Biomolecules 5 Metals Notes PDF

Metals Na/K Ca/Mg Fe/Cu/Zn 1 1  Metals Ligands M+ M+ Tyr M+...

Metals Na/K Ca/Mg Fe/Cu/Zn 1 1  Metals Ligands M+ M+ Tyr M+ O- M+ CH3 O HO Thr H Ser 2 In order to act as a ligand, a molecule must have an atom with a lone pair. The lone pair is slightly negative and sticks to the positive metal ion. The more charged the metal is, the tighter the metal-ligand bond. Only 8 of the amino acid side chains commonly act as ligands to metals. The most common of these are His, Met, Cys and the acids. The protein structure is often used as a rigid framework to hold the metal ions in place. 2  Metals Periodic Table 3 The periodic table contains a large number of metallic elements, but just a few are essential for life. These are present as cations. The bulk metals are Na, K, Mg and Ca. The trace metals are Cr, Mn, Fe, Co, Ni, Cu, Zn and Mo. The bulk metals are present as 1+ or 2+ ions. The trace metals have various oxidation states. Commonly Fe(II)-(III) and Cu(I)-(II). Zn is always 2+. 3  Metals Bulk Metals Skou 1997 Nobel Prize Na+, K+ charge carriers, In Chemistry controlling ionic strength Na+ ions pumped out of the cell Na/K pump – coupled to ATP hydrolysis. Na+ migration back into the cell is coupled to sugar transport 4 Na+ and K+ are used to balance charges inside and outside the cell. A chemical gradient is created with Na+ outside and K+ inside. The gradient is maintained by ATP consumption by a Na/K pump. Na+ re-entry into the cell is couple to sugar transport. Salts concentration is tightly controlled to maintain protein folding and electrostatic associations. 4  Metals Bulk Metals Mg2+ complexes with nucleotides isomerases, hydrolases etc. chlorophyll rubisco Ca2+ signalling – receptor/ion channels, kinases e.g. myosin action 5 Mg2+ is present in numerous enzymes utilising nucleotides for aiding phosphoester cleavage. Ca2+ plays a major role in cell signalling – e.g. voltage gated Ca channels during muscle action. 5  Metals Trace Metals Mn Water splitting enzyme Mo N2 fixation, O atom transfer CMoFe7S9 Mn4Ca Spatzal, (2011) Science 334, 940 Yano (2006) Science 314, 821 6 The trace metals often have very specialized function e.g. Mo in FeMo cofactor during N2 fixation. A Mn cluster is the catalytic site for O2 evolution by plants in the water splitting enzyme. 6  Metals Trace Metals Fe Electron transfer proteins (heme, iron sulfur clusters) O2 transport, O2 activation – oxygenases, cyt P450s, non‐heme iron enzymes. N2 fixation, Ferritin Cu Electron transfer, O2 transport (hemocyanin), O2 activation – oxidases. 7 Fe and Cu use their variable redox states in electron transfer proteins and oxidases – these are present in significant amounts, particularly Fe in mammals. 7  Metals Trace Metals Ni Hydrogenase Co Vitamin B12 – methionine synthesis Zn Numerous enzymes – (e.g. peptidases, carbonic anhydrase) Zinc fingers 8 Ni forms the active site of bacterial hydrogenases. Co sits in the middle of the B12 vitamin and is used in the synthesis of the amino acid methionine. Zn is found abundantly in enzymes and Zn fingers (DNA binding proteins). 8  Metals Carbonic Anhydrase High pH Low H2O + CO2 H2CO3 Lungs Blood Td Zn2+ active site http://pdb101.rcsb.org/motm/49 9 Carbonic anhydrase (present in red blood cells) catalyses the conversion of CO2 in muscles to soluble carbonic acid. This allows the CO2 to dissolve effectively and be transported to the lungs. Within the lungs the carbonic anhydrase can catalyse its conversion back to CO2 for exhaling. Additionally, formation of carbonic acid lowers the pH in the red blood cells causing haemoglobin to lose its O2. In the lungs the consumption of carbonic acid causes the pH to rise and haemoglobin to bind O2 more strongly. 9  Metals Carbonic Anhydrase H2O + CO2 H2CO3 His H2O Td 2+ 2+ Zn Zn C His His ‐ Zn2+ acts as a Lewis acid 2+ ‐ Zn 10 The rate determining step for the reaction is deprotonation of water to make a hydroxyl nucleophile (rate = 0.01 s-1). In the presence of the enzyme coordination to Zn speeds up the deprotonation, so that the reaction in diffusion controlled (10^6 s-1). 10  Metals Haemoglobin His + O2 Haem His 22 tetrameric structure enables O2 binding co‐operativity 11 Haemoglobin is made up of 4 subunits (tetramer). The protein chains are 2 pairs which are similar, but not identical. It uses a haem-based Fe(II) to coordinate O2 reversibly. It can do this without reducing the O2 – it binds and is released in equilibrium. The haem and iron are attached to the protein by a single His ligand. A second His (in the active site) helps to coordinate O2. 