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• Professor Dr. Ernst-Walter Knapp
  Freie Universität Berlin – Fachbereich Biologie, Chemie, Pharmazie
  Institut für Chemie
  Takustraße 6
  14195 Berlin
  
  

  Phone:	+49 (30) 838-54387
  FAX:	+49 (30) 838-56921
  E-Mail:	knapp@chemie.fu-berlin.de

  
  

– Discipline –

• Theoretical Biochemistry/Biophysics

– Systems –

• Photosynthetic systems: photosystem I (PSI), photosystem II (PSII) and bacterial photosynthetic reaction centers
• DNA photolyase (Escherichia coli, Thermus thermophilus, Arabidopsis thaliana)

– Methods –

• Electrostatic energy computation by solving the Poisson-Boltzmann equation
• Quantum-chemical ab initio and density-functional methods
• Conventional molecular-dynamics simulations

• Artur Galstjan
  Freie Universität Berlin – Fachbereich Biologie, Chemie, Pharmazie
  Institut für Chemie
  Takustraße 6
  14195 Berlin
  
  

  Phone:	+49 (30) 838-53612
  FAX:	+49 (30) 838-56921
  E-Mail:	artari@chemie.fu-berlin.de

  
  
• Ana Patricia Gámiz Hernández
  Freie Universität Berlin – Fachbereich Biologie, Chemie, Pharmazie
  Institut für Chemie
  Takustraße 6
  14195 Berlin
  
  

  Phone:	+49 (30) 838-53890
  FAX:	+49 (30) 838-56921
  E-Mail:	apgamiz@chemie.fu-berlin.de

  
  

Reactions in proteins and the functionally related transfer processes of electrons (ET) and protons (PT) are investigated with modeling and computer simulation methods. In essence, we like to understand how proteins steer and optimize enzymatic reactions and transfer processes by recruitment of appropriate cofactors, adjustment of cofactor conformations and tuning specific interactions of the cofactor with charged and polar groups from the protein environment (for instance H-bonds). Special focus are the electron transfer chains and PT-coupled ET events in photosynthesis.
We use conventional techniques of computer simulation and modeling of molecular systems to complement or alternate atomic coordinates from crystal structures to generate different side-chain conformations and mutant structures. The Poisson-Boltzmann equation (PBE) is solved to evaluate the energetics of ET and PT processes in proteins. Quantum-chemical ab initio methods such as density functional theory (DFT) are used to characterize structure and energetics of transition-metal complexes in proteins. The latter technique is used for the non-heme iron centers in bacterial reaction centers (bRCs) and photosystem II (PSII), and for the manganese cluster in PSII.
Problems that we like to address are:

(1) What makes the redox potential of oxidation for the P680 dimer in PSII so high, while the redox potentials of corresponding dimers in bRC and photosystem I (PSI) (P700) are so low?

(2) How can Tyr_Z in PSII transfer electrons from the manganese cluster to P680?

(3) What are the detailed charge states of the manganese cluster in its different redox states S₀ to S₄?

(4) What are the mechanisms that render the two ET branches (branch A and branch B) in bRC asymmetric and what is the degree of asymmetry of the electron-transfer branches in PSI and PSII?

(5) How does the non-heme iron function in PSI, and is there a functional role of this iron center in bRCs, too?

(6) How are the protons transferred that are taken up by the secondary quinone (Q_B) in bRC and PSII?

– 2005 –

• H. Ishikita, B. Loll, J. Biesiadka, W. Saenger, E.W. Knapp
  Redox potentials of chlorophylls in the photosystem II reaction center
  Biochemistry 44 (2005) 4118–4124
  [REPRINT REQUEST]
  
• H. Ishikita, B. Loll, J. Biesiadka, A. Galstyan, W. Saenger, E.W. Knapp
  Tuning electron transfer by ester-group of chlorophylls in bacterial photosynthetic reaction center
  FEBS Letters 579 (2005) 712–716
  [REPRINT REQUEST]
  
• H. Ishikita, E.W. Knapp
  Redox potential of cytochrome c550 in the cyanobacterium Thermosynechococcus elongates
  FEBS Letters 579 (2005) 3190–3194
  [REPRINT REQUEST]
  
• H. Ishikita, E.W. Knapp
  Energetics of proton transfer pathways in reaction centers from Rhodobacter sphaeroides. The Glu-H173 activated mutants
  Journal of Biological Chemistry 280 (2005) 12446–12450
  [REPRINT REQUEST]
  
• A.S. Galstyan, S.D. Zaric, E.W. Knapp
  Computational studies on imidazole heme conformations
  Journal of Biological Inorganic Chemistry 10 (2005) 343–354
  [REPRINT REQUEST]
  
