Application of Probabilistic Roadmaps to the Study of Protein Motion.
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Transcript of Application of Probabilistic Roadmaps to the Study of Protein Motion.
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Application of Probabilistic Roadmaps to
the Study of Protein Motion
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Proteins Proteins are the workhorses of all living organisms They perform many vital functions, e.g:
• Catalysis of reactions• Transport of molecules• Building blocks of muscles• Storage of energy• Transmission of signals• Defense against intruders
They are large molecules (few 100s to several 1000s of atoms)
They are made of building blocks (amino acids) drawn from a small “library” of 20 amino-acids
They have an unusual kinematic structure: long serial linkage (backbone) with short side-chains
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Protein Sequence
O
N
NN
N
OO
O
Long sequence of amino-acids (dozens to thousands), also called residues
Dictionary of 20 amino-acids (several billion years old)
(residue i-1)
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Central Dogma of Molecular Biology
Physiological conditions: aqueous solution, 37°C, pH 7,atmospheric pressure
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Mad cow disease is caused by mis-folding
Drug molecules act bybinding to proteins
Molecular motion is an essential process of life
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So, studying molecular motion is of critical importance in
molecular biology
Stanford BioX cluster
NMR spectrometer
However, few tools are available
Computer simulation:- Monte Carlo simulation- Molecular Dynamics
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Motion occurs at very different frequencies
HIV-1 protease
Low-frequency motions (diffusive motions) are more directly related to protein functions
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I ntermediate states
I ntermediate states
Unfolded (denatured) state
Folded (native) stateMany pathwaysMany pathways
Two Major Drawbacks of MD and MC Simulation
1) Each simulation run yields a single pathway, while molecules tend to move along many different pathways
Interest in ensemble properties
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Two Major Drawbacks ofMD and MC Simulation
1) Each simulation run yields a single pathway, while molecules tend to move along many different pathways
2) Each simulation run tends to waste much time in local minima
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Kinematic Models Atomistic model: The position of each
atom is defined by its coordinates in 3-D space
(x4,y4,z4)
(x2,y2,z2)(x3,y3,z3)
(x5,y5,z5)
(x6,y6,z6)
(x8,y8,z8)(x7,y7,z7)
(x1,y1,z1)
p atoms 3p parameters
Drawback: The bond structure is not taken into account
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Kinematic Models Linkage model: The protein consists of
atoms connected by rotatable bonds
NN
NN
C’
C’
C’
C’
O
O O
O
C
C
C
C
C
C C
C
Resi Resi+1 Resi+2 Resi+3
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Roadmap-Based Representation
Compact representation of many motion pathways Coarse resolution relative to MC and MD simulation ( only low-frequency motions are represented) Efficient algorithms for analyzing multiple pathways
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Initial Work A.P. Singh, J.C. Latombe, and D.L. Brutlag.
A Motion Planning Approach to Flexible Ligand Binding. Proc. 7th ISMB, pp. 252-261, 1999
Study of ligand-protein binding The ligand is a small flexible molecule, but the protein is assumed rigid A fixed coordinate system P is
attached to the protein and a moving coordinate system L is defined using three bonded atoms in the ligand
A conformation of the ligand is defined by the position and orientation of L relative to P and the torsional angles of the ligand
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Roadmap Construction (Node Generation)
The nodes of the roadmap are generated by sampling conformations of the ligand uniformly at random in the parameter space (around the protein)
The energy E at each sampled conformation is computed: E = Einteraction + Einternal
Einteraction = electrostatic + van der Waals potentialEinternal = non-bonded pairs of atoms electrostatic + van der Waals
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Roadmap Construction (Node Generation)
The nodes of the roadmap are generated by sampling conformations of the ligand uniformly at random in the parameter space (around the protein)
The energy E at each sampled conformation is computed: E = Einteraction + Einternal
Einteraction = electrostatic + van der Waals potentialEinternal = non-bonded pairs of atoms electrostatic + van der Waals
A sampled conformation is retained as a node of the roadmap with probability:
0 if E > Emax
Emax-EEmax-Emin
1 if E < Emin
Denser distribution of nodes in low-energy regions of conformational space
P = if Emin E Emax
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Roadmap Construction (Edge Generation)
q q’
Each node is connected to its closest neighbors by straight edges
Each edge is discretized so that between qi and qi+1 no atom moves by more than some ε (= 1Å)
If any E(qi) > Emax , then the edge is rejected
qi qi+
1
E
Emax
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Heuristic measureof energetic difficultyor moving from q to q’
