Publications


2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997 1996 1995

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2019

  • Ingo Schelter, Johannes M Foerster, Alastair T Gardiner, Aleksander W Roszak, Richard Cogdell, G. Matthias Ullmann, Thiago Branquinho de Queiroz, Stephan Kuemmel Assessing Density Functional Theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2. submitted

  • Max Willistein, Dominique F Bechtel, Christina S Müller, Ulrike Demmer, Larissa Heimann, Kanwal Kayastha, Volker Schünemann, Antonio J Pierik, G Matthias Ullmann, Ulrich Ermler, Matthias Boll Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors. Nature communications, 10: 2074, 2019



    • 2018

  • JM Foerster, I Poehner, GM Ullmann. MCMap - A Computational Tool for Mapping Energy Landscapes of Transient Protein–Protein Interactions. ACS Omega, 3: 6465-6475, 2018



    • 2017

  • M Culka, SG Huwiler, M Boll, GM Ullmann. Breaking Benzene Aromaticity - Computational Insights into the Mechanism of the Tungsten-Containing Benzoyl-CoA Reductase. J. Amer. Chem. Soc., 139: 14488-14500, 2017

  • M Culka, FJ Gisdon, GM Ullmann. Computational Biochemistry - Enzyme Mechanisms Explored. Adv. Prot. Chem. Struct. Biol., 109, Pages 77-112, 2017

  • E Bombarda, GM Ullmann. Continuum Electrostatic Calculation on Bovine Rhodopsin: Protonation and the Effect of the Membrane Potential. Photochemistry and Photobiology, in press, 2017

  • Andreas F Geiss, Raghav Khandelwal, Dieter Baurecht, Christina Bliem, Ciril Reiner-Rozman, Michael Boersch, G Matthias Ullmann, Leslie M Loew, Renate LC Naumann. pH and Potential Transients of the bc1 Complex Co-Reconstituted in Proteo-Lipobeads with the Reaction Center from Rb. sphaeroides. J. Phys. Chem. B , 121, 143-152, 2017

  • C. Diederich, M. Leypold, M. Culka, H. Weber, R. Breinbauer, G. M. Ullmann, W. Blankenfeldt. Mechanisms and Specificity of Phenazine Biosynthesis Protein PhzF. Scientific Reports , 7, 6272, 2017


    • 2016

  • Florian J. Gisdon, Martin Culka, G. Matthias Ullmann. PyCPR -- A Python-based Implementation of the Conjugate Peak Refinement (CPR) Algorithm for Finding Transition State Structures. J. Mol. Model., 22: 242, 2016
    [PDF File] [Software]

  • G. Matthias Ullmann, Lars Mueller, and Elisa Bombarda. Theoretical Analysis of Electron Transfer in Proteins: From Simple Proteins to Complex Machineries. In Advances in Photosynthesis and Respiration Vol. 41: Cytochromes and Cytochrome Complexes: Structure and Function. (William A. Cramer and Toivo Kallas eds), Springer Verlag. pp.99-127, 2016
    [PDF File]

  • Matthias Boll, Oliver Einsle, Ulrich Ermler, Peter Kroneck, Matthias Ullmann. Structure and function of tungsten-containing acetylene hydratase and benzoyl-CoA reductase. J. Mol. Microbiol. Biotech., 26: 119-137, 2016
    [PDF File]

  • Brinda Selvaraja, Wolfgang Buckel, Bernard T. Golding, G. Matthias Ullmann and Berta M. Martins. Structure and function of 4-hydroxyphenylacetate decarboxylase and its cognate activating enzyme. J. Mol. Microbiol. Biotech., 26: 76-91, 2016
    [PDF File]

  • Ralf Rabus, Matthias Boll, Johann Heider, Rainer U. Meckenstock, Wolfgang Buckel, Oliver Einsle, Ulrich Ermler, Bernard T. Golding, Robert Gunsalus, Peter M.H. Kroneck, Martin Krüger, Tillmann Lueders, Berta M. Martins, Florin Musat, Hans H. Richnow, Bernhard Schink, Jana Seifert, Maciej Szaleniec, Tina Treude, G. Matthias Ullmann, Carsten Vogt, Martin von Bergen, and Heinz Wilkes. Anaerobic Microbial Degradation of Hydrocarbons: From Enzymatic Reactions to the Environment J. Mol. Microbiol. Biotech., 26: 5-28, 2016
    [PDF File]


    • 2015

  • G. Matthias Ullmann. Mit Computern die Bausteine des Lebens erschließen. UBT Spektrum, 2/15, 22-25, 2015
    [PDF File]

  • Silke A. Wieninger and G. Matthias Ullmann. CoMoDo: Identifying Dynamic Protein Domains Based on Covariances of Motion. J. Chem. Theory Comput. , 11: 2841–2854, 2015
    [PDF File] [Supporting Informations] [Software]

