CB  //  Theory Department  //  Fritz Haber Institute  //  Max Planck Society
Carsten Baldauf
last updated:
October 24, 2018

Publications in Reviewed Journals:

2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2003 to 2008 | theses

2018

  1. Lokare, K.S.; Braun-Cula, B.; Limberg, C.; Jorewitz, M.; Kelly, J.T.; Asmis, K.R.; Leach, S.; Baldauf, C.; Goikoetxea, I.; Sauer, J.:
    Structure and Reactivity of Al-O(H)-Al Moieties in Siloxide Frameworks - Solution and Gasphase Model Studies
    2018 submitted.

  2. Klyne, J.; Bouchet, A.; Ishiuchi, S.; Fujii, M.; Schneider, M.; Baldauf, C.; Dopfer, O.:
    Probing chirality recognition of protonated glutamic acid dimers by gas-phase vibrational spectroscopy and first-principles simulations
    2018 submitted.

  3. Schneider, M.; Baldauf, C.:
    Relative energetics of acetyl-histidine protomers with and without Zn2+ and a benchmark of energy methods
    arXiv.org 2018 to be submitted.


  4. Scutelnic, V.; Perez, M.A.S.; Marianski, M.; Warnke, S.; Gregor, A.; Röthlisberger, U.; Bowers, M.T.; Baldauf, C.; von Helden, G.; Rizzo, T.R.; Seo, J.:
    The Structure of the Protonated Serine Octamer
    J. Am. Chem. Soc. 2018 (140), 7554-7560.


  5. Butera, D.; Passam, F.; Ju, L.; Cook, K.M.; Woon, H.; Aponte-Santamaría, C.; Gardiner, E.; Davis, A.K.; Murphy, D.A.; Bronowska, A.; Luken, B.M.; Baldauf, C.; Jackson, S.; Andrews, R.; Gräter, F.; Hogg, P.J.:
    Autoregulation of von Willebrand factor function by a disulfide bond switch
    Sci. Adv. 2018 (4), eaaq1477.


2017

  1. Schneider, M.; Masellis, C.; Rizzo, T.; Baldauf, C.:
    Kinetically Trapped Liquid-State Conformers of a Sodiated Model Peptide Observed in the Gas Phase
    J. Phys. Chem. A 2017 (121), 6838-6844.


    TOC Figure

  2. Supady, A.; Hecht, S.; Baldauf, C.:
    About Underappreciated Yet Active Conformations of Thiourea Organocatalysts
    Org. Lett. 2017 (19), 4199-4202.

    TOC Figure

  3. De, S.; Musil, F.; Ingram, T.; Baldauf, C.; Ceriotti, M.:
    Mapping and Classifying Molecules from a High-Throughput Structural Database
    J. Cheminform. 2017 (9), 6.

    TOC Figure

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


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


2016

  1. Marianski, M.; Supady, A.; Ingram, T.; Schneider, M.; Baldauf, C.:
    Assessing the accuracy of across-the-scale methods for predicting carbohydrate conformational energies on the example of glucose and α-maltose
    J. Chem. Theory Comput. 2016 (12), 6157-6168.

    TOC Figure

  2. Ropo, M.; Blum, V.; Baldauf, C.:
    Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead
    Sci. Rep. 2016 (6), 35772.


  3. Struwe, W. B.; Baldauf, C.; Hofmann, J.; Rudd, P. M.; Pagel, K.:
    Ion mobility separation of deprotonated oligosaccharide isomers - Evidence for gas-phase charge migration
    Chem. Comm. 2016 (52), 12353-12356.

    The movie (5 MB, mp4) illustrates the movement of protons, and therewith the traversing of the negative charge over the whole molecule. Underlying this visualization is a 20ps ab initio molecular dynamics simulation.



  4. Hoffmann, W.; Marianski, M.; Warnke, S.; Seo, J.; Baldauf, C.; von Helden, G.; Pagel, K.:
    Assessing the stability of alanine-based helices by conformer-selective IR spectroscopy
    Phys. Chem. Chem. Phys. 2016 (18), 19950-19954.


  5. Voronina, L.; Masson, A.; Kamrath, M.Z.; Schubert, F.; Clemmer, D.E.; Baldauf, C.; Rizzo, T.R.:
    Conformations of prolyl-peptide bonds in the bradykinin 1-5 fragment in solution and in the gas phase
    J. Am. Chem. Soc. 2016 (138), 9224-9233.