Roadmap Construction (Edge Generation)
q q’
Any two nodes closer apart than some threshold distance are connected by a straight edge
Each edge is discretized so that between qi and qi+1 no atom moves by more than some ε (= 1Å)
If all E(qi) Emax , then the edge is retained and is assigned two weights w(qq’) and w(q’q)
where:
(probability that the ligand moves from qi to qi+1 when it is constrained to move along the edge)
qi qi+
1
i i+1i
w(q q') = -ln(P[q q ])
ii+1
i ii+1 i-1
-(E -E )/ kT
i i+1 -(E -E )/ kT -(E -E )/ kT
eP[q q ] =
e e
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For a given goal node qg (e.g., binding conformation), the Dijkstra’s single-source algorithm computes the lowest-weight paths from qg to each node (in either direction) in O(N logN) time, where N = number of nodes
Various quantities can then be easily computed in O(N) time, e.g., average weights of all paths entering qg and of all paths leaving qg (~ binding and dissociation rates Kon and Koff)
Querying the Roadmap
Protein: Lactate dehydrogenaseLigand: Oxamate (7 degrees of freedom)
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Computation of Potential Binding Conformations
1) Sample many (several 1000’s) ligand’s conformations at random around protein
2) Repeat several times: Select lowest-energy
conformations that are close to protein surface
Resample around them
3) Retain k (~10) lowest-energy conformations whose centers of mass are at least 5Å apart
lactate dehydrogenase
active site
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Experiments on 3 Complexes
1) PDB ID: 1ldmReceptor: Lactate Dehydrogenase (2386 atoms, 309 residues)Ligand: Oxamate (6 atoms, 7 dofs)
2) PDB ID: 4ts1Receptor: Mutant of tyrosyl-transfer-RNA synthetase (2423
atoms, 319 residues)Ligand: L- leucyl-hydroxylamine (13 atoms, 9 dofs)
3) PDB ID: 1stpReceptor: Streptavidin (901 atoms, 121 residues)Ligand: Biotin (16 atoms, 11 dofs)
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Results for 1ldm
Some potential binding sites have slightly lower energy than the active site Energy is not a discriminating factor
Average path weights (energetic difficulty) to enter and leave binding site are significantly greater for the active site Indicates that the active site is surrounded by an energy barrier that “traps” the ligand
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Energy
ConformationPotential binding
site
Potential binding
site
Active site
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Known native state Degrees of freedom: φ-ψ angles Energy: van der Waals, hydrogen bonds,
hydrophobic effect New idea: Sampling strategy Application: Finding order of SSE
formation
Application of Roadmaps to Protein Folding
N.M. Amato, K.A. Dill, and G. Song. Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of
Known Native Structures. J. Comp. Biology, 10(2):239-255, 2003
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High dimensionality non-uniform sampling
Conformations are sampled using Gaussian distribution around native state
Conformations are sorted into bins by number of native contacts (pairs of C atoms that are closeapart in native structure)
Sampling ends when all bins have minimum number of conformations “good” coverage of conformational space
Sampling Strategy(Node Generation)
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The lowest-weight path is extracted from each denatured conformation to the folded one
The order of formation of SSE’s is computed along each path
The formation order that appears the most often over all paths is considered the SSE formation order of the protein
Application: Order of Formation of Secondary
Structures
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1) The contact matrix showing the time step when each native contact appears is built
Method
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Protein CI2 (1 + 4 )
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Protein CI2(1 + 4 )
60
5
The native contact between residues 5 and 60 appears at step 216
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1) The contact matrix showing the time step when each native contact appears is built
2) The time step at which a structure appears is approximated as the average of the appearance time steps of its contacts
Method
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Protein CI2(1 + 4 )
forms at time step 122 (II)3 and 4 come together at 187 (V)2 and 3 come together at 210 (IV)1 and 4 come together at 214 (I) and 4 come together at 214 (III)
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1) The contact matrix showing the time step when each native contact appears is built
2) The time step at which a structure appears is approximated as the average of the appearance time steps of its contacts
Method
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Comparison with Experimental Data
CI2
1+5
31+4
1+4 5126, 70k
5471, 104k7975, 104k8357, 119k
roadmap sizeSSE’s
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Stochastic Roadmaps M.S. Apaydin, D.L. Brutlag, C. Guestrin, D. Hsu, J.C. Latombe and C.
Varma. Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion. J. Comp. Biol., 10(3-4):257-
281, 2003
New Idea: Capture the stochastic nature of molecular motion by assigning probabilities to edges
vi
vj
Pij
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Edge probabilities
Follow Metropolis criteria:
ijij
iij
i
exp(-ΔE / kT), if ΔE >0;
NP =
1, otherwise.