  • Sebastian R Beyer, Lars Müller, June Southall, Richard J Cogdell, G Matthias Ullmann, Jürgen Köhler. The Open, the Closed, and the Empty: Time-Resolved Fluorescence Spectroscopy and Computational Analysis of RC-LH1 Complexes from Rhodopseudomonas palustris. J. Chem. Phys. B, 119: 1362-1373, 2015
    [PDF File] [Supporting Informations]

    • 2014

  • Irene Díaz-Moreno, Rinske Hulsker, Pavol Skubak, Johannes M. Foerster, Davide Cavazzini, Michelina G. Finiguerra, Antonio Díaz-Quintana, Blas Moreno-Beltrán, Gian-Luigi Rossi, G. Matthias Ullmann, Navraj S. Pannu, Miguel A. De la Rosa, Marcellus Ubbink. The dynamic complex of cytochrome c6 and cytochrome f studied with paramagnetic NMR spectroscopy. BBA Bioenergetics, 1837: 1305-1315, 2014
    [PDF File]

  • G. Matthias Ullmann and Elisa Bombarda. Continuum Electrostatic Analysis of Proteins. In G. Náray-Szabó (ed.), Protein Modelling; Springer : 135-163, 2014
    [PDF File]

  • Jia-Ying Guan, Johannes M. Foerster, Jan W. Drijfhout, Monika Timmer, Anneloes Blok, G. Matthias Ullmann, and Marcellus Ubbink. An Ensemble of Rapidly Interconverting Orientations in Electrostatic Protein–Peptide Complexes Characterized by NMR Spectroscopy. ChemBioChem, 15: 556-566, 2014
    [PDF File] [Supporting Informations]

    • 2013

  • Mikolaj Feliks, Berta M. Martins, and G. Matthias Ullmann. Catalytic Mechanism of the Glycyl Radical Enzyme 4-Hydroxyphenylacetate Decarboxylase from Continuum Electrostatic and QC/MM Calculations. J. Amer. Chem. Soc., 135: 14574-14585, 2013
    [PDF File] [Supporting Informations] [Supporting Informations - Structures] [Movie]

  • Sandra Scanu, Johannes M. Foerster, G. Matthias Ullmann, and Marcellus Ubbink. Loss of electrostatic interactions causes increase of dynamics within the plastocyanin-cytochrome f complex. Biochemistry., 52: 6615–6626, 2013
    [PDF File] [Supporting Informations]

  • Johannes W.R. Martini, G. Matthias Ullmann, and Martin Schlather. The Meaning of the Decoupled Sites Representation in Terms of Statistical Mechanics and Stochastics. MATCH - Comm. Math. Comp. Chem., 70: 829-850, 2013
    [PDF File]

  • Sandra Scanu, Johannes M. Foerster, G. Matthias Ullmann, and Marcellus Ubbink. Role of Hydrophobic Interactions in the Encounter Complex Formation of the Plastocyanin and Cytochrome Complex Revealed by Paramagnetic NMR Spectroscopy. J. Amer. Chem. Soc., 135: 7681–769, 2013
    [PDF File] [Supporting Informations]

  • G. Matthias Ullmann and Elisa Bombarda. pKa values and redox potentials of proteins. What do they mean? Biol. Chem., 394: 611-619, 2013
    [PDF File]

  • Johannes W.R. Martini, Martin Schlather, and G. Matthias Ullmann. On the interaction of two different types of ligands binding to the same molecule. Part I: basics and the transfer of the decoupled sites representation to systems with n and one binding sites. J. Math. Chem., 51: 672-695, 2013
    [PDF File]

  • Johannes W.R. Martini, Martin Schlather, and G. Matthias Ullmann. On the interaction of different types of ligands binding to t he same molecule. Part II: systems with n to 2 and n to 3 binding sites. J. Math. Chem., 51: 696-714, 2013
    [PDF File]

  • Johannes W.R. Martini and G. Matthias Ullmann. A mathematical view on the decoupled sites representation. J. Math. Biol., 66: 477-503, 2013
    [PDF File]

    • 2012

  • Pia Rücker, Silke A. Wieninger, G. Matthias Ullmann, and Heinrich Sticht. pH-Dependent Molecular Dynamics of Vesicular Stomatitis Virus Glycoprotein G. Proteins, 80: 2601–2613, 2012
    [PDF File] [Supporting Informations]

  • G. Matthias Ullmann, Veronica I. Dumit, and Elisa Bombarda. Methods Based on Continuum Electrostatics and Their Application to Flavoproteins. In "Handbook of Flavoproteins" (Susan Miller, Bruce Palfey and Russ Hille, eds), in press, 2012

