Molecular dynamics methods applied to food chemistry › uploads › originals › ... · IMS...
Transcript of Molecular dynamics methods applied to food chemistry › uploads › originals › ... · IMS...
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Axel Bidon-Chanal Badia
Department of Nutrition, food sciences and gastronomy
Faculty of Pharmacy and Food sciences, Food Science Campus, University of Barcelona
Molecular dynamics methods applied to food chemistry
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Molecular dynamics
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QnQm
Estr
Eang
Eele
Etor
othernbtorbndstr EEEEEE
Bonded-terms Non bonded-terms
Other
)ncos(V
Etor n
ntor
12
3
1
2)( o
bonds
strstr llKE 2)( o
angles
angbnd KE
nm mnmn
nm
eleRR
QQE
, )(
EvW =Aij
Rij12
-Cij
Rij6
æ
èçç
ö
ø÷÷
i, j
å
Polarization
Restraints
Molecular dynamics
EvW
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Structural analysis
Solvent accessible
surface
Radius of gyration
Root-mean
Square deviation Specific interactions
Conformational families (clustering)
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Molecular Dynamics example
Folding
Time evolution of the hydrogen bond formation between the backbone NH··O=C groups of both ß-sheet strands
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Structural Flexibility: Essential Dynamics
Trajectory
Covariance
matrix
Diagonalization Eigenvalues frequencies Eigenvectors
Type of movement
For a set of principal eigenvectors,
absolute similarity index
relative similarity index
2
11
)(1 B
j
n
i
A
i
n
j
ABn
BBAA
ABAB
2
FLEXIBILITY ANALYSIS
Entropy
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Mechanisms of ligand activity: enzyme activator
Haohao Fu; Yingzhe Liu; Ferran Adrià; Xueguang Shao; Wensheng Cai; Christophe Chipot; J. Phys. Chem. B 2014, 118, 11747-11756.
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AMPK (AMP-activated protein kinase) • Ser/Thr protein kinase
• Activated by low levels of ATP and high levels of
AMP/ADP
• Sensor of energy homeostasis in the cell
Nat Cell Biol. 2012, 13, 1016. BMC Biology 2013, 11, 36.
Mechanisms of ligand activity: enzyme activator
AMPK
LKB1
CaMKKb
Anabolic Pathways inhibited by the activated AMPK
Synthesis of fatty acids
ACC1
Protein synthesis mTORC1*
Translation of ribosomal proteins
mTORC1*
Transcription of ribosomal RNA
TIF-1A
Catabolic Pathways activated by the activated AMPK
Glycolysis PFKFB2/3
Autophagy
ULK1
Mitochondrial biogenesis oxidative
metabolism PGC-1a? / SIRT1?
Upstream Kinases
Downstream Kinases
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a
b
a
b
a
b a
b
Phosphorylation
@Thr172
Autophosphorylation
@Ser108
Dephosphorylation
@Thr172
Dephosphorylation
@Ser108
A-769662 AMP 2-13x >90x
2- 4x 2-13x
≈1000x
Chem. Biol., 2014, 21, 619.
Structure vs. Function
Mechanisms of ligand activity: enzyme activator
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10
APO HOLO + ATP HOLO
How does A-769662 trigger AMPK activation?
Mechanisms of ligand activity: enzyme activator
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11
P-loop
C-interacting
helix
Active
loop
CBM
αC-helix
Mechanisms of ligand activity: enzyme activator
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12
The effect of activator and ATP in the conformational and dynamic behaviour
Mechanisms of ligand activity: enzyme activator
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13
The activator acts like a glue between the α-kinase domain
and the CBM domain of β-subunit
Mechanisms of ligand activity: enzyme activator
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Allosteric Hypothesis
The activator pre-organizes the ATP-Binding Site
Mechanisms of ligand activity: enzyme activator
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Mechanisms of ligand activity: enzyme mutations
Haohao Fu; Yingzhe Liu; Ferran Adrià; Xueguang Shao; Wensheng Cai; Christophe Chipot; J. Phys. Chem. B 2014, 118, 11747-11756.
