tripeptide by NMR spectroscopy and compared this peptide to Ac-Pro-Gly-OH (a weaker chemoattractant), and to Ac-Pro-OH (inactive). The NMR data were consistent with Ac-Pro-Gly-Pro-OH existing in solution as a mixture of four isomers with different cis and trans conformations about the two X-proline amide bonds. The isomer with two trans conformations (trans-trans) was the most dominant (41%) in aqueous solution. This was followed by the isomers with mixed cis and trans conformations (trans-cis, 26% and cis-trans, 20%). The isomer with two cis conformations (cis-cis) was the least favored (13%). The populations of these isomers were investigated in DMSO and they were similar to those reported in aqueous solutions except that the ordering of the trans-cis and cis-trans isomers were reversed. NMR NH temperature coefficients and nuclear Overhauser effect (NOE) measurements as well as CD spectroscopy were used to demonstrate that the four isomers exist primarily in an extended conformation with little hydrogen bonding. The available (NOE) information was used with molecular dynamics calculations to construct a dominant solution conformation for each isomer of the tripeptide. This information will serve as a model for the design of peptide and nonpeptide inhibitors of the chemoattractant., (Copyright 2001 John Wiley & Sons, Inc. Biopolymers 58: 548-561, 2001)

The 3D NMR structures of the scorpion neurotoxin, CsE-v5, were determined from the same NOESY spectra with NOAH/DIAMOD, an automated assignment and 3D structure calculation software package, and with a conventional manual assignment combined with a distance geometry/simulated annealing (X-PLOR) refinement method. The NOESY assignments and the 3D structures obtained from the two independent methods were compared in detail. The NOAH/DIAMOD program suite uses feedback filtering and self-correcting distance geometry methods to automatically assign NOESY spectra and to calculate the 3D structure of a protein. NOESY cross peaks were automatically picked using a standard software package and combined with 74 manually assigned NOESY peaks to start the NOAH/DIAMOD calculations. After 63 NOAH/DIAMOD cycles, using REDAC procedures in the last 8 cycles, and final FANTOM constrained energy minimization, a bundle of 20 structures with the smallest target functions has a RMSD of 0.81 A for backbone atoms and 1.11 A for all heavy atoms to the mean structure. Despite some missing chemical shifts of side chain protons, 776 (including 74 manually assigned) of 1130 NOE peaks were unambiguously assigned, 150 peaks have more than one possible assignment compatible with the bundle structures, and only 30 peaks could not be assigned within the given chemical shift tolerance ranges in either the D1 or the D2 dimension. The remaining 174, mainly weak NOE peaks were not compatible with the final 20 best bundle structures at the last NOAH/DIAMOD cycle. The automatically determined structures agree well with the structures determined independently using the conventional method and the same NMR spectra, with the mean RMSD in well-defined regions of 0.84 A for bb and 1.48 A for all heavy atoms from residues 2-5, 18-26, 32-36, and 39-45. This study demonstrates the potential of the NOAH/DIAMOD program suite to automatically assign NMR data for proteins and determine their structure., (Copyright 2001 Academic Press.)

We report the detailed solution structure of the 7.2 kDa protein CsE-I, a beta-neurotoxin from the New World scorpion Centruroides sculpturatus Ewing. This toxin binds to sodium channels, but unlike the alpha-neurotoxins, shifts the voltage of activation toward more negative potentials causing the membrane to fire spontaneously. Sequence-specific proton NMR assignments were made using 600 MHz 2D-NMR data. Distance geometry and dynamical simulated annealing refinements were performed using experimental distance and torsion angle constraints from NOESY and pH-COSY data. A family of 40 structures without constraint violations was generated, and an energy-minimized average structure was computed. The backbone conformation of the CsE-I toxin shows similar secondary structural features as the prototypical alpha-neurotoxin, CsE-v3, and is characterized by a short 2(1/2)-turn alpha-helix and a 3-strand antiparallel beta-sheet, both held together by disulfide bridges. The RMSD for the backbone atoms between CsE-I and CsE-v3 is 1.48 A. Despite this similarity in the overall backbone folding, the these two proteins show some important differences in the primary structure (sequence) and electrostatic potential surfaces. Our studies provide a basis for unravelling the role of these differences in relation to the known differences in the receptor sites on the voltage sensitive sodium channel for the alpha- and beta-neurotoxins., (Copyright 1999 Academic Press.)

