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., in press, 2010
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]
Matthias Ullmann