  • R. Thomas Ullmann, Susana L. A. Andrade, and G. Matthias Ullmann. Thermodynamics of transport through the ammonium transporter Amt-1 investigated with free energy calculations. J. Phys. Chem. B, 116: 9690-9703, 2012
    [PDF File] [Supporting Informations]

  • Siriporn Promsri, G. Matthias Ullmann, and Supot Hannongbua. Molecular dynamics simulation of HIV-1 fusion domain-membrane complexes: Insight into the N-terminal gp41 fusion mechanism. Biophys. Chem., 170: 9-16, 2012
    [PDF File]

  • Mikolaj Feliks and G. Matthias Ullmann. Glycerol Dehydratation by the B12-Independent Enzyme May Not Involve the Migration of a Hydroxyl Group: A Computational Study J. Phys. Chem. B, 116: 7076-7087, 2012
    [PDF File] [Supporting Informations] [Movie]

  • R. Thomas Ullmann and G. Matthias Ullmann. GMCT : A Monte Carlo Simulation package for macromolecular receptors. J. Comput. Chem., 33: 887-900, 2012
    [PDF File] [Software]

  • Tijana Grove, G. Matthias Ullmann, and Nenad M. Kostic. Simultaneous True, Gated, and Coupled Electron-Transfer Reactions and the Energetics of Protein Rearrangement. J. Inorg. Biochem., 106: 143–150, 2012
    [PDF File] [Supporting Informations]

    • 2011

  • Berta M. Martins, Martin Blaser, Mikolaj Feliks, G. Matthias Ullmann, Wolfgang Buckel and Thorsten Selmer. Crystal structure of 4-hydroxyphenylacetate decarboxylase, a two [4Fe-4S] clusters-containing glycyl radical enzyme. J. Am. Chem. Soc., 133: 14666–14674, 2011
    [PDF File] [Supporting Informations]

  • R. Thomas Ullmann and G. Matthias Ullmann. Coupling of Protonation, Reduction and Conformational Change in Azurin from Pseudomonas aeruginosa Investigated with Free Energy Measures of Cooperativity. J. Phys. Chem. B, 115: 10346-10359, 2011
    [PDF File] [Supporting Informations]

  • Silke A. Wieninger, Engin H. Serpersu and G. Matthias Ullmann. Differential effects of ligand binding on protein dynamics. In Proceedings of the 4th European Conference on Chemistry for Life Science. Medimon International Proceedings, 2011
    [PDF File]

  • Tobias J. Pflock, Lisa Krapf, Silke Oellerich, June Southall, Richard J. Cogdell, G. Matthias Ullmann and Jürgen Köhler. The electronically excited states of LH2 complexes from Rps. acidophila strain 10050 studied by time-resolved spectroscopy and Dynamic Monte Carlo simulations. I: Isolated, Non-Interacting LH2 complexes. J. Phys. Chem. B., 115: 8813-8820, 2011
    [PDF File] [Supporting Informations]

  • Tobias J. Pflock, Lisa Krapf, Silke Oellerich, June Southall, Richard J. Cogdell, G. Matthias Ullmann and Jürgen Köhler. The electronically excited states of LH2 complexes from Rps. acidophila strain 10050 studied by time-resolved spectroscopy and Dynamic Monte Carlo simulations. II: Homo-Arrays of LH2 complexes reconstituted into phospholipid model membranes. J. Phys. Chem. B., 115: 8821-8831, 2011
    [PDF File] [Supporting Informations]

  • Veronica I. Dumit, Nestor Cortez and G. Matthias Ullmann. Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid. Proteins: Structure, Function, and Bioinformatics, 79: 2076–2085, 2011
    [PDF File]

  • Silke A. Wieninger, Engin H. Serpersu and G. Matthias Ullmann. ATP Binding Enables Broad Antibiotic Selectivity of Aminoglycoside Phosphotransferase(3)-IIIa: An Elastic Network Analysis. J. Mol. Biol., 409 : 450-465, 2011
    [PDF File] [Supporting Informations]

  • Elisa Bombarda and G. Matthias Ullmann. Continuum electrostatic investigations of charge transfer processes in biological molecules using a microstate description. Faraday Discussions, 148: 173-193, 2011
    [PDF File]

  • E.-M. Krammer, S. Bernad, G. M. Ullmann, A Hickman and P. Sebban. Chemical Evidence for the Dawn of Life on Earth. Aust. J. Chem., 64 : 16-22, 2011
    [PDF File]

  • R. Thomas Ullmann and G. Matthias Ullmann. A Generalized Free Energy Perturbation Theory Accounting for End States with Differing Configuration Space Volume. J. Phys. Chem. B, 115 : 507-521, 2011
    [PDF File] [Supporting Informations]