Assembly of double-stranded DNA viruses and bacteriophages involves the polymerization of several hundred molecules of coat protein, directed by an internal scaffolding protein. A 163-amino acid carboxyl-terminal fragment of the 303-amino acid bacteriophage P22 scaffolding protein was cloned, overexpressed, and purified. This fragment is active in procapsid assembly reactions in vitro. The circular dichroism spectrum of the fragment, as well as the 1D-NMR and 15N-1H HSQC spectra of the uniformly-labeled protein, indicate that stable secondary structure elements are present. Determination of the three dimensional packing of these elements into the folded scaffolding protein fragment is underway. Structure-based drug design targeted at structural proteins required for viral assembly may have potential as a therapeutic strategy.

We have used 600 MHz 1H NMR spectroscopy data to determine the solution structure of a 31-residue domain of a murine class II major histocompatibility (MHC) protein. This domain, I-Ab(beta)-(60-90), binds to the superantigen staphylococcal enterotoxin A. Distance geometry and dynamical simulated annealing calculations were performed using NOESY- and COSY-deduced constraints. I-Ab(beta)-(60-90), which is mostly alpha-helical, is more similar to the corresponding region of the class II MHC protein HLA-DR1 than to the class I MHC protein HLA-A2. Arg-72 and Arg-80 lie on the same side of the helix and face away from the antigenic peptide binding groove. His-81, implicated in both superantigen and peptide binding, is located midway between the surface defined by Arg-72/Arg-80 and residues that define the inside of the peptide binding groove, allowing for its participation in both types of binding.

We have demonstrated previously that murine interferon-gamma (MuIFN-gamma) binds to the extracellular domain of the receptor alpha chain through its N-terminus and subsequently to the cytoplasmic domain of the receptor via its C-terminus. Binding of the C-terminus to the cytoplasmic domain of the receptor is thought to occur following endocytosis of the IFN-gamma-receptor complex. In fact, the MuIFN-gamma C-terminus peptide, MuIFN-gamma (95-133), has full agonist activity on macrophages where it is internalized through pinocytosis. Here we examine the structural elements required for the agonist activity of MuIFN-gamma (95-133). Disruption of the alpha helical structure of the peptide by proline substitutions or truncation of the helix resulted in significant loss of binding or loss of antiviral activity or both and induction of MHC class II molecules. Further, removal of the polycationic sequence RKRKR in the tail beyond the helical structure also resulted in loss of agonist activity. Thus, we have isolated the functional site on MuIFN-gamma to the C-terminus and have shown that its helical structure and polycationic tail are required for binding to the cytoplasmic domain of the receptor and induction of biologic activity.

We present complete 1H NMR assignments for two synthetic glycopeptides representative of the carbohydrate-protein linkage region of serglycin proteoglycans. The peptides are: Ser(Galp-Xylp)-Gly-Ser-Gly-Ser(Galp-Xylp)-Gly and, Ser(Galp-Xylp)-Gly-Ser(Galp-Xylp)-Gly-Ser(Galp-Xylp)-G ly. A number of 2D NMR spectra together with a 3D NOESY-TOCSY spectrum were acquired at 600 MHz to complete the assignments of the glycopeptides dissolved in water with 40% trifluoroethanol. Preliminary analysis of the NMR data suggests folded structures for the glycopeptides.

We have determined the solution structure of an alpha-toxin, CsE-V, isolated from the venom of the New World scorpion Centruroides sculpturatus Ewing (CsE). This toxin causes spontaneous rhythmic contractions in muscle. Unlike other New World toxins from CsE, this protein exhibits amino acid insertions and deletions at locations similar to Old World toxins and may thus represent a transition protein between the New World and Old World scorpion alpha-toxins. Sequence-specific assignments were made using 600 MHz 1H two-dimensional NMR data. NOESY, PH-COSY and amide-exchange data were used to deduce constraints for molecular modeling calculations. Distance geometry and dynamical simulated annealing calculations were performed to generate a family of 70 structures free of constraint violations. With respect to this family of structures, the energy-minimized average structure had root-mean-square deviations of 0.74 and 1.32 A for backbone and all atoms, respectively (excluding the C-terminal dipeptide, which is disordered). As with other scorpion toxins, the secondary structure of CsE-V consists of an alpha-helix, a three-strand anti-parallel beta-sheet, four beta-turns, and a hydrophobic patch that includes tyrosine residues in herringbone configuration. Unlike the CsE-v3 and -v1 proteins from C. sculpturatus, all of the proline residues were found to be in the trans configuration. The alpha-helix is slightly longer in CsE-V. The overall structure is more similar to the Old World alpha-toxin AaH-II from Androctonus australis Hector (r.m.s.d 1.59 A for backbone atoms of matching residues) than to the New World alpha-toxin CsE-v3 (r.m.s.d. 1.91 A). These structural data on CsE-V add further to our knowledge of the conformational repertoire exhibited by these sodium channel-binding neurotoxins.

