Prof. Dr. G. Matthias Ullmann

Professor and Chair Holder

+49 921 55 3545

Curriculum Vitae

Year	Description
1970	Born in Stollberg, Saxony, Germany
1977-1987	Primary and secondary school in Lugau
1987-1989	Carl-von-Bach-Gymnasium in Stollberg
1990-1995	Studies at the Friedrich-Schiller University Jena and at the University Witten/Herdecke
1994-1995	Diploma study at the Free University Berlin in the group of Prof. E. W. Knapp (Theoretical and Computational Molecular Biophysics)
1993 & 1996	Two research visits at the Iowa State University in the laboratory of Prof. Nenad M. Kostic (Bioinorganic and Bioorganic Chemistry)
1996-1998	Ph. D. study at the Free University Berlin in the group of Prof. E. W. Knapp (Theoretical and Computational Molecular Biophysics)
1998	Ph. D. at the Department of Chemistry of the Free University Berlin. 1. Reviewer: Prof. E. W. Knapp; 2. Reviewer: Prof. W. Saenger; 3. Reviewer: Prof. D. Haase (Grade: Summa Cum Laude)
1999-2000	Postdoc at The Scripps Research Institute in the group of Prof. David A. Case in collaboration with Prof. Louis Noodlemann and Prof. Donald Bashford
2001-2003	Group leader in the Emmy-Noether Program (Phase II) of the DFG at the Chair for Computational Molecular Biophysics (Prof. Jeremy Smith) at the IWR of the Ruprecht-Karls-Universität Heidelberg
since 2003	Professor for Structural Biology and Bioinformatics at the Chemistry Department of the University of Bayreuth
since 2004	Member of the BZMB
since 2007	Member of the Biomac
2010-2012	Member of the international scientific board of the University of Science and Technology of Hanoi (USTH)
since 2013	Member of the SEN-1 Commission of the FNRS (Belgian Science Foundation)

Fellowships

Year	Description
1991-1995	Scholar of the German National Merit Foundation (Studienstiftung) (German Page)
1996-1998	Ph. D. Scholar of the Boehringer Ingelheim Fonds
1999-2000	Postdoctoral Fellowship of the Deutsche Forschungsgemeinschaft (DFG)
2001-2003	Group leader in the Emmy-Noether Program (Phase II) of the Deutsche Forschungsgemeinschaft (DFG)

Memberships

Year	Description
since 1994	German Society of Biophysics
since 2002	Gesellschaft für Biochemie und Molekularbiologie

Publications

2026

R.R. Roy, M. Janzen, and G.M. Ullmann, Fundamental electrostatics explains why ferredoxin- and HiPIP-type proteins favor different redox transitions in [4Fe-4S]-Cys4 clusters, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 130, no. 14, pp. 3855–3866, 2026. doi:10.1021/acs.jpcb.6c00593
R.R. Roy, M. Janzen, and G.M. Ullmann, Protein-based determination of model redox potentials for the high-potential and low-potential redox transition of [4Fe-4S]-Cys4 clusters using continuum electrostatics, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 22, no. 1, pp. 738–749, 2026. doi:10.1021/acs.jctc.5c01761

2025

J. Fuchs, U. Fernandez-Arevalo, U. Demmer, E. Diaz, G.M. Ullmann, A.J. Pierik, U. Ermler, and M. Boll, Enzymatic birch reduction via hydrogen atom transfer at [4Fe-4S]-OH2 and [8Fe-9S] clusters, NATURE COMMUNICATIONS, vol. 16, no. 1, 2025. doi:10.1038/s41467-025-58418-w
M. Akram, D. Hauser, A. Dietl, M. Steigleder, G.M. Ullmann, and T.R.M. Barends, Redox potential tuning by calcium ions in a novel c-type cytochrome from an anammox organism, JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 301, no. 2, 2025. doi:10.1016/j.jbc.2024.108082

2023

R.R. Roy and G.M. Ullmann, Virtual model compound approach for calculating redox potentials of [Fe2S2]-Cys4 centers in proteins - structure quality matters, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 19, no. 23, pp. 8930–8941, 2023. doi:10.1021/acs.jctc.3c00779
C.S. Seelmann, S.G. Huwiler, M. Culka, M.J.F. Strampraad, T. Biskup, S. Weber, G.M. Ullmann, V. Schunemann, P. Hagedoorn, A.J. Pierik, and M. Boll, Enzymatic birch reduction via hydrogen atom transfer at an aqua-tungsten-bis-metallopterin cofactor, ACS CATALYSIS, vol. 13, no. 13, pp. 8631–8641, 2023. doi:10.1021/acscatal.3c01781

