Theoretische Chemie, Ruhr-Universität Bochum Up

Publications in Peer-Reviewed Journals


[70]    S. Mukherjee, L. V. Schäfer. Spatially Resolved Hydration Thermodynamics in Biomolecular Systems. J. Phys. Chem. B, 2022, DOI: 10.1021/acs.jpcb.2c01088.
[69]    L. Weirich, G. Tusha, E. Engelage, L. V. Schäfer, C. Merten. VCD Spectroscopy Reveals Conformational Changes of Chiral Crown Ethers Upon Complexation of Potassium and Ammonium Cations. Phys. Chem. Chem. Phys., 2022, 24 (19), 11721-11728. DOI: 10.1039/D2CP01309F
[68]    A. Alibakhshi, L. V. Schäfer. Accurate Evaluation of Combustion Enthalpy by Ab-Initio Computations. Sci. Rep., 2022, 12, 5834. DOI: 10.1038/s41598-022-09844-z
[67]    F. Hoffmann, F. A. A. Mulder, L. V. Schäfer. How Much Entropy Is Contained in NMR Relaxation Parameters? J. Phys. Chem. B, 2022, 126 (1), 54-68. DOI: 10.1021/acs.jpcb.1c07786
[66]    A. Dhamija, C. K. Das, Y. H. Ko, Y. Kim, R. D. Mukhopadhyay, A. Gunnam, X. Yu, I.-C. Hwang, L. V. Schäfer, K. Kim. Remotely Controllable Supramolecular Rotor Mounted inside a Porphyrinic Cage. Chem, 2022, 8 (2), 543-556. DOI: 10.1016/j.chempr.2021.12.008


[65]    M. Osorio-Valeriano, F. Altegoer, C. K. Das, W. Steinchen, G. Panis, L. Connolley, G. Giacomelli, H. Feddersen, L. Corrales-Guerrero, P. I. Giammarinaro, J. Hanßmann, M. Bramkamp, P. H. Viollier, S. Murray, L. V. Schäfer, G. Bange, M. Thanbichler. The CTPase Activity of ParB Determines the Size and Dynamics of Prokaryotic DNA Partition Complexes. Mol. Cell, 2021, 81 (19), 3992-4007. DOI: 10.1016/j.molcel.2021.09.004
[64]    C. Päslack, C. K. Das, J. Schlitter, L. V. Schäfer. Spectrally Resolved Estimation of Water Entropy in the Active Site of Human Carbonic Anhydrase II. J. Chem. Theory Comput., 2021, 17 (8), 5409-5418. DOI: 10.1021/acs.jctc.1c00554
[63]    S. Juber, S. Wingbermühle, P. Nuernberger, G. H. Clever, L. V. Schäfer. Thermodynamic Driving Forces of Guest Confinement in a Photoswitchable Cage. Phys. Chem. Chem. Phys., 2021, 23 (12), 7321-7332. DOI: 10.1039/D0CP06495E
[62]    C. Päslack, L. V. Schäfer, M. Heyden. Protein Flexibility Reduces Solvent-Mediated Friction Barriers of Ligand Binding to a Hydrophobic Surface Patch. Phys. Chem. Chem. Phys., 2021, 23 (9), 5665-5672. DOI: 10.1039/D1CP00181G
[61]    S. M. Gopal, S. Wingbermühle, J. Schnatwinkel, S. Juber, C. Herrmann, L. V. Schäfer. Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields. J. Phys. Chem. B, 2021, 125 (1), 24-35. DOI: 10.1021/acs.jpcb.0c08702