    • 2010

  • Qamar Bashir, Alexander Volkov, G. Matthias Ullmann, and Marcellus Ubbink. Visualization of the Encounter Ensemble of the Transient Electron Transfer Complex of Cytochrome c and Cytochrome c Peroxidase. J. Am Chem. Soc., 132 : 241-247, 2010
    [PDF File] [Supporting Informations] [Zip-File] [Distribution - PDB-File]

  • Mirco S. Till and G. Matthias Ullmann. McVol - A program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm. J. Mol. Mod., 16 : 419-429, 2010
    [PDF File] [Software]

  • Elisa Bombarda and G. Matthias Ullmann. pH-dependent pKa Values in Proteins - A Theoretical Analysis of Protonation Energies with Practical Consequences for Enzymatic Reactions. J. Phys. Chem. B, 114 : 1994-2003, 2010
    [PDF File]

  • Veronica Dumit, Timm Essigke, Nestor Cortez, and G. Matthias Ullmann. Electrostatics Calculations on the Reaction Mechanism of Ferredoxin-NADH-Reductase. J. Mol. Biol.,397 : 814-825, 2010
    [PDF File] [Supporting Informations]

  • Alexander Volkov, Qamar Bashir, Jonathan A. R Worrall, G. Matthias Ullmann, and Marcellus Ubbink. Shifting the Equilibrium between the Encounter State and the Specific Form of a Protein Complex by Interfacial Point Mutations. J. Am Chem. Soc., 132 : 11487-11495, 2010
    [PDF File] [Supporting Informations]

  • Olivia Spiegelhauer, Sophia Mende, Frank Dickert, Dimitry Nicks, Stefan H. Knauer, G. Matthias Ullmann and Holger Dobbek. Cysteine as a Modulator Residue in the Active Site of Xenobiotic Reductase A: A Structural, Thermodynamic and Kinetic Study. J. Mol. Biol., 398 : 66-82, 2010
    [PDF File] [Supporting Informations]

    • 2009

  • Eva-Maria Krammer, Pierre Sebban and G. Matthias Ullmann. Conservation of cofactor binding motifs and proton transfer pathways in photosynthetic reaction centers analyzed by profile Hidden Markov Models. Biochemistry, 48 : 1230-1243, 2009
    [PDF File] [Supporting Informations] [Zip-File - Alignments]
    [Sequence Alignment Information]

  • Eva-Maria Krammer, Mirco S. Till, Pierre Sebban and G. Matthias Ullmann. Proton Transfer Pathways in Photosynthetic Reaction Centers Analyzed by Profile Hidden Markov Models and Network Calculations. J. Mol. Biol., 388 : 631-643, 2009
    [PDF File] [Supporting Informations] [TGZ-File - Alignments]
    [Sequence Alignment Information]

  • Olivia Spiegelhauer, Frank Dickert, Sophia Mende, Dimitry Nicks, Russ Hille, G. Matthias Ullmann and Holger Dobbek. The reductive and oxidative half-reactions of Xenobiotic Reductase A from Pseudomonas putida 86. Biochemistry, 48 : 11412-11420, 2009
    [PDF File]

    • 2008

  • Mirco S. Till, Torsten Becker, Timm Essigke and G. Matthias Ullmann. Simulating the Proton Transfer in Gramicidin A by a Sequential Dynamical Monte Carlo Method. J. Phys. Chem. B, 112: 13401-13410, 2008
    [PDF File]

  • G. Matthias Ullmann, Edda Kloppmann, Timm Essigke, Eva-Maria Krammer, Astrid R. Klingen, Torsten Becker, Elisa Bombarda. Investigating the Mechanisms of Photosynthetic Proteins Using Continuum Electrostatics. Photosynth. Res., 97: 33-53, 2008
    [PDF File]

  • Durba Sengupta, Jeremy C. Smith, and G. Matthias Ullmann. Partitioning of Side-chain Analogues in a Five-slab Membrane Model BBA Biomembranes, 1778: 2234-2243, 2008
    [PDF File]

  • Verena Becker, Durba Sengupta, Stephan Heinzer, Robin Ketteler, G. Matthias Ullmann, Jeremy C. Smith, Matthias Weiss, and Ursula Klingmüller. Packing Density of the Erythropoietin Receptor Transmembrane Domain Correlates with Amplification of Biological Responses. Biochemistry, 47: 11771-11782, 2008
    [PDF File]

  • Torsten Becker and G. Matthias Ullmann. Kinetic Simulations of the C-Subunit of the Bacterial Reaction Center. In: Photosynthesis. Energy from the Sun. Allen, J.F.; Osmond, B.; Goldbeck, J.H.; Gantt, E. (Eds.), Springer, Dordrecht: 553-557
    [PDF File]

