Publications
Publications of the Holzhütter group
Previous publications of Prof. Holzhütter
Other publications of group members
Publications of the Holzhütter group
2011
Berndt N, Hoffmann S, Benda J, Holzhütter HG. (2011)
The influence of the chloride currents on action potential firing and volume regulation of excitable cells studied by a kinetic model.
J Theor Biol., 276(1):42-49.
[PubMed]
Herling A, König M, Bulik S, Holzhütter HG. (2011)
Enzymatic Features of the Glucose Metabolism in Tumor Cells.
FEBS J., doi: 10.1111/j.1742-4658.2011.08174.x.
[PubMed]
Hoppe A, Hoffmann S, Gerasch A, Gille C, Holzhutter HG. (2011)
FASIMU: flexible software for flux-balance computation series in large metabolic networks.
BMC Bioinformatics., 12(1):28.
[PubMed]
Hoppe A, Richter C, Holzhütter HG. (2011)
Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes.
BioSystems.,
[in print]
2010
Gille C, Bölling C, Hoppe A, Bulik S, Hoffmann S, Hübner K, Karlstädt A, Ganeshan R, König M, Rother K, Weidlich M, Behre J, Holzhütter HG. (2010)
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology.
Mol Syst Biol., 6:411.
[PubMed]
Huthmacher C, Hoppe A, Bulik S, Holzhutter HG. (2010)
Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis.
BMC Syst Biol., 4(1):120. [Epub ahead of print]
[PubMed]
König M and Holzhütter HG. (2010)
FluxViz - Cytoscape Plug-in for Vizualisation of Flux Distributions in Networks.
Genome Informatics, 24, p.96-103
Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhütter HG. (2010)
IGERS: Inferring Gibbs energy changes of biochemical reactions from reaction similarities.
Biophys J., 98(11):2478-86.
[PubMed]
Sun G, Rosu DM, Zhang X, Hovestädt M, Pop S, Schade U, Aulich D, Gensch M, Ay B, Holzhütter HG, Zahn DRT, Esser N, Volkmer R, Rappich J and Hinrichs K (2010)
Synchrotron infrared spectroscopic ellipsometry (IRSE) for characterization of biofunctional surfaces.
physica status solidi (b), 247: 1925–1931.
[doi]
2009
Bech-Otschir D, Helfrich A, Enenkel C, Consiglieri G, Seeger M, Holzhütter HG, Dahlmann B, Kloetzel PM. (2009)
Polyubiquitin substrates allosterically activate their own degradation by the 26S proteasome.
Nat Struct Mol Biol., 16(2):219-25.
[PubMed]
Binder B, Goede A, Berndt N, Holzhütter HG. (2009)
A conceptual mathematical model of the dynamic self-organisation of distinct cellular organelles.
PLoS One, 4(12):e8295.
[PubMed]
Bulik S, Grimbs S, Huthmacher C, Selbig J, Holzhütter HG. (2009)
Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws: A promising method for speeding up the kinetic modelling of complex metabolic networks.
FEBS Journal, 276:410-424
[PubMed]
Hoffmann S and Holzhütter HG. (2009)
Uncovering metabolic objectives pursued by changes of enzyme levels.
Ann N Y Acad Sci., 1158:57-70.
[PubMed]
Lock JF, Taheri P, Bauer S, Holzhütter HG, Malinowski M, Neuhaus P, Stockmann M. (2009)
Interpretation of Non-Invasive Breath Tests Using 13C-labeled Substrates - A Preliminary Report With superset13 C-Methacetin.
Eur J Med Res., 14(12):547-50.
[PubMed]
Schlüter H, Apweiler R, Holzhütter HG, Jungblut PR. (2009)
Finding one's way in proteomics: a protein species nomenclature.
Chem Cent J., 3:11.
[PubMed]
2008
Gille C, Hoppe A, Holzhütter HG. (2008)
Web-Links as a Means to Document Annotated Sequence and 3D-Structure Alignments in Systems Biology.
Genome Inform., 20:277-84.
[PubMed]
Hübner K, Schwager T, Winkler K, Reich JG, Holzhütter HG. (2008)
Computational lipidology: predicting lipoprotein density profiles in human blood plasma.
PLoS Comput Biol., 23;4(5):e1000079.
[PubMed]
Huthmacher C, Gille C, Holzhütter HG. (2008)
A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling.
J Theor Biol., 252(3):456-64.
