Engineering topics
Publications and source records attributed to Michalczyk, Ryszard.
A nuclear magnetic resonance (NMR) system is configured to detect combinatorial signatures stemming from homonuclear and heteronuclear J-couplings. The system comprises a pre-polarization system, a detector, and NMR electronics, wherein the detector includes an NMR magnet with a magnetic field of strength between 300 mT and 10 μT.
A nuclear magnetic resonance (NMR) system is configured to detect chemical threat material. The system comprises a magnet configured to generate a magnetic field of about 300 millitesla or less; and a probe configured to detect nuclear relaxation of at least two nuclei selected from the group consisting of 1H, 19F, 31P and 14N, and detect the spin density of nuclei selected from the group consisting of 1H, 19F, 31P and 14N, following excitation.
Structured water-soluble and hetero-oligomeric peptoids: the importance of peptoid-specific backbone restrictions.
Isotopologues are molecular species differing only in their stable isotope composition. For example, the isotopologues of water include HOH , DOD , and HOD . The possibility of reactive azeotropy among isotopologues of the same molecule is explored within the ideal gas/ideal solution assumption. The chemical equilibrium enabling azeotropy may involve isotope exchange reactions or may involve more complicated dissociation/solvation chemistry. Azeotropy among isotopologues appears possible in the presence of isotope exchange reactions and with simple dissociation or combination reactions. However, for such chemical reactions, the isotope fractionation factors must be unity, that is, isotope ratios are identical in the vapor and liquid phases. This is not consistent with experimental observations that isotope fractionation factors can differ from unity at an azeotrope. More complex solvation chemistry, wherein the isotopic composition in the solvation shell differs slightly from that of the bulk solvent, can lead to an azeotrope for which the isotope fractionation factor is not unity. Possible azeotropy among the isotopologues of water is then considered. Experiments to directly quantify water isotopologue compositions at the elevated temperatures and pressures anticipated for azeotropy are described. Furthermore the paper concludes with a discussion of the potential impact of azotropic isotopologues on the azeotropic extraction and isotopic analysis of soil water and on the interpretation of isotopic signatures in geological and cosmological samples.
Protein–ligand conjugations are usually carried out in aqueous media in order to mimic the environment within which the conjugates will be used. Here, we focus on the conjugation of amphiphilic variants of elastin-like polypeptide (ELP), short elastin (sEL), to poorly water-soluble compounds like OPPVs (p-phenylenevinylene oligomers), triarylamines, and polypyridine-metal complexes. These conjugations are problematic when carried out in aqueous phase because hydrophobic ligands tend to avoid exposure to water, which in turn causes the ligand to self-aggregate and/or interact noncovalently with hydrophobic regions of the amphiphile. Ultimately, this behavior leads to low conjugation efficiency and contamination with strong noncovalent “conjugates”. After exploring the solubility of sEL in various organic solvents, we have established an efficient conjugation methodology for obtaining covalent conjugates virtually free of contaminating noncovalent complexes. When conjugating carboxylated ligands to the amphiphile amines, we demonstrate that even when only one amine (the N-terminus) is present, its derivatization is 98% efficient. When conjugating amine moieties to the amphiphile carboxyls (a problematic configuration), protein multimerization is avoided, 98–100% of the protein is conjugated, and the unreacted ligand is recovered in pure form. Our syntheses occur in “one pot”, and our purification procedure is a simple workup utilizing a combination of water and organic solvent extractions. This conjugation methodology might provide a solution to problems arising from solubility mismatch of protein and ligand, and it is likely to be widely applied for modification of recombinant amphiphiles used for drug delivery (PEG-antibodies, polymer-enzymes, food proteins), cell adhesion (collagen, hydrophobins), synthesis of nanostructures (peptides), and engineering of biocompatible optoelectronics (biological polymers), to cite a few.
We synthesized and characterized the title compound, (E)-1-(2,6-diisopropylphenyl)-2-phenyldiazine (I) using a combination of 1 H, 13 C, and 15 N NMR spectroscopy, infrared and UV/Vis spectroscopy, X-ray crystallography, and GC mass spectrometry. The solid-state structure is also reported. The unsymmetric azobenzene crystallizes in the space group P2 1 /c with unit cell parameters a = 8.001(7) Å, b = 17.827(16) Å, c = 11.129(10) Å, β = 101.960(10)°, V = 1553(2) Å 3 , Z = 4, D calc = 1.139 g/cm 3 .
