Overview & Applications
Transcript of Overview & Applications
![Page 1: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/1.jpg)
Overview & ApplicationsT. Lezon
Hands-on Workshop in Computational BiophysicsPittsburgh Supercomputing Center
04 June, 2015
![Page 2: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/2.jpg)
Simulations still take time
Coarse-grained Elastic Network Models are fast
Lane et al. 2013
2
Bakan et al. Bioinformatics 2011.
![Page 3: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/3.jpg)
The structural data explosionMultiple structures for a single sequence
Dynamics may be inferred from structural data.
Nature, 15 May 2014.
3
![Page 4: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/4.jpg)
>1A9U:A|PDBID|CHAINGSSHHHHHHSSGLVPRGSHMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTG......
User inputs a sequenceUser inputs a sequence
identifies, retrieves, aligns, and analyzes (PCA) structures matching input sequence
identifies, retrieves, aligns, and analyzes (PCA) structures matching input sequence User can
• Compare experimental and theoretical models• Sample conformations along normal modes
User can• Compare experimental and theoretical models• Sample conformations along normal modes
p38 network model (ANM)
p38 ensemble(PCA)
Experiment/Theory
Usage example
Exploiting the PDB since 2010• High-throughput analysis of structural data• Application Programming Interface (API) for
development of tools • Suitable for interactive usage
Bakan, Meireles & Bahar. Bioinformatics 2011.
MD trajectory analysis (EDA)
4
![Page 5: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/5.jpg)
An Interactive Tool
5
![Page 6: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/6.jpg)
An evolving suite of toolsPrincipal Component AnalysisElastic Network ModelsNormal Mode AnalysisTrajectory Analysis
Computational Drug DiscoveryBinding Site PredictionAffinity Estimation
Call ProDy from VMDNormal Mode Visualization
6
Multiple Sequence AlignmentCorrelated Mutation AnalysisStructural Evolution
![Page 7: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/7.jpg)
Tutorials: ProDy & Structure Analysis
• Obtaining PDB Files• BLAST Searching the
PDB• Constructing
Biomolecules from Transformations
• Aligning and Comparing Structures
• Identifying Intermolecular Contacts
7
![Page 8: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/8.jpg)
Tutorial: Elastic Network Models
• Gaussian Network Model (GNM)
• Anisotropic Network Model (ANM)
• Normal Mode Algebra• Deformation Analysis• Customizing ENMs
8
![Page 9: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/9.jpg)
Elastic Network Model• Useful for finding global
equilibrium motions of proteins
• Employs harmonic potential about native state
• Coarse-grained (Cα-only description)
• Residue pairs are connected via springs
• Normal modes are found analytically
9
![Page 10: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/10.jpg)
Elastic Network Model• Useful for finding global
equilibrium motions of proteins
• Employs harmonic potential about native state
• Coarse-grained (Cα-only description)
• Residue pairs are connected via springs
• Normal modes are found analytically
10
![Page 11: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/11.jpg)
Elastic Network Model• Useful for finding global
equilibrium motions of proteins
• Employs harmonic potential about native state
• Coarse-grained (Cα-only description)
• Residue pairs are connected via springs
• Normal modes are found analytically
11
![Page 12: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/12.jpg)
Hinsen et al. Proteins 33 (1998).
Yang et al. PNAS 106 (2009).
Tirion, PRL 77 (1996).
Hinsen et al. Chem Phys 261 (2000).
