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MBM Group - Publications


2012

S. Edwards, J. Wagner, and F. Gräter (2012).
Dynamic prestress in a globular protein.
PLoS Comput. Biol..

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


2011

F. Xia, A. K. Bronowska, S. Cheng, and F. Gräter (2011).
Base-catalyzed peptide hydrolysis is insensitive to mechanical stress.
The Journal of Physical Chemistry B., 115. PDF

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

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. PDF

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. PDF

M. Cetinkaya, S. Xiao, and F. Gräter (2011).
Effects of crystalline subunit size on silk fiber mechanics.
Soft Matter. PDF

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.. PDF

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

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):6963-6968, PDF

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, PDF

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.. PDF

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. PDF

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. PDF


2010

M. Geisler, S. Xiao, E. Puchner, F. Gräter, and T. Hugel (2010).
Controlling the structure of proteins at surfaces.
J. Amer. Chem. Soc..

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

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

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. DOI link

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

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.

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 DOI

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. DOI


2008

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


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. DOI

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. DOI 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. DOI 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. DOI

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. DOI link

F. Gräter, W. Xu, and H. Grubmüller (2006).
Pheromone discrimination by the pheromone-binding protein of bombyx mori.
Structure, pages 1577 - 1586. DOI 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. DOI 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. DOI 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. DOI 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, DOI link
PMID: 16852269.