[60]    H. Singh, C. K. Das, S. K. Vasa, K. Grohe, L. V. Schäfer, R. Linser. The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics. Angew. Chem. Int. Ed., 2020, 59 (51), 22916-22921. DOI: 10.1002/anie.202009348
[59]    O. Fisette, G. F. Schröder, L. V. Schäfer. Atomistic Structure and Dynamics of the Human MHC-I Peptide-Loading Complex. Proc. Natl. Acad. Sci. U. S. A., 2020, 117 (34), 20597-20606. DOI: 10.1073/pnas.2004445117
[58]    H. Göddeke, L. V. Schäfer. Capturing Substrate Translocation in an ABC Exporter at the Atomic Level. J. Am. Chem. Soc., 2020, 142 (29), 12791-12801. DOI: 10.1021/jacs.0c05502
[57]    S. Wingbermühle, L. V. Schäfer. Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques. J. Chem. Theory Comput., 2020, 16 (7), 4615-4630. DOI: 10.1021/acs.jctc.9b01150
[56]    K. Grohe, S. Patel, C. Hebrank, S. Medina, A. Klein, P. Rovó, S. K. Vasa, H. Singh, B. Vögeli, L. V. Schäfer, R. Linser. Protein Motional Details Revealed by Complementary Structural Biology Techniques. Structure, 2020, 28 (9), 1024-1034. DOI: 10.1016/j.str.2020.06.001
[55]    F. Hoffmann, F. A. A. Mulder, L. V. Schäfer. Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers. J. Chem. Phys., 2020, 152, 084102. DOI: 10.1063/1.5135379
[54]    C. D. Beyer, M. L. Reback, S. M. Gopal, K. A. Nolte, J. A. Finlay, A. S. Clare, L. V. Schäfer, N. Metzler-Nolte, A. Rosenhahn. α-Aminoisobutyric Acid-Stabilized Peptide SAMs with Low Nonspecific Protein Adsorption and Resistance against Marine Biofouling. ACS Sustainable Chem. Eng., 2020, 8 (7), 2665-2671. DOI: 10.1021/acssuschemeng.9b05889


[53]    H. Singh, S. K. Vasa, H. Jangra, P. Rovó, C. Päslack, C. K. Das, H. Zipse, L. V. Schäfer, R. Linser. Fast-Microsecond Dynamics of the Protein-Water Network in the Active Site of Human Carbonic Anhydrase II by Solid-State NMR Spectroscopy. J. Am. Chem. Soc., 2019, 141 (49), 19276-19288. (doi) Supplementary cover
[52]    C. Päslack, L. V. Schäfer, M. Heyden. Atomistic Characterization of Collective Protein-Water-Membrane Dynamics. Phys. Chem. Chem. Phys., 2019, 21, 15958-15965. (doi) Inside back cover
[51]    C. Päslack, J. C. Smith, M. Heyden, L. V. Schäfer. Hydration-Mediated Stiffening of Collective Membrane Dynamics by Cholesterol. Phys. Chem. Chem. Phys., 2019, 21, 10370-10376. (doi)
[50]    C. A. J. Hutter, M. H. Timachi, L. M. Hürlimann, I. Zimmermann, P. Egloff, H. Göddeke, S. Kucher, S. Štefanić, M. Karttunen, L. V. Schäfer, E. Bordignon, M. A. Seeger. The Extracellular Gate Shapes the Energy Profile of an ABC Exporter. Nature Commun., 2019, 10, 2260. (doi)
[49]    S. Wingbermühle, L. V. Schäfer. On Obtaining Boltzmann-Distributed Configurational Ensembles from Expanded Ensemble Simulations with Fast State Mixing. J. Chem. Theory Comput., 2019, 15 (5), 2774-2779. (doi)
[48]    M. Blech, S. Hörer, A. B. Kuhn, S. Kube, H. Göddeke, H. Kiefer, Y. Zang, Y. Alber, S. M. Kast, M. Westermann, M. D. Tully, L. V. Schäfer, P. Garidel. Structure of a Therapeutic Full-Length anti-NPRA IgG4 Antibody: Dissecting Conformational Diversity. Biophys. J., 2019, 116 (9), 1637-1649. (doi)