[PubMed]
Jungblut PR, Holzhütter HG, Apweiler R, Schlüter H. (2008)
The speciation of the proteome.
Chem Cent J., 2:16.
[PubMed]
Menküc BS, Gille C, Holzhütter HG. (2008)
Computer aided optimization of carbon atom labeling for tracer experiments.
Genome Inform., 20:270-6.
[PubMed]
Mishto M, Luciani F, Holzhütter HG, Bellavista E, Santoro A, Textoris-Taube K, Franceschi C, Kloetzel PM, Zaikin A. (2008)
Modeling the in vitro 20S proteasome activity: the effect of PA28-alphabeta and of the sequence and length of polypeptides on the degradation kinetics.
J Mol Biol., 377(5):1607-17.
[PubMed]
Schatz MM, Peters B, Akkad N, Ullrich N, Martinez AN, Carroll O, Bulik S, Rammensee HG, van Endert P, Holzhütter HG, Tenzer S, Schild H. (2008)
Characterizing the N-terminal processing motif of MHC class I ligands.
J Immunol., 180(5):3210-7.
[PubMed]
2007 & 2006
Gille C, Hoffmann S, Holzhütter HG. (2007)
METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks.
BMC Syst Biol., 1:5.
[PubMed]
Grimbs S, Selbig J, Bulik S, Holzhütter HG, Steuer R. (2007)
The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks.
Mol Syst Biol., 3:146.
[PubMed]
Hoffmann S, Hoppe A and Holzhütter HG. (2007)
Pruning genome-scale metabolic models to consistent ad functionem networks.
Genome Informatics, 18(1), 308-19.
[pdf]
Hoppe A, Hoffmann S, Holzhütter HG. (2007)
Including
metabolite concentrations into flux-balance analysis:
Thermodynamic realizability as a constraint on flux
distributions in metabolic networks BMC Syst. Biol.,
1(1): 23. [pdf,
journal, PubMed]
Huthmacher C, Gille C, Holzhütter HG. (2007)
Computational analysis of protein-protein interactions in metabolic networks of Escherichia coli and yeast.
Genome Inform., 18:162-72.
[PubMed]
Saam J, Ivanov I, Walther M, Holzhütter H, and Kuhn H. (2007)
Molecular dioxygen enters the active site of 12/15-lipoxygenase
via dynamic oxygen access channels.
Proc. Natl. Acad. Sci., 104(33), 13319-13324
[PubMed]
Hoffmann S, Hoppe A, Holzhütter
HG. (2006)
Composition of Metabolic Flux Distributions by Functionally Interpretable Minimal Flux Modes (MinModes).
Genome Informatics, 17(1), 195-207. [pdf, PubMed]
Holzhütter HG. (2006)
The generalized flux-minimization method and its application to metabolic networks affected by enzyme deficiencies.
Biosystems., 83(2-3):98-107.
[PubMed]
2005
Bulik S, Peters B, Holzhütter HG. (2005)
Quantifying the contribution of defective ribosomal products to antigen production: a model-based computational analysis.
J Immunol., 175(12):7957-64.
[PubMed]
Gille C, Hoffmann S, Holzhütter HG. (2005)
Combining bioinformatics resources for the structural modelling
of eukaryotic metabolic networks.
Genome Inform., 16, 223-32.
[PubMed]
Ivanov I, Saam J, Kühn H, Holzhütter HG. (2005)
Dual role of oxygen during lipoxygenase reactions.
FEBS Journal, 272, 2523-2535.
[PubMed,
pdf]
Kühn H, Saam J, Eibach S, Holzhütter HG, Ivanov I, Walther M. (2005)
Structural biology of mammalian lipoxygenases: Enzymatic
consequences of targeted alterations of the protein structure.
Biochem. Biophys. Res. Commun., 338, 93-101.
[PubMed]
Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG,
Schild H, Holzhütter HG. (2005).
Modeling the MHC class I pathway by combining predictions of
proteasomal cleavage, TAP transport and MHC class I binding.
Cell. Mol. Life Sci., 62(9), 1025-37.
[PubMed]
2004
Bulik S, Peters B, Ebeling C, Holzhütter HG. (2004)
Cytosolic processing of proteasomal cleavage products can enhance the presentation
efficiency of MHC-1 epitopes. Genome Inform Ser Workshop Genome Inform, 15(1), 24-34.
