Publications

2017

C. Daday, K. Kolšek, F. Gräter (2017).
The mechano-sensing role of the unique SH3 insertion in plakin domains revealed by Molecular Dynamics simulations.
Sci Rep. 2017; 7: 11669 Link

C. Aponte-Santamaría, J. Brunken, F. Gräter (2017).
Stress propagation through biological lipid bilayers in silico.
J Am Chem Soc. 2017 Aug 30 [Epub ahead of print] Link

K. Kolšek, C. Aponte-Santamaría, F. Gräter (2017).
Accessibility explains preferred thiol-disulfide isomerization in a protein domain.
Scientific Reports 7, Article number: 9858 Link

D. Mercadante, J. A. Wagner, I. V. Aramburu, E. A. Lemke, F. Gräter (2017).
Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins.
J Chem Theory Comput. 2017 Aug 28 [Epub ahead of print] Link

G. Fuertes, N. Banterle, K. M. Ruff, A. Chowdhury, D. Mercadante, C. Koehler, M. Kachala, G. Estrada Girona, S. Milles, A. Mishra, P. R. Onck, F. Gräter, S. Esteban-Martín, R. V. Pappu, D. I. Svergun, E. A. Lemke (2017).
Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.
Proc Natl Acad Sci U S A. 2017 Aug 1; 114(31): E6342–E6351 Link

E. R. Cruz-Chú, S. Xiao, S. P. Patil, K. Gkagkas, F. Gräter (2017).
Organic Filling Mitigates Flaw-Sensitivity of Nanoscale Aragonite
ACS Biomater. Sci. Eng., 2017, 3 (3), pp 260–268 Link

B. Zhou, P. J. Hogg, F. Gräter (2017).
One-Way Allosteric Communication between the Two Disulfide Bonds in Tissue Factor.
Biophys. J. 112(1):78-86 Link

C. Aponte-Santamaría, S. Lippok, J. J. Mittag, T. Obser, R. Schneppenheim, C. Baldauf, F. Gräter, U. Budde, J. O. Rädler (2017).
Mutation G1629E Increases von Willebrand Factor Cleavage via a Cooperative Destabilization Mechanism.
Biophys. J. 112(1):57-65 Link

M. Imber, N. T. Huyen, A. J. Pietrzyk-Brzezinska, V. V. Loi, M. Hillion, J. Bernhardt, L. Thärichen, K. Kolšek, M. Saleh, C. J. Hamilton, L. Adrian, F. Gräter, M. Wahl, H. Antelmann (2017).
Protein S-bacillithiolation functions in thiol-protection and redox regulation of the glyceraldehyde-3-phosphate dehydrogenase Gap in Staphylococcus aureus under hypochlorite stress.
Antioxid Redox Signal.  [Epub ahead of print] Link

B. I. Costescu, S. Sturm, F. Gräter (2017).
Dynamic disorder can explain non-exponential kinetics of fast protein mechanical unfolding.
J Struct Biol.197(1):43-49 Link

S. Posch, C. Aponte-Santamaría, R. Schwarzl, A. Karner, M. Radtke, F. Gräter, T. Obser, G. König, M. A. Brehm, H. J. Gruber, R. R. Netz, C. Baldauf, R. Schneppenheim, R. Tampé, P. Hinterdorfer (2017).
Mutual A domain interactions in the force sensing protein von Willebrand factor.
J Struct Biol. 197(1):57-64 Link

2016

A. Tursch, D. Mercadante, J. Tennigkeit, F. Gräter, S. Özbek (2016).
Minicollagen cysteine-rich domains encode distinct modes of polymerization to form stable nematocyst capsules.
Sci Rep. 6:25709 Link

S. Lippok, K. Kolšek, A. Löf, D. Eggert, W. Vanderlinden, J. P. Müller, G. König, T. Obser, K. Röhrs, S. Schneppenheim, U. Budde, C. Baldauf, C. Aponte-Santamaría, F. Gräter, R. Schneppenheim, J. O. Rädler, M. A. Brehm (2016).
von Willebrand factor is dimerized by protein disulfide isomerase.
Blood. 127(9):1183-91 Link

