Chemistry
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Item 5-G MD Simulations(Wiley VCH, 2022) Lewis, Jared C.; Roux, Benoit; Li, Ying; Upp, DavidSee https://doi.org/10.1002/anie.202107982 An excerpt from the experimental of that manuscript is provided here: To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D. MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 3/2 100 3/2 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size. Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24Item A Top-Down/Bottom-Up Study of the Ribosomal Proteins of Caulobacter crescentus(Journal of Proteome Research, 2007) Running, W. E.; Ravipaty, S.; Karty, Jonathan; Reilly, J. P.Ribosomes from the Gram-negative α-proteobacterium Caulobacter crescentus were isolated using standard methods. Proteins were separated using a two-dimensional liquid chromatographic system that allowed the analysis of whole proteins by direct coupling to an ESI-QTOF mass spectrometer and of proteolytic digests by a number of mass spectrometric methods. The masses of 53 of 54 ribosomal proteins were directly measured. Protein identifications and proposed post-translational modifications were supported by proteolysis with trypsin, endoprotease Glu-C, and exoproteases carboxypeptidases Y and P. Tryptic peptide mass maps show an average sequence coverage of 62%, and carboxypeptidase C-terminal sequence tagging provided unambiguous identification of the small, highly basic proteins of the large subunit. C. crescentus presents some post-translational modifications that are similar to those of Escherichia coli (e.g., N-terminal acetylation of S9 and S18) along with some unique variations, such as a near absence of L7 and extensive modification of L11. The comprehensive description of this organism's ribosomal proteome provides a foundation for the study of ribosome structure, dependence of post-translational modifications on growth conditions, and the evolution of subcellular organelles.Item Activation of Atmospheric Small Molecules by Transition Metals(2004) Kilgore, UriahItem Activity of the tetrapyrrole regulator CrtJ is controlled by oxidation of a redox active cysteine located in the DNA binding domain(Molecular Microbiology, 2012) Cheng, Z.; Wu, J.; Setterdahl, A.; Reddie, K.; Carroll, K.; Hammad, L.A.; Karty, Jonathan; Bauer, C.E.CrtJ from Rhodobacter capsulatus is a regulator of genes involved in the biosynthesis of haem, bacteriochlorophyll, carotenoids as well as structural proteins of the light harvesting-II complex. Fluorescence anisotropy-based DNA-binding analysis demonstrates that oxidized CrtJ exhibits ??20-fold increase in binding affinity over that of reduced CrtJ. Liquid chromatography electrospray tandem ionization mass spectrometric analysis using DAz-2, a sulfenic acid (-SOH)-specific probe, demonstrates that exposure of CrtJ to oxygen or to hydrogen peroxide leads to significant accumulation of a sulfenic acid derivative of Cys420 which is located in the helix-turn-helix (HTH) motif. In vivo labelling with 4-(3-azidopropyl)cyclohexane-1,3-dione (DAz-2) shows that Cys420 also forms a sulfenic acid modification in vivo when cells are exposed to oxygen. Moreover, a Cys420 to Ala mutation leads to a ∼ 60-fold reduction of DNA binding activity while a Cys to Ser substitution at position 420 that mimics a cysteine sulfenic acid results in a ∼ 4-fold increase in DNA binding activity. These results provide the first example where sulfenic acid oxidation of a cysteine in a HTH-motif leads to differential effects on gene expression.Item 𝑛-alkanes on MgO(100). I. Coverage-dependent desorption kinetics of 𝑛-butane(Journal of Chemical Physics, 2005-04-27) Tait, Steven; Dohnálek, Zdenek; Campbell, Charles; Kay, BruceItem 𝑛-alkanes on MgO(100). II. Chain length dependence of kinetic desorption parameters for small 𝑛-alkanes(The Journal of Chemical Physics, 2005) Tait, Steven; Dohnalek, Zdenek; Campbell, Charles T.; Kay Bruce D.Item 𝑛-alkanes on Pt(111) and on C(0001) / Pt(111): Chain length dependence of kinetic desorption parameters(The Journal of Chemical Physics, 2006) Tait, Steven; Dohnalek, Zdenek; Campbell, Charles T.; Kay Bruce D.Item The art of stacking: structural folding and self-assembly of branched p-conjugation assisted by O–H...O and C–H...F hydrogen bonds(Royal Society of Chemistry, 2010-10-11) Lee, Dongwhan; Park, Hyunsoo; Pink, Maren; Olasz, Andras; Lee, Ho YongAn intimate interplay of O–H O/C–H F hydrogen bonds and p–p stacking interactions allows a phenyleneethynylene based dendritic molecule to fold and self-assemble into two distinctively different molecular crystals as pseudopolymorphs.Item Automated, Multistep Continuous-Flow Synthesis of 2,6-Dideoxy and 3-Amino-2,3,6-trideoxy Monosaccharide Building Blocks(2021) Subbarao, Yalamanchili; Nguyen, Tu-Anh; Zsikla, Alexander; Stamper, Gavin; DeYong, Ashley; Florek, John; Vasquez, Olivea; Pohl, Nicola; Bennett, ClayAn automated continuous flow system capable of producing protected deoxy-sugar donors from commercial material is described. Four 2,6-dideoxy and two 3-amino-2,3,6-trideoxy sugars with orthogonal protecting groups were synthesized in 11-32% overall yields in 74-131.5 minutes of total reaction time. Several of the reactions were able to be concatenated into a continuous process, avoiding the need for chromatographic purification of intermediates. The modular nature of the experimental setup allowed for reaction streams to be split into different lines for the parallel synthesis of multiple donors. Further, the continuous flow processes were fully automated and described through the design of an open-source Python-controlled automation platform.Item A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics(Mary Ann Liebert, Inc., 2009-08-18) Tang, Haixu; Sheng, Quanhu; Radivojac, Predrag; Li, Yixue; Arnold, Randy J.; Li, Yong FugaThe protein inference problem represents a major challenge in shotgun proteomics. In this article, we describe a novel Bayesian approach to address this challenge by incorporating the predicted peptide detectabilities as the prior probabilities of peptide identification. We propose a rigorous probabilistic model for protein inference and provide practical algorithmic solutions to this problem. We used a complex synthetic protein mixture to test our method and obtained promising results.Item Bistable [2]Catenate-Based Functional Surfaces(2005) McNitt, KristyItem Bronsted Acid-Promoted Olefin Anti-Dihydroxylation(2004) Hong, Ki BumItem Capillary electrophoresis–mass spectrometry for direct structural identification of serum N-glycans(Journal of Chromatography A, 2017) Fonslow, Bryan; Jacobson, Stephen; Karty, Jonathan; Novotny, Milos; Snyder, Christa; Zhou, XiaomeiItem Charge Detection Mass Spectrometry(2005) Maze, JoshuaItem Chelation-induced diradical formation as an approach to modulation of the amyloid-b aggregation pathway(Chemical Science, 2015) Karty, Jonathan; Kochi, Akiko; Lim, Mi Hee; Porter, Meghan; Zaleski, JeffreyItem Chemistry of Mixed Donor Pincer Ligand Nickel Complexes(2005) Fullmer, BenjaminItem Cloning/Expression of TGF-beta Signal Antagonist Smad6/Smad7(2005) Tatge, Tim