Retrieving%20and%20Viewing%20Protein%20Structures%20from%20the%20Protein%20Data%20Base - PowerPoint PPT Presentation

About This Presentation
Title:

Retrieving%20and%20Viewing%20Protein%20Structures%20from%20the%20Protein%20Data%20Base

Description:

Purpose: Make protein structure data available to the entire ... Bovine Pancreatic Ribonuclease. 124 amino acids. 8 cysteines (4 di-sulfide bonds) 26-84 ... – PowerPoint PPT presentation

Number of Views:155
Avg rating:3.0/5.0
Slides: 26
Provided by: davego2
Learn more at: http://web.mit.edu
Category:

less

Transcript and Presenter's Notes

Title: Retrieving%20and%20Viewing%20Protein%20Structures%20from%20the%20Protein%20Data%20Base


1
Retrieving and Viewing Protein Structures from
the Protein Data Base
  • 7.88J Protein Folding
  • Prof. David Gossard
  • Room 3-336, x3-4465
  • gossard_at_mit.edu
  • September 15, 2004

2
Protein Data Base
  • Established in 1971
  • Funded by NSF, DOE, NIH
  • Operated by Rutgers, SDSC, NIST
  • Purpose Make protein structure data available to
    the entire scientific community
  • In the beginning less than a dozen protein
    structures
  • Currently has 27,112 protein structures
  • Growing at 20 per year
  • New structures 50 times larger than those in 1971
    are commonplace

3
PDB Growth
4
Why the Knee in the Curve?
  • Engineered bacteria as a source of proteins
  • Improved crystal-growing conditions
  • More intense sources of X-rays
  • Cryogenic treatment of crystals
  • Improved detectors data collection
  • New method - NMR
  • Accounts for 15 of new structures in PDB
  • Enables determination of structure of proteins in
    solution

Protein Structures From Famine to Feast,
Berman, et.al. American Scientist v.90,
p.350-359, July-August 2002
5
Why is the PDB Important?
  • Rapid, extensive access to new structure data
  • Collective Leverage for
  • Understanding molecular machinery
  • Rational drug design
  • Engineering new molecules
  • Structural genomics
  • etc

6
Not all Structures are Different
  • PDB Growth in New Folds

7
Structure vs Sequence
  • New protein sequences are being discovered much
    more quickly than new protein structures are
    being solved
  • Currently, known protein sequences vastly
    outnumber known protein
    structures
  • The sequence-structure gap continues to widen

8
Point of Information
  • Todays material is
  • a subset of the information available to you in
    online tutorials
  • presented to get you started quickly and to
    shorten the learning curve
  • not exhaustive or even sufficient
  • gt should be augmented by actually working
    through the online tutorials

9
PDB Website
  • http//www.rcsb.org/pdb/

Enter what you know
10
Query Result Browser
Which one do I want?
Lets look at this one
11
Structure Explorer
Yep, thats the right one
View it
Download it
12
View Structure
Static Images
13
Download/Display
Display the file header
Download the file (Select this file format)
14
Header Information
15
Visualizing Proteins
  • High complexity
  • Multiple levels of structure
  • Important properties are distributed
  • throughout the 3D structure

Branden Tooze
16
Visualization Objectives
  • Structure
  • Backbone secondary, tertiary quaternary
  • Side chain groups
  • Hydrophobic, charged, polar, acidic/base, etc.
  • Cross-links
  • Hydrogen bonds, disulfide bonds
  • Surfaces
  • VanderWaals, solvent-accessible
  • Charge distributions, distances angles, etc.

17
Display Conventions
Wireframe
Ribbon
Molecular Surface
Spacefill
18
History of Visualization of Macromolecules
  • http//www.umass.edu/microbio/rasmol/history.htm
  • Sculpture of human
  • neutrophil collagenase
  • by Byron Rubin
  • on permanent exhibition at
  • the Smithsonian Institution
  • Washington DC

19
Important URLs
  • Protein Data Base
  • http//www.rcsb.org/pdb/
  • Chime
  • http//www.mdlchime.com/chime/
  • SwissPDB
  • http//www.expasy.ch/spdbv/

20
Visualization Tools
  • Viewers (free)
  • 1960s MAGE, RasMol, Chime
  • 2004 SwissPDB, Protein Explorer, Cn3D, etc.
  • Operating systems Unix, Windows, Mac
  • Our choice (arbitrary)
  • Chime (plug-in to NETSCAPE)
  • SwissPDB (stand-alone)

21
SwissPDB
22
SwissPDB Toolbar
Center
Distance between two atoms Angle between three
atoms Measure omega, phi and psi angles
Provenance of an atom Display groups a certain
distance from an atom
Translate
Zoom
Rotate
23
Control Panel
Chain
Helix/sheet
Residue
Color target
Main chain
Color
Side chain
Label
Surface
Ribbon
24
Demo
  • Bovine Pancreatic Ribonuclease
  • 124 amino acids
  • 8 cysteines (4 di-sulfide bonds)
  • 26-84
  • 40-95
  • 58-110
  • 65-72

25
END
Write a Comment
User Comments (0)
About PowerShow.com