2015

J. Zhou, C. Aponte-Santamaria, S. Sturm, J. T. Bullerjahn, A. Bronowska, F. Gräter (2015).
Mechanism of focal adhesion mechanosensing.
PLoS Comput. Biol. 11(11):e1004593 Link

S. Milles, D. Mercadante, V. I. Aramburu, M. R. Jensen, N. Banterle, C. Koehler, S. Tyagi, J. Clarke, S. L. Shammas, M., Blackledge, F. Gräter, E. A. Lemke (2015). 
Plasticity of an Ultrafast Interaction between Nucleoporins and Nuclear Transport Receptors.
Cell. 163(3):734-45 Link

M. Louet, C. Seifert, U. Hensen, F. Gräter (2015).
Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces.
PLoS Comput. Biol. 11(8):e1004358 Link

J.A. Wagner, D. Mercadante, I. Nikić, E. A. Lemke, F. Gräter (2015). 
Origin of Orthogonality of Strain-Promoted Click Reactions.
Chem. Eur. J. 119(25):7975-84 Link

D. Mercadante, S. Milles, G. Fuertes, D. I. Svergun, E. A. Lemke, F. Gräter (2015).
Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields.
J. Phys. Chem. B. 119(25):7975-84 Link

C. Aponte-Santamaría, V. Huck, S. Posch, A. K. Bronowska, S. Grässle, M. A. Brehm, Obser, R. Schneppenheim, P. Hinterdorfer, S. W. Schneider, C. Baldauf, F. Gräter (2015).
Force-sensitive autoinhibition of the von Willebrand factor is mediated by interdomain interactions.
Biophys. J. 108(9):2312-21 Link

W. Li, I. B. Baldus, F. Gräter (2015).
Redox potentials of protein disulfide bonds from free-energy calculations.
J. Phys. Chem. B. 119(17):5386-5391 Link

J. Zhou, A. K. Bronowska, J. Le Coq, D. Lietha, F. Gräter (2015).
Allosteric regulation of focal adhesion kinase by PIP₂ and ATP.
Biophys. J. 108(3):698-705 Link

A. Beckmann, S. Xiao, J. P. Müller, D. Mercadante, T. Nüchter, N. Kröger, F. Langhojer, W. Petrich, T. W. Holstein, M. Benoit, F. Gräter, S. Özbek (2015).
A fast recoiling silk-like elastomer facilitates nanosecond nematocyst discharge.
BMC Biol. 13(1):3 Link

D. Peralta, A. K. Bronowska. B. Morgan, Dóka É, K. Van Laer, P. Nagy, F. Gräter, T. P. Dick (2015).
A proton relay enhances H₂O₂ sensitivitz of GADPH to facilitate metabolic adaptation.
Nat. Chem. Biol. 11(2):156-63 Link

F. Gräter, W. Li (2015).
Transition path sampling with quantum/classical mechanics for reaction rates.
J. Methods Mol. Biol., 1215:27-45 Link

2014

U. Hensen, F. Gräter, R. H. Henchman (2014).

Macromolecular entropy can be accurately computed from force.
J. Chem. Theory Comput., 10:4777-4781 Link

S. Xiao and F. Gräter (2014).
Molecular basis of the mechanical hierarchy in myomesin dimers for sarcomere integrity.
Biophys J., 107(4):965-73. Link

S. P. Patil, S. Xiao, K. Gkagkas, B. Markert, F. Gräter (2014).
Viscous friction between crystalline and amorphous phase of dragline silk.
PLoS One., 9(8):e104832. Link

B. Zhou, I. B. Baldus, W. Li, S. A. Edwards, F. Gräter (2014).
Identification of allosteric disulfides from prestress analysis.
Biophys J., 107(3):672-81. Link

G. M. Goñi, C. Epifano, J. Boskovic, M. Camacho-Artacho M, J. Zhou, A. Bronowska, M. T. Martín, M. J. Eck, L. Kremer, F. Gräter, F. L. Gervasio, M. Perez-Moreno, D. Lietha (2014). 
Phosphatidylinositol 4,5-bisphosphate triggers activation of focal adhesion kinase by inducing clustering and conformational changes.
Proc Natl Acad Sci U S A., 111(31):E3177-86. Link