• G. Morra, U. Koert, E.W. Knapp
  Role of ions on structure and stability of a synthetic gramicidin ion channel in solution. A molecular dynamics study
  Journal of Physical Chemistry B 109 (2005) 10441–10448
  [REPRINT REQUEST]
  
• H. Ishikita, E.W. Knapp
  Redox potentials of chlorophylls and beta-carotene in the antenna complexes of photosystem II
  Journal of the American Chemical Society 127 (2005) 1963–1968
  [REPRINT REQUEST]
  

– 2004 –

• P.M. Kekenes-Huskey, I. Muegge, M. von Rauch, R. Gust, E.W. Knapp
  A molecular docking study of estrogenically active compounds with 1,2-diarylethane and 1,2-diarylethene pharmacophores
  Bioorganic & Medicinal Chemistry 12 (2004) 6527–6537
  [REPRINT REQUEST]
  
• H. Riedesel, B. Kolbeck, O. Schmetzer, E.W. Knapp
  Peptide binding at class I major histocompatibility complex scored with linear functions and support vector machines
  Genome Informatics 15 (2004) 198–212
  [REPRINT REQUEST]
  
• H. Ishikita, E.W. Knapp
  Variation of Ser-L223 hydrogen bonding with the Q_B redox state in reaction centers from Rhodobacter sphaeroides
  Journal of the American Chemical Society 126 (2004) 8059–8064 [REPRINT REQUEST]
  

– 2003 –

• H. Ishikita, G. Morra, E.W. Knapp
  Redox potential of quinones in photosynthetic reaction centers from Rhodobacter sphaeroides: dependence on protonation of Glu-L212 and Asp-L213
  Biochemistry 42 (2003) 3882–3892
  [REPRINT REQUEST]
  
• P. Voigt, E.W. Knapp
  Tuning heme redox potentials in the cytochrome c subunit of photosynthetic reaction centers
  Journal of Biological Chemistry 278 (2003) 51993–52001
  [REPRINT REQUEST]
  
• H. Ishikita, E.W. Knapp
  Redox potential of quinones in both electron transfer branches of photosystem I
  Journal of Biological Chemistry 278 (2003) 52002–52011
  [REPRINT REQUEST]
  
• G. Morra, M. Hodoscek, E.W. Knapp
  Unfolding of the cold shock protein studied with biased molecular dynamics
  Proteins: Structure, Function, and Genetics 53 (2003) 597–606
  [REPRINT REQUEST]
  

– 2002 –

• P. Vagedes, W. Saenger, E.W. Knapp
  Driving forces of protein association: the dimer-octamer equilibrium in arylsulfatase A
  Biophysical Journal 83 (2002) 3066–3078
  [REPRINT REQUEST]
  
• D.M. Popovic, A. Zmiric, S.D. Zaric, E.W. Knapp
  Energetics of radical transfer in DNA photolyase
  Journal of the American Chemical Society 124 (2002) 3775–3782
  [REPRINT REQUEST]
  

– 2001 –

• S.D. Zaric, D.M. Popovic, E.W. Knapp
  Factors determining the orientation of axially coordinated imidazoles in heme proteins
  Biochemistry 40 (2001) 7914–7928
  [REPRINT REQUEST]
  
• B. Rabenstein, E.W. Knapp
  Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers
  Biophysical Journal 80 (2001) 1141–1150
  [REPRINT REQUEST]
  
• D.M. Popovic, S.D. Zaric, B. Rabenstein, E.W. Knapp
  Artificial cytochrome b: computer modeling and evaluation of redox potentials
  Journal of the American Chemical Society 123 (2001) 6040–6053
  [REPRINT REQUEST]
  
• U. Bastolla, J. Farwer, E.W. Knapp, M. Vendruscolo
  How to guarantee optimal stability for most representative structures in the Protein Data Bank
  Proteins: Structure, Function, and Genetics 44 (2001) 79–96
  [REPRINT REQUEST]
  

– 2000 –

• B. Rabenstein, G.M. Ullmann, E.W. Knapp
  Electron transfer between the quinones in the photosynthetic reaction center and its coupling to conformational changes
  Biochemistry 39 (2000) 10487–10496
  [REPRINT REQUEST]
  
• S.D. Zaric, D.M. Popovic, E.W. Knapp
  Metal ligand aromatic cation–pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues
  Chemistry – A European Journal 6 (2000) 3935–3942
  [REPRINT REQUEST]
  
• P. Vagedes, B. Rabenstein, J. Åqvist, J. Marelius, E.W. Knapp
  The deacylation step of acetylcholinesterase: computer simulation studies
  Journal of the American Chemical Society 122 (2000) 12254–12262
  [REPRINT REQUEST]
  

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