2021
Acón M, Geiß C, Torres-Calvo J, Bravo-Estupiñan D, Oviedo G, Arias-Arias JL, Rojas-Matey LA, Baez E, Vásquez-Vargas G, Oses-Vargas Y, Guevara-Coto J, Segura-Castillo A, Siles-Canales F, Quirós-Barrantes S, Régnier-Vigouroux A, Mendes P, Mora-Rodríguez R (2021) MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer. iScience. 24:103407
Genetics
Biochemistry
Computational Method
Link
Chushak Y, Harbaugh S, Zimlich K, Alfred B, Chávez J, Kelley-Loughnane N (2021) Characterization of synthetic riboswitch in cell-free protein expression systems. RNA Biology doi:10.1080/15476286.2020.1868149
Biochemistry
Genetics
Link
Kleineberg C (2021) Bottom-up assembly of a light-driven ATP regeneration module in lipid, polymer and hybrid vesicles. Ph.D. Thesis, Otto-von-Guericke Universität Magdeburg, Germany.
Synthetic Biology
Biochemistry
Link
Novichkov AI, Hanopolskyi AI, Miao X, Shimon LJW, Diskin-Posner Y, Semenov SN (2021) Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization. Nature Communications 12:2994
Biochemistry
Link
Ritis D (2021) Dynamical modeling in biological networks. Masters Thesis, Democritus University of Thrace, Greece.
Biochemistry
Link
5 publications
2020
Barrett TM (2020) Thioamides and proteolysis: Examining the effects and applications of a single-atom substitution. PhD Thesis, University of Pennsylvania.
Biochemistry
Link
Benchoam D, Semelak JA, Cuevasanta E, Mastrogiovanni M, Grassano JS, Ferrer-Sueta G, Zeida A, Trujillo M, Möller MN, Estrin DA, Alvarez B (2020) Acidity and nucleophilic reactivity of glutathione persulfide. Journal of Biological Chemistry 295:15466–15481
Biochemistry
Link
Benedek Z, Papp M, Oláh J, Szilvási T (2020) Demonstrating the Direct Relationship between Hydrogen Evolution Reaction and Catalyst Deactivation in Synthetic Fe Nitrogenases. ACS Catalysis 10:12555–12568
Biochemistry
Link
Bragança CE, Kraut DA (2020) Mode of targeting to the proteasome determines GFP fate. Journal of Biological Chemistry 295:15892–15901
Biochemistry
Link
Fournié M, Truan G (2020) Multiplicity of carotene patterns derives from competition between phytoene desaturase diversification and biological environments. Scientific Reports 10:21106
Biochemistry
Metabolism
Link
Padayachee L, Rohwer JM, Pillay CS (2020) The thioredoxin redox potential and redox charge are surrogate measures for flux in the thioredoxin system. Archives of Biochemistry and Biophysics 680:108231
Biochemistry
Metabolism
Link
Schmallegger M, Barbon A, Bortolus M, Chemelli A, Bilkis I, Gescheidt G, Weiner L (2020) Systematic Quantification of Electron Transfer in a Bare Phospholipid Membrane Using Nitroxide-Labeled Stearic Acids: Distance Dependence, Kinetics, and Activation Parameters. Langmuir 36:10429–10437
Biophysics
Biochemistry
Link
Vasil’ev RF, Kancheva VD, Naumov VV, Slavova-Kazakova AK, Trofimov AV, Fedorova GF, Yablonskaya OI (2020) Extreme Kinetics of Chemiluminescence in the Initiated Oxidation of Vegetable Lipids. Russian Journal of Physical Chemistry B 14:479–482
Biochemistry
Link
Zhu H, Poojary MM, Andersen ML, Lund MN (2020) The effect of molecular structure of polyphenols on the kinetics of the trapping reactions with methylglyoxal. Food Chemistry 319:126500
Biochemistry
Link
9 publications
2019
