Structural biology should be computable!
description
Transcript of Structural biology should be computable!
![Page 1: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/1.jpg)
Structural biology should be computable!
• Protein structures determined by amino acid sequences
• Protein structures and complexes correspond to global free energy minima
• Fundamental test of understanding and huge practical relevance
![Page 2: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/2.jpg)
Model of energetics of inter and intramolecular
interactions
Design(Given Structure, OptimizeSequence)
Prediction(Given Sequence, OptimizeStructure)
Ab initio structure Protein Structure Protein designprediction
Protein-protein docking Protein-protein Interface design interactions
ROSETTA
![Page 3: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/3.jpg)
Model of macromolecular interactions
• Removal of single methyl groups can destabilize proteins --> jigsaw puzzle-like packing crucial
• Buried polar atoms almost always hydrogen bonded --> treat hydrogen bonding as accurately as possible
• Exposed charge substitutions generally have little effect --> damp long range elctrostatics
• Focus on short range interactions!
![Page 4: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/4.jpg)
Random Start
Low-Resolution Monte Carlo Search
(integrate out sidechain degrees of
freedom)
High-Resolution Refinement with full atomic detail
105
Predictions
Conformational sampling
Select lowest energy models
Jeff Gray (Hopkins),Ora Furman (Hebrew University), Chu Wang
![Page 5: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/5.jpg)
Docking Low-Resolution Search
• Monte Carlo Search• Rigid body translations and
rotations• Residue-scale interaction
potentials
Protein representation: backbone atoms + average centroids
N
O
OO
N
O
N
O
N
N
O
......
![Page 6: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/6.jpg)
![Page 7: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/7.jpg)
Docking Protocol
(Target 12: cohesin-dockerin; unbound-bound) 1. Initial Search 2. Refinement
RMSD to arbitrary starting structure
Ene
rgy
RMSD to starting structure of refinement
(Å)
![Page 8: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/8.jpg)
red,orange– xrayblue – model; green – unbound
0.46Å interface rmsd 87% native contacts 6% wrong contacts
Target 12Cohesin-Dockerin
Side Chain Flexibility
dockerin
cohesinOra Furman,Chu Wang
![Page 9: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/9.jpg)
Details of T12 Interface
D39
N37
S45
L83
E86
Y74
L22
R53
dockerin
cohesin
red,orange– xrayblue - model
![Page 10: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/10.jpg)
red,orange– xrayblue - model
0.23Å interface rmsd
Target 15immunity protein D-colicin D tRNase
Accurate Side Chain Modeling
colicin
immunity proteinScience 310, 638-642
![Page 11: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/11.jpg)
Details of T15 Interface
H611
red,orange– xrayblue - model
E56
K610K608
K607
E68
E59D61
colicin
immunity protein
![Page 12: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/12.jpg)
red,orange– xrayblue – model; green – unbound
2.34Å interface rmsd 36% native contacts
Target 20HemK-RF1
Modeling Backbone Movement
RF1
HemK
Loop with methylated Gln
Chu Wang
![Page 13: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/13.jpg)
QuickTime™ and aYUV420 codec decompressor
are needed to see this picture.
![Page 14: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/14.jpg)
CASP6 T0198: PhoU domain repeat
Model 2: 4A over 210 rsds
(Model 1: 3.94 over 198)
Phil Bradley
![Page 15: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/15.jpg)
CASP6 T0212
Model 2: 3.97 over 109 rsds(Model 1: 4.0 over 104)
![Page 16: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/16.jpg)
![Page 17: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/17.jpg)
QuickTime™ and aDV/DVCPRO - NTSC decompressor
are needed to see this picture.
![Page 18: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/18.jpg)
T0281 ab initio prediction (1.59Å)Phil Bradley
![Page 19: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/19.jpg)
![Page 20: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/20.jpg)
1r69
![Page 21: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/21.jpg)
![Page 22: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/22.jpg)
1ubq
Science 309, 1868-1871
![Page 23: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/23.jpg)
![Page 24: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/24.jpg)
2REB
![Page 25: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/25.jpg)
Boinc.bakerlab.org/rosettaDavid Kim
High resolution ab initio structure prediction from single sequences by enhanced diversity “barcode” directed samplingOutreach!
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
![Page 26: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/26.jpg)
![Page 27: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/27.jpg)
![Page 28: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/28.jpg)
![Page 29: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/29.jpg)
![Page 30: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/30.jpg)
High Resolution Refinement of CASP target 199 - remote homology model
Calculations performed on SDSC teragrid clustersBin Qian
![Page 31: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/31.jpg)
High Resolution NMR Model Refinement
Vatson Raman
Disulfide Bond Formation Protein
Blue - X-ray structure Green - NMR models Red - Rosetta models
![Page 32: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/32.jpg)
Computing Structural Biology• Free energy function reasonable => Computing simple
protein structures and interactions now appears to be within reach
• Implications for structural genomics? • More cpu power => more accurate predictions for larger
proteins• For larger complexes, experimental data essential (low
resolution electron density!).• Symmetry helps!
Modeling accuracy also illustrated by structures of designed proteins
![Page 33: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/33.jpg)
Top7 X-ray structure has correct topology. Backbone RMSD to design only 1.2Å!!
C- Backbone Overlay
Red : X-ray structure
Blue : Design modelBrian Kuhlman, Gautam Dantas;Science 302 1364-8
![Page 34: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/34.jpg)
Design of novel H bond network
interface
G177
Q51
Q180
Q169
Y35
G177Q180
Q169
Q51
Y35
G177
Y35
Design X-ray
Lukasz Joachimiak
![Page 35: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/35.jpg)
Design of new protein functions
• Design of new protein-protein interactions• Design of enzymes catalyzing novel
chemical reactions • Design of new transcription factor and
endonuclease specificities• Design of HIV vaccine
![Page 36: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/36.jpg)
HIV vaccine design
• Present HIV coat protein epitopes locked into conformation observed in complexes with neutralizing antibodies using designed scaffolds
• Preliminary results: designed proteins fold and bind neutralizing antibodies (5nM affinity). One design confirmed crystallographically.
Bill Schief in collaboration with Peter Kwong
![Page 37: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/37.jpg)
Crystal structure of Mab 2F5in complex with its HIV epitope
Model of non-HIV scaffold-epitope (red)
Computational design of non-HIV immunogens to elicit broadly-neutralizing antibodies
Bill Schief
![Page 38: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/38.jpg)
WT-WT Design-WT
WT-Design Design-Design
Redesign ofDNA cleavage specificity of MsoIhoming endonuclease using ROSETTA
Justin Ashworth,Jim HavranekNature in press
![Page 39: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/39.jpg)
Specific DNA cleavage by designed nuclease
wild-type I-Mso
Design
-1/2n1
wild-type
design
wild-type
design
Cleavage
targets
½ ¼
-
1/29
5uMnuclease
![Page 40: Structural biology should be computable!](https://reader035.fdocuments.net/reader035/viewer/2022062314/568149ed550346895db71c3a/html5/thumbnails/40.jpg)
Acknowledgements
Design• Brian Kuhlman (UNC)• Gautam Dantas• Justin Ashworth• Jim Havranek
Robetta.bakerlab.org
prediction and design server: David Kim (domain parsing, boinc) and Dylan Chivian
Rosetta software freely available for academic use
Boinc.bakerlab.org/rosetta
Protein structure prediction• Phil Bradley (MIT) • Rhiju Das• Lars Marlstrom• Bin Qian• Vatson RamanProtein-protein docking• Ora Furman (Hebrew
University)• Chu Wang• Jeff Gray (Johns
Hopkins)