Publications
2024 Seute L, Hartmann E, Stühmer J, Gräter F (2024). Grappa – A Machine Learned Molecular Mechanics Force Field 1828 Roessner R, Michelarakis N, Gräter F, Aponte-Santamaría C (2024). Mechanical control of the adhesion of malaria-infected erythrocytes to the placenta 1787 Riedmiller K, Reiser P, Bobkova E, Maltsev K, Gryn’ova G, Friederich P, Gräter F (2024). Substituting density functional theory in reaction barrier calculations for hydrogen atom transfer in proteins 1770 Richter S, Jin F, Ritterhoff T, Fergin A, Maurer E, Frank A, Hajnal A, Klevit R, Gräter F, Flotho A, Melchior F (2024). SUMO’s intrinsically disordered N-terminus is an intramolecular inhibitor of SUMO – SIM interactions 1763 2023 Buhr Sd, Gräter F (2023). Myristoyl’s dual role in allosterically regulating and localizing Abl kinase 1556 Herrera-Rodríguez AM, Dasanna AK, Daday C, Cruz-Chú ER, Aponte-Santamaría C, Schwarz US, Gräter F (2023). The role of flow in the self-assembly of dragline spider silk proteins 1715 Franz F, Tapia-Rojo R, Winograd-Katz S, Boujemaa-Paterski R, Li W, Unger T, Albeck S, Aponte-Santamaría C, Garcia-Manyes S, Medalia O, Geiger B, Gräter F (2023). Allosteric activation of vinculin by talin 1505 Rennekamp B, Karfusehr C, Kurth M, Ünal A, Riedmiller K, Gryn’ova G, Hudson DM, Gräter F (2023). Collagen breaks at weak sacrificial bonds taming its mechanoradicals 1540 Kutzki F, Butera D, Lay AJ, Maag D, Chiu J, Woon H, Kubař T, Elstner M, Aponte-Santamaría C, Hogg PJ, Gräter F (2023). Disulfide Bond Reduction and Exchange in von-Willebrand-Factor’s C4-Domain Undermines Platelet Binding 1651 Dupuy A, Santamaría CA, Yeheskel A, Hortle E, Oehlers SH, Gräter F, Hogg PJ, Passam FH, Chiu J (2023). Mechano-Redox Control of Macrophage-1 Antigen De-Adhesion From ICAM-1 (Intercellular Adhesion Molecule 1) by Protein Disulfide Isomerase Promotes Directional Movement Under Flow 1652 Kurth M, Barayeu U, Gharibi H, Kuzhelev A, Riedmiller K, Zilke J, Noack K, Denysenkov V, Kappl R, Prisner TF, Zubarev RA, Dick TP, Gräter F (2023). DOPA Residues Endow Collagen with Radical Scavenging Capacity 1566 Diedrich L, Brosz M, Abele T, Steinke S, Gräter F, Göpfrich K, Aponte-Santamaría C (2023). Energetics and kinetics of membrane permeation of photoresists for bioprinting 1676 Ehret T, Heißenberg T, Buhr Sd, Aponte-Santamaría C, Steinem C, Gräter F (2023). FERM domains recruit ample PI(4,5)P2s to form extensive protein-membrane attachments 1649 Buhr J, Franz F, Gräter F (2023). Intrinsically disordered region of talin’s FERM domain functions as an initial PIP2 recognition site 1650 Riedmiller K, Reiser P, Bobkova E, Maltsev K, Gryn’ova G, Friederich P, Gräter F (2023). Predicting reaction barriers of hydrogen atom transfer in proteins 1621 2022 Treyde AW, Riedmiller K, Gräter F (2022). Bond dissociation energies of X–H bonds in proteins 1506 Chen P, Kutzki F, Mojzisch A, Simon B, Xu E, Aponte-Santamaría C, Horny K, Jeffries C, Schneppenheim R, Wilmanns M, Brehm MA, Gräter F, Hennig J (2022). Structure and dynamics of the von Willebrand Factor C6 domain 1553 Barayeu U, Schilling D, Eid M, Silva TNXd, Schlicker L, Mitreska N, Zapp C, Gräter F, Miller AK, Kappl R, Schulze A, Angeli JPF, Dick TP (2022). Hydropersulfides inhibit lipid peroxidation and ferroptosis by scavenging radicals 1512 Gruber