Adelson CN, Johnston EM, Hilmer KM, Watts H, Dey SG, Brown DE, Broderick JB, Shepard EM, Dooley DM, Solomon EI (2019) Characterization of the Preprocessed Copper Site Equilibrium in Amine Oxidase and Assignment of the Reactive Copper Site in Topaquinone Biogenesis. Journal of the American Chemical Society 141:8877–8890
Enzymology
Biochemistry
Link
Faraj SE, Noguera ME, Delfino JM, Santos J (2019) Global Implications of Local Unfolding Phenomena, Probed by Cysteine Reactivity in Human Frataxin. Scientific Reports 9:1–12
Biochemistry
Link
Hochberg D, Ribó JM (2019) Entropic Analysis of Mirror Symmetry Breaking in Chiral Hypercycles. Life 9:28
Biochemistry
Link
Macikova L, Sinica V, Kadkova A, Villette S, Ciaccafava A, Faherty J, Lecomte S, Alves ID, Vlachova V (2019) Putative interaction site for membrane phospholipids controls activation of TRPA1 channel at physiological membrane potentials. FEBS Journal 286:3664–3683
Signaling
Biochemistry
Link
Möller MN, Denicola A (2019) Acceleration of the autoxidation of nitric oxide by proteins. Nitric Oxide: Biology and Chemistry 85:28–34
Biochemistry
Link
Muth M, Jänsch N, Kopranovic A, Krämer A, Wössner N, Jung M, Kirschhöfer F, Brenner-Weiß G, Meyer-Almes F-J (2019) Covalent inhibition of histone deacetylase 8 by 3,4-dihydro-2H-pyrimido[1,2-c][1,3]benzothiazin-6-imine. Biochimica et Biophysica Acta (BBA) - General Subjects 1863:577–585
Enzymology
Biochemistry
Link
Pawłowski PH, Szczęsny P, Rempoła B, Poznańska A, Poznański J (2019) Combined in silico and 19F NMR analysis of 5-fluorouracil metabolism in yeast at low ATP conditions. Bioscience Reports 39 9:BSR20192847
Biochemistry
Link
Reader P (2019) in vitro Characterisation of the Complement Cascade for Predicting Patient Outcome Post-operatively. Ph.D. Thesis, University of Exeter
Biochemistry
Physiology
Link
Sheppard S, Dikicioglu D (2019) Dynamic modelling of the killing mechanism of action by virus-infected yeasts. Journal of the Royal Society Interface 16:20190064
Biochemistry
Signaling
Link
Taheri M, Nouri K, Asgari Y, Zabihinpour Z, Sadeghi M (2019) The Significance of Noise in the Evolution of Negative and Positive Cooperativity in Protein Complexes. MATCH Communications in Mathematical and Computer Chemistry 81:177–192
Biochemistry
Macromolecular Biochemistry
Link
Virtanen O, Valev D, Kruse O, Wobbe L, TYYSTJÄRVI E (2019) Photoinhibition and continuous growth of the wild-type and a high-light tolerant strain of Chlamydomonas reinhardtii. Photosynthetica 57:617–626
Biochemistry
Microbiology
Link
Yu T (2019) Oxidative Protein Folding: Investigating New Enzymes, New Assays, and New Locations. PhD Thesis, University of Delaware.
Biochemistry
Link
12 publications
2018
Carpine R, Raganati F, Olivieri G, Hellingwerf KJ, Pollio A, Salatino P, Marzocchella A (2018) Poly-β-hydroxybutyrate (PHB) production by Synechocystis PCC6803 from CO2: Model development. Algal Research 29:49–60
Microbiology
Biochemistry
Link
Coulthard SA, McGarrity S, Sahota K, Berry P, Redfern CP (2018) Three Faces of Mercaptopurine Cytotoxicity in vitro: Methylation, Nucleotide Homeostasis and Deoxythioguanosine in DNA. Drug Metabolism and Disposition 46:1191–1199
Toxicology
Biochemistry
Link
da Silva, LHG (2018) Self-Replication and Non-enzymatic Catalytic Networks subject to Open Flow. MS Thesis, University of Porto.