The sequence-specific proton resonance assignments for the variant-1 (CsE-v1) neurotoxin from the venom of the New World scorpion Centruroides sculpturatus Ewing (range Southwestern United States) have been performed by 2D 1H NMR spectroscopy at 600 MHz. The stereospecific assignments for the beta-methylene protons of 19 non-proline residues have been determined. A number of short-, medium-, and long-range NOESY contacts as well as the backbone and the side-chain vicinal coupling constants for several residues have been determined. Slowly exchanging amide hydrogens from a number of residues have been identified. On the basis of the NMR data, the solution structure of this protein has been determined by a hybrid procedure consisting of distance geometry and dynamical simulated annealing refinement calculations. Distance constraints from the NOESY data and torsion angle constraints from proton vicinal coupling constant data were used in the simulated annealing calculations. The three-dimensional structure of CsE-v1 is characterized by a three-stranded antiparallel beta-sheet, a short alpha-helix, a cis-proline, and intervening loops. A comparison with the solution NMR data of a homologous protein (CsE-v3) from the Centruroides venom, shows that the structures are essentially similar, except for some minor differences. Some of the NMR spectral perturbations are felt in regions far removed from sites of amino acid substitutions. The hydrophobic surface in CsE-v1 is slightly more extended than in CsE-v3.

Nuclear magnetic resonance (NMR) spectra for [2-amino,3-15N2]folate and [2-13C]folate complexed with human dihydrofolate reductase, and for complexes of similarly labeled dihydrofolate, show that the N-3 proton of bound folate or dihydrofolate exchanges slowly with solvent and that the bound substrates are in the imino-keto tautomeric form. Previously proposed schemes for substrate protonation that require bound substrate to be in the enolic tautomer are therefore unlikely. The NMR spectra for bound folate are unchanged by raising the pH from 7 to 9.5, whereas those for free folate show marked changes due to ionization for the N-3 proton. The fraction of bound folate with the N-3 proton ionized at pH 9.5 is therefore very small, and the rate constant for the dissociation of the ionized species must be at least 320 times faster than for the protonated species. Comparison of NMR spectra over the pH range 5 to 7 gives no indication of a change in ionization state of the Glu30 carboxyl group over this pH range. This raises doubts about whether the apparent pKa of approximately 6 that describes pH dependence of hydride transfer is due to ionization of this carboxyl group.

Previous studies using synthetic peptides and monoclonal antibodies have implicated the N-terminal 39-residue segment as a receptor binding region of mouse gamma-interferon (MuIFN gamma). In this work, we report the solution structure of this fragment (dissolved in water with 40% trifluoroethanol) as determined by proton NMR spectroscopy. The proton sequence-specific assignments were determined from TOCSY and NOESY spectra using established procedures. The secondary structure is characterized by two well-defined alpha-helical regions composed of residues 5-16 and 22-37. These two helices are joined by a loop. No NOESY contacts between the two helical regions were detected. Molecular models consistent with the NMR data were generated for MuIFN gamma (1-39) using distance geometry and restrained molecular dynamics/energy minimization calculations. Comparison with similar N-terminal domains in the published NMR and crystallographic studies on the dimeric human and rabbit IFN gamma suggests some similarities in the structures except that the helical regions in the fragment are longer, and considerable variation may exist in the relative orientation of the two helices in the solution phase. The presence of stronger alpha N sequential NOE's suggests that this peptide is flexible. The absence of NOESY contacts involving the N-terminal tripeptide suggests that this region undergoes rapid segmental motion. The data presented here on MuIFN gamma (1-39), combined with the studies on human and rabbit IFN gamma, suggest that the N-terminal receptor binding domain of the protein can undergo structural changes, the understanding of which may provide insight into the basis for receptor interaction by this lymphokine.