Flexible force constants
12
![Page 13: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/13.jpg)
Optimizing force constants
• Download NMR structures from PDB• Calculate residue MSFs for each protein• Assign ENM topology• Optimize force constants to reproduce structural
dynamics• Search for trends in force constant values with
structure
13
fetchPDB()
calcMSF()
buildHessian()
![Page 14: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/14.jpg)
Fine-tuning force constants
black: NMRred: ENMblue: modified ENM
• Distance-dependence• 1st neighbors• 2nd neighbors• H bonds
GammaStructureBased()
R=0.91R=0.91
R=0.76R=0.79
R=0.31R=0.57
Learn more at prody.csb.pitt.edu 15
![Page 15: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/15.jpg)
Tutorial: Ensemble Analysis
• NMR Models• Homologous Proteins• Multiple X-ray
Structures• Multimeric Proteins
16
![Page 16: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/16.jpg)
Example: Comparing PCA and ENM
17
Structures of HIV1-RTUnboundInhibitor boundDNA bound
Bakan & Bahar. PNAS 106 (2009).
![Page 17: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/17.jpg)
Example: Comparing PCA and ENM
18Bakan & Bahar. PNAS 106 (2009).
Structures of p38 MAPKUnboundInhibitor boundGlucose boundPeptide bound
![Page 18: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/18.jpg)
Tutorial: Trajectory Analysis
• Fast processing of long trajectories
• Enables comparison of MD trajectories and structural data or ENM results
19
![Page 19: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/19.jpg)
Tutorial: Conformational Sampling
• Sample structures along normal modes
• Refine structures using NAMD
20
![Page 20: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/20.jpg)
Tutorial: Druggability
• Set up NAMD simulations
• Analyze trajectories to identify binding hot spots
21
![Page 21: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/21.jpg)
Exploring binding with probe molecules
22Bakan et al. J Chem Theor Comput (2012).
![Page 22: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/22.jpg)
Tutorial: Evol
23
![Page 23: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/23.jpg)
Tutorial: Normal Mode Wizard
24
![Page 24: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/24.jpg)
Global transitions
30Å
Outward Facing (OF) Inward Facing (IF)
25Yernool et al. Nature 431 (2004).Reyes et al. Nature 462 (2009).
![Page 25: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/25.jpg)
Global transitions
Reyes et al. Nature 462 (2009).
Single subunit showing the transport domain moving across the membrane
27
![Page 26: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/26.jpg)
Rotations-Translations of Blocks
28
HRTBP
HAA PT
(3N × 3N)
(6Nb × 3N)
(3N × 6Nb)(6Nb × 6Nb)
H: ANM Hessian (3 rows/cols per residue)P: Projection matrix from all-residue space to rigid block spaceHRTB: RTB Hessian (no internal motions of blocks)V’AA: Approximate ANM motions
VRTB
PTV’AA
Smaller Hessian can be more easily diagonalized...
...and modes projected back into all-residue spaceMing & Wall. PRL 95 (2005).Zheng & Brooks. Biophys J 89 (2005).
RTB.buildHessian()
![Page 27: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/27.jpg)
Exploring structural transitions: Glutamate transporter
Lezon & Bahar. Biophys J 102 (2012).
ANM predicts large radial motions of the trimer. Can we invent a better model?
200000
002000
000020
20
ijijijijij
ijijijijij
ijijijijij
ij zzyzx
zyyyx
zxyxx
R
ijH
200000
002000
000020
20
zijzyijijzxijij
zyijijyijyxijij
zxijijyxijijxij
ij
zzyzx
zyyyx
zxyxx
R
ijH
Altered radial force constants:
RTB.buildHessian()
30
Hij = -g
Rij0( )2
xij0( )2 xij
0yij0 cxij
0zij0
xij0yij0 yij
0( )2 cyij0zij0
cxij0zij0 cyij
0zij0 czij
0( )2
é
ë
êêêêêê
ù
û
úúúúúú
![Page 28: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/28.jpg)
Exploring structural transitions: Glutamate transporter
ANM: Large radial motions imANM
32
![Page 29: Overview & Applications](https://reader031.fdocuments.us/reader031/viewer/2022012414/616eb6d485bd405965090980/html5/thumbnails/29.jpg)
Explicit membrane models
Hss
HEEHSE
HES
“system”
“environment”
As the environment fluctuates randomly, the effective motion of the system is given by
reduceModel()
33