2024
Akune-Taylor Y, Kon A, Aoki-Kinoshita KF (2024) In silico simulation of glycosylation and related pathways. Analytical and Bioanalytical Chemistry. 416:3687-3696
Biochemistry
Link
Angeli L, Morozova K, Dawid C, Scampicchio M, Stark TD (2024) UPLC-ESI-TOF MS Profiling Discriminates Biomarkers in Authentic and Adulterated Italian Samples of Saffron (Crocus sativus L.). ACS Food Science & Technology 4:1783–1794
Chemistry
Biochemistry
Link
Angeli L, Populin F, Morozova K, Ding Y, Asma U, Bolchini S, Cebulj A, Busatto N, Costa F, Ferrentino G, Scampicchio M (2024) Comparative analysis of antioxidant activity and capacity in apple varieties: Insights from stopped flow DPPH• kinetics, mass spectrometry and electrochemistry. Food Bioscience 58:103729
Biochemistry
Link
Asma U, Bertotti ML, Zamai S, Arnold M, Amorati R, Scampicchio M (2024) A Kinetic Approach to Oxygen Radical Absorbance Capacity (ORAC): Restoring Order to the Antioxidant Activity of Hydroxycinnamic Acids and Fruit Juices. Antioxidants 13:222
Laboratory Method
Biochemistry
Link
Deng M, Yu J, Blackmond DG (2024) Symmetry breaking and chiral amplification in prebiotic ligation reactions. Nature 626:1019–1024
Chemistry
Biochemistry
Link
Erbez JP, Rangel GH, Davila M, Englade JA, Erbez AD, Rattanpal J, Li H, Chen Y, Toney MD (2024) Activation Heat Capacities in Pyridoxal Phosphate Enzymes. ACS Catalysis 14:11178–11195
Biochemistry
Enzymology
Link
Faustino M, Lourenço T, Strobbe S, Cao D, Fonseca A, Rocha I, Van Der Straeten D, Oliveira MM (2024) OsTH1 is a key player in thiamin biosynthesis in rice. Scientific Reports 14:13591
Biochemistry
Metabolism
Plant Biology
Link
Høyland LE, VanLinden MR, Niere M, Strømland Ø, Sharma S, Dietze J, Tolås I, Lucena E, Bifulco E, Sverkeli LJ, Cimadamore-Werthein C, Ashrafi H, Haukanes KF, van der Hoeven B, Dölle C, Davidsen C, Pettersen IKN, Tronstad KJ, Mjøs SA, Hayat F, Makarov MV, Migaud ME, Heiland I, Ziegler M (2024) Subcellular NAD+ pools are interconnected and buffered by mitochondrial NAD+. Nature Metabolism 6:2319–2337
Metabolism
Biochemistry
Link
Marchetti T, Roberts BMW, Frezzato D, Prins LJ (2024) A Minimalistic Covalent Bond-Forming Chemical Reaction Cycle that Consumes Adenosine Diphosphate. Angewandte Chemie International Edition 63:e202402965
Chemistry
Biochemistry
Link
Nguyen PH, Cui S, Kozarich AM, Rautio A, Roberts AG, Xiong MP (2024) Utilizing surface plasmon resonance as a novel method for monitoring in-vitro P-glycoprotein efflux. Frontiers in Biophysics 2:1367511
Laboratory Method
Biochemistry
Link
Olsen LF (2024) Stern–Brocot arithmetic in dynamics of a biochemical reaction model. Chaos: An Interdisciplinary Journal of Nonlinear Science 34:123107
Biochemistry
Link
Pulsford SB, Outram MA, Förster B, Rhodes T, Williams SJ, Badger MR, Price GD, Jackson CJ, Long BM (2024) Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP. Science Advances 10:eadk7283
Biochemistry
Plant Biology
Metabolism
Link
Rettenbacher LA (2024) Quantifying oxidative folding. Ph.D. Thesis, University of Kent, U.K.
Biochemistry
Link
Riepl D, Gamiz-Hernandez AP, Kovalova T, Król SM, Mader SL, Sjöstrand D, Högbom M, Brzezinski P, Kaila VRI (2024) Long-range charge transfer mechanism of the III2IV2 mycobacterial supercomplex. Nature Communications 15:5276
Biochemistry
Link
Sánchez-Campillo I, Blanco-Canosa JB (2024) Kinetic and Mechanistic Studies of Native Chemical Ligation with Phenyl α-Selenoester Peptides. JACS Au 4:4374–4382
Chemistry
Biochemistry
Link
Węgrzyn E, Mejdrová I, Müller FM, Nainytė M, Escobar L, Carell T (2024) RNA-Templated Peptide Bond Formation Promotes L-Homochirality. Angewandte Chemie International Edition 63:e202319235
Biochemistry
Link
16 publications
2023
Angeli L, Morozova K, Scampicchio M (2023) A kinetic-based stopped-flow DPPH• method. Scientific Reports 13:7621
Laboratory 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
Pozdnyakov EM, Korneichuk AD, Rogacheva AV, Vasilev GA (2023) Polymerase β Limits the Rate of DNA Single-Strand Break Repair. Mathematical Biology and Bioinformatics 18:294–307
Genetics
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, Stillman MJ (2023) Arsenic binding to human metallothionein-3. Chemical Science 14:5756–5767
Biochemistry
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
18 publications
2022
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
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 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
2020
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
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 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
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 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
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
Cabezas Pérez RJ (2017) Mecanismos de protección frente a rotenona por PDGF-BB en un modelo astrocitario. Ph.D. Thesis, Pontificia Universidad Javeriana, Bogotá, Colombia. http://repository.javeriana.edu.co/handle/10554/38509
Toxicology
Biochemistry
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
10 publications
2016
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
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
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
2009
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
