molecular dynamics simulations: an useful tool to ...€¦ · 24 technical details systems studied:...
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![Page 1: Molecular Dynamics Simulations: an Useful Tool to ...€¦ · 24 Technical Details Systems studied: Fe(III)-sTf and Al(III)-sTf Gromacs 4.5.3 Initial geometry: 1A8E (iron-loaded human](https://reader033.vdocuments.site/reader033/viewer/2022060608/605fec3ef4256d4fad59b656/html5/thumbnails/1.jpg)
J. I. Mujika
University of the Basque Country
Molecular Dynamics Simulations: an Useful Tool to Investigate the Metal Release
Mechanism from Serum Transferrin Protein
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Theoretical Chemistry group at the University of the Basque Country
Group web page: http://www.ehu.es/chemistry/theory/
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Outline:
Motivation of the project: 'Aluminum Age'
Mechanim of Serum Transferrin protein.
Biological role of serum transferrin (sTf) Results Conclusions
Acknowledgments
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Part I: Aluminum Age
Aluminum in biological systems
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Oxygen (46.6%)Silicon (27.7%)Aluminium (8.1%)Iron (5.0%)Calcium (3.6%)...
Abundance of elements in Earth's crust
% in mass
But Al(III) is not essential in the human body
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2) Low absorption
Al(III) intake in the human body
Figure taken from Exley C. J. Inorg. Biochem. 2003, 97, 1
1) Biogeochemical control
Al(III)
Low traces of Al(III) in the human body
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2) Aging
1) Human interventionAl(III)
Significant Al(III) concentration in the human body
water treatment pharmaceuticals drugs foodstuffs acidification of water and soil …
Al(III) intake in the human body
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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
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Al(III) Speciation
90% Transferrin
8% Citrate
2% Others
Percentages refer to amount of Al(III) interacting with each species
In blood
Brain extracellular fluid
Cells
Blood brain barrier
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Part II: Serum Transferrin
Understanding the mechanism
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● 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).
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In serum (pH=7.4), metal load Tf is recognized by Transferrin receptor I (TFR) and introduced in cell (pH=5.5) by endocytosis.
TfMC
Tf
C
TfM
C
TFRTf
MC
TFRTf
MC
TFRTf
M
C
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Metal binding site
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N I
N II
ᄎ
ᄎ
X-ray structures (holo- vs apo-form)
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Lateral view
N I
N II
Top view of N II subdomain
N II
X-ray structures (holo- vs apo-form)
Hinge bending + hinge twistingHow these global motions are modulated?
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17Lys206-Lys296 interaction modulates the protein opening
”Dilysine trigger” explanation
Lys206
N I
N II
Lys296
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Some authors(1) pointed out that dilysine trigger is insufficient to explain the domain opening
(1) H. M. Baker et al. (2007) Acta Cryst., D63, 404-414
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(1) H. M. Baker et al. (2007) Acta Cryst., D63, 404-414
● Protonation of carbonate ion
● Protonation and posterior dissosiaction of His249
● Protonation of Tyr188 by Lys296
Some authors(1) pointed out that dilysine trigger is insufficient to explain the domain opening
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But, this is a mere hypothesis!
● Protonation of carbonate ion
● Protonation and posterior dissosiaction of His249
● Protonation of Tyr188 by Lys296
(1) H. M. Baker et al. (2007) Acta Cryst., D63, 404-414
Some authors(1) pointed out that dilysine trigger is insufficient to explain the domain opening
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Physiol. pH
Acid pH (Tyr188O-)
Systems Simulated with MM Molecular Dynamis
Mujika et al. Biochemistry (2012), 51, 7017
Acid pH (Tyr188OH(1)) Acid pH (Tyr188OH(2))
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Technical Details
● Systems studied: Fe(III)-sTf and Al(III)-sTf
● Gromacs 4.5.3
● 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, 114509
● 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 + 100 ns production (time step of 2 fs)
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MD analysis on Al(III)-sTf system
(similar conclusions with Fe(III)
Mujika et al. Biochemistry (2012), 51, 7017
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Phys pHAcid pH (Tyr188O-)
Acid pH (Tyr188OH(1))
Acid pH (Tyr188OH(2))
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Thr120
Arg124
Tyr95
Tyr188
Lys296
Lys206
Asp63
His249
Glu83
Tyr85
CO3
MDPhys
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Thr120
Arg124
Tyr95
Tyr188
Lys296
Lys206
Asp63
His249
Glu83
Tyr85
CO3H
MDAcid (Tyr188O-)
Dilysine trigger does not prompt the protein opening
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Thr120
Arg124
Tyr95
Tyr188
Lys296Lys206
Asp63
His249
Glu83
Tyr85
CO3H
(Waters not shown)
MDAcid (Tyr188OH(1))
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Arg124
Tyr95
Tyr188
Lys296
Lys206
Asp63
His249
Glu83
CO3H
(Waters not shown)
MDAcid (Tyr188OH(2))
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31Arg124 has been involved in metal release(1)
(1) T. E. Adams et al. (2003) J. Biol. Chem., 278, 6027-6033
Position of Arg124
Phys pHAcid pH (Tyr188O-)
Acid pH (Tyr188OH(1))
Acid pH (Tyr188OH(2))
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d
N I
N II
Phys pHAcid pH (Tyr188O-)
Acid pH (Tyr188OH(1))
Acid pH (Tyr188OH(2))
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Principle component analysis
1st Principle Component 2nd Principle Component
Technique to identify main global motions during a MD trajectory
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Release mechanism
Lateral view Top view of N II subdomain
N II
MD structures (MDPhys
vs MDAcid (Tyr188OH(1))
)
N I
N II
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A stepwise mechanism
1) Hinge-bending
2) Hinge-twisting
Release mechanism
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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
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Acknowledgments
● Group of Theoretical Chemistry at the University of the Basque Country
● Elena Akhmatskaya and Bruno Escribano
● All of you for your attention!!