future directions in research on biomolecular structure nsls-ii workshop july 17,2007
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Future directions in research onbiomolecular structure
NSLS-II Workshop
July 17,2007
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Molecular structure and dynamics in biology
1. Where are we?2. Where are we going?3. How will NSLS-II (and similar installations) help us get there?
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The molecular biological sciences:
1. Structure
2. Information transfer: “Molecular Biology” and “Systems’ Biology”
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The molecular biological sciences:
1. Structure
2. Information transfer: “Molecular Biology” and “Systems’ Biology”
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Structural biology in the twentieth century
1953 1961 1977 1998 2000
DNA Protein Virus Ion channel Ribosome
Molecules:
Cells:
1950’s:
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NMRX-ray
EMOpt.
10 Å
100 Å
10,000 Å
Chemistry,genetic
“engineering”
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c-Src
kinase
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c-Src tyrosine kinase
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QuickTime™ and aYUV420 codec decompressor
are needed to see this picture.
HIV-1 envelope glycoprotein
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Nitrogenase
Howard & Rees, 200650 Å
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F1 ATPaseSource of intracellular energy
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Reinisch et al, 2000
Reovirus core
100 Å
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R. Kornberg & coworkers, 2001
Yeast RNA polymerase II
25 A
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Cate & co-workers, 2005
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Limitations of crystallographyfor structure determination:
Inhomogeneity, even modest,is generally incompatible with
crystallization
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Viral entry via the endosome
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Fotin et al, 2004a100 Å
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Anatomy of a clathrin coat
Triskelion = 3 x (Heavy Chain + Light Chain)
N
CC
N
proximal
knee
distal
linker
terminal domain
Clathrin lattice
ankle
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NMRX-ray
EMOpt.
10 Å
100 Å
10,000 Å
Chemistry,genetic
“engineering”
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QuickTime™ and aCinepak decompressor
are needed to see this picture.
~1 m
clathrin
reovirus
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“Molecular movies”: to link live-cell dynamics and molecular structure.
The goal is a data-based dynamic picturerather than simply an imaginative animation
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How will we get the requisite atomic-resolutionsnapshots of various substructures?
X-ray crystallography will continue to bethe principal method, and adequate progresswill depend on being able to get good datafrom very small and weakly diffractingcrystals
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What are the critical technical problems?
Signal-to-noise: Signal is restricted by damage Noise is determined by characteristics of the sample (and by the extent to which the measurements can minimize it)
Sources of noise1. Scatter from interstitial solvent in crystal2. Scatter from surrounding solvent and mount3. Beam-path scatter4. Detector a. Pixels too large b. Detector noise
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What is needed to optimize datacollection from such crystals?
1. Very small beam2. Positionally very stable beam3. Very low divergence4. Suitably precise sample handling instruments5. Large detectors with very small pixel sizes to match
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3.5 ÅDengue sE trimerP3221 a=b=159Å c=145Å1° rotation D=450 mm
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Small and weakly diffracting crystals
For a protein crystal, damage from inelastic scatter ~ Bragg photon/unit cell (Sliz et al, 2003. Structure 11:13-19)
Example: 20x20x20 3 crystal with 100x100x100 Å3 cellAbout 500 photons/reflection if you “burn up” crystal (inpractice, long-range order disappears much sooner).
Data from multiple crystals can be scaled and merged
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Summary
1. “Molecular movies” are a goal of structural cell biology2. The fundamental elements of cellular molecular movies will continue to be provided by x-ray crystallography3. Critical barriers: the x-ray optical precision needed to make many accurate measurements from small crystals and new kinds of beamline instrumentation4. NSLS-II appears to have many of the characteristics suitable for surmounting these barriers
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Sources of noise
1. Scatter from interstitial solvent in crystal2. Scatter from surrounding solvent and mount3. Beam-path scatter4. Detector a. Pixels too large b. Detector noise