  • Eva-Maria Krammer and G. Matthias Ullmann. The role of AspL213 for stabilizing semiquinone binding to the photosynthetic reaction center. In: Photosynthesis. Energy from the Sun. Allen, J.F.; Osmond, B.; Goldbeck, J.H.; Gantt, E. (Eds.), Springer, Dordrecht: 127-131
    [PDF File]

  • Eva-Maria Krammer and G. Matthias Ullmann. Functional Important Residues of the Oxygen Evolving Mechanism Located in the D1 Subunit of Photosystem II. In: From Computational Biophysics to Systems Biology (CBSB08),Edt.: U. H. E. Hansmann, J. Meinke, S. Mohanty, W. Nadler, O. Zimmermann, NIC Series, 265-268, 2008.
    [PDF File]

    • 2007

  • Lars V. Schäfer, Gerrit Groenhof, Astrid R. Klingen, G. Matthias Ullmann, Martial Boggio-Pasqua, Michael A. Robb, and Helmut Grubmüller. Photoswitching Mechanism of the Fluorescent Protein asFP595: Proton Pathways, pH Dependence, and Absorption Spectra. Angewandte Chemie, 46, 530-536, 2007
    [PDF File]

  • Nadine Homeyer, Timm Essigke, Heike Meiselbach, G. Matthias Ullmann, Heinrich Sticht. Effect of HPr Phosphorylation on Structure, Dynamics, and Interactions in the Course of Transcriptional Control. J. Mol. Mod., 13, 431-444, 2007
    [PDF File] [Supporting Informations]

  • Zoe Cournia, G. Matthias Ullmann, Jeremy C. Smith. Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine (DPPC) membrane: A Molecular Dynamics Simulation Study. J. Phys. Chem. B, 111, 1786-1801, 2007
    [PDF File] [Supporting Informations]

  • Grazyna B. Seiffert, G. Matthias Ullmann, Albrecht Messerschmidt, Bernhard Schink, Peter M. H. Kroneck and Oliver Einsle. Structure of the Non Redox-Active Tungsten/[4Fe:4S] Enzyme Acetylene Hydratase. Proc. Natl. Acad. Sci. USA, 104, 3073-3077, 2007
    [PDF File]

  • Torsten Becker, R. Thomas Ullmann and G. Matthias Ullmann. Simulation of the Electron Transfer between the Tetraheme-Subunit and the Special Pair of the Photosynthetic Reaction Center using a Microstate Description. J. Phys. Chem. B, 1111, 2957-2968, 2007
    [PDF File]

  • Astrid R. Klingen, Hildur Palsdottir, Carola Hunte, and G. Matthias Ullmann. Redox-linked Protonation State Changes in Cytochrome bc1 Identified by Poisson-Boltzmann Electrostatics Calculations. Biochem. Biophys. Acta Bioenergetics, 1767, 204-221, 2007
    [PDF File] [Supporting Informations]

  • Edda Kloppmann, G. Matthias Ullmann and Torsten Becker. An Extended Dead-End Elimination Algorithm to Determine Gap-Free Lists of Low Energy States. J. Comp. Chem., 28: 2325-2335 J. Comp. Chem., in press
    [PDF File]
  • Jürgen Koepke, Eva-Maria Krammer, Astrid R. Klingen, P. Sebban, G. Matthias Ullmann and G. Fritzsch. pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states. J. Mol. Biol., 371: 396-409, 2007
    [PDF File]

  • Nadine Homeyer, Timm Essigke, G. Matthias Ullmann, and Heinrich Sticht. Effects of Histidine Protonation and Phosphorylation on HPr Structure, Dynamics and Physicochemical Properties. Biochemistry, 46: 12314-12326, 2007
    [PDF File]

  • Alexei Toutchkine, Wen-Ge Han, G. Matthias Ullmann, Tiqing Liu, Donald Bashford, Louis Noodleman, and Klaus M. Hahn. (2007): Experimental and DFT Studies: Novel Structural Modifications Generate Greatly Enhanced Solvent Sensitivity of Live Cell Imaging Dyes. J. Phys. Chem. A, 111: 10849-10860, 2007
    [PDF File]

    • 2006

  • Astrid R. Klingen, Elisa Bombarda, and G. Matthias Ullmann. Theoretical Investigation of the Behavior of Titratable Groups in Proteins. Photochem. Photobiol. Sci., 5, 588-596, 2006
    [PDF File]

  • Astrid R. Klingen and G. Matthias Ullmann. Computer in der Biochemie. Computer helfen Struktur-Funktions-Beziehungen von Biomolekülen zu verstehen. UBT Spektrum, 2/06, 38-39, 2006
    [PDF File]

  • Elisa Bombarda, Torsten Becker, and G. Matthias Ullmann. The Influence of the Membrane Potential on the Protonation of Bacteriorhodopsin: Insights from Electrostatic Calculations into the Regulation of Proton Pumping. J. Amer. Chem. Soc. , 128, 12129-12139, 2006
    [PDF File] [Supporting Informations]