2022

S. Weigert, P. Perez-Garcia, F.J. Gisdon, A. Gagsteiger, K. Schweinshaut, G.M. Ullmann, J. Chow, W.R. Streit, and B. Hoecker, Investigation of the halophilic PET hydrolase PET6 from vibrio gazogenes, PROTEIN SCIENCE, vol. 31, no. 12, 2022. doi:10.1002/pro.4500
F.J. Gisdon, E. Bombarda, and G.M. Ullmann, Serine and cysteine peptidases: So similar, yet different. How the active-site electrostatics facilitates different reaction mechanisms, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 126, no. 22, pp. 4035–4048, 2022. doi:10.1021/acs.jpcb.2c01484
F.J. Gisdon, C.G. Feiler, O. Kempf, J.M. Foerster, J. Haiss, W. Blankenfeldt, G.M. Ullmann, and E. Bombarda, Structural and biophysical analysis of the phytochelatin-synthase-like enzyme fromNostocsp. Shows that its protease activity isSensitive to the redox state of the substrate, ACS CHEMICAL BIOLOGY, vol. 17, no. 4, pp. 883–897, 2022. doi:10.1021/acschembio.1c00941
A.H. Schweiger, G.M. Ullmann, N.M. Nuerk, D. Triebel, R. Schobert, and G. Rambold, Chemical properties of key metabolites determine the global distribution of lichens, ECOLOGY LETTERS, vol. 25, no. 2, pp. 416–426, 2022. doi:10.1111/ele.13930
A. Di Savino, J.M. Foerster, G.M. Ullmann, and M. Ubbink, Enhancing the population of the encounter complex affects protein complex formation efficiency, FEBS JOURNAL, vol. 289, no. 2, pp. 535–548, 2022. doi:10.1111/febs.16159

2021

O. Kempf, G.M. Ullmann, R. Schobert, K. Kempf, and E. Bombarda, Chemoselective attachment of the water-soluble dark quencher hydrodabcyl to amino groups in peptides and preservation of its spectroscopic properties over a wide pH range, ACS OMEGA, vol. 6, no. 48, pp. 32896–32903, 2021. doi:10.1021/acsomega.1c04891
A. Di Savino, J.M. Foerster, G.M. Ullmann, and M. Ubbink, The charge distribution on a protein surface determines whether productive or futile encounter complexes are formed, BIOCHEMISTRY, vol. 60, no. 10, pp. 747–755, 2021. doi:10.1021/acs.biochem.1c00021
N. Chrysochos, M. Ahmadi, I. Trentin, M. Lokov, S. Tshepelevitsh, G.M. Ullmann, I. Leito, and C. Schulzke, Aiding a better understanding of molybdopterin: Syntheses, structures, and pKa value determinations of varied pterin-derived organic scaffolds including oxygen, sulfur and phosphorus bearing substituents, JOURNAL OF MOLECULAR STRUCTURE, vol. 1230, 2021. doi:10.1016/j.molstruc.2020.129867

2020

A. Di Savino, J.M. Foerster, T. La Haye, A. Blok, M. Timmer, G.M. Ullmann, and M. Ubbink, Efficient encounter complex formation and electron transfer to cytochrome c peroxidase with an additional, distant electrostatic binding site, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, vol. 59, no. 51, pp. 23239–23243, 2020. doi:10.1002/anie.202010006

2019

I. Schelter, J.M. Foerster, A.T. Gardiner, A.W. Roszak, R.J. Cogdell, G.M. Ullmann, T.B. Queiroz, and S. Kuemmel, Assessing density functional theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2, JOURNAL OF CHEMICAL PHYSICS, vol. 151, no. 13, 2019. doi:10.1063/1.5116779
M. Willistein, D.F. Bechtel, C.S. Mueller, U. Demmer, L. Heimann, K. Kayastha, V. Schuenemann, A.J. Pierik, G.M. Ullmann, U. Ermler, and M. Boll, Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors, NATURE COMMUNICATIONS, vol. 10, 2019. doi:10.1038/s41467-019-10078-3

2018

J.M. Foerster, I. Poehner, and G.M. Ullmann, MCMap-computational tool for mapping energy landscapes of transient protein-protein interactions, ACS OMEGA, vol. 3, no. 6, pp. 6465–6475, 2018. doi:10.1021/acsomega.8b00572

2017

E. Bombarda and G.M. Ullmann, Continuum electrostatic calculation on bovine rhodopsin: Protonation and the effect of the membrane potential, PHOTOCHEMISTRY AND PHOTOBIOLOGY, vol. 93, no. 6, SI, pp. 1388–1398, 2017. doi:10.1111/php.12777
M. Culka, S.G. Huwiler, M. Boll, and G.M. Ullmann, Breaking benzene aromaticity-computational insights into the mechanism of the tungsten-containing benzoyl-CoA reductase, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 139, no. 41, pp. 14488–14500, 2017. doi:10.1021/jacs.7b07012
C. Diederich, M. Leypold, M. Culka, H. Weber, R. Breinbauer, G.M. Ullmann, and W. Blankenfeldt, Mechanisms and specificity of phenazine biosynthesis protein PhzF, SCIENTIFIC REPORTS, vol. 7, 2017. doi:10.1038/s41598-017-06278-w
A.F. Geiss, R. Khandelwal, D. Baurecht, C. Bliem, C. Reiner-Rozman, M. Boersch, G.M. Ullmann, L.M. Loew, and R.L.C. Naumann, pH and potential transients of the bc1 complex co-reconstituted in proteo-lipobeads with the reaction center from rb. sphaeroides, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 121, no. 1, pp. 143–152, 2017. doi:10.1021/acs.jpcb.6b11116
M. Culka, F.J. Gisdon, and G.M. Ullmann, Computational biochemistry-enzyme mechanisms explored, in STRUCTURAL AND MECHANISTIC ENZYMOLOGY, T. KarabenchevaChristova, Eds. 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA: ELSEVIER ACADEMIC PRESS INC, 2017, vol. 109, pp. 77–112.doi:10.1016/bs.apcsb.2017.04.004

