COPASI's Use In Biochemistry


0 publication
Angeli L, Morozova K, Scampicchio M (2023) A kinetic-based stopped-flow DPPH• method. Scientific Reports 13:7621 Experimental Method Biochemistry Link
Cardozo G, Mastrogiovanni M, Zeida A, Viera N, Radi R, Reyes AM, Trujillo M (2023) Mitochondrial Peroxiredoxin 3 Is Rapidly Oxidized and Hyperoxidized by Fatty Acid Hydroperoxides. Antioxidants 12:408 Biochemistry Link
Ferreira MJ, Rodrigues TA, Pedrosa AG, Gales L, Salvador A, Francisco T, Azevedo JE (2023) The mammalian peroxisomal membrane is permeable to both GSH and GSSG – Implications for intraperoxisomal redox homeostasis. Redox Biology 63:102764 Biochemistry Link
Jannsen N, Jurrat J, Neumann H, Fischer C, Thede R, Heller D (2023) Major–minor concept revisited: causes for the reversal of thermodynamically determined intermediate ratios under reaction conditions. Catalysis Science & Technology 13:4498–4505 Chemistry Biochemistry Link
Katsyv A, Kumar A, Saura P, Pöverlein MC, Freibert SA, Stripp ST, Jain S, Gamiz-Hernandez AP, Kaila VRI, Müller V, Schuller JM (2023) Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC. Journal of the American Chemical Society 145:5696–5709 Enzymology Biochemistry Link
Korkola NC, Stillman MJ (2023) Structural Role of Cadmium and Zinc in Metallothionein Oxidation by Hydrogen Peroxide: The Resilience of Metal–Thiolate Clusters. Journal of the American Chemical Society 145:6383–6397 Biochemistry Link
Masison J, Mendes P (2023) Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics. PLoS One 18:e0281401 Biochemistry Link
Mattila H, Mishra S, Tyystjärvi T, Tyystjärvi E (2023) Singlet oxygen production by photosystem II is caused by misses of the oxygen evolving complex. The New Phytologist 237:113–125 Biochemistry Plant Biology Link
Naumov VV, Trofimov AV, Fedorova GF, Yablonskaya OI, Vasil’ev RF (2023) Kinetic Intricacies of the Light Emission and Antiradical Influence of Exogenous Bioantioxidants Transformation Products in the Chemiluminescence Bioantioxidant Assay. International Journal of Molecular Sciences 24:8486 Biochemistry Biophysics Link
Olsen LF (2023) Complex dynamics in an unexplored simple model of the peroxidase–oxidase reaction. Chaos 33:023102 Biochemistry Enzymology Link
Palermo JC, Colombo MC, Scocozza MF, Murgida DH, Estrín DA, Bari SE (2023) Reduction of metmyoglobin by inorganic disulfide species. Journal of Inorganic Biochemistry 245:112256 Biochemistry Link
Saffioti NA, Alvarez CL, Bazzi Z, Gentilini MV, Gondolesi GE, Schwarzbaum PJ, Schachter J (2023) Dynamic recycling of extracellular ATP in human epithelial intestinal cells. PLOS Computational Biology 19:e1011196 Biochemistry Link
Siedentop R, Dziennus M, Lütz S, Rosenthal K (2023) Debottlenecking of an In Vitro Enzyme Cascade Using a Combined Model- and Experiment-Based Approach. Chemie Ingenieur Technik 95:543–548 Biochemistry Metabolism Link
Suárez H, Guerra A, Mansilla R, Nieto-Villar JM (2023) Ferroptosis as a biological Phase transition II: Chronotherapy of avascular and vascular tumor growth. Biological Rhythm Research 54:722–731 Biochemistry Signaling Link
Yalçınkaya BH, Genc S, Yılmaz B, Özilgen M (2023) How does exercise affect energy metabolism? An in silico approach for cardiac muscle. Heliyon 9:e17164 Biochemistry Physiology Link
Yuan AT, Korkola NC, Stillman MJ (2023) Apo-metallothionein-3 cooperatively forms tightly compact structures under physiological conditions. Journal of Biological Chemistry 299:102899 Biochemistry Biophysics Link