[47]    C. Bock, F. Löhr, F. Tumulka, K. Reichel, J. Würz, G. Hummer, L. Schäfer, R. Tampé, B. Joseph, F. Bernhard, V. Dötsch, R. Abele. Structural and Functional Insights into the Interaction and Targeting Hub TMD0 of the Polypeptide Transporter TAPL. Sci. Rep., 2018, 8, 15662. (doi)
[46]    M. Prieß, H. Göddeke, G. Groenhof, L. V. Schäfer. Molecular Mechanism of ATP Hydrolysis in an ABC Transporter. ACS Cent. Sci., 2018, 4 (10), 1334-1343. (doi) See also First Reactions in ACS Central Science
[45]    F. Hoffmann, M. Xue, L. V. Schäfer, F. A. A. Mulder. Narrowing the Gap Between Experimental and Computational Determination of Methyl Group Dynamics in Proteins. Phys. Chem. Chem. Phys., 2018, 20, 24577-24590. (doi)
[44]    R. Zhu, W. M. Bloch, J. J. Holstein, S. Mandal, L. V. Schäfer, G. H. Clever. Donor-Site-Directed Rational Assembly of Heteroleptic cis-[Pd2L2L'2] Coordination Cages from Picolyl Ligands. Chem. Eur. J., 2018, 24 (49), 12976-12982. (doi)
[43]    F. Hoffmann, F. A. A. Mulder, L. V. Schäfer. Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields. J. Phys. Chem. B, 2018, 122 (19), 5038-5048. (doi)
[42]    H. Göddeke, M. H. Timachi, C. A. J. Hutter, L. Galazzo, M. A. Seeger, M. Karttunen, E. Bordignon, L. V. Schäfer. Atomistic Mechanism of Large-Scale Conformational Transition in a Heterodimeric ABC Exporter. J. Am. Chem. Soc., 2018, 140 (13), 4543-4551. (doi)


[41]    A. B. Kuhn, S. Kube, A. R. Karow-Zwick, D. Seeliger, P. Garidel, M. Blech, L. V. Schäfer. Improved Solution-State Properties of Monoclonal Antibodies by Targeted Mutations. J. Phys. Chem. B, 2017, 121 (48), 10818-10827. (doi)
[40]    P. Garidel, A. B. Kuhn, L. V. Schäfer, A. R. Karow-Zwick, M. Blech. High-Concentration Protein Formulations: How High is High? Eur. J. Pharm. Biopharm., 2017, 119, 353-360. (doi)
[39]    O. Fisette, S. Wingbermühle, L. V. Schäfer. Partial Dissociation of Truncated Peptides Influences the Structural Dynamics of the MHC I Binding Groove. Front. Immunol., 2017, 8, 408. (doi)
[38]    S. M. Gopal, F. Klumpers, C. Herrmann, L. V. Schäfer. Solvent Effects on Ligand Binding to a Serine Protease. Phys. Chem. Chem. Phys., 2017, 19, 10753-10766. (doi)
[37]    J. Michalowsky, L. V. Schäfer, C. Holm, J. Smiatek. A Refined Polarizable Water Model for the Coarse-Grained MARTINI Force Field with Long-Range Electrostatic Interactions. J. Chem. Phys., 2017, 146, 054501. (doi)
[36]    K. Reichel, O. Fisette, T. Braun, O. F. Lange, G. Hummer, L. V. Schäfer. Systematic Evaluation of CS-Rosetta for Membrane Protein Structure Prediction with Sparse NOE Restraints. Proteins, 2017, 85 (5), 812-826. (doi)


[35]    O. Fisette, C. Päslack, R. Barnes, J. M. Isas, R. Langen, M. Heyden, S. Han, L. V. Schäfer. Hydration Dynamics of a Peripheral Membrane Protein. J. Am. Chem. Soc., 2016, 138 (36), 11526-11535. (doi)
[34]    M. Prieß, L. V. Schäfer. Release of Entropic Spring Reveals Conformational Coupling Mechanism in the ABC Transporter BtuCD-F. Biophys. J., 2016, 110 (11), 2407-2418. (doi)
[33]    O. Fisette, S. Wingbermühle, R. Tampé, L. V. Schäfer. Molecular Mechanism of Peptide Editing in the Tapasin-MHC I Complex. Sci. Rep., 2016, 6, 19085. (doi)