2016

F.J. Gisdon, M. Culka, and G.M. Ullmann, PyCPR - a python-based implementation of the conjugate peak refinement (CPR) algorithm for finding transition state structures, JOURNAL OF MOLECULAR MODELING, vol. 22, no. 10, 2016. doi:10.1007/s00894-016-3116-8
M. Boll, O. Einsle, U. Ermler, P.M.H. Kroneck, and G.M. Ullmann, Structure and function of the unusual tungsten enzymes acetylene hydratase and class II benzoyl-coenzyme a reductase, JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY, vol. 26, no. 1-3, pp. 119–137, 2016. doi:10.1159/000440805
R. Rabus, M. Boll, J. Heider, R.U. Meckenstock, W. Buckel, O. Einsle, U. Ermler, B.T. Golding, R.P. Gunsalus, P.M.H. Kroneck, M. Krueger, T. Lueders, B.M. Martins, F. Musat, H.H. Richnow, B. Schink, J. Seifert, M. Szaleniec, T. Treude, G.M. Ullmann, C. Vogt, M. Bergen, and H. Wilkes, Anaerobic microbial degradation of hydrocarbons: From enzymatic reactions to the environment, JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY, vol. 26, no. 1-3, pp. 5–28, 2016. doi:10.1159/000443997
B. Selvaraj, W. Buckel, B.T. Golding, G.M. Ullmann, and B.M. Martins, Structure and function of 4-hydroxyphenylacetate decarboxylase and its cognate activating enzyme, JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY, vol. 26, no. 1-3, pp. 76–91, 2016. doi:10.1159/000440882

2015

S.A. Wieninger and G.M. Ullmann, CoMoDo: Identifying dynamic protein domains based on covariances of motion, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 11, no. 6, pp. 2841–2854, 2015. doi:10.1021/acs.jctc.5b00150
S.R. Beyer, L. Mueller, J. Southall, R.J. Cogdell, G.M. Ullmann, and J. Koehler, The open, the closed, and the empty: Time-resolved fluorescence spectroscopy and computational analysis of RC-LH1 complexes from rhodopseudomonas palustris, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 119, no. 4, pp. 1362–1373, 2015. doi:10.1021/jp510822k

2014

I. Diaz-Moreno, R. Hulsker, P. Skubak, J.M. Foerster, D. Cavazzini, M.G. Finiguerra, A. Diaz-Quintana, B. Moreno-Beltran, G. Rossi, G.M. Ullmann, N.S. Pannu, M.A. De la Rosa, and M. Ubbink, The dynamic complex of cytochrome c6 and cytochrome f studied with paramagnetic NMR spectroscopy, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, vol. 1837, no. 8, pp. 1305–1315, 2014. doi:10.1016/j.bbabio.2014.03.009
J. Guan, J.M. Foerster, J.W. Drijfhout, M. Timmer, A. Blok, G.M. Ullmann, and M. Ubbink, An ensemble of rapidly interconverting orientations in electrostatic protein-peptide complexes characterized by NMR spectroscopy, CHEMBIOCHEM, vol. 15, no. 4, pp. 556–566, 2014. doi:10.1002/cbic.201300623

2013

M. Feliks, B.M. Martins, and G.M. Ullmann, Catalytic mechanism of the glycyl radical enzyme 4-hydroxyphenylacetate decarboxylase from continuum electrostatic and QC/MM calculations, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 135, no. 39, pp. 14574–14585, 2013. doi:10.1021/ja402379q
S. Scanu, J.M. Foerster, M. Timmer, G.M. Ullmann, and M. Ubbink, Loss of electrostatic interactions causes increase of dynamics within the plastocyanin-cytochrome f complex, BIOCHEMISTRY, vol. 52, no. 38, pp. 6615–6626, 2013. doi:10.1021/bi400450q
S. Scanu, J.M. Foerster, G.M. Ullmann, and M. Ubbink, Role of hydrophobic interactions in the encounter complex formation of the plastocyanin and cytochrome f complex revealed by paramagnetic NMR spectroscopy, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 135, no. 20, pp. 7681–7692, 2013. doi:10.1021/ja4015452
G.M. Ullmann and E. Bombarda, pKa values and redox potentials of proteins. What do they mean?, BIOLOGICAL CHEMISTRY, vol. 394, no. 5, pp. 611–619, 2013. doi:10.1515/hsz-2012-0329
J.W.R. Martini and G.M. Ullmann, A mathematical view on the decoupled sites representation, JOURNAL OF MATHEMATICAL BIOLOGY, vol. 66, no. 3, pp. 477–503, 2013. doi:10.1007/s00285-012-0517-x
J.W.R. Martini, M. Schlather, and G.M. 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, JOURNAL OF MATHEMATICAL CHEMISTRY, vol. 51, no. 2, pp. 672–695, 2013. doi:10.1007/s10910-012-0107-6
J.W.R. Martini, M. Schlather, and G.M. Ullmann, On the interaction of different types of ligands binding to the same molecule part II: Systems with n to 2 and n to 3 binding sites, JOURNAL OF MATHEMATICAL CHEMISTRY, vol. 51, no. 2, pp. 696–714, 2013. doi:10.1007/s10910-012-0108-5
J.W.R. Martini, G.M. Ullmann, and M. Schlather, The meaning of the decoupled sites representation in terms of statistical mechanics and stochastics, MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTER CHEMISTRY, vol. 70, no. 3, pp. 829–850, 2013.

