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Bioinorganic Chemistry & Biophysics of Plants Bioinorganic Chemistry & Biophysics of Plants University of Konstanz, SS 2012 [email protected] 1 Bioinorganic Chemistry & Biophysics of Plants Lectures P. Kroneck 1. Basics of Coordination Chemistry in Biological Systems (transition metals – general properties – structural/functional aspects) 2. Magnetic Resonance Spectroscopy as Structural Tool (electron paramagnetic resonance, nuclear magnetic resonance) 3. Global Cycles of the Elements (nitrogen, sulfur, metals, and metalloenzymes) 4. From Physiology to Biochemistry to Spectroscopy and Protein Structure (copper and iron proteins) 5. How to give a good seminar & how to prepare a good poster 2 "Bioinorganic Chemistry & Biophysics of Plants" Introductory Books & References Frausto da Silva, Williams, 2001 The biological chemistry of the elements, Oxford University Press H. B. Gray, E. I. Stiefel, J. Selverstone Valentine, I. Bertini, 2007 Biological Inorganic Chemistry: Structure and Reactivity, University Science Books R. R. Crichton, 2012 Biological Inorganic Chemistry, 2nd edition, Elsevier Messerschmidt, Huber, Poulos, Wieghardt (eds), 2001; 2004; 2009 on-line Handbook of Metalloproteins, John Wiley & Sons, LTD Chemical Reviews, 1996; 2004 Special Issues on Bioinorganic Enzymology, 96, 2237; 104, 347 3 Useful web sites http://http://www.ebi.ac.uk/pdbe/ comprehensive database of all published protein structures http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi comprehensive databases (genomes, genes, proteins, inherited diseases...etc) and various search tools http://www.brenda-enzymes.org/ comprehensive enzyme database including information on metal requirements http://www.webelements.com periodic table of the elements including useful information on each element 4 PDB and PROMISE Databases • PDB = Protein Data Bank: http://www.rcsb.org/pdb/home.do; type in the search field the PDB number: • 1A70 (for Ferredoxin), 3SBP for Nitrous Oxide Reductase • PROMISE at Scripps, San Diego: htpp://metallo.scripps.edu/PROMISE/ 5 Bringing Inorganic Chemistry to Life... Biochemistry Biogeochemistry Physiology Molecular Biology Biophysics Bioinorganic Chemistry Microbiology Environmental Spectroscopy Chemistry Structural Biology Catalysis Physical Chemistry Medical Chemistry/Toxicology 6 Part 1: Basics of Coordination Chemistry in Biological Systems (transition metals – general properties – structural and functional aspects) “The application of metals to treat human ailments dates back at least to the fifth century B.C., and the study and mimicry of metals in biology is a vibrant subject today”…. Stephen Lippard, J Am Chem Soc (2010), 132, 141689-14693 7 The elements/metals of life H He www.webelements.com Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Essential Transition metals (ions) are Ca: 1.2 kg Transition Metals under strict control within the K: 150 g Fe: 4.5 g living cell; usually bound to Na: 70 g Zn: 2.3 g proteins, peptides, or other Mg: 20-30 g Cu: 72 mg molecules. Mo: 9 mg