Future directions in research on biomolecular structure NSLS-II Workshop July 17,2007.

Slides:



Advertisements
Similar presentations
Introduction to Virology
Advertisements

9 September, 2005 A quantitative description of the invasion of bacteriophage T4 R. D. James IMA and Aerospace Engineering and Mechanics University of.
Gihan E-H Gawish, MSc, PhD Ass. Professor Molecular Genetics and Clinical Biochemistry Molecular Genetics and Clinical BiochemistryKSU SECOND WEEK.
Determination of Protein Structure. Methods for Determining Structures X-ray crystallography – uses an X-ray diffraction pattern and electron density.
NSLS-II Life Science Breakout Session. Agenda  Introduction (Miller)  Keynote Speaker: Carolyn Larabell (ALS, UCSF) (30 min)  Technique talks (4 min.
Class I and II Fusion Proteins To reproduce, enveloped viruses must enter a host cell by fusing their own membrane coat with that of the cell. Fusion is.
 A cell is an organization of millions of molecules  Proper communication between these molecules is essential to the normal functioning of the cell.
16 November 2004Biomedical Imaging BMEN Biomedical Imaging of the Future Alvin T. Yeh Department of Biomedical Engineering Texas A&M University.
Optical Tweezers F scatt F grad 1. Velocity autocorrelation function from the Langevin model kinetic property property of equilibrium fluctuations For.
Biochemistry 301 Overview of Structural Biology Techniques Jan. 19, 2004.
Pathways Bioinformatics & Biomolecular Center at the City College of New York Marshak Science Building, Room 1102 Tel: 212/ Fax: 212/
Biosensors for efficient capture of biological information Current technology relies on inefficient systems for capture of biological information: –Information.
Genetics of Viruses.
(X-Ray Crystallography) X-RAY DIFFRACTION. I. X-Ray Diffraction  Uses X-Rays to identify the arrangement of atoms, molecules, or ions within a crystalline.
A U.S. Department of Energy laboratory managed by The University of Chicago X-Ray Damage to Biological Crystalline Samples Gerd Rosenbaum Structural Biology.
Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)
BY SANTANU PRAMANIK(09369) HITESH KUMAR GUPTA(09320) CHANDAN SINGH(09260) SCANNING ELECTRON MICROSCOPE MATERIAL SCIENCE ASSIGNMENT.
1 Bi 1 Lecture 3 Thursday, March 30, 2006 What is a Receptor? Receptors and Ion Channels as Examples of Proteins.
Protein Structure Determination Part 2 -- X-ray Crystallography.
Biochemistry 300 Introduction to Structural Biology Walter Chazin 5140 BIOSCI/MRBIII
Bioinformatics for biomedicine Protein domains and 3D structure Lecture 4, Per Kraulis
The Structure and Function of DNA CHAPTER 10 Transcription (DNA  RNA) RNA Polymerase Processing of Eukaryotic RNA Translation (mRNA  Protein) The Three.
Bioinformatics Module Lecture 1 Cell biology. Introduction to lecture 1 Introduction to cellular and multicellular biology: – Our current understanding.
Chem X-ray Crystallography X-ray crystallography is an experimental technique that exploits the fact that X-rays are diffracted by the periodic.
Virus Notes. Basic Definition Viruses Viruses: Submicroscopic, parasitic, acellular entity composed of a nucleic acid core surrounded by a protein coat.
 Four levels of protein structure  Linear  Sub-Structure  3D Structure  Complex Structure.
Chapter 19~Viruses.
X-Ray Crystallography Susan Ahrens February 3, 2004.
Single-crystal X-ray Crystallography ● The most common experimental means of obtaining a detailed picture of a large molecule like a protein. ● Allows.
Announcements Lec 10 Quiz today--ATPase Homework #5 Assigned includes Reading, Chpt 3 ECB Most students like in-class assignments (good!)
Viruses. Biology of Viruses Structure of Viruses: Size -Less then 0.2 microns Parts of the Virus 1)Capsid: -Made of protein subunits 2) Inner core: made.
Structural Biomedicine
Macromolecular Crystallography Summary of the July 18, 2007 Breakout Session.
Structural proteomics
STRUCTURAL BIOLOGY Martina Mijušković ETH Zürich, Switzerland.
Biomedical Week 2 This is a very brief review of biochemistry and how this effects cells.
Managed by UT-Battelle for the Department of Energy Dynamically Polarized Solid Target for Neutron Scattering Josh Pierce, J.K. Zhao Oak Ridge National.
The Virus.
Structural proteomics Handouts. Proteomics section from book already assigned.
Pattersons The “third space” of crystallography. The “phase problem”
Atomic structure model
Virus: A biological particle composed of nucleic acid and protein Intracellular Parasites: organism that must “live” inside a host What is a Virus?
Viruses Mader-Chapter 21.
Past and Future Insights from Neutron Scattering Collin Broholm * Johns Hopkins University and NIST Center for Neutron Research  Virtues and Limitations.
Using Technology to Study Cellular and Molecular Biology.
Dynamically Polarized Solid Target for Neutron Scattering at the SNS PST 07 J.K. Zhao Neutron Scattering Sciences Division, Spallation Neutron Source Oak.
Sébastien Boutet LUSI DOE Review July 23, 2007 CXI (WBS 1.3) 1 Coherent X-ray Imaging (WBS 1.3) Sébastien Boutet System Specifications.
Viruses A “borrowed life”. Characteristics of Life All living things exhibit the following four characteristics: 1.Carry out metabolic activities to meet.
 Virus: A biological particle composed of nucleic acid and protein  Intracellular Parasites: organism that must “live” inside a host.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings PowerPoint ® Lecture Presentations for Biology Eighth Edition Neil Campbell.
Lecture 53: X-ray crystallography. Electrons deflect x-rays We try to recreate electron density from the x-ray diffraction pattern Each point in space.
Cont. Proteomics Structural Genomics Describes the experimental and analytical techniques that are used to determine the structure of proteins and RNA.
Why are. we not solving more struct tures? James Holton University of California San Francisco and Advanced Light Source Lawrence.
Viruses.
MSc-Student Activities at the European XFEL
Organic Chemistry Lesson 21 X-ray crystallography.
MeV Ion Microbeams and Radiation Biology at the University of Surrey
The Scale of the Biological World
Data processing Creative Biostructure now can provide a collection of tools and analysis package for biomolecular structure determination, refinement and.
Concept 4: Analyzing Cell Communication
Virus Chapter 2 Lesson 1.
Cells Chapter 3.
Viral Structure.
VIRUS.
Viruses Are obligate intracellular parasites
Unit III Information Essential to Life Processes
Key Interactions for Clathrin Coat Stability
Yeast RNA Polymerase II at 5 Å Resolution
MIRACLES budget: Summary of the 3 configurations
Pick up a book (pg 338) and present trp operon with your team
Presentation transcript:

Future directions in research on biomolecular structure NSLS-II Workshop July 17,2007

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?

The molecular biological sciences: 1.Structure 2.Information transfer: “Molecular Biology” and “Systems’ Biology”

The molecular biological sciences: 1.Structure 2.Information transfer: “Molecular Biology” and “Systems’ Biology”

Structural biology in the twentieth century DNA Protein Virus Ion channel Ribosome Molecules: Cells: 1950’s:

NMR X- ray EM Opt. 10 Å 100 Å 10,000 Å Chemistry, genetic “engineering”

c-Src kinase

c-Src tyrosine kinase

HIV-1 envelope glycoprotein

Nitrogenase Howard & Rees, Å

F1 ATPase Source of intracellular energy

Reinisch et al, 2000 Reovirus core 100 Å

R. Kornberg & coworkers, 2001 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 100 Å

Anatomy of a clathrin coat Triskelion = 3 x (Heavy Chain + Light Chain) N C C N proximal knee distal linker terminal domain Clathrin lattice ankle

NMR X- ray EM Opt. 10 Å 100 Å 10,000 Å Chemistry, genetic “engineering”

~1  m clathrin 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? 1.Very small beam 2.Positionally very stable beam 3.Very low divergence 4.Suitably precise sample handling instruments 5.Large detectors with very small pixel sizes to match

3.5 Å Dengue sE trimer P 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, Structure 11:13-19) Example: 20x20x20  3 crystal with 100x100x100 Å 3 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 1.“Molecular movies” are a goal of structural cell biology 2.The fundamental elements of cellular molecular movies will continue to be provided by x-ray crystallography 3.Critical barriers: the x-ray optical precision needed to make many accurate measurements from small crystals and new kinds of beamline instrumentation 4.NSLS-II appears to have many of the characteristics suitable for surmounting these barriers

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