S, Löf A, Hausch A, Kutzki F, Jöhr R, Obser T, König G, Schneppenheim R, Aponte-Santamaría C, Gräter F, Brehm MA, Benoit M, Lipfert J (2022). A Conformational Transition of the D’D3 Domain primes von Willebrand Factor for Multimerization 1507 Brosz M, Michelarakis N, Bunz UHF, Aponte-Santamaría C, Gräter F (2022). Martini 3 coarse-grained force field for poly(para-phenylene ethynylene)s. 1478 Dupuy A, Aponte-Santamaría C, Yeheskel A, Gräter F, Hogg PJ, Passam FH, Chiu J (2022). Mechano-redox control of Mac-1 de-adhesion from ICAM-1 by protein disulfide isomerase promotes directional movement of neutrophils under flow 1509 Martin I, Nava M, Wickström S, Gräter F (2022). ATP allosterically stabilizes integrin-linked kinase for efficient force generation 1257 Gómez-Flores CL, Maag D, Kansari M, Vuong V, Irle S, Gräter F, Kubař T, Elstner M (2022). Accurate Free Energies for Complex Condensed-Phase Reactions Using an Artificial Neural Network Corrected DFTB/MM Methodology. 1454 Daday C, Buhr Sd, Mercadante D, Gräter F (2022). Mechanical force can enhance c-Src kinase activity by impairing autoinhibition. 1453 Martin IM, Aponte-Santamaría C, Schmidt L, Hedtfeld M, Iusupov A, Musacchio A, Gräter F (2022). Phosphorylation tunes elongation propensity and cohesiveness of INCENP’s intrinsically disordered region. 1438 2021 Michelarakis N, Franz F, Gkagkas K, Gräter F (2021). Longitudinal strand ordering leads to shear thinning in Nafion. 1358 Banterle N, Nievergelt AP, Buhr Sd, Hatzopoulos GN, Brillard C, Andany S, Hübscher T, Sorgenfrei FA, Schwarz US, Gräter F, Fantner GE, Gönczy P (2021). Kinetic and structural roles for the surface in guiding SAS-6 self-assembly to direct centriole architecture 1360 Obarska-Kosinska A, Rennekamp B, Ünal A, Gräter F (2021). ColBuilder: A server to build collagen fibril models. 1295 Jin F, Gräter F (2021). How multisite phosphorylation impacts the conformations of intrinsically disordered proteins. 1294 Zha J, Zhang Y, Xia K, Gräter F, Xia F (2021). Coarse-Grained Simulation of Mechanical Properties of Single Microtubules With Micrometer Length. 1293 Maag D, Putzu M, Gómez-Flores CL, Gräter F, Elstner M, Kubař T (2021). Electrostatic interactions contribute to the control of intramolecular thiol–disulfide isomerization in a protein 1320 2020 Huck V, Chen P, Xu E, Tischer A, Klemm U, Aponte-Santamaría C, Mess C, Obser T, Kutzki F, König G, Denis CV, Gräter F, Wilmanns M, Auton M, Schneider SW, Schneppenheim R, Hennig J, Brehm MA (2020). Gain-of-Function Variant p.Pro2555Arg of von Willebrand Factor Increases Aggregate Size through Altering Stem Dynamics. 1292 Cruz-Chú ER, Villegas-Rodriguez G, Jäger T, Valentini L, Pugno N, Gkagkas K, Gräter F (2020). Mechanical characterization and induced crystallization in nanocomposites of thermoplastics and carbon nanotubes 1255 Acebrón I, Righetto RD, Schoenherr C, Buhr Sd, Redondo P, Culley J, Rodríguez CF, Daday C, Biyani N, Llorca O, Byron A, Chami M, Gräter F, Boskovic J, Frame MC, Stahlberg H, Lietha D (2020). Structural basis of Focal Adhesion Kinase activation on lipid membranes. 