In CHEMISTRY we call this a TRANSITION METAL COMPLEX 8 Why Investigate Metals in Biology ? • There is hardly any important process in nature which does not depend on a metal ion; ~ 1/3 of the proteins of the human genome depend on metal ions • Novel Materials, Structures and Reactions • Trigger - Signaling - Sensing - Regulation • Acid-Base Catalysis • Redox – Proton & Electron Transfer (coupled, conservation of energy) 9 Case 1:Metals in Medicine - DNA – cis-platin 10 Case 2: Nitrogen Fixation - Nitrogenase http://en.wikipedia.org/wiki/Nitrogen_cycle 11 Case 3: Respiration – Reduction of O2 to H2O Synthesis of ATP – proton-coupled electron transfer (PCET) 12 Goal: From highly resolved 3D & Electronic Structure to Function to Mechanism ABS 4 ) 1 - m c 1 - M m 2 ( 0 25000 20000 15000 10000 Wavenumber (cm-1) EPR 2800 3000 3200 3400 Magnetic field (G) 13 Why (Transition)Metal Ions ? • Positively Charged • Open Shell Systems – Lewis Acids – No Problems with Spin Restriction – Stabilization of Anions • Sterochemically Flexible • Loosely Bound Electrons – Large Variety of – Redox Active Structures. – Multiple Redox States – Little Reorganization – Easily tunable Redox – Facile Ligand Addition/Dissociation Potential • Facilitate Reactions of • Coupled Redox/Acid Base Bound Ligands Chemistry 14 (Bio)Metals – Perodic Table - Electrons H www.webelements.com He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Mo W 3d i 4s 3p 3s 2p 2s 1s 15 3d-Orbitals z d 2 2 y z r x z z y d yz d xz y x x z z y y d 2 2 d x y xy x x 16 Basic Features of a Metal Protein Complex Chem. Rev. 1996, 96, 2239-2314 (1996) RH Holm, P Kennepohl, E I Solomon, Structural and Functional Aspects of Metal Sites in Biology Prot-L| -------- M d- d+ strong attraction - + CH4 + O2 +2e +2H H3COH + H2O Chemistry at the Catalytic Center (Active site) of the Iron Enzyme Methane Monooxygenase 17 Protein Ligands – Amino Acid Residues N O S Tyr His Cys Glu(+Asp) Met Lys Ser 18 Tetrapyrrole - Versatile Ligand in Biology O2 Respiration Photosynthesis O O O O O O O A B O NH HN (Bacterio)- NH HN Chlorophylls (Mg+2) +2 D C Hemes (Fe ) O O O O O O O O Sirohemes VitB (Co+2) +2 12 (Fe , +2 F430 (Ni ) Fe-S cluster) N & S Cycles Met biosynthesis 19 Methanogenesis Molybdopterin, a Dithiolene Ligand (binds both Mo and W) JOURNAL of BIOLOGICAL CHEMISTRY (2009) Vol. 284, p. e10, N Kresge, R D Simoni, R L Hill: The Discovery and Characterization of Molybdopterin - the Work of K. V. Rajagopalan Mo-S-Cu Cluster in CO Dehydrogenase from Oligotropha carboxidovorans : + - CO + H2O → CO2 + 2 H + 2e H Dobbek et al., Proceedings National Academy of Sciences/USA, 99, 15971-15976 ( 2002) 20 Geometry – Coordination Number 3 Trigonal Trigonal pyramidal T-shape 4 Square planar Tetrahedral 5 Square pyramidal Trigonal bipyramidal 6 21 Octahedral Geometry is important: Iron Proteins Trigonal Tetragonal Octahedron Tetrahedron Bipyramide Pyramide Rubredoxin 3,4-Protocatechoate Tyrosine Lipoxygenase Dioxygenase Hydroxylase 22 EI Solomon, et al. (2000), Chem. Rev., 100, 235–350 Color and Magnetism Co[(NH3)6]Cl3 Co[(NH3)5Cl]Cl2 