2012

P. Ruecker, S.A. Wieninger, G.M. Ullmann, and H. Sticht, pH-dependent molecular dynamics of vesicular stomatitis virus glycoprotein g, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol. 80, no. 11, pp. 2601–2613, 2012. doi:10.1002/prot.24145
R.T. Ullmann, S.L.A. Andrade, and G.M. Ullmann, Thermodynamics of transport through the ammonium transporter amt-1 investigated with free energy calculations, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 116, no. 32, pp. 9690–9703, 2012. doi:10.1021/jp305440f
S. Promsri, G.M. Ullmann, and S. Hannongbua, Molecular dynamics simulation of HIV-1 fusion domain-membrane complexes: Insight into the n-terminal gp41 fusion mechanism, BIOPHYSICAL CHEMISTRY, vol. 170, pp. 9–16, 2012. doi:10.1016/j.bpc.2012.07.002
M. Feliks and G.M. Ullmann, Glycerol dehydratation by the B12-independent enzyme may not involve the migration of a hydroxyl group: A computational study, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 116, no. 24, pp. 7076–7087, 2012. doi:10.1021/jp301165b
R.T. Ullmann and G.M. Ullmann, GMCT: A monte carlo simulation package for macromolecular receptors, JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 33, no. 8, pp. 887–900, 2012. doi:10.1002/jcc.22919
T.Z. Grove, G.M. Ullmann, and N.M. Kostic, Simultaneous true, gated, and coupled electron-transfer reactions and energetics of protein rearrangement, JOURNAL OF INORGANIC BIOCHEMISTRY, vol. 106, no. 1, pp. 143–150, 2012. doi:10.1016/j.jinorgbio.2011.09.017

2011

B.M. Martins, M. Blaser, M. Feliks, G.M. Ullmann, W. Buckel, and T. Selmer, Structural basis for a kolbe-type decarboxylation catalyzed by a glycyl radical enzyme, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 133, no. 37, pp. 14666–14674, 2011. doi:10.1021/ja203344x
R.T. Ullmann and G.M. Ullmann, Coupling of protonation, reduction, and conformational change in azurin from pseudomonas aeruginosa investigated with free energy measures of cooperativity, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, no. 34, pp. 10346–10359, 2011. doi:10.1021/jp204644h
T.J. Pflock, S. Oellerich, J. Southall, R.J. Cogdell, G.M. Ullmann, and J. Koehler, The electronically excited states of LH2 complexes from rhodopseudomonas acidophila strain 10050 studied by time-resolved spectroscopy and dynamic monte carlo simulations. I. Isolated, non-interacting LH2 complexes, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, no. 28, pp. 8813–8820, 2011. doi:10.1021/jp202353c
T.J. Pflock, S. Oellerich, L. Krapf, J. Southall, R.J. Cogdell, G.M. Ullmann, and J. Koehler, The electronically excited states of LH2 complexes from rhodopseudomonas acidophila strain 10050 studied by time-resolved spectroscopy and dynamic monte carlo simulations. II. Homo-arrays of LH2 complexes reconstituted into phospholipid model membranes, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, no. 28, pp. 8821–8831, 2011. doi:10.1021/jp2023583
V.I. Dumit, N. Cortez, and G.M. Ullmann, Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol. 79, no. 7, pp. 2076–2085, 2011. doi:10.1002/prot.23027
S.A. Wieninger, E.H. Serpersu, and G.M. Ullmann, ATP binding enables broad antibiotic selectivity of aminoglycoside phosphotransferase(3′)-IIIa: An elastic network analysis, JOURNAL OF MOLECULAR BIOLOGY, vol. 409, no. 3, pp. 450–465, 2011. doi:10.1016/j.jmb.2011.03.061
S.A. Wieninger, E.H. Serpersu, and G.M. Ullmann, Ligand-dependent dynamics of aminoglycoside phosphotransferase(3R′)-IIIa explains unusual solvent effects and h/d exchange behaviour of the enzyme, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 241, 2011.
R.T. Ullmann and G.M. Ullmann, A generalized free energy perturbation theory accounting for end states with differing configuration space volume, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 115, no. 3, pp. 507–521, 2011. doi:10.1021/jp1093838
E. Bombarda and G.M. Ullmann, Continuum electrostatic investigations of charge transfer processes in biological molecules using a microstate description, FARADAY DISCUSSIONS, vol. 148, pp. 173–193, 2011. doi:10.1039/c003905e
E. Krammer, S. Bernad, G.M. Ullmann, A. Hickman, and P. Sebban, Chemical evidence for the dawn of life on earth, AUSTRALIAN JOURNAL OF CHEMISTRY, vol. 64, no. 1, pp. 16–22, 2011. doi:10.1071/CH10427
E. Krammer, S. Bernad, G.M. Ullmann, A. Hickman, and P. Sebban, Chemical evidence for the dawn of life on earth (vol 64, pg 16, 2011), AUSTRALIAN JOURNAL OF CHEMISTRY, vol. 64, no. 2, pp. 228–U7, 2011. doi:10.1071/CH10427\_CO
S.A. Wieninger, E.H. Serpersu, and G.M. Ullmann, Differential effects of ligand binding on protein dynamics, In Proc. 4TH EUROPEAN CONFERENCE ON CHEMISTRY FOR LIFE SCIENCES, 2011, pp. 113–115.