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IMS
matrix
me
mb
ran
e
H1-H2
H3-H4
H5-H6 Pebay-Peyroula, E., et al., Nature, 2003, 426,
39–44
• Mitochondrial Carrier Family member.
• 6 TM helices
• Imports ADP to the matrix of the
mitochondria and exports ATP to the
Inter-membrane space (IMS)
• Two possible conformations, but only
one has been crystalized
ADP
ATP
Capacity to interconvert between two different
conformations to achieve proper nucleotide
transport
AAC + CATR
Fixed
conformation
Falconi, M., et al.,Proteins, 2006, 65, 681-689
Mechanisms of ligand activity: enzyme mutations
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Localization in the protein structure
Measured Activity in E. Coli membrane
KM Vmax
Wild-Type 23.7 ± 5 14.6 ± 0.6
A90D 82.1 ± 7.8 7.8 ± 0.4
L98P 18.5 ± 9.8 1.7 ± 0.3
D104G 15.9 ± 6.4 4.1 ± 0.4
A114P 104.1 ± 47.9 4.5 ± 1.1
A123D ND ND
V289M 17.0 ± 2.4 10.3 ± 0.4
A114P
D104G
V289M
A90D
L98P
A123D
Ravaud, S., Bidon-Chanal, A., et al., ACS Chem. Biol.,
2012
6 pathological mutations have been detected, all of them in the IMS
Mechanisms of ligand activity: enzyme mutations
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• Wild-type or mutant protein immersed in a lipid bilayer of united atom POPC lipids
• 114 lipids per leaflet
• System solvated with TIP3P waters
• 0.15 M NaCl concentration
• Total system box size of 90x81x81
• charmm27 forcefield with CMAP
corrections.
• NPT ensemble. PBC and PME. • 100 ns MD simulations for each system
Simulated systems
RMSD Backbone
Atoms All Heavy Atoms
WT 1.9 ± 0.2 2.4 ± 0.2
A90D 1.6 ± 0.3 2.0 ± 0.3
A114P 1.5 ± 0.2 1.7 ± 0.2
L98P 1.5 ± 0.2 1.9 ± 0.2
D104G 1.7 ± 0.3 2.2 ± 0.5
A123D 1.5 ± 0.2 1.8 ± 0.2
V289M 1.5 ± 0.2 1.9 ± 0.2
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Electrostatic funnel
Path to the bottom of the cavity is nearly barrier
less and is modulated by two basic patches Dehez, F., et al.,J. Am. Chem. Soc., 2008, 130,
12725-12733
Binding of the ADP molecule is driven by an electrostatic funnel that
attracts the phosphate moiety of ADP
Mechanisms of ligand activity: enzyme mutations
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N(∆B
-facto
r)
∆B-factor (BfactWT-BfactMut)
L98P
Entropy
N(∆B
-facto
r)
∆B-factor (BfactWT-BfactMut)
A114P
D103G
N(∆B
-facto
r)
∆B-factor (BfactWT-BfactMut) ∆B-factor (BfactWT-BfactMut)
N(∆B
-facto
r) A90D
•B-factors were inferred from the atomic
positional fluctuations computed for the
backbone atoms along the molecular
dynamics trajectory multiplied by
(8/3)π2.
•Configurational entropies were obtained
using the Schlitter approximation with
the eigenvalues that result from
diagonalisation of the mass weightened
covariance matrix, and differences were
obtained as Tx(SinfWT-SinfMUT). Sinf was
obtained by curve fitting of the
configurational entropy computed at
different times along the MD trajectory to
the formula S(t)=Sinf-atb
Atomic positional fluctuations
• Mutations A114P, L98P, A90D and
D103G have a clear impact on the flexibility of the carrier which is reflected in a lower nucleotide uptake.
Mechanisms of ligand activity: enzyme mutations
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Spherification: Role of calcium cations
in alginate aggregation
Haohao Fu; Yingzhe Liu; Ferran Adrià; Xueguang Shao; Wensheng Cai; Christophe Chipot; J. Phys. Chem. B 2014, 118, 11747-11756.