[PubMed]
Epple G, Langfeld K, Baier M, Holzhütter HG, Schleuning WD, Köttgen E, Gessner R, Praus M. (2004)
Both lysine-clusters of the NH(2)-terminal prion-protein fragment PrP23 are essential for t-PA mediated plasminogen activation.
Thromb Haemost., 91(3):465-72.
[PubMed]
Holzhütter HG. (2004)
Mathematische Zellmodelle - Fiktion oder greifbare Wirklichkeit?
Bioforum.
[pdf]
Holzhütter, HG. (2004)
Studying enzyme kinetics by means of progress-curve analysis.
In: Proc. of the 1st International Beilstein Workshop on Exp. Standard Conditions of Enzyme Characterizations, 5.-8.Oct. 2003. Logos Verlag Berlin, pp. 99-113
Holzhütter HG. (2004)
The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur J Biochem 271, 2905-2922.
[PubMed]
Holzhütter S, Holzhütter HG. (2004)
Computational design of reduced metabolic networks.
Chembiochem, 5, 1401-1422.
[PubMed]
Ivanov I, Romanov S, Ozdoba C, Holzhütter HG, Myagkova G, Kuhn H. (2004)
Enantioselective substrate specificity of 15-lipoxygenase 1.
Biochemistry, 43(50):15720-8.
[PubMed]
2003 & 2002
Hakenberg J, Nussbaum AK, Schild H, Rammensee HG, Kuttler C, Holzhütter HG, Kloetzel PM, Kaufmann SH, Mollenkopf HJ. (2003)
MAPPP: MHC class I antigenic peptide processing prediction.
Appl Bioinformatics., 2(3):155-8.
[PubMed]
Holzhütter HG, Genschow E, Diener W, Schlede E. (2003)
Dermal and inhalaton acute toxic class methods: test procedures and biometric avaluations for the Globally Harmonized Classification System.
Arch Toxicol., 77(5):243-54.
[PubMed]
Peters B, Bulik S, Tampe R, van Endert PM, and Holzhütter HG. (2003)
Identifying MHC-I epitopes by predicting the TAP transport efficiency of epitope precursors.
J. Immunol., 171(4), 1741-1749.
[PubMed]
Praus M, Kettelgerdes G, Baier M, Holzhütter HG, Jungblut PR, Maissen M, Epple G, Schleuning WD, Köttgen E, Aguzzi A, Gessner R. (2003)
Stimulation of plasminogen activaton by recombinant cellular prion protein is conserved in the NH2-terminal fragment PrP23-10.
Thromb Haemost., 89(5):812-9.
[PubMed]
Stohwasser R, Holzhütter HG, Lehmann U, Henklein P and Kloetzel PM. (2003)
Hepatitis B virus HBx peptide 116-138 and proteasome activator PA28 compete
for binding to the proteasome alpha4/MC6 subunit.
Biol. Chem., 384(1), 39-49.
[PubMed]
Klipp E, Heinrich R and Holzhütter HG. (2002)
Prediction of temporal gene expression. Metabolic opimization by re-distribution of enzyme activities.
Eur. J. Biochem., 269(22), 5406-5413.
[PubMed]
Peters B and Holzhütter HG. (2002)
In vitro phototoxicity testing: Development and validation of a new concentration response
analysis software and biostatistical analyes relates to the use of various prediction models.
ATLA, 30, 415-432.
[PubMed]
Peters B, Janek K, Kuckelkorn U and Holzhütter HG. (2002)
Assessment of proteasomal cleavage probabilities from kinetic analysis of time-dependent
product formation.
J. Mol. Biol., 318, 847-862.
[PubMed]
Previous publications of Prof. Holzhütter
2001 & 2000
Kuon W, Holzhütter HG, Appel H, Grolms M, Kollnberger S, Traeder A, Henklein P, Weiss E,
Thiel A, Lauster R, Bowness P, Radbruch A, Kloetzel PM and Sieper J. (2001)
Identification of HLA-B27-restricted peptides from the Chlamydia trachomatis proteome
with possible relevance to HLA-B27-associated diseases.
J. Immunol., 167(8), 4738-4746.
[PubMed]
Pospisil H and Holzhütter HG. (2001)
A compartment model to calculate time-dependent concentration profiles topically applied
chemical compounds in the anterior compartments of the eye.
ATLA, 29, 347-365.
[PubMed]
Schreiber S, Ludwig K, Herrmann A and Holzhütter HG. (2001)
Stochastic simulation of hemagglutinin-mediated fusion pore formation.
