david m. smith div. org. chem. and biochem., institut ruđer bošković, zagreb
DESCRIPTION
Specific Interactions Between Sense and Complementary Peptides: What Can Molecular Dynamics Tell Us?. David M. Smith Div. Org. Chem. and Biochem., Institut Ruđer Bošković, Zagreb. Sense Peptide. N → Tyr-Gly-Gly-Phe-Met → C. Translation. Sense mRNA (+). 5’ → UAU-CCC-GGC-UUC-AUG → 3’. - PowerPoint PPT PresentationTRANSCRIPT
David M. SmithDiv. Org. Chem. and Biochem., Institut Ruđer Bošković, Zagreb
Specific Interactions Between Sense and Complementary Peptides:
What Can Molecular Dynamics Tell Us?
Complementary Peptides: What are they ?
3’ ← AUA-CCC-CCG-AAG-UAC ← 5’Complementary mRNA (-)
5’ → TAT-GGG-GGC-TTC-ATG → 3’Sense DNA
3’ ← ATA-CCC-CCG-AAG-TAC ← 5’Complementary DNA
C ← Ile-Pro-Ala-Glu-His ← NComplementary Peptide
5’ → UAU-CCC-GGC-UUC-AUG → 3’Sense mRNA (+) Transcription
N → Tyr-Gly-Gly-Phe-Met → CSense PeptideTranslation
ChemBioChem. 2002, 3, 136
Some Mekler-Idlis Pairs
CysArgGlySer
Ala
TrpGlyArgArg
Pro
SerAlaThrPro
Gly
CysAgrGlySer
Thr
Sense Complementary Sense Complementary
Biophyzika. 1969, 14, 581
Hydropathicity and the Molecular Recognition Theory
NH2CHC
CH2
O
N
HN
HNCHC
CH2
O
CH2
C
OH
O
HNCHC
CH3
O
NC
NHCHC
CH
HO
O
H3C
CH2
CH3
O
Hydrophobic HydrophobicHydrophilic
Hydrophilic
H2N CH C
CH2
O
OH
NH CH C
H
OHN CH C
H
OHN CH C
CH2
OHN CH C
CH2
OH
O
CH2
S
CH3 HydrophobicHydrophobic
Hydrophilic
Hydrophilic
Biochem. Biophys. Res. Commun. 1984, 121, 203
An Alternative Definition of Complementary Peptides:
3’ → AUA-CCC-CCG-AAG-UAC → 5’Complementary mRNA (-)
N → Ile-Pro-Pro-Lys-Tyr → CComplementary Peptide
5’ → TAT-GGG-GGC-TTC-ATG → 3’Sense DNA
3’ ← ATA-CCC-CCG-AAG-TAC ← 5’Complementary DNA
5’ → UAU-CCC-GGC-UUC-AUG → 3’Sense mRNA (+)
N → Tyr-Gly-Gly-Phe-Met → CSense Peptide
Pro. Nat. Acad. Sci. 1985, 82, 1372
Some Root-Bernstein Pairs
ArgArgArgArg
Ala
GlyGlyGlyGly
Pro
ProProProPro
Gly
CysCysTrpstop
Thr
Sense Complementary Sense Complementary
J. Theor. Biol. 1983, 100, 99
The SystemNH CH C
CH2
O
OH
NH CH C
H
OHN CH C
H
OHN CH C
CH2
OHN CH C
CH2
HN
O
CH2
S
CH3
CH3C
O
H3C
HN CH C
CH
O
CH2
CH3
NC
O
N
C
O
HN CH C
CH2
O
CH2
CH2
CH2
NH2
NH CH C
CH2
NH
O
OH
CH3
H3C
C
O
H3C
Ace-Tyr-Gly-Gly-Phe-Met-NmeAce-Ile-Pro-Pro-Lys-Tyr-Nme
Croat. Chem. Acta. 1998, 71, 591
Molecular Dynamics: The Force Field
U(R) = bonds
Kr (r - req)2 angles
K ( - eq)2+
Bonds Angles
Dihedrals
Van der Waals Electrostatic
Vn
2dihedrals
(1 + cos[n - +
i<j
Aij
rij12
-atoms
Bij
rij6
+qi qj
riji<j
atoms
+
+
+
Implicit Solvation (Elec.)
qi qj
f gb(rij,Ri,Rj)
i<j
atoms
+ + A+
Implicit Solvation (Non Elec.)
