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Various Representations of 3° Structure 1 Various representations of 3° structure 1 Ras, a guanine nucleotide– binding protein. • The simplest way to represent three-dimensional structure is to trace the course of the backbone atoms with a solid line; the most complex model shows the location of every atom. • The former shows the overall organization of the polypeptide chain without consideration of the amino acid side chains; the latter details the interactions among atoms that form the backbone and that stabilize the protein’s conformation. Even though both views are useful, the elements of secondary structure are not easily discerned in them. • Another type of representation uses common shorthand symbols for depicting secondary structure, cylinders or fancy cartoon helices for α-helices, arrows for β-strands, and a flexible string-like form for parts of the backbone without any regular structure. This type of representation emphasizes the organization of the secondary structure of a protein, and various combinations of secondary structures are easily seen. • Computer analysis in which a water molecule is rolled around the surface of a protein can identify the atoms that are in contact with the watery environment. On this water-accessible surface, regions having a common chemical (hydrophobicity or hydrophilicity) and electrical (basic or acidic) character can be mapped. Such models show the texture of the protein surface and the distribution of charge, both of which are important parameters of binding sites. This view represents a protein as seen by another molecule. • Question: What do you mean by "rendered images"? I remember you said high quality about this in class, but could you give me more details about this explanation? • Answer: Compare this image: http://www.pymolwiki.org/index.php/File:No_ray_trace.png and this image: http://www.pymolwiki.org/index.php/File:Ray_traced.png. You could read the wikipedia entry on Rendering (http://en.wikipedia.org/wiki/Rendering_(computer_graphics)), but this is way more information than you need. Essentially, 'Rendering' refers to generating high (that is, publication) quality images. Images that could be printed in high resolution on the glossy cover of a journal and still look good. Every visualization program will handle things a bit differently. I recommend using Pymol, which you can learn more about here: http://www.pymol.org/ and http://www.pymolwiki.org/index.php/Main_Page. Here is the information about ray- tracing: http://www.pymolwiki.org/index.php/Ray www.rcsb.org 2 • The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium dedicated to improving our understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. RCSB members work cooperatively and equally through joint grants and subsequently provide free public resources and publications to assist others and further the fields of bioinformatics and biology. • The RCSB maintains the Protein Data Bank; the freely available database of all protein structures. • Follow the education links (bottom left hand corner) to learn more about ‘Methods for determining structures’ and ‘Software programs for looking at structures’: • http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/methods.html • http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/graphics.html www.rcsb.org 3 • The Protein Data Bank is the repository of all atomic structures for proteins as determined by x-ray crystallography, NMR, and (more rarely) electron microscopy. • Each structure is indicated by a 4 character code. In this example the code is 2i5j. • The real fun begins when you start looking at protein structures in 3 dimensions. To do this you require a molecular visualization tool. Their are a wide variety of these currently available. It seems as though everyone has their favorite one and this is strongly influenced by what they need to use it for and what operating system they are running. • You can view 3-D structures online using interactive tools such as Jmol, which is now built in to every PDB webpage. • Alternatively, a structure file can be downloaded to your computer by clicking on the link on the left hand side of the page. • The classic visualizer is RasMol. It is very simple and sufficient for most purposes. However, I don’t recommend it for creation of publication quality images. I think that RasMol is still available for all platforms, but it is no longer updated and has been superseded by other programs. • For example, in terms of ease of use and versatility, RasMol has now been surpassed by Jmol which is a Java based visualizer that works in your web browser. Essentially it does everything that RasMol does and looks a lot nicer. I like to use iMol for simple visualization on the mac. Once again, it is not great for publication quality images. www.rcsb.org 4 • Some other promising visualization programs for producing publication quality images are QuteMol (it really is Cute!!) and VMD (looks intimidating...). Molscript is probably the most powerful program for creating figures, but it has a very steep learning curve. There are probably many others out there that I don’t know about (i.e., because they are Windows only) • Using either online tools or programs on your computer, the protein can be represented in a variety of different styles. • Typical options include: • protein backbone representation style and color • atom representation (ball-and-stick vs. spacefill) and colors • showing/hiding various parts • zoom, rotation • molecular surfaces • By combining these options, attractive and informative figures can be created. • Some software will allow you to create animations in which the structure is rotating • To get ‘publication quality’ pictures it is typically necessary to use proper rendering or ray-tracing software. Popular options include Raster3D (http://skuld.bmsc.washington.edu/raster3d/) and POV-ray. • Rendering is the process of generating a high quality image in which aspects such as light source, reflections, transparencies, and shadows are all taken into account. • Ray tracing is a rendering technique that produces some of the most photo-realistic images 5 • PyMOL is currently the most popular software for making rendered images of proteins. • PyMol has a fairly easy to understand interface and a built in rendering function. • There is a free version for educational use.
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