Biochemistry
Theory
Link
da Silva LHG, Hochberg D (2018) Open flow non-enzymatic template catalysis and replication. Physical Chemistry Chemical Physics 20:14864–14875
Biochemistry
Link
Fiebig D, Storka J, Roeder M, Meyners C, Schmelz S, Blankenfeldt W, Scrima A, Kolmar H, Fuchsbauer H-L (2018) Destructive twisting of neutral metalloproteases: the catalysis mechanism of the Dispase autolysis-inducing protein from Streptomyces mobaraensis DSM 40487. FEBS Journal 285:4246–4264
Biochemistry
Link
Haffez H, Chisholm DR, Tatum NJ, Valentine R, Redfern C, Pohl E, Whiting A, Przyborski S (2018) Probing biological activity through structural modelling of ligand-receptor interactions of 2,4-disubstituted thiazole retinoids. Bioorganic & Medicinal Chemistry 26:1560–1572
Biochemistry
Link
Kaushik AC, Kumar A, Dwivedi VD, Bharadwaj S, Kumar S, Bharti K, Kumar P, Chaudhary RK, Mishra SK (2018) Deciphering the Biochemical Pathway and Pharmacokinetic Study of Amyloid βeta-42 with Superparamagnetic Iron Oxide Nanoparticles (SPIONs) Using Systems Biology Approach. Molecular Neurobiology 55:3224–3236
Biochemistry
Pharmacology
Laboratory Method
Link
Rossi F., Torbensen K., Ristori S., Abou-Hassan A. (2018) Signal Transduction and Communication Through Model Membranes in Networks of Coupled Chemical Oscillators. In: Pelillo M., Poli I., Roli A., Serra R., Slanzi D., Villani M. (eds.) Artificial Life and Evolutionary Computation. WIVACE 2017. Communications in Computer and Information Science, vol 830. Springer
Biochemistry
Signaling
Link
Semenov SN, Ainla A, Skorb EV, Postma SG (2018) Four-Variable Model of an Enzymatic Oscillator Based on Trypsin. Israel Journal of Chemistry 58:781–786
Biochemistry
Link
Wang M, Wölfer C, Otrin L, Ivanov I, Vidaković-Koch T, Sundmacher K (2018) Transmembrane NADH Oxidation with Tetracyanoquinodimethane. Langmuir 34:5435–5443
Biochemistry
Biotechnology
Link
Ximing L (2018) Insights into Delivery of Somatic Calcium Signals to the Nucleus During LTP Revealed by Computational Modeling. PhD Thesis, Ohio University
Signaling
Biochemistry
Link
Xu H, Curtis TY, Powers SJ, Raffan S, Gao R, Huang J, Heiner M, Gilbert DR, Halford NG (2018) Genomic, biochemical and modelling analyses of asparagine synthetases from wheat. Frontiers in Plant Science 8:2237
Biochemistry
Link
Yeom K-H, Mitchell S, Linares AJ, Zheng S, Lin C-H, Wang X-J, Hoffmann A, Black DL (2018) Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proceedings of the National Academy of Sciences USA 115:E11061–E11070
Genetics
Biochemistry
Link
13 publications
2017
Amdahl MB, Sparacino-Watkins CE, Corti P, Gladwin MT, Tejero J (2017) Efficient Reduction of Vertebrate Cytoglobins by the Cytochrome b 5/Cytochrome b 5 Reductase/NADH System. Biochemistry 56:3993–4004
Biochemistry
Enzymology
Link
Haffez H, Chisholm DR, Valentine R, Pohl E, Redfern C, Whiting A (2017) The molecular basis of the interactions between synthetic retinoic acid analogues and the retinoic acid receptors. MedChemComm 8:578
Biochemistry
Pharmacology
Link
Orlenko A, Chi PB, Liberles DA (2017) Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways. BMC Evolutionary Biology 17:117
Biochemistry
Genetics
Link
Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT (2017) A proteomic approach to analyse the aspirin-mediated lysine acetylome. Molecular & Cellular Proteomics 16:310–326
Pharmacology
Biochemistry
Laboratory Method
Link
Tikidji-Hamburyan A, Reinhard K, Storchi R, Dietter J, Seitter H, Davis KE, Idrees S, Mutter M, Walmsley L, Bedford RA, Ueffing M, Ala-Laurila P, Brown TM, Lucas RJ, Münch TA (2017) Rods progressively escape saturation to drive visual responses in daylight conditions. Nature Communications 8:1813
Biochemistry
Biophysics
Physiology
Link
Wang H, Ray JCJ (2017) Dynamical predictors of an imminent phenotypic switch in bacteria. Physical Biology 14:045007
Microbiology
Biochemistry
Link
Zaccarin M, Bosello-Travain V, Di Paolo ML, Falda M, Maiorino M, Miotto G, Piccolo S, Roveri A, Ursini F, Venerando R, Toppo S (2017) Redox status in a model of cancer stem cells. Archives of Biochemistry and Biophysics 617:120–128
Biochemistry
Cell Biology
Link
7 publications
2016
Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T (2016) Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science Advances 2:e1600823
Biochemistry
Signaling
Link
Haffez HRS (2016) Design, synthesis and biological evaluation of small molecules for controlling cellular development. PhD Thesis, Durham University, UK.