16 publications
Angelini AAR, Gache SAM, Lurdes Sabeckis M, Melian NA, Flecha FLG (2022) On the role of citrate in 12-molybdophosphoric-acid methods for quantification of phosphate in the presence of ATP. New Journal of Chemistry 46:12401–12409 Chemistry Biochemistry Link
Bourdon-García RD, Ágreda J, Burgos-Salcedo J, Hochberg D, Ribó JM, Bargueño P, Salamanca AE (2022) Stoichiometric network analysis in reaction networks yielding spontaneous mirror symmetry breaking in a prebiotic atmosphere. Physical Chemistry Chemical Physics 24:20788–20802 Biochemistry Chemistry Link
Faraj SE, Valsecchi WM, Ferreira-Gomes MS, Centeno M, Saint Martin EM, Fedosova NU, Rossi JPFC, Montes MR, Rossi RC (2022) Measurements of Na+-occluded intermediates during the catalytic cycle of the Na+/K+-ATPase provide novel insights into the mechanism of Na+ transport. Journal of Biological Chemistry 299:102811 Biochemistry Biophysics Link
Gallas JAC, Olsen LF (2022) Complexity in subnetworks of a peroxidase-oxidase reaction model. Chaos 32:063122 Biochemistry Enzymology Link
Knox HL, Sinner EK, Townsend CA, Boal AK, Booker SJ (2022) Structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis. Nature 602:343–348 Biochemistry Enzymology Link
Mattila H, Tyystjärvi E (2022) Light-induced damage to photosystem II at a very low temperature (195 K) depends on singlet oxygen. Physiologia Plantarum 174:e13824 Plant Biology Biochemistry Link
Orrico F, Lopez AC, Saliwonczyk D, Acosta C, Rodriguez-Grecco I, Mouro-Chanteloup I, Ostuni MA, Denicola A, Thomson L, Möller MN (2022) The permeability of human red blood cell membranes to hydrogen peroxide is independent of aquaporins. Journal of Biological Chemistry 298:101503 Biophysics Biochemistry Link
Rettenbacher LA, von der Haar T (2022) A quantitative interpretation of oxidative protein folding activity in Escherichia coli. Microbial Cell Factories 21:268 Biochemistry Microbiology Link
Ulrich EC, Drennan CL (2022) The Atypical Cobalamin-Dependent S-Adenosyl-l-Methionine Nonradical Methylase TsrM and Its Radical Counterparts. Journal of the American Chemical Society 144:5673–5684 Biochemistry Link
White C, Rottschäfer V, Bridge LJ (2022) Insights into the dynamics of ligand-induced dimerisation via mathematical modelling and analysis. Journal of Theoretical Biology 538:110996 Signaling Biochemistry Link
Xu Q, Rose JJ, Chen X, Wang L, DeMartino AW, Dent MR, Tiwari S, Bocian K, Huang XN, Tong Q, McTiernan CF, Guo L, Alipour E, Jones TC, Ucer KB, Kim-Shapiro DB, Tejero J, Gladwin MT (2022) Cell-free and alkylated hemoproteins improve survival in mouse models of carbon monoxide poisoning. JCI Insight 7:e153296 Biochemistry Toxicology Physiology Link

11 publications
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 18:1727-1738 Biochemistry Genetics Link
Erlendsson S, Teilum K (2021) Binding Revisited-Avidity in Cellular Function and Signaling. Frontiers in Molecular Biosciences 7:615565 Biochemistry Immunology 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
Silva PJ (2021) Response to “Molecular-level understanding of biological energy coupling and transduction: Response to ‘Chemiosmotic misunderstandings’”. Biophysical Chemistry 269:106512 Biochemistry Link

7 publications
Barrett TM (2020) Thioamides and proteolysis: Examining the effects and applications of a single-atom substitution. Ph.D. Thesis, University of Pennsylvania, USA. 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
Horváth D, Taricska N, Keszei E, Stráner P, Farkas V, Tóth GK, Perczel A (2020) Compactness of Protein Folds Alters Disulfide-Bond Reducibility by Three Orders of Magnitude: A Comprehensive Kinetic Case Study on the Reduction of Differently Sized Tryptophan Cage Model Proteins. ChemBioChem 21:681–695 Biochemistry Link
Kolodkin AN, Sharma RP, Colangelo AM, Ignatenko A, Martorana F, Jennen D, Briedé JJ, Brady NR, Barberis M, Mondeel TDGA, Papa M, Kumar V, Peters B, Skupin A, Alberghina L, Balling R, Westerhoff HV (2020) ROS networks: designs, aging, Parkinson’s disease and precision therapies. npj Systems Biology and Applications 6:34 Biochemistry 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
Soares DMM, Gonçalves LCP, Machado CO, Esteves LC, Stevani CV, Oliveira CC, Dörr FA, Pinto E, Adachi FMM, Hotta CT, Bastos EL (2020) L-DOPA dioxygenase of the fly agaric toadstool: revision of the dodA gene sequence and mechanism of enzymatic pigment production. bioRxiv 2020.08.03.235077 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 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

