# Presentation: 611436

## Future directions in research on

- biomolecular structure
- NSLS-II  Workshop
- July 17,2007

## Molecular structure and dynamics in biology

- Where are we?
- Where are we going?
- How will NSLS-II (and similar installations)
-             help us get there?

## The molecular biological sciences:

- Structure
- Information transfer:  “Molecular Biology” and “Systems’ Biology”

## The molecular biological sciences:

**Structure**
- Information transfer:  “Molecular Biology” and “Systems’ Biology”

## Structural biology in the twentieth century

- 1953		1961		1977		1998		2000

- DNA                Protein                Virus             Ion channel        Ribosome

- Molecules:

- Cells:

- 1950’s:

## Chemistry,

- 100 Å

- 10,000 Å

**Chemistry,**
**genetic **
**“****engineering”**

## c-Src

**c-Src**

**kinase**

## c-Src tyrosine kinase

## HIV-1 envelope glycoprotein

## Nitrogenase

- Howard & Rees, 2006

**50 Å**

## F1 ATPase

- Source of intracellular energy

## Reovirus core

- Reinisch et al, 2000

**100 Å**

## Yeast RNA polymerase II

- 25 A

## Cate & co-workers, 2005

## Limitations of crystallography

- for structure determination:
- Inhomogeneity, even modest,
- is generally incompatible with
- crystallization

## Viral entry via the endosome

## Fotin et al, 2004a

**Fotin et al, 2004a**

- 100 Å

## Anatomy of a clathrin coat

**Triskelion = 3 x (Heavy Chain + Light Chain)**

**N**

**C**

**proximal**

**knee**

**distal**

**linker**

**terminal domain**

**Clathrin lattice**

**ankle**

## Chemistry,

- 100 Å

- 10,000 Å

**Chemistry,**
**genetic **
**“****engineering”**

## clathrin

- ~1 m

- reovirus

## “Molecular movies”: 

- to link live-cell dynamics and molecular structure.
- The goal is a data-based dynamic picture
- rather than simply an imaginative animation

## How will we get the requisite atomic-resolution

- snapshots of various substructures?
- X-ray crystallography will continue to be
- the principal method, and adequate progress
- will depend on being able to get good data
- from very small and weakly diffracting
- crystals

## 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 noise
- 1. Scatter from interstitial solvent in crystal
- 2. Scatter from surrounding solvent and mount
- 3. Beam-path scatter
- 4. Detector
-     a. Pixels too large
-     b. Detector noise

## What is needed to optimize data

- collection from such crystals?
- Very small beam
- Positionally very stable beam
- Very low divergence
- Suitably precise sample handling instruments
- Large detectors with very small
-             pixel sizes to match

## Dengue sE trimer

- 3.5 Å

- P3221 a=b=159Å c=145Å
- 1° rotation  D=450 mm

## 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 cell
- About 500 photons/reflection if you “burn up” crystal (in
- practice, long-range order disappears much sooner).
- Data from multiple crystals can be scaled and merged

## Summary

- “Molecular movies” are a goal of structural cell biology
- The fundamental elements of cellular molecular movies
-             will continue to be provided by x-ray crystallography
- Critical barriers: the x-ray optical precision needed to
-             make many accurate measurements from small
-             crystals and new kinds of beamline instrumentation
- NSLS-II appears to have many of the characteristics
-             suitable for surmounting these barriers

## Slide 28

## Slide 29

## Sources of noise

- 1. Scatter from interstitial solvent in crystal
- 2. Scatter from surrounding solvent and mount
- 3. Beam-path scatter
- 4. Detector
-     a. Pixels too large
-     b. Detector noise