2010

A.N. Volkov, Q. Bashir, J.A.R. Worrall, G.M. Ullmann, and M. Ubbink, Shifting the equilibrium between the encounter state and the specific form of a protein complex by interfacial point mutations, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 132, no. 33, pp. 11487–11495, 2010. doi:10.1021/ja100867c
O. Spiegelhauer, S. Mende, F. Dickert, S.H. Knauer, G.M. Ullmann, and H. Dobbek, Cysteine as a modulator residue in the active site of xenobiotic reductase a: A structural, thermodynamic and kinetic study, JOURNAL OF MOLECULAR BIOLOGY, vol. 398, no. 1, pp. 66–82, 2010. doi:10.1016/j.jmb.2010.02.044
V.I. Dumit, T. Essigke, N. Cortez, and G.M. Ullmann, Mechanistic insights into ferredoxin-NADP(h) reductase catalysis involving the conserved glutamate in the active site, JOURNAL OF MOLECULAR BIOLOGY, vol. 397, no. 3, pp. 814–825, 2010. doi:10.1016/j.jmb.2010.01.063
M.S. Till and G.M. Ullmann, McVol - a program for calculating protein volumes and identifying cavities by a monte carlo algorithm, JOURNAL OF MOLECULAR MODELING, vol. 16, no. 3, pp. 419–429, 2010. doi:10.1007/s00894-009-0541-y
E. Bombarda and G.M. Ullmann, pH-dependent pKa values in proteins-a theoretical analysis of protonation energies with practical consequences for enzymatic reactions, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 114, no. 5, pp. 1994–2003, 2010. doi:10.1021/jp908926w
Q. Bashir, A.N. Volkov, G.M. Ullmann, and M. Ubbink, Visualization of the encounter ensemble of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 132, no. 1, pp. 241–247, 2010. doi:10.1021/ja9064574

2009

E. Krammer, M.S. Till, P. Sebban, and G.M. Ullmann, Proton-transfer pathways in photosynthetic reaction centers analyzed by profile hidden markov models and network calculations, JOURNAL OF MOLECULAR BIOLOGY, vol. 388, no. 3, pp. 631–643, 2009. doi:10.1016/j.jmb.2009.03.020
E. Krammer, P. Sebban, and G.M. Ullmann, Profile hidden markov models for analyzing similarities and dissimilarities in the bacterial reaction center and photosystem II, BIOCHEMISTRY, vol. 48, no. 6, pp. 1230–1243, 2009. doi:10.1021/bi802033k

2008

V. Becker, D. Sengupta, R. Ketteler, G.M. Ullmann, J.C. Smith, and U. Klingmueller, Packing density of the erythropoietin receptor transmembrane domain correlates with amplification of biological responses, BIOCHEMISTRY, vol. 47, no. 45, pp. 11771–11782, 2008. doi:10.1021/bi801425e
M.S. Till, T. Essigke, T. Becker, and G.M. Ullmann, Simulating the proton transfer in gramicidin a by a sequential dynamical monte carlo method, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 112, no. 42, pp. 13401–13410, 2008. doi:10.1021/jp801477b
D. Sengupta, J.C. Smith, and G.M. Ullmann, Partitioning of amino-acid analogues in a five-slab membrane model, BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, vol. 1778, no. 10, pp. 2234–2243, 2008. doi:10.1016/j.bbamem.2008.06.014
G.M. Ullmann, E. Kloppmann, T. Essigke, E. Krammer, A.R. Klingen, T. Becker, and E. Bombarda, Investigating the mechanisms of photosynthetic proteins using continuum electrostatics, PHOTOSYNTHESIS RESEARCH, vol. 97, no. 1, pp. 33–53, 2008. doi:10.1007/s11120-008-9306-1