  6. Posch, S.; Aponte-Santamaría, C.; Schwarzl, R,; Karner, A.; Radtke, M.; Gräter, F.; Obser, T.; König, G.; Brehm, M.A.; Gruber, H.J.; Netz, R.R.; Baldauf, C.; Schneppenheim, R.; Tampé, R.; Hinterdorfer, P.:
    Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor
    Data in Brief 2016 (8), 1080-1087.


  7. Ropo, M.; Schneider, M.; Baldauf, C.; Blum, V.:
    First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids
    Sci. Data 2016 (3), 160009.
    Website: http://aminoaciddb.rz-berlin.mpg.de/


  8. Pecina, A.; Meier, R.; Fanfrlík, J.; Lepšík, M.; Řezáč, J.; Hobza, P.; Baldauf, C.:
    The SQM/COSMO Filter: Reliable Native Pose Identification Based on the Quantum-Mechanical Description of Protein-Ligand Interactions and Implicit COSMO Solvation
    Chem. Comm. 2016 (52), 3312-3315.


    TOC Figure

  9. Lippok, S.; Kolšek, K.; Löf, A.; Eggert, D.; Vanderlinden, W.; Müller, J.P.; König, G.; Obser, T.; Röhrs, K.; Schneppenheim, S.; Budde, U.; Baldauf, C.; Aponte-Santamaría, C.; Gräter, F.; Schneppenheim, R.; Rädler, J.O.; Brehm, M.A.:
    Von Willebrand Factor is dimerized by Protein Disulfide Isomerase
    Blood 2016 (127), 1183-1191.


  10. Chen, P.; Marianski, M.; Baldauf, C.:
    H-Bond Isomerization in Crystalline Cellulose IIII: Proton Hopping versus Hydroxyl Flip-Flop
    ACS Macro Lett. 2016 (5), 50-54.


2015

  1. Baldauf, C.; Rossi, M.:
    Going Clean: Structure and Dynamics of Peptides in the Gas Phase and Paths to Solvation
    J. Phys.: Cond. Matt. 2015 (49), 493002.


  2. Supady, A.; Blum, V.; Baldauf, C.:
    First-Principles Molecular Structure Search with a Genetic Algorithm
    J. Chem. Inf. Model. 2015 (55), 2338-2348.

    Flexible algorithm for optimization of molecules (Fafoom)
    Source code: https://github.com/adrianasupady/fafoom

  3. Aponte-Santamaría, C.; Huck, V.; Posch, S.; Bronowska, A.K.; Grässle, S.; Brehm, M.A.; Obser, T.; Schneppenheim, R.; Hinterdorfer, P.; Schneider, S.W.; Baldauf, C.; Gräter, F.:
    Force-sensitive autoinhibition of the von Willebrand factor mediated by interdomain interactions
    Biophys. J. 2015 (108), 2312-2321.


  4. Schubert, F.; Rossi, M.; Baldauf, C.; Pagel, K.; Warnke, S.; von Helden, G.; Filsinger, F.; Kupser, P.; Meijer, G.; Salwiczek, M.; Koksch, B.; Scheffler, M.; Blum, V.:
    Exploring the conformational preferences of 20-residue peptides in isolation: Ac-Ala19-Lys + H+ vs. Ac-Lys-Ala19 + H+ and the current reach of DFT
    Phys. Chem. Chem. Phys. 2015 (17), 7373-7385.


  5. Mortier, J.; Nyakatura, E.K.; Reimann, O., Huhmann, S.; Daldrop, J.O.; Baldauf, C.; Wolber, G.; Miettinen, M.S.; Koksch, B.:
    Coiled-coils in phage display screening: Insight into exceptional selectivity provided by molecular dynamics
    J. Chem. Inf. Model. 2015 (55), 495-500.


  6. Schubert, F.; Pagel, K.; Rossi, M.; Warnke, S.; Salwiczek, M.; Koksch, B.; von Helden, G.; Blum, V.; Baldauf, C.; Scheffler, M.:
    Native like helices in a specially designed β peptide in the gas phase
    Phys. Chem. Chem. Phys. 2015 (17), 5376-5385.


2014

  1. Nyakatura, E.K.; Mortier, J.; Radtke, V.S.; Wieczorek, S.; Rezaei Araghi, R.; Baldauf, C.; Wolber, G.; Koksch, B.;
    β- and γ-Amino Acids at α-Helical Interfaces: Toward the Formation of Highly Stable Foldameric Coiled Coils
    ACS Med. Chem. Lett. 2014 (5), 1300-1303.


  2. Warnke, S.; Baldauf, C.; Bowers, M.T.; Pagel, K.; von Helden, G;
    Photodissociation of Conformer-Selected Ubiquitin Ions Reveals Site-Specific cis/trans Isomerization of Proline Peptide Bonds
    J. Am. Chem. Soc. 2014 (136), 10308-10314.