    • 2005

  • Durba Sengupta, Raghu Nath Behera, Jeremy C. Smith and G. Matthias Ullmann. The α-Helix Dipole - Screened Out? Structure, 13, 849-855, 2005
    [PDF File]

  • Durba Sengupta, Lars Meinhold, Dieter Langosch, G. Matthias Ullmann, and Jeremy C. Smith. Energetics of Helical-Peptide Orientations in Membranes. Proteins, 58, 913 - 922, 2005
    [PDF File]

  • Zoe Cournia, Jeremy C. Smith and G. Matthias Ullmann. A Molecular Mechanics Force-Field for Biologically-Important Sterols. J. Comp. Chem., 26, 1383-1399, 2005
    [PDF File] [Supporting Information] [Parameter Files]

  • Emmanuelle Pion, G. Matthias Ullmann, Joan-Claude Ame, Dominique Gerard, Gilbert De Murcia, and Elisa Bombarda. DNA induced dimerization of Poly (ADP-ribose) polymerase-1 triggers its enzymatic activity. Biochemistry, 44, 14670-14681, 2005
    [PDF File]

  • Edda Kloppmann, Torsten Becker, and G. Matthias Ullmann. Electrostatic Potential at the Retinal of Three Archaeal Rhodopsins: Implications for Their Different Absorption Spectra. Proteins, 61, 953 -965, 2005
    [PDF File]

  • Zoe Cournia, Jeremy C. Smith, G. Matthias Ullmann. Development and Validation of a Force-Field for Biologically Important Sterols in Biomembranes. In: Lecture Series on Computer and Computational Sciences. Brill Academic Publishers, Leiden, in press, 2005

    • 2004

  • Nicolas Calimet and G. Matthias Ullmann. The Influence of a Transmembrane pH Gradient on Protonation Probabilities of Bacteriorhodopsin: The Structural Basis of the Back-Pressure Effect. J. Mol. Biol., 339, 571-589, 2004
    [PDF File]

  • Ellen J. Leggate, Eckhard Bill, Timm Essigke, G. Matthias Ullmann, and Judy Hirst. Formation and Characterization of an All-Ferrous Rieske Cluster, and Stabilization of the[2Fe-2S]0 Core by Protonation. Proc. Natl. Acad. Sci. USA , 101, 10913-10918,2004
    [Abstract] [PDF File]

  • Tiqing Liu, Wen-Ge Han, Fahmi Himo, G. Matthias Ullmann, Donald Bashford, Alexei Toutchkine, Klaus M. Hahn, and Louis Noodleman. Density Functional Vertical Self-consistent Reaction field Theory for Solvatochromism studies of Solvent-Sensitive Dyes. J. Phys. Chem. A 108, 3545-3555, 2004
    [PDF File]

  • Alexey Onufriev and G. Matthias Ullmann. Decomposing Complex Ligand Binding into Simple Components: Connections between Microscopic and Macroscopic models. J. Phys. Chem. B, 108, 11157 - 11169, 2004
    [PDF File] [Supporting Informations]

  • Andrei Borodich and G. Matthias Ullmann. Internal Hydration of Protein Cavities: Studies on BPTI. PCCP, 6, 1906-1911, 2004
    [PDF File]

  • Jeremy C. Smith, Zoe Cournia, Antoine Taly, Alexander C. Tournier, Dan Mihailescu, and G. Matthias Ullmann. Conformational Transitions in Proteins and Membranes. In: Novel Approaches to the Structure and Dynamics of Liquids: Experiments, Theories and Simulations. Eds. J. Samios, V.A.Durov, Kluwer Academic Publishers, Dordrecht: 485-502, 2004

  • Zoe Cournia, Andrea Vaiana, G. Matthias Ullmann and Jeremy C. Smith. Derivation of a Molecular Mechanics Force Field for Cholesterol. Pure Appl. Chem., 76, 189-196, 2004
    [PDF File]

  • Dan Mihailescu, G. Matthias Ullmann, and Jeremy C. Smith. Computer Simulation of Energy-Transducing Proteins and Peptides:Membrane Interactions. In: Molecular Bioenergetics Simulations of Electron, Proton, and Energy Transfer. Ed. R. A. Wheeler, Oxford University Press: 175-186

  • Astrid R. Klingen and G. Matthias Ullmann. Negatively-charged Aminoacids and Hydrogen Bond Pattern Tune the pKa Values of the Rieske-type Iron-Sulfur Proteins. Biochemistry, 43, 12383 -12389, 2004
    [Supporting Informations] [PDF File]