Biochemistry
Pharmacology
Link
Ledwitch KV, Barnes RW, Roberts AG (2016) Unravelling the complex drug–drug interactions of the cardiovascular drugs, verapamil and digoxin, with P-glycoprotein. Bioscience Reports 36:e00309
Pharmacology
Biochemistry
Link
Ledwitch KV, Gibbs ME, Barnes RW, Roberts AG (2016) Cooperativity between verapamil and ATP bound to the efflux transporter P-glycoprotein. Biochemical Pharmacology 118:96–108
Pharmacology
Biochemistry
Link
McClary WD (2016) Interactions of Cytochrome P450 3A4 with Phospholipid Bilayer Nanodiscs. PhD Thesis, Seattle, University of Washington.
Biochemistry
Macromolecular Biochemistry
Link
Olajuyigbe FM, Demitri N, De Zorzi R, Geremia S (2016) Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals. Molecules 21:1458
Biochemistry
Link
Reichard EL, Chirico GG, Dewey WJ, Nassif ND, Bard KE, Millas NE, Kraut DA (2016) Substrate Ubiquitination Controls the Unfolding Ability of the Proteasome. Journal of Biological Chemistry 291:18547–18561
Biochemistry
Macromolecular Biochemistry
Link
Rentergent J, Driscoll MD, Hay S (2016) Time course analysis of enzyme-catalyzed DNA polymerization. Biochemistry 55:5622–5634
Biochemistry
Enzymology
Macromolecular Biochemistry
Link
Semenov SN, Kraft LJ, Ainla A, Zhao M, Baghbanzadeh M, Campbell VE, Kang K, Fox JM, Whitesides GM (2016) Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions. Nature 537:656–660
Chemistry
Biochemistry
Link
Vranish JN, Das D, Barondeau DP (2016) Real-Time Kinetic Probes Support Monothiol Glutaredoxins As Intermediate Carriers in Fe–S Cluster Biosynthetic Pathways. ACS Chemical Biology 11:3114–3121
Enzymology
Biochemistry
Link
10 publications
2012
Hamberg A, Maurer S, Hult K (2012) Rational engineering of Candida antarctica lipase B for selective monoacylation of diols. Chemical Communications 48:10013
Biochemistry
Link
Kraut DA, Israeli E, Schrader EK, Patil A, Nakai K, Nanavati D, Inobe T, Matouschek A (2012) Sequence- and Species-Dependence of Proteasomal Processivity. ACS Chemical Biology 7:1444–1453
Biochemistry
Macromolecular Biochemistry
Link
Witmer JR (2012) Quantitative analysis and modeling of redox networks in biology. PhD Thesis, University of Iowa.
Biochemistry
Link
3 publications
2009
Friedrich A, Ghosh R, Kolb R, Herdtweck E, Schneider S (2009) Iridium Olefin Complexes Bearing Dialkylamino/amido PNP Pincer Ligands: Synthesis, Reactivity, and Solution Dynamics. Organometallics 28:708-718
Biochemistry
Link
Katzberg, M., Wechler, K., Müller, M., Dünkelmann, P., Stohrer, J., Hummel, W., & Bertau, M. (2009). Biocatalytical production of (5S)-hydroxy-2-hexanone. Organic and Biomolecular Chemistry 7:304-314
Biochemistry
Link
Kona F, Tao P, Martin P, Xu X, Gatti DL (2009) Electronic Structure of the Metal Center in the Cd 2+ , Zn 2+ , and Cu 2+ Substituted Forms of KDO8P Synthase: Implications for Catalysis. Biochemistry 48:3610–3630
Enzymology
Biochemistry
Link
3 publications
