Publications
Publications of the Holzhütter group
Publications of the Holzhütter group in cooperation with other groups
Other publications of group members
Publications of the Holzhütter group
2010
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(1): accepted
2009
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]
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]
Menküc BS, Gille C, Holzhütter HG. (2008)
Computer aided optimization of carbon atom labeling for tracer experiments.
Genome Inform., 20:270-6.
[PubMed]
2007
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]
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]
2006 & 2005
Gille C. (2006)
Structural interpretation of mutations and SNPs using STRAP-NT.
Protein Science., 15, 208-210.
[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]
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]
2002-2004
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]
Holzhütter HG. (2004)
Mathematische Zellmodelle - Fiktion oder greifbare Wirklichkeit?
Bioforum.
[pdf]
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]
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]
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]
2001 & 2000
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]
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]
1999 & before
Holzhütter HG, Frommel C and Kloetzel PM. (1999)
A theoretical approach towards the identification of cleavage-determining amino acid motifs of
the 20 S proteasome.
J. Mol. Biol., 286(4), 1251-65.
[PubMed]
Zaiss DM, Standera S, Holzhütter H, Kloetzel PM and Sijts AJ. (1999)
The proteasome inhibitor PI31 competes with PA28 for binding to 20S proteasomes.
FEBS Lett., 457(3), 333-338.
[PubMed]
Schuster R and Holzhütter HG. (1995)
Use of Mathematical Models for Predicting the Metabolic Effect of Evolution of Large-Scale
Enzyme Activity Alteration: Application to Enzyme Deficiencies of Red Blood Cells.
Eur. J. Biochem., 229, 403-418.
[PubMed]
Holzhütter HG, Schwendel A, Grune T, Quedenau J, Siems W. (1993)
Estimation of steady-state flux rates in metabolic systems by computer simulations of
radioactive tracer experiments.
Comput Appl Biosci., 9(5), 573-580.
[PubMed]
Bartel T and Holzhütter HG. (1990)
Mathematical modelling of the purine metabolism of the rat liver
Biochim. Biophys. Acta, 1035, 331-339.
[PubMed]
Holzhütter HG, Henke W, Dubiel W and Gerber G. (1985)
A mathematical model to study the short-term regulation of mitochondrial energy transduction.
Biochim. Biophys. Acta, 810, 252-268.
[PubMed]
Publications of the Holzhütter group in cooperation with other groups
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]
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
Jungblut PR, Holzhütter HG, Apweiler R, Schlüter H. (2008)
The speciation of the proteome.
Chem Cent J., 2:16.
[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]
2001-2007
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]
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]
Holzhütter S, Holzhütter HG. (2004)
Computational design of reduced metabolic networks.
Chembiochem, 5, 1401-1422.
[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]
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]
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]
2000 & before
Belkner J, Stender H, Holzhütter HG, Holm C and 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., 352, 125-133.
[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.
[Abstract]
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]
Schmidtke G, Holzhütter HG, Bogyo M, Kairies N, Groll M, de Giuli R, Emch S and Groettrup M. (1999)
How an inhibitor of the HIV-I protease modulates proteasome activity.
J. Biol. Chem., 274(50), 35734-35740.
[PubMed]
Other publications of group members
2009 & 2008
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]
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]
Bauer RA, Bourne PE, Formella A, Frömmel C, Gille C, Goede A, Guerler A, Hoppe A, Knapp EW, Pöschel T, Wittig B, Ziegler V, Preissner R. (2008)
Superimpose: a 3D structural superposition server.
Nucleic Acids Res., 36(Web Server issue):W47-54.
[PubMed]
Flajolet M, Wang Z, Futter M, Shen W, Nuangchamnong N, Bendor J, Wallach I, Nairn AC, Surmeier DJ, Greengard P. (2008) FGF acts as a co-transmitter through adenosine A(2A) receptor to regulate synaptic plasticity. Nat Neurosci., 11(12):1402-9. [PubMed]
Hildebrand PW, Günther S, Goede A, Forrest L, Frömmel C, Preissner R. (2008)
Hydrogen-bonding and packing features of membrane proteins: functional implications.
Biophys J., 94(6):1945-53.
[PubMed]