  • Astrid R. Klingen and G. Matthias Ullmann. Biochemie im Computer. BIOforum, 12/2004, 28-29, 2004
    [PDF File]

    • 2003

  • Antoine Taly, Pierre Sebban, Jeremy C. Smith, and G. Matthias Ullmann. The structural changes in the QB pocket of the photosynthetic reaction center depend on pH: a theoretical analysis of the proton uptake upon QB reduction.
    Biophys. J., 84, 2090-2098, 2003
    [PDF File]

  • G. Matthias Ullmann. Relations between Protonation Constants and Titration Curves in Polyprotic Acids: A Critical View. J. Phys. Chem. B, 107, 1263-1271, 2003
    [PDF File] [Supporting Informations]

  • Timm Essigke, G. Matthias Ullmann, Rebecca C. Wade. What Determines the Redox Potential of Ferredoxins? In: Proceedings of the 13th International Conference on Cytochromes P450'', Monduzzi Editore, Bologna: 25-30, 2003

  • Torsten Becker, Stefan Fischer, Frank Noe, Alexander L. Tournier, G. Matthias Ullmann, and Jeremy C. Smith. Protein Dynamics - Glass Transition and Mechanical Function. Advances in Solid State Physics, 43: 677-694, 2003

  • Emmanuelle Pion, Elisa Bombarda, Patrick Stiegler, G. Matthias Ullmann, Yves Mely, Gilbert de Murcia, and Dominique Gerard. Poly (ADP-ribose) polymerase-1 dimerizes at a 5' recessed DNA end in vitro: a fluorescence study. Biochemistry, 42: 12409-12417, 2003
    [PDF File]

    • 2002

  • Reinhard Grebe, Markus Gumbel, Michaela Knapp-Mohammady, G. Matthias Ullmann, and Jörg Langowski: Modellierung biologischer Prozesse. In: Handbuch Medizinische Informatik. T. Lehmann and E. M. zu Bexten (Eds.), 179-223; Carl Hanser Verlag, München, 2002

  • G. Matthias Ullmann, Louis Noodleman, and David A. Case. Density Functional Calculation of pKa values and Redox Potentials in the Bovine Rieske Iron-Sulfur Protein. J. Biol. Inorg. Chem. 7, 632-639, 2002
    [Supporting Informations] [PDF File]

    • 2001

  • Alexey Onufriev, David A. Case, and G. Matthias Ullmann. A Novel View of pH Titration in Biomolecules. Biochemistry (New Concepts) 40, 3413-3419, 2001
    [PDF File]

  • G. Matthias Ullmann. Charge Transfer Properties of Photosynthetic and Respiratory Proteins. In: Supramolecular Photosensitive and Electroactive Materials. H. S. Nalwa (Ed.) pg. 525-584 (Invited Review), Academic Press, New York, 2001.

  • Milan Crnogorac,* G. Matthias Ullmann,* and Nenad M. Kostic. Effects of pH on Protein Association: The Case of Zinc Cytochrome c and Plastocyanin. Extension of the Proton Linkage Model and Experimental Verification of the Extended Model. J. Amer. Chem. Soc. 123, 10789-10798, 2001
    [Supporting Informations] [PDF File]

    • 2000

  • G. Matthias Ullmann, Markus Hauswald, Axel Jensen, and Ernst-Walter Knapp. Superposition of Ferredoxin and Flavodoxin Using Their Electrostatic Potentials. Implications for Their Interactions with Photosystem I and Ferredoxin:NADP Reductase. Proteins 38, 301-309, 2000
    [PDF File]

  • G. Matthias Ullmann. The Coupling of Protonation and Reduction in Proteins with Multiple Redox Centers. Theory, Computational Method, and Application to Cytochrome c3. J. Phys. Chem. B 104, 6293-6301, 2000
    [Supporting Informations] [PDF File]

  • Björn Rabenstein, G. Matthias Ullmann, and Ernst-Walter Knapp. Electron Transfer between the Quinones in the Photosynthetic Reaction Center and its Coupling to Conformational Changes. Biochemistry 39, 10487-10496, 2000
    [PDF File]

  • Natalia V. Kaminskaia, G. Matthias Ullmann, D. Bruce Fulton, and Nenad M. Kostic. Spectroscopic, Kinetic, and Mechanistic Study of a New Mode of Coodination of Indole Derivatives to Platinum(II) and Palladium(II) Ions in Complexes. Inorg. Chem. 39, 5004-5013, 2000
    [Supporting Informations] [PDF File]

    • 1999

  • G. Matthias Ullmann and Ernst-Walter Knapp. Electrostatic Computations of Protonation and Redox Equilibria in Proteins. Eur. Biophys. J. 28, 533-551,1999
    [PDF-File] [PDF File]