2007

E. Kloppmann, G.M. Ullmann, and T. Becker, An extended dead-end elimination algorithm to determine gap-free lists of low energy states, JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 28, no. 14, pp. 2325–2335, 2007. doi:10.1002/jcc.20749
N. Homeyer, T. Essigke, G.M. Ullmann, and H. Sticht, Effects of histidine protonation and phosphorylation on histidine-containing phosphocarrier protein structure, dynamics, and physicochernical properties, BIOCHEMISTRY, vol. 46, no. 43, pp. 12314–12326, 2007. doi:10.1021/bi701228g
J. Koepke, E. Krammer, A.R. Klingen, P. Sebban, G.M. Ullmann, and G. Fritzsch, pH modulates the quinone position in the photosynthetic reaction center from rhodobacter sphaeroides in the neutral and charge separated states, JOURNAL OF MOLECULAR BIOLOGY, vol. 371, no. 2, pp. 396–409, 2007. doi:10.1016/j.jmb.2007.04.082
M. Punnagai and G.M. Ullmann, Does the deprotonation of CuB ligands play a role in reaction mechanism of cytochrome c oxidase?, JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, vol. 12, no. SUPPL 1, 1, SI, p. S87, 2007.
T. Becker, R.T. Ullmann, and G.M. Ullmann, Simulation of the electron transfer between the tetraheme subunit and the special pair of the photosynthetic reaction center using a microstate description, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 111, no. 11, pp. 2957–2968, 2007. doi:10.1021/jp066264a
N. Homeyer, T. Essigke, H. Meiselbach, G.M. Ullmann, and H. Sticht, Effect of HPr phosphorylation on structure, dynamics, and interactions in the course of transcriptional control, JOURNAL OF MOLECULAR MODELING, vol. 13, no. 3, pp. 431–444, 2007. doi:10.1007/s00894-006-0162-7
A.R. Klingen, H. Palsdottir, C. Hunte, and G.M. Ullmann, Redox-linked protonation state changes in cytochrome bc1 identified by poisson-boltzmann electrostatics calculations, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, vol. 1767, no. 3, pp. 204–221, 2007. doi:10.1016/j.bbabio.2007.01.016
G.B. Seiffert, G.M. Ullmann, A. Messerschmidt, B. Schink, P.M.H. Kroneck, and O. Einsle, Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 104, no. 9, pp. 3073–3077, 2007. doi:10.1073/pnas.0610407104
Z. Cournia, G.M. Ullmann, and J.C. Smith, Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: A molecular dynamics simulation study, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 111, no. 7, pp. 1786–1801, 2007. doi:10.1021/jp065172i
E. Krammer, A.R. Klingen, and G.M. Ullmann, The role of AspL213 for the binding of coenzyme q to the photosynthetic reaction center, PHOTOSYNTHESIS RESEARCH, vol. 91, no. 2-3, pp. 141–142, 2007.
L.V. Schaefer, G. Groenhof, A.R. Klingen, G.M. Ullmann, M. Boggio-Pasqua, M.A. Robb, and H. Grubmueller, Photoswitching of the fluorescent protein asFP595:: Mechanism, proton pathways, and absorption spectra, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, vol. 46, no. 4, pp. 530–536, 2007. doi:10.1002/anie.200602315

2006

E. Bombarda, T. Becker, and G.M. Ullmann, Influence of the membrane potential on the protonation of bacteriorhodopsin: Insights from electrostatic calculations into the regulation of proton pumping, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 128, no. 37, pp. 12129–12139, 2006. doi:10.1021/ja0619657
A.R. Klingen and G.M. Ullmann, Redox-linked protonation state changes in cytochrome bc1 complex identified by poisson-boltzmann electrostatics calculations, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, no. S, pp. 190–191, 2006.
A.R. Klingen, E. Bombarda, and G.M. Ullmann, Theoretical investigation of the behavior of titratable groups in proteins, PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, vol. 5, no. 6, pp. 588–596, 2006. doi:10.1039/b515479k
E.-. Krammer, A.R. Klingen, and G.M. Ullmann, The binding behavior of coenzyme q to the photosynthetic reaction center, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, no. S, p. 285, 2006.
J. Smith, T. Becker, S. Fischer, F. Noe, A. Tournier, G. Ullmann, and V. Kurkal, Physical and functional aspects of protein dynamics, In Proc. SOFT CONDENSED MATTER PHYSICS IN MOLECULAR AND CELL BIOLOGY, 2006, pp. 225–241.

2005

E. Kloppmann, T. Becker, and G. Ullmann, Electrostatic potential at the retinal of three archaeal rhodopsins: Implications for their different absorption spectra, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol. 61, no. 4, pp. 953–965, 2005. doi:10.1002/prot.20744
E. Pion, G. Ullmann, J. Amé, D. Gérard, G. Murcia, and E. Bombarda, DNA-induced dimerization of poly(ADP-ribose) polymerase-1 triggers its activation, BIOCHEMISTRY, vol. 44, no. 44, pp. 14670–14681, 2005. doi:10.1021/bi050755o
Z. Cournia, J. Smith, and G. Ullmann, A molecular mechanics force field for biologically important sterols, JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 26, no. 13, pp. 1383–1399, 2005. doi:10.1002/jcc.20277
D. Sengupta, R. Behera, J. Smith, and G. Ullmann, The α helix dipole: Screened out?, STRUCTURE, vol. 13, no. 6, pp. 849–855, 2005. doi:10.1016/j.str.2005.03.010
D. Sengupta, L. Meinhold, D. Langosch, G. Ullmann, and J. Smith, Understanding the energetics of helical peptide orientation in membranes, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol. 58, no. 4, pp. 913–922, 2005. doi:10.1002/prot.20383
Z. Cournia, J.C. Smith, and G.M. Ullmann, Development and validation of a force-field for biologically important sterols in biomembranes, In Proc. ADVANCES IN COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2005, VOLS 4 a & 4 b, 2005, vol. 4A-4B, pp. 949–953.