11  Metals Haemoglobin O2 release Cooperativity enables efficient uptake and release of O2 by Mb haemoglobin (Hb) to myoglobin (Mb) Hb O2 uptake sigmoidal 12 Haemoglobin binds O2 cooperatively, so its binding curve is sigmoidal. This helps in the uptake and release of oxygen in high and low O2 environments respectively – making it a very effective transporter. 12  Metals Haemoglobin His + T‐state heme FeII O 2 Heme His FeII heme pulled in His R‐state on O2 binding His Movement of the His displaces the attached ‐helix, inducing a T‐state to R‐state protein conformation change 0.6 A The R‐state binds O2 more strongly than the T‐state. The tetramer is more stable if all the conformations are the same, so if one subunit changes, the others are induced to change. 13 The mechanism of cooperativity centres around the very small movement of the Fe and attached His ligand. On binding O2 the Fe becomes smaller and is pulled into the heme plane. This moves the His slightly affecting the folded conformation of the haemoglobin tetramer. In the T-state the tetramer has low O2 affinity, in the R-state it has high O2 affinity. The tetramer is most stable when all subunits are R or all are T. Therefore binding of one O2 triggers the binding of more – same with release. 13  Metals Haemoglobin cooperative O2 binding is caused by interactions between different subunits within the tetramer O2 His moves in 14 Motion of the His and the protein conformation change can be seen in the O2 bound and free X-ray structures. 14  Metals Bioenergetics Electron transfer through complexes I‐IV 2NAD+ + 4H+ + 4 e‐ 4 e‐ + O 2 2NADH Respiration Stored Released C6H12O6 + 6O2 6CO2 + 6H2O + Energy Energy Photosynthesis 2NADPH 4 e‐ + O 2 2NADP+ + 4H+ + 4 e‐ Electron transfer through photosystems I‐II etc 15 Bioenergetics is the study of energy storage and release in biological systems. The two main processes at work are photosynthesis – the storage of energy from the sun in plant matter and atmospheric oxygen – and respiration, the controlled consumption of this biomatter in reaction with oxygen. The two process form a large energy cycle encompassing most of biology. Remarkably, both processes store and release energy using similar energy transport molecules and by electron transfer processes. These are made possible by metal ions with different redox states. 15  Metals Respiration Anatomy of a eukaryotic cell Mitochondrion Krebs cycle NAD+ NADH 16 The energy transport molecule ATP is generated by respiration in the inner membrane of mitochondria 16  Metals Respiration Proton translocation drives ATP synthesis Mitchell 1978 Nobel Prize for Chemistry ‐320 mV +800 mV 17 Protons are pumped across the membrane by a series of electron transfer events through Complexes I-IV. The electrons start on the NADH hydride and end up on O2. The protons eventually push their way back through the membrane via ATP synthase. 17  Metals Respirasome Complexes I,II2 and IV of the Respirasome J A Letts et al. Nature 1–5 (2016) doi:10.1038/nature19774 18 A structure of the respiration machinery determined by electron microscopy. The metal centres are shown in the diagram. 18  Metals Cytochrome c His Heme heme c + Axial ligation Met + Met FeIII heme + His 19 The electron transfer protein cytochrome c from the mitochondrial electron transport chain. The heme group contains iron, bound by His and Met residues. 19  Metals Cytochrome c Heme e.g. in cytochrome c Axial ligation Met Met e‐ FeIII heme FeII heme His His 20 The function of cyt c is to simply pass on an electron. It can do this by using its Fe(III)/Fe(II) oxidation states. The electron is picked up from complex II and passed to complex (IV) where it will be used to reduce O2 to H2O. 20  Metals Iron‐Sulfur Clusters FeIIIFeIII + e- FeIIFeIII ‐300 mV Fe4S44+ + e- Fe4S43+ +350 mV HiPIP NB/ There are many other variants 21 Iron-sulfur clusters or ferredoxins contain Fe ions and S2- ions. These also pass on single electrons. The reduction potential depends on the type of cluster. 21  Metals Plastocyanin Cu(II) + e- Cu(I) An electron carrier during photosynthesis Blue-copper centre Ligands 22 Plastocyanin operates during photosynthesis and uses a copper centre to pass on a single electron. The Cu is bound by 4 amino acid residues and goes between the Cu(I) and (II) oxidation states. 22  Metals Plastocyanin Antiparallel -sheets create a rigid framework for Cu binding. Even when Cu is removed, the structure is retained 23 The Cu is held in a very rigid environment by the protein (see all the B-sheets) The rigid environment helps to ensure very fast electron transfer by making interconversion between Cu(I) and Cu(II) easier. 23  Metals Summary Amino Acid Sidechains as Ligands Metals involved in biology His O2 Electron transfer Carbonic anhydrase Haem Zn2+ as a Lewis acid His Haemoglobin: O2 binding and transport 24 24