Molecular Dynamics in Practise
Fi = mi ai
-dUdri
= mid2ri
dt2
In practise we must numerically integrate these equations with a finite time step
(typically 1-2 fs)
In principle, doing MDs is simply a matter of solving Newton’s equations of motion
Molecular Dynamics in Action
50 ps of MD at 300 K with implicit solvation
Analysis: Structural Deviations
Root Mean Square Deviation from a reference structure vs time
Analysis: Clustering
BackboneOverlay
Cluster 1, Pop. = 28%<E> = -57.5 kcal/mol
Cluster 2, Pop. = 45%<E> = -58.6 kcal/mol
Cluster 3, Pop. = 27%<E> = -58.5 kcal/mol Minimum Energy Structure
E= -16.7 kcal/mol
Analysis: Clustering
28%
27%
45%
Implicit solvent, 150 ns
Principle Component Analysis
Projections onto the eigenvectors of the covariance matrix
Principle Component Analysis
28%
27%
45%
What about the force field?FF94, Implict solvent, 150 ns
Differences in the Force Field
12%
58%
27%
FF99, Implict solvent, 150 ns4%
Differences in the Force Field
51%
16%
33%
FF03, Implict solvent, 150 ns
What Does Experiment SayNMR experiments in water show an essentially random distribution of conformers
Biophys. J. 2004, 86, 1587
NMR, experiments in binary bilayered mixed micelles(bicelles) show a well-defined structure:
Explicit Solvation
50 ps of MD at 300 K with explicit solvation (NVT)
Explicit Solvation: Analysis
54 %
19%
27%
40 ns of MD at 300 K with explicit solvation (FF03)
Replica Exchange DynamicsSingle simulations, especially in explicit solvent, are prone to become trapped in potential energy minima
Increasing the temperature can facilitate barrier crossingsbut can lead to irrelevant results
P(exchange) = exp -kBTi
1
kBTj
1Ei - Ej
A modern solution is to construct several replica simulationswith different temperatures and allow them to exchange according to:
Replica Exchange Dynamics
16 replicas simulated for 2.5 ns each, implying 40ns in total.The temperatures range between 275K and 420K such that P≈0.2.
Replica Exchange Dynamics
27%
33%
40%
40 ns (16 x 2.5) of MD at 275-420 K with explicit solvation (FF03)
Non-Exchanging Replicas
Replica exchange MD is an inherently parallel method
An alternative approach is to construct several non-interacting replicas (distributed computing)
An efficient way to implement this is to first run one simulation at high temperature and to cluster the results
The structure closest to the centroid of each cluster canthen be used as a starting point for each replica
Non-Exchanging Replicas
30%
33%
37%
40 ns (8 x 5) of MD at 300 K with explicit solvation (FF03)
Sense and Complementary Peptides
1 ns of MD at 300 K with explicit solvation
Sense and Complementary Peptides
40 ns (8 x 5) of MD at 300 K with explicit solvation
19%
30%
23% 13%
16%
A Closer Look at the Clusters
Cluster 1: Population 30 %
A Closer Look at the Clusters
Cluster 2: Population 19 %
A Closer Look at the Clusters
Cluster 3: Population 23 %
A Closer Look at the Clusters
Cluster 4: Population 13 % Cluster 5: Population 16 %
Analysis: Structural Properties
Separation of the centres of mass of the two peptides
Analysis: Structural Properties
Separation of the centres of mass of the complementary residues
Conclusions• The force field can have a strong influence on the structural properties. FF03 can probably be trusted.
• Met-enkephalin does not have a well-defined native structure in aqueous solution at 300 K.
• Met-enkephalin does exhibit some affinity for its complementary counterpart but this is apparently not based on the specific interactions predicted by the Molecular Recognition Theory.
• Non-interacting replicas constitute a good approximation to the replica exchange method and a good alternative to a single long simulation, at least for small peptides.
BackboneOverlay
Analysis: Clustering (ff03)
Cluster 1, Pop. = 51%<E> = 0.4 kcal/mol
Cluster 2, Pop. = 33%<E> = -0.5 kcal/mol
Cluster 3, Pop. = 16%<E> = 0.4 kcal/mol Minimum Energy Structure
E= -16.7 kcal/mol
Analysis: Clustering (ff03)
51%
16%
33%
Principle Component Analysis (ff03)
51%
16%
33%