2004

A. Klingen and G. Ullmann, Negatively charged residues and hydrogen bonds tune the ligand histidine pKa values of rieske iron-sulfur proteins, BIOCHEMISTRY, vol. 43, no. 39, pp. 12383–12389, 2004. doi:10.1021/bi0488606
A. Onufriev and G. Ullmann, Decomposing complex cooperative ligand binding into simple components: Connections between microscopic and macroscopic models, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 108, no. 30, pp. 11157–11169, 2004. doi:10.1021/jp049961g
E. Leggate, E. Bill, T. Essigke, G. Ullmann, and J. Hirst, Formation and characterization of an all-ferrous rieske cluster and stabilization of the [2Fe-2S]0 core by protonation, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 101, no. 30, pp. 10913–10918, 2004. doi:10.1073/pnas.0402711101
N. Calimet and G. Ullmann, The influence of a transmembrane pH gradient on protonation probabilities of bacteriorhodopsin: The structural basis of the back-pressure effect, JOURNAL OF MOLECULAR BIOLOGY, vol. 339, no. 3, pp. 571–589, 2004. doi:10.1016/j.jmb.2004.03.075
T. Liu, W. Han, F. Himo, G. Ullmann, D. Bashford, A. Toutchkine, K. Hahn, and L. Noodleman, Density functional vertical self-consistent reaction field theory for solvatochromism - studies of solvent-sensitive dyes, JOURNAL OF PHYSICAL CHEMISTRY A, vol. 108, no. 16, pp. 3545–3555, 2004. doi:10.1021/jp031062p
A. Borodich and G. Ullmann, Internal hydration of protein cavities: Studies on BPTI, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 6, no. 8, pp. 1906–1911, 2004. doi:10.1039/b313238m
Z. Cournia, A. Vaiana, G. Ullmann, and J. Smith, Derivation of a molecular mechanics force field for cholesterol, PURE AND APPLIED CHEMISTRY, vol. 76, no. 1, pp. 189–196, 2004. doi:10.1351/pac200476010189
A. Klingen and G. Ullmann, A comparative structure-based analysis of the pH-dependent reduction potentials of rieske iron-sulphur proteins, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, vol. 1658, no. S, p. 165, 2004.
J. Smith, Z. Cournia, A. Taly, A. Tournier, D. Mihailescu, and G. Ullmann, Conformational transitions in proteins and membranes, In Proc. NOVEL APPROACHES TO THE STRUCTURE AND DYNAMICS OF LIQUIDS: EXPERIMENTS, THEORIES AND SIMULATIONS, 2004, pp. 485–502.
G. Ullmann and N. Calimet, Influence of a transmembrane pH gradient on protonation probabilities of bacteriorhodopsin, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, vol. 1658, no. S, p. 263, 2004.

2003

E. Pion, E. Bombarda, P. Stiegler, G. Ullmann, Y. Mély, G. Murcia, and D. Gérard, Poly(ADP-ribose) polymerase-1 dimerizes at a 5′ recessed DNA end in vitro:: A fluorescence study, BIOCHEMISTRY, vol. 42, no. 42, pp. 12409–12417, 2003. doi:10.1021/bi0344432
T. Essigke, R. Wade, and G. Ullmann, Calculation of the redox potential of iron-sulfur proteins, JOURNAL OF INORGANIC BIOCHEMISTRY, vol. 96, no. 1, p. 127, 2003. doi:10.1016/S0162-0134(03)80607-4
A. Taly, P. Sebban, J. Smith, and G. Ullmann, The position of QB in the photosynthetic reaction center depends on pH: A theoretical analysis of the proton uptake upon QB reduction, BIOPHYSICAL JOURNAL, vol. 84, no. 3, pp. 2090–2098, 2003. doi:10.1016/S0006-3495(03)75016-4
G. Ullmann, Relations between protonation constants and titration curves in polyprotic acids: A critical view, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 107, no. 5, pp. 1263–1271, 2003. doi:10.1021/jp026454v
T. Becker, S. Fischer, F. Noe, A. Tournier, G. Ullmann, and J. Smith, Protein dynamics: Glass transition and mechanical function, In Proc. ADVANCES IN SOLID STATE PHYSICS 43, 2003, vol. 43, pp. 677–692.
T. Essigke, G. Ullmann, and R. Wade, What determines the redox potential of ferredoxins?, In Proc. CYTOCHROMES P450, BIOCHEMISTRY, BIOPHYSICS AND DRUG METABOLISM, 2003, pp. 25–30.