Biophy. J., 81, 1360-1372.
[PubMed]
Velders MP, Macedo MF, Provenzano M, Elmishad AG, Holzhütter HG, Carbone M, Kast WM. (2001)
Human T cell responses to endogenously presented HLA-A*0201 restric peptides of simian virus
40 large T antigen.
J. Cell Biochem., 82, 155-162.
[PubMed]
Belkner J, Stender H, Holzhütter HG, Holm C, Kühn H. (2000)
Macrophage cholesteryl ester hydrolases and hormone-sensitive lipase prefer specifically oxidized cholesteryl esters as substrates over their non-oxidized counterparts.
Biochem J., 352Pt 1:125-33.
[PubMed]
Holzhütter HG and Kloetzel PM. (2000)
A kinetic model of vertebrate 20S proteasome accounting for the generation of major
proteolytic fragments from oligomeric peptide substrates.
Biophys. J., 79(3), 1196-1205.
[PubMed]
Liebsch M, Traue D, Barrabas C, Spielmann H, Uphill P, Wilkins S, McPherson JP, Wiemann C, Kaufmann T, Remmele M and Holzhütter HG (2000)
The ECVAM prevalidation study on the use of EpiDerm for skin corrosivity testing.
ATLA, 28, 371-401.
Marx U, Lassmann G, Holzhütter HG, Wüstner D, Müller P, Höhlig A, Kubelt J,
Herrmann. (2000)
A. Rapid Flip-Flop of Phospholipids in Endoplasmatic Reticulum Membranes Studied by a
Stopped-Flow Approach.
Biophys. J., 78, 2628-2640
[PubMed]
Schmidtke G, Emch S, Groettrup M, Holzhütter HG. (2000)
Evidence for the existence of a non-catalytic modifier site of peptide hydrolysis by the
20S proteasome.
J. Biol. Chem., 275, 22056-22063.
[PubMed]
Stohwasser R, Salzmann U, Giesebrecht J, Kloetzel PM and Holzhütter HG.(2000)
Kinetic evidences for facilitation of peptide channeling by the proteasomal activator PA28.
Eur. J. Biochem., 267, 6221-6230.
[PubMed]
Other publications of group members
2010 & 2009
Rose A, Goede A, Hildebrand PW. (2010)
MPlot--a server to analyze and visualize tertiary structure contacts and geometrical features of helical membrane proteins.
Nucleic Acids Res., 38(Web Server issue):W602-8.
[PubMed]
Sereda MJ, Hartmann S, Büttner DW, Volkmer R, Hovestädt M, Brattig N, Lucius R. (2010)
Characterization of the allergen filarial tropomyosin with an invertebrate specific monoclonal antibody.
Acta Trop., 116(1):61-7.
[PubMed]
Zhang X, Sun G, Hovestädt M, Syritski V, Esser N, Volkmer R, Janietz S, Rappich J, Hinrichs K (2010)
A new strategy for the preparation of maleimide-functionalised gold surfaces.
Electrochemistry Communications, 12(10):1403-1406
[doi]
Hildebrand PW, Goede A, Bauer RA, Gruening B, Ismer J, Michalsky E, Preissner R. (2009)
SuperLooper - a prediction server for the modeling of loops in globular and membrane proteins.
Nucl. Acids Res. 37, Web Server issue, W571-W574
[PubMed]
Rose A, Lorenzen S, Goede A, Gruening B, Hildebrand PW. (2009)
RHYTHM - a server to predict the orientation of transmembrane helices in channels and membrane-coils.
Nucl. Acids Res. 37, Web Server issue, W575-W580
[PubMed]
Rother K, Hildebrand PW, Goede A, Gruening B, Preissner R. (2009)
Voronoia: analyzing packing in protein structures.
Nucleic Acids Res., 37(Database issue):D393-5.
[PubMed]
Scheerer P, Heck M, Goede A, Park JH, Choe HW, Ernst OP, Hofmann KP, Hildebrand PW. (2009)
Structural and kinetic modeling of an activating helix switch in the rhodopson-transducin interface.
PNAS 106(26):10660-5
[PubMed]
Wallach I, Zhang J, Hartmann A, van Landeghem FKH, Ivanova A, Klar M, Dame C. (2009)
Erythropoietin-Receptor gene regulation in neuronal cells.
Pediatr Res., 65(6):619-24.
[PubMed]