S. P. Patil, B. Markert, F. Gräter (2014).
Rate-dependent behavior of the amorphous phase of spider dragline silk.
Biophys J., 106(11):2511-8. Link

B. I. Costescu, F. Gräter (2014).
Graphene mechanics: II. Atomic stress distribution during indentation until rupture.
Phys Chem Chem Phys., 16(24):12582-90. Link

B. I. Costescu, I. B. Baldus, F. Gräter (2014).
Graphene mechanics: I. Efficient first principles based Morse potential.
Phys Chem Chem Phys., 16(24):12591-8. Link

S. Grässle, V. Huck, K. I. Pappelbaum, C. Gorzelanny, C. Aponte-Santamaría, C. Baldauf, F. Gräter, R. Schneppenheim, T. Obser, S. W. Schneider (2014).
von Willebrand factor directly interacts with DNA from neutrophil extracellular traps.
Arterioscler Thromb Vasc Biol., 34(7):1382-9. Link

M. A. Brehm, V. Huck, C. Aponte-Santamaría, T. Obser, S. Grässle, F. Oyen, U. Budde, S. Schneppenheim, C. Baldauf, F. Gräter, S. W. Schneider, R. Schneppenheim (2014).
von Willebrand disease type 2A phenotypes IIC, IID and IIE: A day in the life of shear-stressed mutant von Willebrand factor.
Thromb Haemost., 112(1):96-108. Link

Z. Palmai, C. Seifert, F. Gräter, E. Balog (2014).
An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis.
PLoS Comput Biol., 10(1):e1003444. Link

2013

C. Seifert and F. Gräter (2013).
Protein mechanics: How force regulates molecular function.
Biochim. Biophys. Acta – General Subjects, 1830(10):4762-8. Link

W. Li, S. A. Edwards, L. Lu, T. Kubar, Patil S. P., H. Grubm, G. Groenhof, and F. Gräter (2013).
Force distribution analysis of mechanochemically reactive dimethylcyclobutene.
ChemPhysChem., 14(12):2687-97. Link

Se. Xiao, Sh. Xiao, and F. Gräter (2013).
Dissecting the structural determinants for the difference in mechanical stability of silk and amyloid beta-sheet stacks.
Phys. Chem. Chem. Phys., 15(22):8765-71. Link

I. B. Costescu and F. Gräter (2013).
Time-resolved force distribution analysis.
BMC Biophys., 6(5):1-5. Link

H. Young, S. A. Edwards, and F. Gräter (2013).
How fast does a signal propagate through proteins.
PLoS One., 8(6):1-5. Link

B. Wang, S. Xiao, S. A. Edwards, and F. Gräter (2013).
Isopeptide bonds mechanically stabilize spy0128 in bacterial pili.
Biophys. J., 104(9):2051-7. Link Additional Resources

C. Debès, M. Wang, G. Caetano-Anollés, and F. Gräter (2013).
Evolutionary optimization of protein folding.
PLoS Comput. Biol., 9(1):1-9. Link

2012

C. Seifert and F. Gräter (2012).
Force distribution reveals signal transductionn in E. coli Hsp90.
Biophys. J., 103(10):2195-2202. Link

M. Kolar, P Hobza, and A. K. Bronowska (2012).
Plugging the explicit sigma-holes in molecular docking.
Chem. Cummun., 49(10):981-3. Link

J. Chen, S. A. Edwards, F. Gräter, and C. Baldauf (2012).
On the cis to trans isomerization of prolyl-peptide bonds under tension.
J. Phys. Chem. B, 116(31):9346-51. Link

W. Li, T. Rudack, K. Gerwert, F. Gräter, and J. Schlitter (2012).
Exploring the multi-dimensional free energy surface of phosphoester hydrolysis with constrained QM/MM dynamics.
J. Chem. Theory Comput., 8(10):3596-3604. Link

S. Edwards, J. Wagner, and F. Gräter (2012).
Dynamic prestress in a globular protein.
PLoS Comput. Biol., 8(5):1-11. Link

I. B. Baldus and F. Gräter (2012).
Mechanical force can fine-tune redox potentials of disulfide bonds.
Biophys. J., 102(3):622-629. Link