Alfred Werner (University of Zürich/CH, Nobel Prize in Inorganic Chemistry, 1913) 23 Remember: Valence Bond Theory L. Pauling 3+ 3- 6 [Co(NH3]6 and [CoF6] d 3d 4s 4p 4d 3- [CoF6] sp3d2 d d d d 2 d 2 2 xy xz yz z x -y F- F- F- F- F- F- paramagnetic, S=2 3+ [Co(NH3)6] d2sp3 NH3 NH3 NH3 NH3 NH3 NH3 diamagnetic, S=0 3 2 2 3 sp d and d sp hybridization 24 Color and Magnetism Variable Spin States of Metal Centers For a d5 configuration, Fe(III) OR High-Spin, S= 5/2 Low-Spin, S= 1/2 Depending on the METAL ION ENVIRONMENT, balance of Crystal Field Splitting, 10Dq and Spin-Pairing Energy, P 10Dq > 10Dq < Strong Field Weak Field High Spin Low-Spin 25 Metals – Biological Functions Metal Function, Enzymes Na Charge Carrier, Osmolysis/equilibrium K Charge Carrier, Osmolysis/equilibrium Mg Structure, ATP/ThDP Binding, Photosynthesis,... Ca Structure, Signaling, Charge Carrier V Nitrogen Fixation, Oxidases, O2 Carrier Cr Unknown! (glucose metabolism ???) Mo Nitrogen Fixation, Oxidoreductase, O-Transfer W Oxidoreductases, Acetylene Hydratase Mn Photosynthesis, Oxidases, Structure,... - Fe Oxidoreductase, O2 Transport + Activation,e -Transfer,... Co Oxidoreductase, Vitamin B12 (Alkyl Group Transfer) Ni Hydrogenase, CO Dehydrogenase, Hydrolases, Urease - Cu Oxidoreductases, O2 Transport, e -Transfer Zn Structure, Hydrolases, Acid-Base Catalysis... 26 Oxidation States of Metals in Biology Metal Valence state (Electron configuration) Na Na(I) K K(I) Mg Mg(II) Ca Ca(II) V V(V)=(d0), V(IV)=(d1), V(III)=(d2) Cr Cr(III)=(d3),Cr(IV)=(d2),Cr(V)=(d1) Mo Mo(III)=(d3),Mo(IV)=(d2),Mo(V)=(d1), Mo(VI)=(d0) W W(IV)=(d2) ,W(V) =(d1), W(VI)=(d0) Mn Mn(V)=(d2),Mn(IV) =(d3),Mn(III) =(d4),Mn(II) =(d5) Fe Fe(V)=(d3), Fe(IV)=(d4),Fe(III)=(d5),Fe(II)=(d6), Fe(I)?=(d7) Co Co(III)=(d6), Co(II)=(d7), Co(I)=(d8) Ni Ni(III)=(d7), Ni(II)=(d8), Ni(I)=(d9) Cu Cu(III)=(d8), Cu(II)=(d9), Cu(I)=(d10) Zn Zn(II) =(d10) 27 Exogenous ligands Ligand pKa - 2- Acid/base H2O/OH ,O 14,~34 - 2- HCO3 /CO3 10.3 2- 3- HPO4 /PO4 12.7 - H3CCOO /H3CCOOH 4.7 - HO2 /H2O2 11.6 + NH3 /NH4 9.3 - N3 /N3H 4.8 F-, Cl- Br-, I-/XH 3.5, -7, -9, -11 Neutral O2, CO, NO, RNC d+ d- H n+ 28 M O Hd+ Modulation of pKa + n+ -H - n+ H2O + M HO -M +H+ Metal pKa none 14.0 2+ Ca 13.4 4 orders of 2+ Mn 11.1 magnitude ! Cu2+ 10.7 Zn2+ 10.0 d+ d- H n+ M O Hd+ 29 Kinetic Control -H2O [Mn+(H O) ] [Mn+(H O) ] 2 m 2 m-1 +H2O -1 Metal k (s ) K+ 1x109 Ca2+ 3x108 Mn2+ 2x107 Fe2+ 4x106 15 orders of Co2+ 3x106 magnitude! Ni2+ 4x104 Fe3+ 2x102 3+ -6 Co <10 30 Water exchange rates M. Eigen, Nobel Prize Lecture 1967 Expressed as lifetime of complexes Useful to look at reactivity in ligand exchange reactions - catalysis inert labile 31 Stability of Metal Ion Complexes: The Irving-Williams Series Stability order for high-spin divalent metal ion complexes: Peak at Cu(II), Minimum at Mn(II) 32 Strong chelating ligand: EDTA N N HOOC COOH HOOC COOH +M -4H+ Hexadentate Ligand => strong complexing agent; can be applied to remove metal ions from biological samples (proteins, nucleic acids).
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