[32]    A. Blees, K. Reichel, S. Trowitzsch, O. Fisette, C. Bock, R. Abele, G. Hummer, L. V. Schäfer, R. Tampé. Assembly of the MHC I Peptide-Loading Complex Determined by a Conserved Ionic Lock-Switch. Sci. Rep., 2015, 5, 17341. (doi)
[31]    G. Fleischmann, O. Fisette, C. Thomas, R. Wieneke, F. Tumulka, C. Schneeweiss, S. Springer, L. V. Schäfer, R. Tampé. Mechanistic Basis for Epitope Proofreading in the Peptide Loading Complex. J. Immunol., 2015, 195 (9), 4503-4513. (doi) See also "In This Issue" highlight in The Journal of Immunology.
[30]    A. B. Kuhn, S. M. Gopal, L. V. Schäfer. On Using Atomistic Solvent Layers in Hybrid All-Atom/Coarse-Grained Molecular Dynamics Simulations. J. Chem. Theory Comput., 2015, 11 (9), 4460-4472. (doi)
[29]    A. Debnath, L. V. Schäfer. Structure and Dynamics of Phospholipid Nanodiscs from All-Atom and Coarse-Grained Simulations. J. Phys. Chem. B, 2015, 119 (23), 6991-7002. (doi)
[28]    S. M. Gopal, A. B. Kuhn, L. V. Schäfer. Systematic Evaluation of Bundled SPC Water for Biomolecular Simulations. Phys. Chem. Chem. Phys., 2015, 17, 8393-8406. (doi)

2012 - 2014

[27]    S. Eggensperger, O. Fisette, D. Parcej, L. V. Schäfer, R. Tampé. An Annular Lipid Belt is Essential for Allosteric Coupling and Viral Inhibition of the Antigen Translocation Complex TAP. J. Biol. Chem., 2014, 289 (48), 33098-33108. (doi) COVER
[26]    P. Lloris-Garcerá, J. S. Slusky, S. Seppälä, M. Prieß, L. V. Schäfer, G. von Heijne. In vivo Trp-Scanning of the Small Multidrug Resistance Protein EmrE Confirms 3D Structure Models. J. Mol. Biol., 2013, 425 (22), 4642-4651. (doi)
[25]    M. Majsnerowska, I. Hänelt, D. Wunnicke, L. V. Schäfer, H.-J. Steinhoff, D. J. Slotboom. Substrate-Induced Conformational Changes in the S-Component ThiT from an Energy Coupling Factor Transporter. Structure, 2013, 21 (5), 861-867. (doi)
[24]    T. A. Wassenaar, H. I. Ingólfsson, M. Prieß, S. J. Marrink, L. V. Schäfer. Mixing Martini: Electrostatic Coupling in Hybrid Atomistic/Coarse-Grained Biomolecular Simulations. J. Phys. Chem. B, 2013, 117 (13), 3516-3530. (doi) COVER
[23]    D. H. de Jong, G. Singh, W. F. D. Bennett, C. Arnarez, T. A. Wassenaar, L. V. Schäfer, X. Periole, D. P. Tieleman, S. J. Marrink. Improved Parameters for the Martini Coarse-Grained Protein Force Field. J. Chem. Theory Comput., 2013, 9 (1), 687-697. (doi)
[22]    J. Domański, S. J. Marrink, L. V. Schäfer. Transmembrane Helices can Induce Domain Formation in Crowded Model Membranes. Biochim. Biophys. Acta - Biomembr., 2012, 1818 (4), 984-994. (doi)