  • Tatjana N. Parac, G. Matthias Ullmann, and Nenad M. Kostic. New Regioselectivity in the Cleavage of Histidine-Containing Peptides by Palladium(II) Complexes Studied by Kinetic Experiments and Molecular Dynamics Simulations. J. Amer. Chem. Soc. 121, 3127-3135,1999
    [Supporting Informations] [PDF File]

  • Maja M. Ivkovic-Jensen, G. Matthias Ullmann, Milan Crnogorac, Mikael Ejdeback, Simon Young, Orjan Hansson, and Nenad M. Kostic. Comparing the Rates and the Activation Parameter for the Forward Reaction between the Triplet State of Zinc Cytochrome c and Cupriplastocyanin and the Back Reaction between the Zinc Cytochrome c Cation Radical and Cuproplastocyanin. Biochemistry 38, 1589-1597, 1999
    [PDF File]

  • Ekaterina V. Sokerina, G. Matthias Ullmann, Gertie van Pouderoyen, Gerard W. Canters, and Nenad M. Kostic. Electrostatic Effects on the Kinetics of Photoinduced Electron-Transfer Reactions of the Triplet State of Zinc Cytochrome c with Wild-Type and Mutant Forms of Pseudomonas aeruginosa Azurin. J. Biol. Inorg. Chem. 4, 111-121, 1999
    [Supporting Informations] [PDF File]

    • 1998

  • Björn Rabenstein, G. Matthias Ullmann, and Ernst-Walter Knapp. Calculation of Protonation Patterns in Proteins with Conformational Relaxation - Application to the Photosynthetic Reaction Center. Eur. Biophys. J.27: 628-637, 1998
    [PDF File]

  • Björn Rabenstein, G. Matthias Ullmann, and Ernst-Walter Knapp. Energetics of Electron-Transfer and Protonation Reactions of Quinons in the Photosynthestic Reaction Center of Rhodopseudomonas viridis. Biochemistry, 37: 2488-2495, 1998.
    [Abstract] [Supporting Informations] [PDF File]

  • Maja M. Ivkovic-Jensen, G. Matthias Ullmann, Simon Young, Orjan Hansson, Milan Crnogorac, Mikael Ejdeback, and Nenad M. Kostic. Effects of Single and Double Mutations in Plastocyanin on the Rate Constant and Activation Parameters of the Gated Electron-Transfer Reaction between the Triplet State of Zinc Cytochrome c and Cupriplastocyanin. Biochemistry 37: 9557-9569, 1998.
    [Abstract] [Supporting Informations] [PDF File]

  • G. Matthias Ullmann. Simulation and Analysis of Docking and Dynamics of Electron-Transfer Protein-Complexes. Ph.D. Thesis. Free University Berlin, 1998.

    • 1997

  • G. Matthias Ullmann, Ernst-Walter Knapp, and Nenad M. Kostic. Computational Simulation and Analysis of the Dynamic Assocition between Plastocyanin and Cytochrome f. Consequences for the Electron-transfer Reaction. J. Amer. Chem. Soc. 119: 42-52, 1997.
    [Supporting Informations] [Color Pictures in Postscript] [PDF File]

  • G. Matthias Ullmann, Markus Hauswald, Axel Jensen, Nenad M. Kostic, and Ernst-Walter Knapp. Comparison of the Physiologically-Equivalent Proteins Cytochrome c6 and Plastocyanin on the Basis of Their Electrostatic Potentials. Tryptophane 63 in Cytochrome c6 May Be Isofunctional with Tyrosine 83 in Plastocyanin. Biochemistry 36: 16187-16196, 1997.
    [Supporting Informations] [gzipped Color Pictures in Postscript] [PDF File]

    • 1996

  • G. Matthias Ullmann, Ingo Muegge, and Ernst-Walter Knapp. Shifts of the Special Pair Redox Potential of Mutants of Rhodobacter sphaeroides calculated with Delphi and Charmm Energy Functions. In: Michel-Beyerle, E. M. (Ed.): The Reaction Centers of Photosynthetic Bacteria. Structure and Dynamics. pg. 143-155, Springer Verlag, Heidelberg, 1996

    • 1995

  • G. Matthias Ullmann. Analyse und Auswahl von Konformationen der Aminosäureseitenketten zur Simulation der Langzeitdynamik von Proteinen mit einer Monte-Carlo-Methode. Diplomarbeit. Universität Witten/Herdecke und Freie Universität Berlin, 1995.

  • G. Matthias Ullmann and Nenad M. Kostic. Electron-Tunneling Paths in Various Electrostatic Complexes between Cytochrome c and Plastocyanin . Anisotropy of the Copper-Ligand Interactions and Dependence of the Iron-Copper Electronic Coupling on the Metalloprotein Orientation. J. Amer. Chem. Soc. 117: 4766-4774, 1995.
    [PDF File]