  3. Grässle, S.; Huck, V.; Pappelbaum, K.I.; Gorzelanny, C.; Aponte-Santamaría, C.; Baldauf, C.; Gräter, F.; Schneppenheim, R.; Obser, T.; Schneider, S.W.;
    von Willebrand Factor Directly Interacts With DNA From Neutrophil Extracellular Traps
    Arterioscler. Thromb. Vasc. Biol. 2014 (34), 1382-1389.


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


  5. Nyakatura, E.K.; Rezaei Araghi, R.; Mortier, J.; Wieczorek, S.; Baldauf, C.; Wolber, G.; Koksch, B.;
    An Unusual Interstrand H-Bond Stabilizes the Heteroassembly of Helical αβγ-Chimeras with Natural Peptides
    ACS Chem. Biol. 2014 (9), 613-616.

2013

  1. Baldauf, C.; Pagel, K.; Warnke, S.; von Helden, G.; Koksch, B.; Blum, V.; Scheffler, M.;
    How Cations Change Peptide Structure
    Chem. Eur. J. 2013 (19), 11224-11234.

2012

  1. Baldauf, C.; Hofmann, H.-J.;
    Ab initio MO Theory - An Important Tool in Foldamer Research: Prediction of Helices in Oligomers of ω-Amino Acids
    Helv. Chim. Acta 2012 (95), 2348-2383.

  2. Chen, J.; Edwards, S. A.; Gräter, F.; Baldauf, C.;
    On the cis to trans isomerization of prolyl-peptide bonds under tension
    J. Phys. Chem. B 2012 (116), 9346-9351.

2011

  1. Diwold, K.; Himmelbach, D.; Meier, R.; Baldauf, C.; Middendorf, M.;
    Bonding as a Swarm: Applying Bee Nest-Site Selection Behaviour to Protein Docking
    Peer-reviewed conference article: 13th Annual Genetic and Evolutionary Computation Conference, GECCO 2011, Proceedings, Dublin, Ireland, July 12-16, 2011.

  2. Rezaei Araghi, R.; Baldauf, C.; Gerling, U. I. M.; Cadicamo, C. D.; Koksch, B.;
    A systematic study of fundamentals in α-helical coiled coil mimicry by alternating sequences of β- and γ-amino acids
    Amino Acids 2011 (41), 733-742.

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

2010

  1. Meier, R.; Pippel, M.; Brandt, F.; Sippl, W.; Baldauf, C.;
    Paradocks - A framework for molecular docking with population-based metaheuristics
    J. Chem. Inf. Model. 2010 (50), 879-889.

    The Parallel Docking Suite (Paradocks)
    Source code: https://github.com/cbaldauf/paradocks

    TOC Figure

  2. Rezai Araghi, R.; Jäckel, C.; Cölfen, H.; Salwiczek, M.; Völkel, A.; Wagner, S.C.; Wieczorek, S.; Baldauf, C.; Koksch, B.;
    A β/γ Motif To Mimic α-Helical Turns In Proteins
    ChemBioChem 2010 (11), 335-339.
    DOI: 10.1002/cbic.200900700
    pdf

2009

  1. Baldauf, C.; Schneppenheim, R.; Stacklies, W.; Obser, T.; Pieconka, A.; Schneppenheim, S.; Budde, U.; Gräter, F.;
    Shear-Induced Unfolding Activates von Willebrand Factor A2 Domain for Proteolysis
    J. Thromb. Haemost. 2009 (7), 2096-2105.
    DOI: 10.1111/j.1538-7836.2009.03640.x; arXiv [physics.bio-ph]: arxiv:0904.3951v1
    pdf ; SuppInf ; PDB

    The movie (8.4 MB, mp4) illustrates the forced unfolding of the VWF A2 domain and the exposure of the ADAMTS13 cleavage site (highlighted in green). Simulations were performed with Gromacs and the OPLS-AA force field.