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Spherifications
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https://www.youtube.com/channel/UCxD2E-bVoUbaVFL0Q3PvJTg
http://www.chefsteps.com
Spherifications
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https://www.youtube.com/watch?v=A7QFcP74zyg
http://www.chefsteps.com
Spherifications
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Origin
Obtained from brown algae of the Phaeophyceae
class. Their celullar walls contain alginic acid and
its different sodium, potassium or calcium salts in
different proportions.
Alginate, Soduim Alginate, E-400.
Comercial name
Chemical structure
β-D-mannuronic acid (M units)
α-L-guluronic acid (G units)
Spherifications
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Preferential affinity for G compared to M: ‘egg-box’ model
DFT-MD methods
10 oxygens from the guluronate molecules
Hydroxyl groups coordinating Ca2+.
Molecular Mechanics methods
Grant, G. T. et al. FEBS Lett. 1973, 32, 195−198
I. Braccini and S. Pérez. Biomacromolecules 2001, 2, 1089−1096
Plazinski, W, et al. J. Phys. Chem. B 2013, 117, 12105−12112
Spherifications
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36 linear alginate chains 600 calcium ions randomly placed TIP3P water molecules
Haohao Fu; Yingzhe Liu; Ferran Adrià; Xueguang Shao; Wensheng Cai; Christophe Chipot; J. Phys. Chem. B 2014, 118, 11747-11756.
Spherifications
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mi = mass of atom i M = summed mass of the atoms RC = central reference point coords.
Spherifications
Ca+2 Na+
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Spherifications
Characteristic chain–chain interaction modes in the alginate membrane
Spontaneous association of alginate chains in non-restrained MD simulations of calcium alginate salts in solution.
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Olfactory receptors: the influence of food odor
Olfactory receptors
Anselmi, C.; Buonocore, A.; Centini, M.; Facino, R. M.; Hatt, H. Comp. Biol. Chem. 2011, 35, 159-168.
Lai, P. C.; Guida, B.; Shi, J.; Crasto, C. J. Chem. Senses, 2014, 39, 107-123.
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The actors
Olfactory Receptor Neuron surface
• G-Protein Coupled Receptors
• Odorant binding activates signal cascade pathway
• Promiscuous • Odours are fruit of the cooperativity
Olfactory receptors
Olfactory receptors
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Olfactory receptors
Homology modeling
ß2-adrenergic Rhodopsin
PDB ID: 5D6L PDB ID: 5TE3
Docking
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Olfactory receptors: better binders
Olfactory receptors
Anselmi, C.; Buonocore, A.; Centini, M.; Facino, R. M.; Hatt, H. Comp. Biol. Chem. 2011, 35, 159-168.
Lai, P. C.; Guida, B.; Shi, J.; Crasto, C. J. Chem. Senses, 2014, 39, 107-123.
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Olfactory receptors
OR17-40
Anselmi, C.; Buonocore, A.; Centini, M.; Facino, R. M.; Hatt, H. Comp. Biol. Chem. 2011, 35, 159-168.
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Olfactory receptors
Thermodynamic integration MD simulations
Anselmi, C.; Buonocore, A.; Centini, M.; Facino, R. M.; Hatt, H. Comp. Biol. Chem. 2011, 35, 159-168.
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Olfactory receptors: activators and inactivators
Olfactory receptors
Anselmi, C.; Buonocore, A.; Centini, M.; Facino, R. M.; Hatt, H. Comp. Biol. Chem. 2011, 35, 159-168.
Lai, P. C.; Guida, B.; Shi, J.; Crasto, C. J. Chem. Senses, 2014, 39, 107-123.
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Olfactory receptors
Lai, P. C.; Guida, B.; Shi, J.; Crasto, C. J. Chem. Senses, 2014, 39, 107-123.
Acid
Heptanoic Octanoi
c Nonanedioic
Nonanoic
heptanol heptanoi
c
OR S79 + + + –
S86 + –
Docking +
MD
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Axel Bidon-Chanal Badia Campus de l’Alimentació de Torribera Verdaguer building, office 14. Av. Prat de la Riba 171. 08921 Santa Coloma de Gramenet [email protected]