12 publications
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 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: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, UK 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. Ph.D. Thesis, University of Delaware, USA. Biochemistry Link

12 publications
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 C (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
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 SA (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
Molina-Mora JA, Kop-Montero M, Quirós-Fernández I, Quirós-Barrantes S, Crespo-Mariño JL, Mora-Rodríguez R (2018) A hybrid mathematical modeling approach of the metabolic fate of a fluorescent sphingolipid analogue to predict cancer chemosensitivity. Computers in Biology and Medicine 97:8–20 Biochemistry Pharmacology 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 SGJ (2018) Four-Variable Model of an Enzymatic Oscillator Based on Trypsin. Israel Journal of Chemistry 58:781–786 Biochemistry Link
Silva LHG (2018) Self-Replication and Non-enzymatic Catalytic Networks subject to Open Flow. MS Thesis, University of Porto, Portugal. Biochemistry Theory Link
Silva LHG, Hochberg D (2018) Open flow non-enzymatic template catalysis and replication. Physical Chemistry Chemical Physics 20:14864–14875 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
Wei Y, Mayoral-Delgado I, Stewart NA, Dymond MK (2018) Macromolecular crowding and membrane binding proteins: the case of phospholipase A1. Chemistry and Physics of Lipids 218:91–102 Biochemistry Biophysics Link
Ximing L (2018) Insights into Delivery of Somatic Calcium Signals to the Nucleus During LTP Revealed by Computational Modeling. Ph.D. Thesis, Ohio University, USA 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 Plant Biology 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

15 publications
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
Houwman JA (2017) The ribosome regulates flavodoxin folding. Ph.D. Thesis, Wageningen University, The Netherlands. Biophysics Biochemistry 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
Seitter H (2017) Retinal function of the voltage-gated calcium channel subunit α2δ-3 / Light-dependent effects in α2δ-3 mutant and in wild type retina. Ph.D. Thesis, Universität Tübingen, Germany. Biochemistry Biophysics Physiology 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

9 publications
delToro D, Ortiz D, Ordyan M, Sippy J, Oh C-S, Keller N, Feiss M, Catalano CE, Smith DE (2016) Walker-A Motif Acts to Coordinate ATP Hydrolysis with Motor Output in Viral DNA Packaging. Journal of Molecular Biology 428:2709–2729 Biochemistry Link
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. Ph.D. 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. Ph.D. Thesis, Seattle, University of Washington, USA. 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
Podoplelova NA, Sveshnikova AN, Kurasawa JH, Sarafanov AG, Chambost H, Vasil’ev SA, Demina IA, Ataullakhanov FI, Alessi M-C, Panteleev MA (2016) Hysteresis-like binding of coagulation factors X/Xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization. Biochimica et Biophysica Acta 1858:1216–1227 Immunology Biochemistry Biophysics 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

12 publications
Lai M, Brun D, Edelstein SJ, Le Novère N (2015) Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions. PLoS Computational Biology 11:e1004063 Biochemistry Enzymology Link

1 publication
Sapra A, Ramadan D, Thorpe C (2014) Multivalency in the inhibition of oxidative protein folding by arsenic (III) species. Biochemistry 54:612–621 Biochemistry Link

1 publication
Emiola A, Falcarin P, Tocher J, George J (2013) A model for the proteolytic regulation of LpxC in the lipopolysaccharide pathway of Escherichia coli. Computational Biology and Chemistry 47:1–7 Biochemistry Microbiology Link
Wilcock P (2013) A systems biology approach for investigating oral squamous cell carcinoma (OSCC). Ph.D. Thesis, University of Manchester, UK Metabolism Biochemistry Link

2 publications
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
Krey T, Bontems F, Vonrhein C, Vaney M-C, Bricogne G, Rümenapf T, Rey FA (2012) Crystal structure of the pestivirus envelope glycoprotein E(rns) and mechanistic analysis of its ribonuclease activity. Structure 20:862–873 Biochemistry Link
Witmer JR (2012) Quantitative analysis and modeling of redox networks in biology. Ph.D. Thesis, University of Iowa, USA. Biochemistry Link

4 publications

0 publication
Mizera A, Gambin B (2010) Stochastic modelling of the eukaryotic heat shock response. Journal of Theoretical Biology 265:455–466 Biochemistry Link

1 publication
Chu C-F (2009) Computational characterization of the role of antioxidant potential in the tonifying mechanism of Yang-invigorating Chinese tonifying herbs. Masters Thesis, National Chiao Tung University, Taiwan, Republic of China Biochemistry Link
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 & 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
Stefan MI, Edelstein SJ, Le Novère N (2009) Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters. BMC Systems Biology 3:68 Biochemistry Link

5 publications