  2. Sharma, G. V. M.; Babu, B. S.; Ramakrishna, K. V. S.; Nagendar, P.; Kunwar, A. C.; Schramm, P.; Baldauf, C.; Hofmann, H.-J.;
    Synthesis and Structure of α/δ-Hybrid Peptides - Access to Novel Helix Patterns in Foldamers
    Chem. Eur. J. 2009 (15), 5552-5566.
    DOI: 10.1002/chem.200802078
    pdf

2003 to 2008

  1. Baldauf, C.; Pisabarro, M. T.;
    Stable Hairpins with β-Peptides - Route to Tackle Protein-Protein Interactions
    J. Phys. Chem. B 2008 (112), 7581-7591.
    DOI: 10.1021/jp076838r
    pdf

  2. Scheike, J. A.; Baldauf, C.; Spengler, J.; Albericio, F.; Pisabarro, M. T.; Koksch, B.;
    Amide-to-Ester Substitution in Coiled Coils: The Effect of Removing Hydrogen Bonds on Protein Structure
    Angew. Chem. 2007 (119), 7912-7916. Angew. Chem. Int. Ed. 2007 (46), 7766-7769.
    DOI: 10.1002/anie.200702218
    pdf ; supp

  3. Baldauf, C.; Günther, R.; Hofmann, H.-J.;
    Theoretical Prediction of the Basic Helix Types in α,β-Hybrid Peptides
    Biopolymers: Peptide Science 2006 (84), 408-413.
    DOI: 10.1002/bip.20493
    pdf ; supp

  4. Baldauf, C.; Günther, R.; Hofmann, H.-J.;
    Helices in Peptoids of α- and β-Peptides
    Phys. Bio. 2006 (3), S1-S9.
    DOI: 10.1088/1478-3975/3/1/S01
    pdf ; supp ; supp1

  5. Baldauf, C.; Günther, R.; Hofmann, H.-J.;
    Helix Formation in α,γ- and β,γ-Hybrid Peptides - Theoretical Insights into Mimicry of α- and β-Peptides
    J. Org. Chem. 2006 (71), 1200-1208.
    DOI: 10.1021/jo052340e
    pdf ; supp ; supp1 ; supp2 ; supp3 ; supp4

  6. Lang, M.; De Pol, S.; Baldauf, C.; Hofmann, H.-J.; Reiser, O.; Beck-Sickinger, A. G.;
    Identification of the Key Residue of Calcitonin Gene Related Peptide (CGRP) 27-37 to Obtain Antagonists with Picomolar Affinity at the CGRP Receptor
    J. Med. Chem. 2006 (49), 616-624.
    DOI: 10.1021/jm050613s
    pdf

  7. Baldauf, C.; Günther, R.; Hofmann, H.-J.;
    Side Chain Control of Folding of the Homologous α-, β- and γ-Peptides into "Mixed" Helices (β-Helices)
    Biopolymers: Peptide Science 2005 (80), 675-687.
    DOI: 10.1002/bip.20249
    pdf

  8. Baldauf, C.; Günther, R.; Hofmann, H.-J.;
    Control of Helix Formation in Vinylogous γ-Peptides by (E)- and (Z)- Double Bonds - A Way to Ion Channels and Monomolecular Nanotubes
    J. Org. Chem. 2005 (70), 5351-5361.
    DOI: 10.1021/jo0480489
    pdf ; supp
    TOC Figure

  9. Baldauf, C.; Günther, R.; Hofmann, H.-J.;
    δ-Peptides and δ-Amino Acids as Tools for Peptide Structure Design - A Theoretical Study
    J. Org. Chem. 2004 (69), 6214-6220.
    DOI: 10.1021/jo049535r
    pdf ; supp

  10. Baldauf, C.; Günther, R.; Hofmann, H.-J.;
    Conformational properties of sulfonamido peptides
    J. Mol. Struct. (Theochem) 2004 (675), 19-28.
    DOI: 10.1016/j.theochem.2003.12.029
    pdf

  11. Baldauf, C.; Günther, R.; Hofmann, H.-J.;
    Mixed Helices - A General Folding Pattern in Homologous Peptides?
    Angew. Chem. 2004 (116), 1621-1624. Angew. Chem. Int. Ed. 2004 (43), 1594-1597.
    DOI: 10.1002/anie.200353249
    pdf ; supp

  12. Baldauf, C.; Günther, R.; Hofmann, H.-J.;
    Helix Formation and Folding in γ-Peptides and Their Vinylogues
    Helv. Chim. Acta 2003 (86), 2573-2588.
    DOI: 10.1002/hlca.200390208
    pdf ; supp

Diplomarbeit (Diploma thesis):
Sulfonamidopeptide und vinyloge Peptide als Foldamere. Universität Leipzig 2002.
pdf[1442k]

Doktorarbeit (Ph.D. thesis):
Secondary Structure Formation in Homologous Peptides. Universität Leipzig 2005.
pdf[3663k]

Habilitation:
Biomolecular Simulations - From mechanics of a blood protein to peptides in isolation to molecular structure sampling. Freie Universität Berlin 2016.
pdf[35MB]