2000-02-18 - Part 2 Lecture 20: Chemical visualizations - - PowerPoint PPT Presentation

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2000-02-18 - Part 2 Lecture 20: Chemical visualizations - - PowerPoint PPT Presentation

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Mats Nyl en February 18, 2000 Slide 1 of 23 2000-02-18 - Part 2 Lecture 20: Chemical visualizations Application areas Representations Molecular surfaces The Ras p21 protein VIS00 Mats Nyl en February 18, 2000 Slide

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2000-02-18 - Part 2

  • Lecture 20:

– Chemical visualizations – Application areas – Representations – Molecular surfaces – The Ras p21 protein VIS00

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Mats Nyl´ en February 18, 2000 Slide 2 of 23

Chemical visualization

Lots of software packages exists for chemical visualisation, some examples are rasmol, O, Ribbons, MOLMOL, gOpenMol and ICM. Molecules and other atomic structures can be visualized in a lot of different ways, depending in which information is sought. Various structural representations and colouring schemes may be used. VIS00

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Application areas

This a short, incomplete list of application areas

  • molecular viewing in Chemistry,
  • Biochemistry,
  • Structural Biology,
  • Bioinformatics and microbiology,
  • Solid state Physics (and Chemistry)

And many, many others. VIS00

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Structural represenations

Some structural represenations:

  • atomic positions (primary structure),
  • secondary structure (chains, ribbons etc.),
  • tertiary structure,
  • various surface representations (isovalue elctronic density, Van der Waals

surface, Connolly surface etc.) VIS00

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Colouring schemes

Some useful colouring schemes

  • by atom type (e.g. CPK),
  • by structural part,
  • by property (e.g., map the electrostatic potential as colour on the Con-

nolly surface). VIS00

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Primary Structure

Representations of the primary structure makes sense for smaller molecules, crystals and for details. Common representations are

  • Space filling spheres,
  • Stick models,
  • Ball and Stick models,
  • Ball and structure models.

And, of course, others. In a primary structure representation all atoms are represented (almost). VIS00

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Space filling example

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Ball and Stick

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Solid state physics

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Tl2Ba2Ca0Cu1O6+δ

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Secondary structure

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Secondary structure: Backbone

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Secondary structure: Ribbons

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Molecular surfaces

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Isovalue surfaces

Examples include

  • Electron density,
  • Molecular orbitals (remember hydrogen.fld)
  • Electrostatic potential
  • Spin Density

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Molecular orbitals

Here is a couple of examples showing orbital isovalues: VIS00

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Properties on surfaces

Various properties can be mapped onto various surfaces Properties Surfaces Electron density Molecular orbitals Electrostatic potential Spin density Various energies Connolly surface Electron density isosurface Spin density isosurface Electrostatic potential isosurface VIS00

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Electrostatic potential

Mapped onto the Connolly surface. VIS00

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Combinations

This shows a semitransparent Connolly surface with a Stick model of the molecule VIS00

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Resources and references

A lot of resources are available on the Web. Here are some that I have used

  • The Protein Databank: http://www.rcsb.org/pdb
  • MOLMOL homepage:

http://www.mol.biol.ethz.ch/wuthrich/software/molmol

  • gOpenMol homepage: http://www.csc.fi/~

laaksone/gopenmol/gopenmol.html

  • Rasmol homepage: http://www.umass.edu/microbio/rasmol
  • Overview of representations: http://scsg9.unige.ch/fln/eng/toc.html
  • Linux Chemistry resources: http://chpc06.ch.unito.it/chem linux.html

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The Ras p21 protein

The Ras p21 protein is a central component in the cell-signalling system that transmits extra-cellular growth signals via cell membrane receptors, via a cascade of signalling molecules into the nucleus. It is present in many cell types, and several forms of cancer are associated with a mutated form

  • f the protein, where it is locked in a growth-promoting state.

Ras p21 is an enzyme; it hydrolyzes GTP (guanosine triphosphate) to GDP (guanosine diphosphate); it is a GTPase. The protein exists in vivo as a ternary complex with one magnesium ion (Mg) and GDP (or GTP). VIS00

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Ras p21 on Display

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Summary and Outlook

This has been a very brief overview of some topics in chemical visualization. Espicially in microbiology there is a relation between structure and function

  • f the molecules. So we try to encode function into the visualizations.

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