COPASI

COPASI's Use In Macromolecular Biochemistry

2023

0 publication
2022
Baggett DW, Nath A (2022) Structure–Activity Relationships of Novel Tau Ligands: Passive Fibril Binders and Active Aggregation Inhibitors. ACS Chemical Biology 17:701–708 Macromolecular Biochemistry Link
Kathan M, Crespi S, Thiel NO, Stares DL, Morsa D, de Boer J, Pacella G, van den Enk T, Kobauri P, Portale G, Schalley CA, Feringa BL (2022) A light-fuelled nanoratchet shifts a coupled chemical equilibrium. Nature Nanotechnology 17:159–165 Chemistry Biotechnology Macromolecular Biochemistry Link
Trošanová Z, Louša P, Kozeleková A, Brom T, Gašparik N, Tungli J, Weisová V, Župa E, Žoldák G, Hritz J (2022) Quantitation of Human 14-3-3ζ Dimerization and the Effect of Phosphorylation on Dimer-monomer Equilibria. Journal of Molecular Biology 434:167479 Signaling Macromolecular Biochemistry Link

3 publications
2021
Guzman-Luna V, Fuchs AM, Allen AJ, Staikos A, Cavagnero S (2021) An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel. Communications Biology 4:1236 Macromolecular Biochemistry Link
Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG (2021) Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif. Journal of Biological Chemistry 297:101175 Macromolecular Biochemistry Microbiology Link
Monti M, Guiducci G, Paone A, Rinaldo S, Giardina G, Liberati FR, Cutruzzolá F, Tartaglia GG (2021) Modelling of SHMT1 riboregulation predicts dynamic changes of serine and glycine levels across cellular compartments. Computational and Structural Biotechnology Journal 19:3034–3041 Macromolecular Biochemistry Link
Rosenbloom AD (2021) Mechanism of Actin Filament Nucleation. Ph.D. Thesis, Yale University, New Haven, CT, USA. Macromolecular Biochemistry Cell Biology Link
Rosenbloom AD, Kovar EW, Kovar DR, Loew LM, Pollard TD (2021) Mechanism of actin filament nucleation. Biophysical Journal 120:4399–4417 Macromolecular Biochemistry Biophysics Link
Teilum K, Olsen JG, Kragelund BB (2021) On the specificity of protein-protein interactions in the context of disorder. Biochemical Journal 478:2035–2050 Signaling Macromolecular Biochemistry Link
Zweifel ME, Sherer LA, Mahanta B, Courtemanche N (2021) Nucleation limits the lengths of actin filaments assembled by formin. Biophysical Journal 120:4442–4456 Macromolecular Biochemistry Cell Biology Link

7 publications
2020
Balzer CJ, James ML, Narvaez-Ortiz HY, Helgeson LA, Sirotkin V, Nolen BJ (2020) Synergy between Wsp1 and Dip1 may initiate assembly of endocytic actin networks. eLife 9:e60419 Cell Biology Macromolecular Biochemistry Link
Firczuk H, Teahan J, Mendes P, McCarthy JEG (2020) Multisite rate control analysis identifies ribosomal scanning as the sole high-capacity/low-flux-control step in mRNA translation. FEBS Journal 287:925940 Macromolecular Biochemistry Link
Rana P (2020) Mathematical models of cellular signaling and supramolecular self-assembly. Ph.D. Thesis, Virginia Commonwealth University, USA. Signaling Macromolecular Biochemistry Link
Song X, Yu Y, Shen C, Wang Y, Wang N (2020) Dimerization/oligomerization of the extracellular domain of the GLP-1 receptor and the negative cooperativity in its ligand binding revealed by the improved NanoBiT. FASEB Journal 34:4348–4368 Macromolecular Biochemistry Signaling Link