2009 - 2011

[21]    A. Kazaryan, Z. Lan. L. V. Schäfer, W. Thiel, M. Filatov. Surface Hopping Excited-State Dynamics Study of the Photoisomerization of a Light-Driven Fluorene Molecular Rotary Motor. J. Chem. Theory Comput., 2011, 7 (7), 2189-2199. (doi)
[20]    D. H. de Jong, L. V. Schäfer, A. H. de Vries, S. J. Marrink, H. J. C. Berendsen, H. Grubmüller. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations. J. Comput. Chem., 2011, 32 (9), 1919-1928. (doi)
[19]    L. V. Schäfer, D. H. de Jong, A. Holt, A. J. Rzepiela, A. H. de Vries, B. Poolman, J. A. Killian, S. J. Marrink. Lipid Packing Drives the Segregation of Transmembrane Helices into Disordered Lipid Domains in Model Membranes. Proc. Natl. Acad. Sci. U. S. A., 2011, 108 (4), 1343-1348. (doi)
[18]    L. V. Schäfer, S. J. Marrink. Partitioning of Lipids at Domain Boundaries in Model Membranes. Biophys. J., 2010, 99 (12), L91-L93. (doi)
[17]    S. Ramadurai, A. Holt, L. V. Schäfer, V. V. Krasnikov, D. T. S. Rijkers, S. J. Marrink, J. A. Killian, B. Poolman. Influence of Hydrophobic Mismatch and Amino Acid Composition on the Lateral Diffusion of Transmembrane Peptides. Biophys. J., 2010, 99 (5), 1447-1454. (doi)
[16]    N. Kučerka, D. Marquardt, T. A. Harroun, M. P. Nieh, S. R. Wassall, D. H. de Jong, L. V. Schäfer, S. J. Marrink, J. Katsaras. Cholesterol in Bilayers with PUFA Chains: Doping with DMPC or POPC Results in Sterol Reorientation and Membrane-Domain Formation. Biochemistry, 2010, 49 (35), 7485-7493. (doi)
[15]    S. O. Yesylevskyy, L. V. Schäfer, D. Sengupta, S. J. Marrink. Polarizable Water Model for the Coarse-Grained MARTINI Force Field. PLoS Comput. Biol., 2010, 6 (6), e1000810. (doi)
[14]    A. J. Rzepiela, L. V. Schäfer, N. Goga, H. J. Risselada, A. H. de Vries, S. J. Marrink. Reconstruction of Atomistic Details from Coarse-Grained Structures. J. Comput. Chem., 2010, 31 (6), 1333-1343. (doi)
[13]    A. Kazaryan, J. C. M. Kistemaker, L. V. Schäfer, W. R. Browne, B. L. Feringa, M. Filatov. Understanding the Dynamics Behind the Photoisomerization of a Light-Driven Fluorene Molecular Rotary Motor. J. Phys. Chem. A, 2010, 114 (15), 5058–5067. (doi)
[12]    G. Groenhof, M. Boggio-Pasqua, L. V. Schäfer, M. A. Robb. Computer Simulations of Photobiological Processes: The Effect of the Protein Environment. Adv. Quantum Chem., 2010, 59, 181-212. (doi)