2011

F. Xia, A. K. Bronowska, S. Cheng, and F. Gräter (2011).
Base-catalyzed peptide hydrolysis is insensitive to mechanical stress.
J Phys Chem B., 115(33):10126-32. Link

F. Gräter (2011).
Strained molecules: Insights from force distribution analysis.
In P. Comba, editor, Modeling of Molecular Properties, pages 301-310. Wiley-VCH. Link

S. Xiao, S. A. Edwards, and F. Gräter (2011).
A new transferable forcefield for simulating the mechanics of CaCO3 crystals.
The Journal of Physical Chemistry, 115(41):20067-20075. Link

P. Strnad, V. V. Usachov, C. Debès, F. Gräter, D. A. D. Parry, and B.M Omary (2011).
Unique amino acid signatures that are evolutionarily conserved distinguish simple-type, epidermal and hair keratins.
Journal of Cell Science, 124(24):4221-4232. Link

M. Cetinkaya, S. Xiao, and F. Gräter (2011).
Effects of crystalline subunit size on silk fiber mechanics.
Soft Matter, 7(18):8142-8148. Link

F. Berkemeier, M. Bertz, S. Xiao, N. Pinotsis, M. Wilmanns, F. Gräter, and M. Rief (2011).
Fast folding alpha-helices as reversible strain absorbers in the muscle protein myomesin.
Proc. Nat. Acad. Sci., 108(34):14139-44. Link

W. Stacklies, C. Seifert, and F. Gräter (2011).
Implementation of force distribution analysis for molecular dynamics simulations.
BMC Bioinformatics, 12(101). Link

F. Xia, D. Thirumalai, and F. Gräter (2011).
Minimum energy compact structures in force-quench polyubiquitin folding are domain swapped.
Proc. Nat. Acad. Sci., 108(17):6963-8. Link

M. Cetinkaya, S. Xiao, B. Markert, W. Stacklies, and F. Gräter (2011).
Silk fiber mechanics from multiscale force distribution analysis.
Biophys. J., 100(5):1298-305. Link

M. Cetinkaya, S. Xiao, and F. Gräter (2011).
Bottom-up computational modeling of semi-crystalline fibers: From atomistic to continuum scale.
Phys. Chem. Chem. Phys., 13(22):10426-9. Link

M. Zhou, X. Dong, C. Baldauf, H. Chen, Y. Zhou, T. A. Springer, X. Luo, C. Zhong, F. Gräter, and J. Ding (2011).
A novel calcium-binding site of von Willebrand factor A2 domain regulates its cleavage by ADAMTS13.
Blood., 117(5):4623-4631. Link

S. Xiao, W. Stacklies, C. Debès, and F. Gräter (2011).
Force distribution determines optimal length of beta-sheet crystals for mechanical robustness.
Soft Matter, 7(11):1308 – 1311.  Link

2010

M. Geisler, S. Xiao, E. Puchner, F. Gräter, and T. Hugel (2010).
Controlling the structure of proteins at surfaces.
J. Am. Chem. Soc., 132(38):17277-17281. Link

W. Li and F. Gräter (2010).
Atomistic evidence of how force dynamically regulates thiol/disulfide exchange.
J. Am. Chem. Soc., 132(47):16790-5. Link

S. Cheng, M. Cetinkaya, and F. Gräter (2010).
How sequence determines elasticity of disordered proteins.
Biophys. J., 99(12):3863-9, Link

Y. Leng, J. Chen, B. Zhou, and F. Gräter (2010).
Rupture mechanism of aromatic systems from graphite probed with molecular dynamics simulations.
Langmuir, 26:10791 – 10795. Link

S. Cheng, S.A. Edwards, Y. Jiang, and F. Gräter (2010).
Glycosylation enhances peptide hydrophobic collapse by imparing solvation.
ChemPhysChem, 9999:1439 – 4235. Link

2009

W. Stacklies, F. Xia, and F. Gräter (2009).
Dynamic allostery in the methionine repressor revealed by force distribution analysis.
PLoS Comput. Biol., 5(11):e1000574, 11 Link

S. Xiao, W. Stacklies, M. Cetinkaya, B. Markert, and F. Gräter (2009).
Mechanical response of silk crystalline units from force-distribution analysis.
Biophys. J., 96(10):pp.3997 – 4005. Link