4 publications
2019
Beal DM, Bastow EL, Staniforth GL, von der Haar T, Freedman RB, Tuite MF (2019) Quantitative Analyses of the Yeast Oxidative Protein Folding Pathway In Vitro and In Vivo. Antioxidants & Redox Signaling 31:261–274 Macromolecular Biochemistry Link
Cababie LA, Incicco JJ, González-Lebrero RM, Roman EA, Gebhard LG, Gamarnik AV, Kaufman SB (2019) Thermodynamic study of the effect of ions on the interaction between dengue virus NS3 helicase and single stranded RNA. Scientific Reports 9:10569 Biophysics Macromolecular Biochemistry Link
Chum AP, Shoemaker SR, Fleming PJ, Fleming KG (2019) Plasticity and transient binding are key ingredients of the periplasmic chaperone network. Protein Science 28:1340–1349 Macromolecular Biochemistry Microbiology Link
Erlendsson S, Thorsen TS, Vauquelin G, Ammendrup-Johnsen I, Wirth V, Martinez KL, Teilum K, Gether U, Madsen KL (2019) Mechanisms of PDZ domain scaffold assembly illuminated by use of supported cell membrane sheets. eLife 8:e39180 Macromolecular Biochemistry Cell Biology 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
Wei Y, Mayoral-Delgado I, Stewart NA, Dymond MK (2019) Macromolecular crowding and membrane binding proteins: The case of phospholipase A1. Chemistry and Physics of Lipids 218:91–102 Macromolecular Biochemistry Link
Xie Y, Kazmierczyk M, Graham BP, Dutia MB, Stefan MI, Dutia MB (2019) A multi-scale model reveals cellular and physiological mechanisms underlying hyperpolarisation-gated synaptic plasticity. bioRxiv doi:10.1101/418228 Macromolecular Biochemistry Biophysics Link

7 publications
2018
Hantusch A (2018) Systems Biological Analysis of Bcl-2 Family Interactions and Effector Oligomerization. Ph.D. Thesis, University of Konstanz, Germany Cell Biology Macromolecular Biochemistry Link

1 publication
2017
Badet T, Peyraud R, Mbengue M, Navaud O, Derbyshire M, Oliver RP, Barbacci A, Raffaele S (2017) Codon optimization underpins generalist parasitism in fungi. eLife 6:e22472 Genomics Theory Macromolecular Biochemistry Link
Chizzolini F, Forlin M, Yeh Martín N, Berloffa G, Cecchi D, Mansy SS (2017) Cell-free translation is more variable than transcription. ACS Synthetic Biology 6:638–647 Macromolecular Biochemistry Synthetic Biology Link
Dacheux E, Malys N, Meng X, Ramachandran V, Mendes P, McCarthy JEG (2017) Translation initiation events on structured eukaryotic mRNAs generate gene expression noise. Nucleic Acids Research 45:6981–6992 Macromolecular Biochemistry Link
Meng X, Firczuk H, Pietroni P, Westbrook R, Dacheux E, Mendes P, McCarthy JEG (2017) Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis. Nucleic Acids Research 45:1015–1025 Macromolecular Biochemistry Link
Nakatani-Webster E, Nath A (2017) Inferring Mechanistic Parameters from Amyloid Formation Kinetics by Approximate Bayesian Computation. Biophysical Journal 112:868–880 Macromolecular Biochemistry Computational Method Link
Postma SGJ, te Brinke D, Vialshin IN, Wong ASY, Huck WTS (2017) A trypsin-based bistable switch. Tetrahedron 73:4896–4900 Macromolecular Biochemistry Link
Roy RD, Rosenmund C, Stefan MI (2017) Cooperative binding mitigates the high-dose hook effect. BMC Systems Biology 11:74 Theory Macromolecular Biochemistry Link
Zhao W, Pferdehirt L, Segatori L (2017) Quantitatively predictable control of cellular protein levels through proteasomal degradation. ACS Synthetic Biology 7:540–552 Synthetic Biology Macromolecular Biochemistry Link

8 publications
2016
Jungmann R, Avendaño MS, Dai M, Woehrstein JB, Agasti SS, Feiger Z, Rodal A, Yin P (2016) Quantitative super-resolution imaging with qPAINT. Nature Methods 13:439–442 Laboratory Method Macromolecular 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
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

