Molecular Dynamics Simulations: an Useful Tool to Investigate the Metal Release Mechanism from Serum Transferrin Protein

Transcription

1 Molecular Dynamics Simulations: an Useful Tool to Investigate the Metal Release Mechanism from Serum Transferrin Protein J. I. Mujika University of the Basque Country

2 Theoretical Chemistry group at the University of the Basque Country Group web page: 3

3 Outline: Motivation of the project: 'Aluminum Age' Mechanim of Serum Transferrin protein. Biological role of serum transferrin (stf) Results Conclusions Acknowledgments 4

4 Part I: Aluminum Age Aluminum in biological systems 5

5 Abundance of elements in Earth's crust Oxygen (46.6%) Silicon (27.7%) Aluminium (8.1%) Iron (5.0%) Calcium (3.6%)... % in mass But Al(III) is not essential in the human body 6

6 Al(III) intake in the human body 1) Biogeochemical control 2) Low absorption Al(III) Low traces of Al(III) in the human body Figure taken from Exley C. J. Inorg. Biochem. 2003, 97, 1 7

7 Al(III) intake in the human body 1) Human intervention Al(III) water treatment pharmaceuticals drugs foodstuffs acidification of water and soil 2) Aging Significant Al(III) concentration in the human body 8

8 Aluminium does not present an immediate toxicity, but: Involved in several diseases: dialysis dementia, renal bone diseases, Inhibits the function of Mg or Ca metalloproteins Related with neurodegenerative diseases, such as Alzheimer's disease (AD) or Parkinson disease (PD) Little information about Al(III) at molecular level Computational chemistry can get access to this information 9

9 Al(III) Speciation Cells In blood 90% Transferrin 8% Citrate 2% Others Blood brain barrier Brain extracellular fluid 10 Percentages refer to amount of Al(III) interacting with each species

10 Part II: Serum Transferrin Understanding the mechanism 11

11 Transferrins, a family of iron-binding proteins: lactoferrin, ovotransferrin, serum transferrin. High sequencial similarities between them. Serum transferrin transports iron in blood and delivers it into cells. Tf is 30% saturated with iron, so binds other metals (as aluminium). 12

12 C Tf M Tf Tf M C C TFR In serum (ph=7.4), metal load Tf is recognized by Transferrin receptor I (TFR) and introduced in cell (ph=5.5) by endocytosis. Tf M C M TFR Tf TFR Tf M C C 13

13 Metal binding site 14

14 X-ray structures (holo- vs apo-form) N II ﾺ ﾺ NI 15

15 X-ray structures (holo- vs apo-form) N II N II NI Lateral view Top view of N II subdomain Hinge bending + hinge twisting How these global motions are modulated? 16

16 Dilysine trigger explanation N II Lys206 Lys296 NI Lys206-Lys296 interaction modulates the protein opening 17

17 Some authors(1) pointed out that dilysine trigger is insufficient to explain the domain opening 18 (1) H. M. Baker et al. (2007) Acta Cryst., D63,

18 Some authors(1) pointed out that dilysine trigger is insufficient to explain the domain opening Protonation of carbonate ion Protonation and posterior dissosiaction of His249 Protonation of Tyr188 by Lys (1) H. M. Baker et al. (2007) Acta Cryst., D63,

19 Some authors(1) pointed out that dilysine trigger is insufficient to explain the domain opening Protonation of carbonate ion Protonation and posterior dissosiaction of His249 Protonation of Tyr188 by Lys296 But, this is a mere hypothesis! 20 (1) H. M. Baker et al. (2007) Acta Cryst., D63,

20 Systems Simulated with MM Molecular Dynamis Physiol. ph Acid ph (Tyr188O-) Acid ph (Tyr188OH(1)) Mujika et al. Biochemistry (2012), 51, 7017 Acid ph (Tyr188OH(2))

21 Technical Details Systems studied: Fe(III)-sTf and Al(III)-sTf Gromacs Initial geometry: 1A8E (iron-loaded human Tf) Charmm27 force field (TIP3 water molecules) Al(III) Lennard-Jones parameters taken from Faro et al, J. Chem. Phys. (2010), 132, Periodic Boundary Conditions (NVT ensemble) Short-range electr. and VdW interactions: 14 Å Cut-off Long-range electrostatic calculated with PME Long-range dispersion correction to energy and pressure 1 ns equilibration ns production (time step of 2 fs) 24

22 MD analysis on Al(III)-sTf system (similar conclusions with Fe(III) 25 Mujika et al. Biochemistry (2012), 51, 7017

23 Phys ph Acid ph (Tyr188O-) Acid ph (Tyr188OH(1)) Acid ph (Tyr188OH(2)) 26

24 MDPhys Asp63 Arg124 Tyr95 Thr120 CO3 His249 Lys296 Tyr85 Lys206 Glu83 Tyr188 27

25 MDAcid (Tyr188 O- ) Dilysine trigger does not prompt the protein opening Asp63 Thr120 CO3H Tyr95 His249 Arg124 Lys296 Tyr85 Tyr188 Glu83 Lys206 28

26 MDAcid (Tyr188 OH(1) ) (Waters not shown) Arg124 Asp63 Thr120 Glu83 Tyr188 His249 CO3H Lys296 Lys206 Tyr95 Tyr85 29

27 MDAcid (Tyr188 OH(2) ) (Waters not shown) Arg124 Lys296 Asp63 CO3H Tyr188 His249 Tyr95 Glu83 Lys206 30

28 Phys ph Acid ph (Tyr188O-) Acid ph (Tyr188OH(1)) Acid ph (Tyr188OH(2)) Position of Arg124 Arg124 has been involved in metal release(1) (1) T. E. Adams et al. (2003) J. Biol. Chem., 278,

29 Phys ph Acid ph (Tyr188O-) Acid ph (Tyr188OH(1)) Acid ph (Tyr188OH(2)) N II d NI 32

30 Principle component analysis Technique to identify main global motions during a MD trajectory 1st Principle Component 2nd Principle Component 33

31 Release mechanism MD structures (MDPhys vs MDAcid (Tyr188 ) OH(1) ) N II N II NI Lateral view Top view of N II subdomain 35

32 Release mechanism A stepwise mechanism 1) Hinge-bending 2) Hinge-twisting 36

33 Conclusions MM Molecular Dynamics simulations suitable tool for exploring the stf opening during the metal release process The simulations show the role played by the main amino acids at different ph conditions. Dilysine trigger insufficient to induce the conformational change The simulations provide clear evidences for the Lys296-Tyr188 proton transfer hypothesis The metal release may follow a two-step mechanism initialized by hinge bending 38

34 Acknowledgments Group of Theoretical Chemistry at the University of the Basque Country Elena Akhmatskaya and Bruno Escribano All of you for your attention!! 39