1256 Zapp C, Obarska-Kosinska A, Rennekamp B, Kurth M, Hudson DM, Mercadante D, Barayeu U, Dick TP, Denysenkov V, Prisner T, Bennati M, Daday C, Kappl R, Gräter F (2020). Mechanoradicals in tensed tendon collagen as a source of oxidative stress 1139 Franz F, Daday C, Gräter F (2020). Advances in molecular simulations of protein mechanical properties and function 1095 Rennekamp B, Kutzki F, Obarska-Kosinska A, Zapp C, Gräter F (2020). Hybrid Kinetic Monte Carlo/Molecular Dynamics Simulations of Bond Scissions in Proteins 1096 2019 Suman SK, Daday C, Ferraro T, Vuong-Brender T, Tak S, Quintin S, Robin F, Gräter F, Labouesse M (2019). The plakin domain of C. elegans VAB-10/plectin acts as a hub in a mechanotransduction pathway to promote morphogenesis 1097 Caetano-Anollés G, Aziz MF, Mughal F, Gräter F, Koç I, Caetano-Anollés K, Caetano-Anollés D (2019). Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis. 1120 Zhang Y, Xia K, Cao Z, Gräter F, Xia F (2019). A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data 1104 Herrera-Rodríguez AM, Miletić V, Aponte-Santamaría C, Gräter F (2019). Molecular Dynamics Simulations of Molecules in Uniform Flow 1103 Sheridan S, Gräter F, Daday C (2019). How Fast Is Too Fast in Force-Probe Molecular Dynamics Simulations? 1102 Bauer MS, Baumann F, Daday C, Redondo P, Durner E, Jobst MA, Milles LF, Mercadante D, Pippig DA, Gaub HE, Gräter F, Lietha D (2019). Structural and mechanistic insights into mechanoactivation of focal adhesion kinase 1101 Brehm MA, Klemm U, Rehbach C, Erdmann N, Kolšek K, Lin H, Aponte-Santamaría C, Gräter F, Rauch BH, Riley AM, Mayr GW, Potter BV, Windhorst S (2019). Inositol hexakisphosphate increases the size of platelet aggregates 1099 Daday C, Mateyka LM, Gräter F (2019). How ARVC-Related Mutations Destabilize Desmoplakin: An MD Study 1100 Xu E, Bülow Sv, Chen P, Lenting PJ, Kolšek K, Aponte-Santamaría C, Simon B, Foot J, Obser T, Schneppenheim R, Gräter F, Denis CV, Wilmanns M, Hennig J (2019). Structure and dynamics of the platelet integrin-binding C4 domain of von Willebrand factor 1098 Gräter F, Li W (2019). Studying Functional Disulphide Bonds by Computer Simulations 1105 2018 Imber M, Huyen NTT, Pietrzyk-Brzezinska AJ, Loi VV, Hillion M, Bernhardt J, Thärichen L, Kolšek K, Saleh M, Hamilton CJ, Adrian L, Gräter F, Wahl MC, Antelmann H (2018). Protein S-Bacillithiolation Functions in Thiol Protection and Redox Regulation of the Glyceraldehyde-3-Phosphate Dehydrogenase Gap in Staphylococcus aureus Under Hypochlorite Stress. 1122 Butera D, Passam F, Ju L, Cook KM, Woon H, Aponte-Santamaría C, Gardiner E, Davis AK, Murphy DA, Bronowska A, Luken BM, Baldauf C, Jackson S, Andrews R, Gräter F, Hogg PJ (2018). Autoregulation of von Willebrand factor function by a disulfide bond switch 372 Franz F, Aponte-Santamaría C, Daday C, Miletić V, Gräter F (2018). Stability of Biological Membranes upon Mechanical Indentation 373 Friedman R, Khalid S, Aponte-Santamaría C, Arutyunova E, Becker M, Boyd KJ, Christensen M, Coimbra JTS, Concilio S, Daday C, Eerden FJv, Fernandes PA, Gräter F, Hakobyan D, Heuer A, Karathanou K, Keller F, Lemieux MJ, Marrink SJ, May ER, Mazumdar A, Naftalin R, Pickholz M, Piotto S, Pohl P, Quinn P, Ramos MJ, Schiøtt B, Sengupta D, Sessa L, Vanni S, Zeppelin T, Zoni V, Bondar A, Domene C (2018). Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology 374 Mercadante D, Gräter F, Daday C (2018). CONAN: A Tool to Decode Dynamical Information from Molecular Interaction Maps 375 Passam F, Chiu J, Ju L, Pijning A, Jahan Z, Mor-Cohen R, Yeheskel A, Kolšek K, Thärichen L, Aponte-Santamaría C, Gräter F, Hogg PJ (2018). Mechano-redox control of integrin de-adhesion 376 Putzu M, Gräter F, Elstner M, Kubař T (2018). On the mechanism of spontaneous thiol-disulfide exchange in proteins 377 Ray A, Gräter F, Thukral L (2018). Probing molecular forces in multi-component physiological membranes 378 Tan PS, Aramburu IV, Mercadante D, Tyagi S, Chowdhury A, Spitz D, Shammas SL, Gräter F, Lemke EA (2018). Two Differential Binding Mechanisms of FG-Nucleoporins and Nuclear Transport Receptors 379 2017 Hocq L, Sénéchal F, Lefebvre V, Lehner A, Domon J, Mollet J, Dehors J, Pageau K, Marcelo P, Guérineau F, Kolšek K, Mercadante D, Pelloux J (2017). Combined Experimental and computational approaches reveal distinct pH-dependence of pectin methyl esterase inhibitors 164 Cruz-Chú ER, Xiao S, Patil SP, Gkagkas K, Gräter F (2017). Organic Filling Mitigates Flaw-Sensitivity of Nanoscale Aragonite 162 Posch S, Aponte-Santamaría C, Schwarzl R, Karner A, Radtke M, Gräter F, Obser T, König G, Brehm MA, Gruber HJ, Netz RR, Baldauf C, Schneppenheim R, Tampé R, Hinterdorfer P (2017). Mutual A domain interactions in the force sensing protein von Willebrand factor 161 Mercadante D, Wagner JA, Aramburu IV, Lemke EA, Gräter F (2017). Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins 254 Daday C, Kolšek K, Gräter F (2017). The mechano-sensing role of the unique SH3 insertion in plakin domains revealed by Molecular Dynamics simulations 255 Aponte-Santamaría C, Brunken J, Gräter F (2017). Stress propagation through biological lipid bilayers in silico 256 Kolšek K, Aponte-Santamaría C, Gräter F (2017). Accessibility explains preferred thiol-disulfide isomerization in a protein domain. 257 Aponte-Santamarı́a C, Fischer G, Båth P, Neutze R, Groot Bd (2017). Temperature dependence of protein-water interactions in a gated yeast aquaporin. , Scientific Reports, 7:4016 258 Briones B, Aponte-Santamarı́a C, Groot Bd (2017). Localization and ordering of lipids around Aquaporin-0: Protein and lipid mobility effects. , Frontiers in Physiology, 8:124 259 Aponte-Santamaría C, Lippok S, Mittag JJ, Obser T, Schneppenheim R, Baldauf C, Gräter F, Budde U, Rädler JO (2017). Mutation G1629E increases von Willebrand factor cleavage via a cooperative destabilization mechanism. 260 Wagner JA, Patil SP, Greving I, Lämmel M, Gkagkas K, Seydel T, Müller M, Markert B, Gräter F (2017). Stress-induced long-range ordering in spider silk 261 Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Girona GE, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV, Svergun DI, Lemke EA (2017). Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements. 262 Zhou B, Hogg PJ, Gräter F (2017). One-Way Allosteric Communication between the Two Disulfide Bonds in Tissue Factor 263 Costescu SSB (2017). Dynamic disorder can explain non-exponential kinetics of fast protein mechanical unfolding 264 Miletić V, Odorčić I, Nikolić P, Svedružić Ž (2017). In silico design of the first DNA-independent mechanism-based inhibitor of mammalian DNA methyltransferase Dnmt1 , PLoS ONE, 12:e0174410 265 2016 Posch S, Aponte-Santamaría C, Schwarzl R, Karner A, Radtke M, Gräter F, Obser T, König G, Brehm MA, Gruber HJ, Netz RR, Baldauf C, Schneppenheim R, Tampé R, Hinterdorfer P (2016). Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor. 1121 Dugard CK, Mertz RA, Rayon C, Mercadante D, Hart C, Benatti MR, Olek AT, SanMiguel PJ, Cooper BR, Reiter W, McCann MC, Carpita NC (2016). The Cell Wall Arabinose-Deficient Arabidopsis thaliana Mutant murus5 Encodes a Defective Allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2 165 Lippok S, Kolšek K, Löf A, Eggert D, Vanderlinden W, Müller JP, König G, Obser T, Röhrs K, Schneppenheim S, Budde U, Baldauf C, Aponte-Santamaría C, Gräter F, Schneppenheim R, Rädler JO, Brehm MA (2016). von Willebrand factor is dimerized by protein disulfide isomerase 160 Mercadante D, Milles S, Fuertes G, Svergun D, Lemke EA, Gräter F (2016). Rescuing the Over-Collapse of Intrinsically Disordered Proteins using a Force Field Derived by a New Paradigm , Biophysical Journal, 110(3):556a 163 Aramburu IV, Mercadante D, Milles S, Ringkjøbing M, Banterle N, Koehler C, Tyagi S, Clarke J, Shammas SL, Blackledge M, others (2016). Plasticity of Nucleoporin Nuclear Transport Receptor Interactions-Molecular Description of a Highly Dynamic, Ultrafast Interaction Mechanism , Biophysical Journal, 110(3):357a 166 Tursch A, Mercadante D, Tennigkeit J, Gräter F, Özbek S (2016). Minicollagen cysteine-rich domains encode distinct modes of polymerization to form stable nematocyst capsules 167 Kent LM, Loo TS, Melton LD, Mercadante D, Williams MA, Jameson GB (2016). Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control , Journal of Biological Chemistry, 291(3):1289–1306 168 2015 Gräter F, Li W (2015). Transition Path Sampling with Quantum/Classical Mechanics for Reaction Rates 88 Peralta D, Bronowska AK, Morgan B, Dóka É, Laer KV, Nagy P, Gräter F, Dick TP (2015). A proton relay enhances H2O2 sensitivity of GAPDH to facilitate metabolic adaptation 89 Beckmann A, Xiao S, Müller JP, Mercadante D, Nüchter T, Kröger N, Langhojer F, Petrich W, Holstein TW, Benoit M, others (2015). A fast recoiling silk-like elastomer facilitates nanosecond nematocyst discharge 90 Zhou J, Bronowska A, Le Coq J, Lietha D, Gräter F (2015). Allosteric Regulation of Focal Adhesion Kinase by PIP 2 and ATP 91 Li W, Baldus IB, Gräter F (2015). Redox Potentials of Protein Disulfide Bonds from Free-Energy Calculations 92 Aponte-Santamarı́a C, Huck V, Posch S, Bronowska AK, Graessle S, Brehm MA, Obser T, Schneppenheim R, Hinterdorfer P, Schneider SW, others (2015). Force-Sensitive Autoinhibition of the von Willebrand Factor Is Mediated by Interdomain Interactions 93 Mercadante D, Milles S, Fuertes G, Svergun DI, Lemke EA, Gräter F (2015). Kirkwood–Buff approach rescues overcollapse of a disordered protein in canonical protein force fields 94 Wagner JA, Mercadante D, Nikić I, Lemke EA, Gräter F (2015). Origin of Orthogonality of Strain-Promoted Click Reactions 95 Louet M, Seifert C, Hensen U, Gräter F (2015). Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces 96 Milles S, Mercadante D, Aramburu IV, Jensen MR, Banterle N, Köhler C, Tyagi S, Clarke J, Shammas SL, Blackledge M, others (2015). Plasticity of an ultrafast interaction between nucleoporins and nuclear transport receptors 97 Zhou J, Aponte-Santamaría C, Sturm S, Bullerjahn JT, Bronowska A, Gräter F (2015). Mechanism of Focal Adhesion Kinase Mechanosensing 98 2014
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