N
Self-transition probability:
ii ijj i
P=1- Pvj
vi
Pij
Pii
[Roadmap nodes are sampled uniformly at random and energy profilealong edges is not considered]
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V
Stochastic Roadmap Simulation
Pij
Stochastic roadmap simulation and Monte Carlo simulation converge to the Boltzmann distribution, i.e., the number of times SRS is at a node in V converges towardwhen the number of nodes grows (and they are uniformly distributed)
-E/ kT
Ve dV
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Roadmap as Markov Chain
Transition probability Pij depends only on i and j
Pijij
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Example #1: Probability of Folding pfold
Unfolded state Folded state
pfold1- pfold
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Pii
F: Folded stateU: Unfolded state
First-Step Analysis
Pij
i
k
j
l
m
Pik Pil
Pim
Let fi = pfold(i)After one step: fi = Pii fi + Pij fj + Pik fk + Pil fl + Pim fm
=1 =1
One linear equation per node Solution gives pfold for all nodes No explicit simulation run All pathways are taken into account Sparse linear system
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Number of Self-Avoiding Walks
on a 2D Grid
1, 2, 12, 184, 8512, 1262816,575780564, 789360053252, 3266598486981642,(10x10) 41044208702632496804, (11x11) 1568758030464750013214100,(12x12) 182413291514248049241470885236 > 1028 http://mathworld.wolfram.com/Self-AvoidingWalk.html
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In contrast …
Computing pfold with MC simulation requires:
For every conformation q of interest
Perform many MC simulation runs from q
Count number of times F is attained first
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Computational Tests• 1ROP (repressor of
primer)• 2 helices• 6 DOF
• 1HDD (Engrailed homeodomain)
• 3 helices• 12 DOF
H-P energy model with steric clash exclusion [Sun et al., 95]
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1ROP
Correlation with MC Approach
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pfold for ß hairpin
Immunoglobin binding protein
(Protein G)
Last 16 amino acids
Cα based representation
Go model energy function
42 DOFs
[Zhou and Karplus, `99]
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Computation Times (ß hairpin)
Monte Carlo (30 simulations):
1 conformation ~10 hours ofcomputer time
Over 107 energy
computations
Roadmap:
2000 conformations23 seconds ofcomputer time
~50,000 energycomputations
~6 orders of magnitude speedup!
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Using Path Sampling to Construct Roadmaps
N. Singhal, C.D. Snow, and V.S. Pande. Using Path Sampling to Build Better Markovian State Models: Predicting the Folding Rate
and Mechanism of a Tryptophan Zipper Beta Hairpin, J. Chemical Physics, 121(1):415-425, 2004
New idea:Paths computed with Molecular Dynamics simulation techniques are used to create the nodes of the roadmap
More pertinent/better distributed nodes
Edges are labeled with the time needed to traverse them
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t
U
F
Sampling Nodes from Computed Paths (Path
Shooting)
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Sampling Nodes from Computed Paths (Path
Shooting)
U
Fi
jtij
pij
Example: Langevin dynamics equation of motion is where R is a Gaussian random forceext
dxF -mγ +R=0
dt
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Node Merging
If two nodes are closer apart than some , they are merged into one and merging rules are applied to update edge probabilities and times
4
1
5
3
2P12, t12
P14, t14
1
5
3
2’P12’, t12’
P12’ = P12 + P14 t12’ = P12xt12 + P14xt14
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Node Merging
If two nodes are closer apart than some , they are merged into one and merging rules are applied to update edge probabilities and times
4
1
5
3
2P12, t12
P14, t14
1
5
3
2’P12’, t12’
P12’ = P12 + P14 t12’ = P12xt12 + P14xt14
Approximately uniform distribution of nodes over the reachable subset of
conformational space
Approximately uniform distribution of nodes over the reachable subset of
conformational space
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Application: Computation of MFPT
Mean First Passage Time: the average time when a protein first reaches its folded state
First-Step Analysis yields: MPFT(i) = j Pij x (tij + MPFT(j)) MPFT(i) = 0 if i F
Assuming first-order kinetics, the probability that a protein folds at time t is:
where r is the folding rate
MFPT = =1/r
-rtfP(t) = 1 - e
f0
P(t) tdt
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Computational Test
12-residue tryptophan zipper beta hairpin (TZ2)
Folding@Home used to generate trajectories (fully atomistic simulation) ranging from 10 to 450 ns
1750 trajectories (14 reaching folded state) 22,400-node roadmap MFPT ~ 2-9 s, which is similar to
experimental measurements (from fluorescence and IR)
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Conclusion
Probabilistic roadmaps are a recent, but promising tool for exploring conformational space and computing ensemble properties of molecular pathways
Current/future research:• Better sampling strategies able to handle more
complex molecular models (protein-protein binding)• More work to include time information in roadmaps • More thorough experimental validation to compare
computed and measured quantitative properties