2023
Cook I, Leyh TS (2023) Sterol-activated amyloid beta fibril formation. Journal of Biological Chemistry 299:105445
Macromolecular Biochemistry
Link
Šimek J (2023) Is there a difference between 14-3-3 homo- and heterodimer? Diploma Thesis, Masaryk University, Brno, Czech Republic
Macromolecular Biochemistry
Biophysics
Link
Stanton DA, Ellis EA, Cruse MR, Jedlinski R, Kraut DA (2023) The importance of proteasome grip depends on substrate stability. Biochemical and Biophysical Research Communications 677:162–167
Macromolecular Biochemistry
Link
Tare P, Bhowmick T, Katagi G, China A, Nagaraja V (2023) Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time. ACS Omega 8:47510–47519
Genetics
Macromolecular Biochemistry
Link
4 publications
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
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