W. Stacklies, M. C. Vega, M. Wilmanns, and F. Gräter (2009).
Mechanical network in titin immunoglobulin from force distribution analysis.
PLoS Comput. Biol., 5(3):e1000306, 03 Link

C. Baldauf, R. Schneppenheim, W. Stacklies, T. Obser, A. Pieconka,S. Schneppenheim, U. Budde, J. Zhou, and F. Gräter (2009).
Shear-induced unfolding activates von Willebrand factor A2 domain for proteolysis.
J. Thromb. Haemost., 7:2096 – 2105. Link

2008

F. Gräter, P. Haider, R. Zangi, and B. J. Berne (2008).
Dissecting entropic coiling and poor solvent effects in protein collapse. Link
J. Am. Chem. Soc., 130.

E. Puchner, A. Alexandrovitch, B. Brandmeier, U. Hensen, L. Schaefer, F. Gräter, H. Grubmüller, H. Gaub, and M. Gautel (2008).
Mechanoenzymatics of titin kinase.
Proc. Natl. Acad. Sci. USA, 105(36):13385-13390. Link

2007

K. A. Walther, F. Gräter, L. Dougan, C. L. Badilla, Bruce J. Berne, and J. M (2007).Fernandez.
Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy.
Proc. Natl. Acad. Sci. USA, 104(19):7916-7921. Link

F. Gräter and H. Grubmüller (2007).
Fluctuations of primary ubiquitin folding intermediates in a force clamp.
J. Struct. Biol., 157(3):557 – 569.
ISSN 1047-8477. Link
Advances in Molecular Dynamics Simulations.

A. P. Wiita, R. Perez-Jimenez, K. A. Walther, F. Gräter, B. J. Berne, A. Holmgren, J. M. Sanchez-Ruiz, and J. M. Fernandez (2007).
Probing the chemistry of thioredoxin catalysis with force.
Nature, 450. Link

2006

S. Takamori, M. Holt, K. Stenius, E. A. Lemke, M. Grönborg, D. Riedel, H. Urlaub, S. Schenck, B. Brügger, P. Ringler, S. A. Müller, B. Rammner, F. Gräter, J. S. Hub, B. L. De Groot, G. Mieskes, Y. Moriyama, J. Klingauf, H. Grubmüller, J. Heuser, F. Wieland, and R. Jahn (2006).
Molecular anatomy of a trafficking organelle.
Cell, 127:pp.831 – 846. Link

F. Gräter, B. L. de Groot, and H. Grubmüller (2006).
Ligand-release pathways in the pheromone-binding protein of Bombyx mori.
Structure, pages 1567 – 1576. Link

F. Gräter, W. Xu, and H. Grubmüller (2006).
Pheromone discrimination by the pheromone-binding protein of Bombyx mori.
Structure, pages 1577 – 1586. Link

2005

Frauke Gräter (2005).
Enforced functional protein motions studied by Molecular Dynamics simulations.
PhD thesis, University of Goettingen.

M. Andresen, M. C. Wahl, A. C. Stiel, F. Gräter, L. V. Schäfer, S. Trowitzsch, G. Weber, C. Eggeling, H. Grubmüller, S. W. Hell, and S. Jakobs (2005).
Structure and mechanism of the reversible photoswitch of a fluorescent protein.
Proc. Natl. Acad. Sci. USA, 102(37):13070-13074. Link

F. Gräter, J. Shen, H. Jiang, M. Gautel, and H. Grubmüller (2005).
Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations.
Biophys. J., 88:790-804. Link

W. Li, H. Liu, E. E. Scott, F. Gräter, J. R. Halpert, X. Luo, J. Shen, and H. Jiang (2005).
Possible pathway(s) of testosterone egress from the active site of cytochrome p450 2b1: A steered molecular dynamics simulation.
Drug Metabolism and Disposition, 33(7):910-919. Link

F. Gräter, S. M. Schwarzl, A. Dejaegere, S. Fischer, and J. C. Smith (2005).
Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics.
J. Phys. Chem. B, 109(20):10474-10483, Link
PMID: 16852269.