4 publications
2015
Dacheux E, Firczuk H, McCarthy JEG (2015) Rate control in yeast protein synthesis at the population and single-cell levels. Biochemical Society Transactions 43:1266-70 Macromolecular Biochemistry Link
Daneshjou N, Sieracki N, van Nieuw Amerongen GP, Schwartz MA, Komarova YA, Malik AB, Conway DE (2015) Rac1 functions as a reversible tension modulator to stabilize VE-cadherin trans-interaction. Journal of Cell Biology 208:23-32 Macromolecular Biochemistry Cell Biology Link
Dornseifer S, Willkomm S, Far RK, Liebschwager J, Beltsiou F, Frank K, Laufer SD, Martinetz T, Sczakiel G, Claussen JC, Restle T (2015) RNAi revised - target mRNA-dependent enhancement of gene silencing. Nucleic Acids Research 43:10623-32. Macromolecular Biochemistry Genetics Link
Dutta-Roy R, Rosenmund C, Edelstein SJ, Le Novère N (2015) Ligand-Dependent Opening of the Multiple AMPA Receptor Conductance States: A Concerted Model. PLoS One 10:e0116616 Physiology Macromolecular Biochemistry Link
Hudson DA, Gannon SA, Thorpe C, (2015) Oxidative protein folding: From thiol-disulfide exchange reactions to the redox poise of the endoplasmic reticulum. Free Radical Biology and Medicine 80:171-182 Macromolecular Biochemistry Link
Karapetyan S, Buchler NE (2015) Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators. Physical Review E 92:062712 Macromolecular Biochemistry Theory Link
Lee TW, Yang AS-P, Brittain T, Birch NP (2015) An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: Application to neuroserpin reveals regions that differentially regulate inhibitory activity. Proteins: Structure, Function, and Bioinformatics 83:135-52 Macromolecular Biochemistry Link
Rastgou Talemi S, Kollarovic G, Lapytsko A, Schaber J (2015) Development of a robust DNA damage model including persistent telomere-associated damage with application to secondary cancer risk assessment. Scientific Reports 5:13540 Genetics Macromolecular Biochemistry Link
Sapra A, Ramadan D, Thorpe C (2015) Multivalency in the inhibition of oxidative protein folding by arsenic(III) species. Biochemistry 54:612–621 Macromolecular Biochemistry Link
Subburaj Y, Ros U, Hermann E, Tong R, García-Sáez AJ (2015) Toxicity of an alpha-Pore-forming Toxin Depends on the Assembly Mechanism on the Target Membrane as Revealed by Single Molecule Imaging. Journal of Biological Chemistry 290:4856-4865 Macromolecular Biochemistry Link
Zhou J, Aponte-Santamaría C, Sturm S, Bullerjahn JT, Bronowska A, Gräter F (2015) Mechanism of Focal Adhesion Kinase Mechanosensing. PLoS Computational Biology 11:e1004593 Macromolecular Biochemistry Cell Biology Link

11 publications
2014
Gianni S, Dogan J, Jemth P (2014) Distinguishing induced fit from conformational selection. Biophysical Chemistry 189:33–39 Macromolecular Biochemistry Link
Irving JA, Haq I, Dickens JA, Faull SV, Lomas DA (2014) Altered native stability is the dominant basis for susceptibility of α1-antitrypsin mutants to polymerization. Biochemical Journal 460:103–119 Macromolecular Biochemistry Link
James AI, Imran HAQ, Jennifer AD, Sarah VF, David AL (2014) Altered native stability is the dominant basis for susceptibility of alpha1-antitrypsin mutants to polymerization. Biochemical Journal 460:103-115 Macromolecular Biochemistry Link
Rodriguez Plaza JG, Morales-Nava R, Diener C, Schreiber G, Gonzalez ZD, Lara Ortiz MT, Ortega Blake I, Pantoja O, Volkmer R, Klipp E, Herrmann A, Del Rio G (2014) Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin. Journal of Biological Chemistry 289:14448–14457 Macromolecular Biochemistry Biophysics Microbiology Link
Tunnicliffe RB, Hautbergue GM, Wilson SA, Kalra P, Golovanov AP (2014) Competitive and Cooperative Interactions Mediate RNA Transfer from Herpesvirus Saimiri ORF57 to the Mammalian Export Adaptor ALYREF. PLoS Pathogens 10:e1003907 Macromolecular Biochemistry Link