( iPr PN H P)Mn(CO) 2 (OH) (2; iPr PN H P = HN{CH 2 CH 2 (P i Pr 2 )} 2 ) was formed from the reversible 1,2-addition of water to ( iPr PNP)Mn(CO) 2 (1; iPr PNP = the deprotonated, amide form of the ligand, –N{CH 2 CH 2 (P i Pr 2 )} 2 ). This reversible reaction was probed via variable-temperature NMR experiments, and the energetics of the 1,2-addition/elimination was found to be slightly exothermic (-0.8 kcal/mol). The corresponding manganese hydroxide was found to react with aldehydes, yielding the corresponding manganese carboxylate complexes ( iPr PN H P)Mn(CO) 2 (CO 2 R), where R = H, methyl, phenyl. While no reaction between 1 and neat benzaldehyde was observed, in the presence of water, conversion to the corresponding manganese-bound benzoate with formation of H 2 was observed. The catalytic oxidation of benzaldehyde by water without additives was unsuccessful due to strong product inhibition, with the manganese benzoate formed under a variety of reaction conditions. Upon addition of base, a catalytic cycle for the conversion of aldehyde to carboxylate and hydrogen can be devised.
Significance Enzymes find utility as therapeutics and for the production of specialty chemicals. Changing the amino acid sequence of an enzyme can increase solubility, but many such mutations disrupt catalytic activity. To evaluate this trade-off, we developed an experimental system to evaluate the relative solubility for nearly all possible single point mutants for two model enzymes. We find that the tendency for a given solubility-enhancing mutation to disrupt catalytic activity depends, among other factors, on how far the position is from the catalytic active site and whether that mutation has been sampled during evolution. We develop predictive models to identify mutations that enhance solubility without disrupting activity with an accuracy of 90%. These results have biotechnological applications.
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Synthetic metabolic pathways often suffer from low specific productivity, and new methods that quickly assess pathway functionality for many thousands of variants are urgently needed. Here we present an approach that enables the rapid and parallel determination of sequence effects on flux for complete gene-encoding sequences. We show that this method can be used to determine the effects of over 8000 single point mutants of a pyrolysis oil catabolic pathway implanted in Escherichia coli . Experimental sequence-function data sets predicted whether fitness-enhancing mutations to the enzyme levoglucosan kinase resulted from enhanced catalytic efficiency or enzyme stability. A structure of one design incorporating 38 mutations elucidated the structural basis of high fitness mutations. One design incorporating 15 beneficial mutations supported a 15-fold improvement in growth rate and greater than 24-fold improvement in enzyme activity relative to the starting pathway. Lastly, this technique can be extended to improve a wide variety of designed pathways.
The most abundant carbohydrate product of cellulosic biomass pyrolysis is the anhydrosugar levoglucosan (1,6-anhydro-β-d-glucopyranose), which can be converted to glucose 6-phosphate by levoglucosan kinase (LGK). In addition to the canonical kinase phosphotransfer reaction, the conversion requires cleavage of the 1,6-anhydro ring to allow ATP-dependent phosphorylation of the sugar O6 atom. Using x-ray crystallography, we show that LGK binds two magnesium ions in the active site that are additionally coordinated with the nucleotide and water molecules to result in ideal octahedral coordination. To further verify the metal binding sites, we co-crystallized LGK in the presence of manganese instead of magnesium and solved the structure de novo using the anomalous signal from four manganese atoms in the dimeric structure. The first metal is required for catalysis, whereas our work suggests that the second is either required or significantly promotes the catalytic rate. Although the enzyme binds its sugar substrate in a similar orientation to the structurally related 1,6-anhydro-N-acetylmuramic acid kinase (AnmK), it forms markedly fewer bonding interactions with the substrate. In this orientation, the sugar is in an optimal position to couple phosphorylation with ring cleavage. We also observed a second alternate binding orientation for levoglucosan, and in these structures, ADP was found to bind with lower affinity. These combined observations provide an explanation for the high Km of LGK for levoglucosan. Furthermore, greater knowledge of the factors that contribute to the catalytic efficiency of LGK can be used to improve applications of this enzyme for levoglucosan-derived biofuel production.
Proton transfer is a fundamental mechanism at the core of many enzyme-catalyzed reactions. It is also exquisitely sensitive to a number of factors, including pH, electrostatics, proper active-site geometry, and chemistry. Carbonic anhydrase has evolved a fast and efficient way to conduct protons through a combination of hydrophilic amino acid side chains that coordinate a highly ordered H-bonded water network. This study uses a powerful approach, combining NMR solution studies with neutron protein crystallography, to determine the effect of pH and divalent cations on key residues involved in proton transfer in human carbonic anhydrase. Lastly, the results have broad implications for our understanding of proton transfer and how subtle changes in ionization and H-bonding interactions can modulate enzyme catalysis.