11.4. Visualisation of protein structures by molecular graphics programs

11.4.1. RasMol

RasMol is a free, open-source and stand-alone molecular graphics program. Three-dimensional structures can be constructed and displayed if the atomic-resolution coordinates of a biomolecule or its complex are available. The program consists of two windows: one for the command line, another for providing the graphics. The input file can be in PDB format and can be downloaded from the PDB structure database. The initial image is shown as a „wire” model. However, from the Display menu one can choose other visualisation styles such as „spacefill”, „stick”, „ball and stick” as well as the visually most attractive „ribbon” and „cartoon” models. In the last two styles, alpha helices are rendered as helical ribbons and beta structures as flat arrows pointing in the direction of the polypeptide chain. The atoms of the model can be coloured by the standard CPK (named after Corey, Pauling and Koltun) scheme in which white is hydrogen, black is carbon, blue is nitrogen and red is oxygen. The protein can be coloured based on polypeptide chains („chain” command), the chemical property of the amino acids („shapely” command), or the inner mobility of the atoms (as determined by the crystallographic so-called B-factor; „temperature” command). The structure can be cut in the z-dimension by the „slab” command, can be rendered in a stereo view, and the otherwise invisible hydrogen atoms and hydrogen bonds can also be visualised.

The left and right mouse buttons can be used to rotate the protein along the „x” and „y” axes. Shift + left-click will shrink and enlarge the rendered structure, whereas shift + right click will translate it along the „z” axis. By clicking any part of the structure, the residue number of the given chain and the particular atom will be shown in the command window. One can select a chain, a particular residue or segment of the chain by using the „select” command. „Select 25A” in the command window means that the 25th residue of chain A will be selected. The name of the residue can also be used. A segment of a chain can also be selected: for example, „select 1-33” means that the first 33 residues of the chain will be selected. If the structure contains a ligand (coenzyme, substrate, metal ion etc.) besides the polypeptide chain, it can be selected by the „hetero” command or by its name (e.g. „ca” refers to a Ca2+ ion). By clicking the ligand, we can learn its name. Commands in the menu or in the command line will always be executed on the last selection. Parts of the molecule (chains, segments, residues, ligands) can be changed by the „color” command followed by the name of a particular colour. The background of the image can be set by the „background color” syntax. If we want to remove part of the structure, it can be done by using the „restrict” command (e.g. „restrict 1-56” will remove the rendering of the chain from residue 57 to the C-terminal end). One can save the modified structure (e.g. for later manipulation) by the „write script” command and a file name. To continue working on a particular structure view, the „script” command together with a file name will reload the previously saved script file. The finished structure can be saved in common graphics file formats (gif, jpeg, etc.). The „help” menu can explain many additional commands that can be used to manipulate the structure. RasMol is a powerful program, and it takes time to learn all of its features. Further help for using RasMol can be found at http://www.openrasmol.org/doc/.

It should be noted that RasMol is not suitable for homology modelling, to study the structural effect of mutations, to energy-minimise structures or for molecular dynamics simulations. If the reader is interested in learning such structural modelling software, he/she should search the internet for such programs (many free and commercial programs are available for that purpose) and/or attend a structural bioinformatics course.

In Figure 11.15 and Figure 11.16 we illustrate two protein structures rendered by RasMol. In the first one, an EF-hand Ca2+-binding domain of the ubiquitous eukaryotic Ca2+-modulator protein calmodulin is shown (α-helices are magenta, a short β-sheet at the beginning of the Ca2+-binding loop is shown in yellow, Ca2+ is blue; and the residues participating in the coordination of the divalent ion are shown in a ball-and-stick style). In the second molecular graphics image, the three-dimensional structure of myoglobin is shown in a cartoon model (α-helices are red, the loops are yellow, the ball-and-stick hem atoms are blue, and the Fe2+ ion is shown in magenta in spacefill style).

EF-hand structure of calmodulin

Figure 11.15. An EF-hand of calmodulin rendered by the RasMol program

Structure of myoglobin

Figure 11.16. Myoglobin structure visualised by RasMol

11.4.2. PyMOL

PyMOL is another open-source molecular graphics program. It is probably the one most often used by molecular biologists to visualise three-dimensional structures of macromolecules. The program is free for academic users and students (after registration), except for its molecular modelling modules. Its advantage over RasMol is that it has superb publication-quality graphics outputs. In Figure 11.17, a „publication-ready” structural model is shown: that of the vertebrate-specific Ca2+-binding protein S100A4 in complex with a non-muscle myosin 2a peptide. In Figure 11.18, the three-dimensional structure of hemoglobin is modelled by PyMol in three styles; the polypeptide chains in stick and atoms of the hem prosthetic group in spacefill representation (left), the four chains in four coloured ribbon models (middle) and a van der Waals-surface representation with the hem in wireframe (right). The detailed description of the program is given in M.Sc. programme courses and is also available online (http://pymol.sourceforge.net/newman/user/toc.html).

The complex of S100A4 with a myosin peptide

Figure 11.17. The Complex of the Ca2+-binding protein S100A4 with a non-muscle myosin 2A peptide (figure made using the PyMOL program)

Three molecular graphics representations of hemoglobin

Figure 11.18. Three-dimensional structure of deoxyhemoglobin, visualised by PyMOL as „sticks” (left), as a „cartoon” model (middle) and displaying the surface of the protein (right)

11.4.3. Jmol

Jmol is an open-source molecular graphics application written in Java programming language that can be used either as a browser applet or a downloadable stand-alone program. Its input file can be in PDB file format or many other structural biology or organic chemistry file formats that contain atomic coordinates of a structure. The commands of Jmol are similar to (actually derived from) those of RasMol, and they follow the same logic. Jmol can be used to perform simple molecular modelling tasks such as adding or deleting atoms or residues. The command window can be opened by clicking the right mouse button. Jmol has versions in many languages (including Hungarian). Further information can be read on the Jmol Wiki page.

Jmol is often used for educational purposes as part of e-learning pages or other applications. Any file from the PDB database can be interactively viewed online by using the Jmol applet. In Figure 11.19, a static view of the hemoglobin mutant causing sickle-cell anemia is shown from the interactive Jmol Hemoglobin Tutorial. Other examples of structural biology Jmol tutorials include DNA structure, Antibody, Lipid Bilayers and Membrane Channel, Collagen, Water, and Lac Repressor. In Figure 11.20, we illustrate B-DNA structure (left) and the three-chain collagen helix (right) captured by Jmol.

Detail of a Jmol tutorial

Figure 11.19. Detail of a Jmol tutorial explaining the structural background of the hemoglobin mutation causing sickle-cell anemia. The close-up view of a subunit interface is shown. (The mutant valine 6 of the beta chain binds to alanine 70 and leucine 88 of the beta chain of a second hemoglobin tetramer.)

Structures visualised by Jmol

Figure 11.20. Structure of B-DNA (left) and that of the collagen triple helix (right), visualised by the Jmol program