2002

G. Ullmann, L. Noodleman, and D. Case, Density functional calculation of pKa values and redox potentials in the bovine rieske iron-sulfur protein, JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, vol. 7, no. 6, pp. 632–639, 2002. doi:10.1007/s00775-002-0342-6

2001

M. Crnogorac, G. Ullmann, and N. Kostic, Effects of pH on protein association: Modification of the proton-linkage model and experimental verification of the modified model in the case of cytochrome c and plastocyanin, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 123, no. 44, pp. 10789–10798, 2001. doi:10.1021/ja003818t
G. Ullmann, L. Noodleman, and D. Case, Computing macroscopic and microscopic pKa vaules of the rieske iron-sulfur cluster using a combined electrostatic-density functional method, JOURNAL OF INORGANIC BIOCHEMISTRY, vol. 86, no. 1, p. 464, 2001.
A. Onufriev, D. Case, and G. Ullmann, A novel view of pH titration in biomolecules, BIOCHEMISTRY, vol. 40, no. 12, pp. 3413–3419, 2001. doi:10.1021/bi002740q

2000

N. Kaminskaia, G. Ullmann, D. Fulton, and N. Kostic, Spectroscopic, kinetic, and mechanistic study of a new mode of coordination of indole derivatives to platinum(II) and palladium(II) ions in complexes, INORGANIC CHEMISTRY, vol. 39, no. 22, pp. 5004–5013, 2000. doi:10.1021/ic000254l
B. Rabenstein, G. Ullmann, and E. Knapp, Electron transfer between the quinones in the photosynthetic reaction center and its coupling to conformational changes, BIOCHEMISTRY, vol. 39, no. 34, pp. 10487–10496, 2000. doi:10.1021/bi000413c
G. Ullmann, The coupling of protonation and reduction in proteins with multiple redox centers: Theory, computational method, and application to cytochrome c3, JOURNAL OF PHYSICAL CHEMISTRY B, vol. 104, no. 26, pp. 6293–6301, 2000. doi:10.1021/jp000711j
G. Ullmann, M. Hauswald, A. Jensen, and E. Knapp, Structural alignment of ferredoxin and flavodoxin based on electrostatic potentials: Implications for their interactions with photosystem i and ferredoxin-NADP reductase, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol. 38, no. 3, pp. 301–309, 2000.

1999

G. Ullmann and D. Case, Coupling of electron and proton transfer in proteins. Computational investigations of the redox-bohr effect in cytochromes., JOURNAL OF INORGANIC BIOCHEMISTRY, vol. 74, no. 1-4, p. 322, 1999.
T. Parac, G. Ullmann, and N. Kostic, New regioselectivity in the cleavage of histidine-containing peptides by palladium(II) complexes studied by kinetic experiments and molecular dynamics simulations, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 121, no. 13, pp. 3127–3135, 1999. doi:10.1021/ja982369i
M. Ivkovic-Jensen, G. Ullmann, M. Crnogorac, M. Ejdebäck, S. Young, Ö. Hansson, and N. Kostic, Comparing the rates and the activation parameters 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, vol. 38, no. 5, pp. 1589–1597, 1999. doi:10.1021/bi9817156
E. Sokerina, G. Ullmann, G. Pouderoyen, G. Canters, and N. 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, JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, vol. 4, no. 1, pp. 111–121, 1999. doi:10.1007/s007750050294
G. Ullmann and E. Knapp, Electrostatic models for computing protonation and redox equilibria in proteins, EUROPEAN BIOPHYSICS JOURNAL, vol. 28, no. 7, pp. 533–551, 1999. doi:10.1007/s002490050236

1998

M. Ivkovic-Jensen, G. Ullmann, S. Young, Ö. Hansson, M. Crnogorac, M. Ejdebäck, and N. Kostic, Effects of single and double mutations in plastocyanin on the rate constant and activation parameters for the rearrangement gating the electron-transfer reaction between the triplet state of zinc cytochrome c and cupriplastocyanin, BIOCHEMISTRY, vol. 37, no. 26, pp. 9557–9569, 1998. doi:10.1021/bi9802871
B. Rabenstein, G. Ullmann, and E. Knapp, Energetics of electron-transfer and protonation reactions of the quinones in the photosynthetic reaction center of rhodopseudomonas viridis, BIOCHEMISTRY, vol. 37, no. 8, pp. 2488–2495, 1998. doi:10.1021/bi971921y
B. Rabenstein, G. Ullmann, and E. Knapp, Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles - application to the photosynthetic reaction center, EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, vol. 27, no. 6, pp. 626–637, 1998. doi:10.1007/s002490050174

1997

G. Ullmann, M. Hauswald, A. Jensen, N. Kostic, and E. Knapp, Comparison of the physiologically equivalent proteins cytochrome c6 and plastocyanin on the basis of their electrostatic potentials. Tryptophan 63 in cytochrome c6 may be isofunctional with tyrosine 83 in plastocyanin, BIOCHEMISTRY, vol. 36, no. 51, pp. 16187–16196, 1997. doi:10.1021/bi971241v
G. Ullmann, E. Knapp, and N. Kostic, Computational simulation and analysis of dynamic association between plastocyanin and cytochrome f. Consequences for the electron-transfer reaction, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 119, no. 1, pp. 42–52, 1997. doi:10.1021/ja962237u

1996

G. Ullmann, E. Knapp, and N. Kostic, Modelling of the plastocyanin-cytochrome f-complex using simulation techniques and calculation of electron transfer pathways, PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, vol. 65, no. 1, p. PE207, 1996.

1995

G. ULLMANN and N. 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, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 117, no. 17, pp. 4766–4774, 1995. doi:10.1021/ja00122a005

Theoretical and Computational Biochemistry Group

Prof. Dr. G. Matthias Ullmann

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