5 publications
2013
Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff HV, Mendes P, McCarthy JEG (2013) An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology 9:635 Macromolecular Biochemistry Cell Biology Link
Haq I, Irving JA, Faull SV, Dickens JA, Ordonez A, Belorgey D, Gooptu B, Lomas DA (2013) Reactive centre loop mutants of alpha-1-antitrypsin reveal position-specific effects on intermediate formation along the polymerization pathway. Bioscience Reports 33:499-511 Macromolecular Biochemistry Link
Helgeson LA, Nolen BJ (2013) Mechanism of synergistic activation of Arp2/3 complex by cortactin and N-WASP. eLife 2:e00884 Macromolecular Biochemistry Signaling Link
Incicco JJ, Gebhard LG, González-Lebrero RM, Gamarnik AV, Kaufman SB (2013) Steady-State NTPase Activity of Dengue Virus NS3: Number of Catalytic Sites, Nucleotide Specificity and Activation by ssRNA. PLoS One 8:e58508 Macromolecular Biochemistry Link
Maccari G, Mori M, Rodríguez-Salarichs J, Fang W, Díaz JF, Botta M (2013) Free Energy Profile and Kinetics Studies of Paclitaxel Internalization from the Outer to the Inner Wall of Microtubules. Journal of Chemical Theory and Computation 9:698-706 Cell Biology Macromolecular Biochemistry Pharmacology Link
Proctor CJ, Boche D, Gray DA, Nicoll JAR (2013) Investigating Interventions in Alzheimer's Disease with Computer Simulation Models. PLoS One 8:e73631 Macromolecular Biochemistry Link
Sarma U, Gade PM, Saha B (2013) A mathematical model for dynamics of CD40 clustering. Systems and Synthetic Biology 7:197-208 Macromolecular Biochemistry Link

7 publications
2012
Chang J-Y, Chantrathammachart P, Monroe DM, Key NS (2012) Studies on the mechanism of action of the aptamer BAX499, an Inhibitor of tissue factor pathway inhibitor. Thrombosis Research 130:e151-e157 Macromolecular 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

2 publications
2011
Baez M, Wilson CA, Babul J (2011) Folding kinetic pathway of phosphofructokinase-2 from Escherichia coli: a homodimeric enzyme with a complex domain organization. FEBS Letters 585:2158–2164 Macromolecular Biochemistry Link
Li Y, Cucinotta FA (2011) Modeling non-homologous end joining. Journal of Theoretical Biology 283:122–135 Genetics Theory Macromolecular Biochemistry Link
Proctor CJ, Lorimer IAJ (2011) Modelling the role of the Hsp70/Hsp90 system in the maintenance of protein homeostasis. PLoS One 6:e22038 Macromolecular Biochemistry Link
Rodriguez F, Bustos MA, Zanetti MN, Ruete MC, Mayorga LS, Tomes CN (2011) alpha-SNAP prevents docking of the acrosome during sperm exocytosis because it sequesters monomeric syntaxin. PLoS One 6:e21925 Cell Biology Macromolecular Biochemistry Link

4 publications
2010
Chi CN, Bach A, Gottschalk M, Kristensen AS, Stromgaard K, Jemth P (2010) Deciphering the Kinetic Binding Mechanism of Dimeric Ligands Using a Potent Plasma-stable Dimeric Inhibitor of Postsynaptic Density Protein-95 as an Example. Journal of Biological Chemistry 285:28252–28260 Macromolecular Biochemistry Link
Huang R, Grabarek Z, Wang C-LA (2010) Differential effects of caldesmon on the intermediate conformational states of polymerizing actin. Journal of Biological Chemistry 285:71-79 Macromolecular Biochemistry Link
Samorodnitsky E, Pugh BF (2010) Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data. PLoS Computational Biology 6:e1000733 Macromolecular Biochemistry Genomics Link

3 publications
2009
Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, Mones L, Fuxreiter M, Pingoud A (2009) On the Divalent Metal Ion Dependence of DNA Cleavage by Restriction Endonucleases of the EcoRI Family. Journal of Molecular Biology 393:140-60 Macromolecular Biochemistry Link
Ricagno S, Caccia S, Sorrentino G, Antonini G, Bolognesi M (2009) Human Neuroserpin: Structure and Time-Dependent Inhibition. Journal of Molecular Biology 388:109–121 Enzymology Macromolecular Biochemistry Link

2 publications
2008
Ciocchetta F, Hillston J, Kos M, Tollervey D (2008) Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA. Theoretical Computer Science 408:41–54 Macromolecular Biochemistry Link
Kühnel M, Mayorga LS, Dandekar T, Thakar J, Schwarz R, Anes E, Griffiths G, Reich J (2008) Modelling phagosomal lipid networks that regulate actin assembly. BMC Systems Biology 2:107 Metabolism Macromolecular Biochemistry Link
Stefan MI, Edelstein SJ, Le Novère N (2008) An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. Proceedings of the National Academy of Sciences USA 105:10768-73 Physiology Signaling Macromolecular Biochemistry Link

3 publications
2007
Rippe K, Schrader A, Riede P, Strohner R, Lehmann E,Längst G (2007) DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proceedings of the National Academy of Sciences USA 104:15635-40 Macromolecular Biochemistry Cell Biology Link

1 publication
2006