2004 - 2008

[11]    L. V. Schäfer, G. Groenhof, M. Boggio-Pasqua, M. A. Robb, H. Grubmüller. Chromophore Protonation State controls Photoswitching of the Fluoroprotein asFP595, PLoS Comput. Biol., 2008, 4 (3), e1000034. (doi)
[10]    E. M. Puchner, A. Alexandrovich, A. L. Kho, U. Hensen, L. V. Schäfer, B. Brandmeier, F. Gräter, H. Grubmüller, H. E. Gaub, M. Gautel. Mechanoenzymatics of Titin Kinase. Proc. Natl. Acad. Sci. U. S. A., 2008, 105 (36), 13385-13390. (doi)
  [9]    G. Groenhof, L. V. Schäfer, M. Boggio-Pasqua, H. Grubmüller, M. A. Robb. Arginine52 Controls the Photoisomerization Process in Photoactive Yellow Protein. J. Am. Chem. Soc., 2008, 130 (11), 3250-3251. (doi)
  [8]    M. Boggio-Pasqua, G. Groenhof, L. V. Schäfer, H. Grubmüller, M. A. Robb. Ultrafast Deactivation Channel for Thymine Dimerization. J. Am. Chem. Soc., 2007, 129 (36), 10996-10997. (doi)
  [7]    G. Groenhof, L. V. Schäfer, M. Boggio-Pasqua, M. Goette, H. Grubmüller, M. A. Robb. Ultrafast Deactivation of an Excited Cytosine-Guanine Base Pair in DNA. J. Am. Chem. Soc., 2007, 129, 6812-6819. (doi)
  [6]    L. V. Schäfer, E. M. Müller, H. E. Gaub, H. Grubmüller. Elastic Properties of Photoswitchable Azobenzene Polymers from Molecular Dynamics Simulations. Angew. Chem. Int. Ed., 2007, 46 (13), 2232-2237. (doi)
  [5]    L. V. Schäfer, G. Groenhof, A. R. Klingen, G. M. Ullmann, M. Boggio-Pasqua, M. A. Robb, H. Grubmüller. Photoswitching of the Fluorescent Protein asFP595: Mechanism, Proton Pathways, and Absorption Spectra. Angew. Chem. Int. Ed., 2007, 46 (4), 530-536. (doi)
  [4]    O. F. Lange, L. V. Schäfer, H. Grubmüller. Flooding in GROMACS: Accelerated Barrier Crossings in Molecular Dynamics. J. Comput. Chem., 2006, 27 (14), 1693-1702. (doi)
  [3]    M. Andresen, M. C. Wahl, A. C. Stiel, F. Gräter, L. V. Schäfer, S. Trowitzsch, G. Weber, C. Eggeling, H. Grubmüller, S. W. Hell, S. Jakobs. Structure and Mechanism of the Reversible Photoswitch of a Fluorescent Protein. Proc. Natl. Acad. Sci. U. S. A., 2005, 102 (37), 13070-13074. (doi)
  [2]    A. Chichinin, T. S. Einfeld, K.-H. Gericke, J. Grunenberg, C. Maul, L. V. Schäfer. Photodissociation Dynamics of SOCl2. Phys. Chem. Chem. Phys., 2005, 7, 301-309. (doi)
  [1]    L. Schäfer, N. Gödecke, O. Ott, C. Maul, K.-H. Gericke, P. S. Shternin, E. V. Orlenko, O. S. Vasyutinskii. Recoil Velocity-Dependent Spin-Orbit State Distribution of Chlorine Photofragments. Chem. Phys., 2004, 301, 213-224. (doi)

Book Chapters, Lecture Notes, etc

  -    H. Göddeke, L. Schäfer. Atomistic Dynamics of Alternating Access Mechanism of an ABC Transporter In: High Performance Computing in Science and Engineering '19 pp. 117-124. Editors: W. E. Nagel, D. H. Kröner, M. M. Resch. Springer, 2021. ISBN: 978-3-030-66792-4
  -    L. V. Schäfer. Coarse-Grain Water and Solutions: Hybrid AA/CG with Martini. In: Computational Trends in Solvation and Transport in Liquids, pp. 333-348. Editors: G. Sutmann, J. Grotendorst, G. Gompper, D. Marx. Lecture Notes of the Jülich CECAM School, Jülich Supercomputing Centre, 2015. ISBN: 978-3-95806-030-2 (Open Access)
  -    G. Groenhof, L. V. Schäfer, M. Boggio-Pasqua, M. A. Robb. Excited State Dynamics in Biomolecules. In: Handbook of Molecular Biophysics: Methods and Applications. Editor: H. G. Bohr. WILEY-VCH, 2009. ISBN: 978-3-527-40702-6

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