M.Sc. Project Introduction Nitrogen-fixing Enzymes M.Sc. Candidate: Egill Skulason Supervisor: Hannes Jonsson Co-supervisor: Magnus Mar Kristjansson Raunvisindastofnun Haskola Islands Efnafraedistofa vklubbur 31 st of July 2003
Contents Introduction Background Nitrogenase Methodology FeMo Cofactor Model Structures Reactivity Biological Ammonia Synthesis Summary and Future Study
Introduction Project Goal: Study the biological ammonia synthesis using density functional calculations (DFT) on models of the active center of nitrogenase. Nitrogenase is a catalytic enzyme found in many bacteria, and is central to biological ammonia synthesis. Understanding of this process may lead to a more gentle manufacturing of ammonia, lowering pollution and energy costs. Background: Density Functional Calculations and Modeling of the Biological Ammonia Synthesis by Thomas Holm Rod, Ph. D. (2000) Technical University of Denmark (DTU) and Center for Atomic-Scale Materials Physics (CAMP).
Background The conversion of atmospheric N 2 into a biologically accessible form of nitrogen such as ammonia, is termed nitrogen fixation. Since the element N is present in many biomolecules, such as amino acids, nitrogen fixation is a prerequisite for life. In spite of the vast quantities of atmospheric N 2, the sources of biologically accessible nitrogen are few.
The Main Sources of Biologically Accessible Nitrogen Oxidation of N 2 to nitrogen oxides by lightning and combustion. The commercial Haber-Bosch process where N 2 reacts with hydrogen on a Fe or Ru based catalyst to form ammonia. The enzyme catalyzed ammonia synthesis where N 2 reacts with electrons and protons to form ammonia. Ref: L. Stryer, Biochemistry, 4. Ed. (W.H. Freeman and Company, New York, 1995), p. 714.
Nitrogenase Nitrogenase consists of two metalloproteins: Fe protein and MoFe protein (named after their metal clusters). The Fe protein contains a ferredoxin (4Fe-4S), which is known to play a role in electron transfer in many proteins. W. Kaim and B. Schwederski, Bioinorganic Chemistry: Inorganic Elements in the Chemistry of Life (John Wiley & Sons, New York, 1991). The MoFe protein contains two unique cluster pairs, namely the P-cluster and the FeMo cofactor (FeMoco). FeMoco is most likely the active center where N 2 binds and is reduced.
Nitrogenase Ferredoxin reduced e- are accelerated through the Pcluster towards the FeMoco. N. Schindelin et al., Structure of ADP AlF4- -stabilized nitrogenase complex and its implications for signal transduction, Nature 387, (1997), PDB ID code: 1N2C.
The Metalloclusters Sulfur: yellow Iron: purple Molybdenum: blue N. Schindelin et al., Structure of ADP AlF 4 - -stabilized nitrogenase complex and its implications for signal transduction, Nature 387, (1997), PDB ID code: 1N2C.
The Methodology Density Functional Calculation (DFT) forms the basis in this Ph. D. thesis and will be used in this M.Sc. study. The exchange correlation functionals applied in the Ph. D. study, by Rod, were the PW91 and the RPBE functionals. The latter will probably be used for current study. DACAPO: an DFT calculating program which use planewave pseudo-potentials.
Model Structures of the FeMo Cofactor
N 2 Adsorption on Models I and II Adsorption energies: Model I 0.0 ev Model II -0.1 ev
Reactivity of the FeMoco H bonding (H + + e - ) and H 2 formation N 2 adsorption modeling of the interaction with the surrounding protein The energy of a system is always calculated in relation to model I and the incoming substrate, usually in gas phase.
H Binding and H2 Formation of Model I To study the effect of the e- and H+ flow to the FeMoco, 1-4 H atoms where added to model I.
N2 Adsorption
Modeling of the Interaction with the Surrounding Protein There is a possibility that an e - is transferred to the complex without a simultaneous transfer of a proton. It is clear that the enzyme must have sites close to the active site that can act as proton donors during nitrogen hydrogenation. Such a donor might either be an amino residue or an H 2 O molecule. They therefore add to their system a weak base, NH 4 + or H 3 O +, in the vicinity of the cofactor.
N 2 Adsorption on Model I with and without the Proton Donor NH 4 +
Biological Ammonia Synthesis
A Short Summary In this thesis a simple model of the FeMoco has been investigated theoretically. Two different clusters have been studied to mimic the central part of the FeMoco. The effect of the surroundings have also been included in a crude way by invoking proton donors in the vicinity of the cofactor. The interaction of the FeMoco with the substrates H, H 2 and N 2 have been calculated and most of the observations agree with experimental results. (Not discussed in this presentation). A reaction path, of the biological ammonia synthesis, has been calculated.
For Future Study Investigate the real environment of the nitrogenase and make new models. Simulate the high chemical potential of the electrons and protons.