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Katri Vilkman 67615R Ilkka Koskela 77267R Visualization of RNA molecules using VMD 1 Table of Contents 1 Introduction....................................................................................................................... 3 2 RNA structure................................................................................................................... 4 2.1 Nucleotides............................................................................................................... 4 2.2 Nucleic acids............................................................................................................. 4 2.3 RNA Secondary structures ...................................................................................... 4 2.4 Different kinds of RNA............................................................................................... 5 2.4.1 mRNA................................................................................................................ 5 2.4.2 tRNA.................................................................................................................. 5 2.4.3 rRNA ................................................................................................................. 5 2.4.4 Catalytic RNA..................................................................................................... 5 2.4.5 Double stranded RNA........................................................................................ 6 2.4.6 RNA genes......................................................................................................... 6 3 VMD................................................................................................................................. 6 3.1 Visualisation in VMD................................................................................................. 6 3.1.1 Loading a molecule............................................................................................ 6 3.1.2 Observing the molecule in the Graphics window............................................... 7 3.1.3 Changing the molecule's representation on screen........................................... 7 3.1.4 Extensions......................................................................................................... 7 3.1.5 Rendering.......................................................................................................... 8 3.1.6 Text interfaces................................................................................................... 8 4 References....................................................................................................................... 9 2 1 Introduction WwPDB (Worldwide protein data bank) maintains an extensive databank of macromolecule structures in a standardized file format. These are available in the same file format (.pdb). Organizations that are members of wwPDB: RCSB PDB (USA), MSDEBI (Europe), PDBj (Japan) and BMRB (USA), which joined the organization in 2006. Although originally founded to store protein structure models, the PDB is nowadays used to store other macromolecules as well, such as nucleic acids. We studied the visualization of RNA (Ribonucleic acid). Molecular 3-d structure can be viewed via .pdbs. There are several visualization programs available. Most of them are free for academic use. So is VMD. It is made by University of Illinois. The one we used was VMD (Visual Molecular Dynamics). We will introduce the basic structure of RNA and this program and some of its properties. 3 2 RNA structure Ribonucleic acid (RNA) is the way to transfer information inside the cell. RNA is a chain of nucleotides. It slightly differs from DNA. RNA can also contain genetic information, for example HIV has two single stranded RNA as its genome. 2.1 Nucleotides Nucleotide consists of base (adenine, urasil, cytosine, guanine), phosphate and sugar parts. There are two different groups of bases: purines and pyrimidines. Adenine and guanine are purines and cytosine and urasil pyrimidines. Sugar is pentose and phosphate is bonded to its 5'-carbon. Base is bonded to pentoses 1'-carbon. RNA has urasil instead of thymine as a base pair to adenine. It is also single-stranded in most cases, while DNA is double-stranded. The sugar is ribose in RNA and deoxyribose in DNA. 2.2 Nucleic acids Nucleic acids are nucleotides combined together by phosphodiester bond. Phosphates oxygens are bonded to riboses 3'- and 5'-carbons. Nucleic acids are polymerized to 5'->3'-direction by RNA polymerase enzyme. DNA is used as a template, which is read to 3'->5' direction. 2.3 RNA Secondary structures RNA Molecules are not linear but, much like proteins, take complex two- and three-dimensional structures. The secondary structures of RNA dictate the folding of the RNA molecule and also serve as signals in, for example, terminating RNA polymerase function. As with proteins, the main factors in producing secondary structures are hydrogen bonds between different sections of the molecule. The Hbonds force the polynucleotide chain to form different structures 4 hairpin loop such as hairpin loops, bulges and internal loops. The three-dimensional structure is dependent on the nucleotide sequence; thus a specific sequence is expressed in a specific 3d structure just like the tertiary structure of proteins is dependent on the aminoacid sequence. Indeed, some RNA molecules even exhibit enzyme-like catalytic abitilies. 2.4 Different kinds of RNA There are six main types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), catalytic RNA, double stranded RNA (dsRNA) and non-coding RNA (”RNA” genes). Each one has its own specific way to function. 2.4.1 mRNA Messenger RNA (mRNA) is for carrying the information out of the nucleus to protein synthesis site in the cytoplasm. In eucaryotes the strand is spliced before the transportation. 2.4.2 tRNA Transfer RNA is for bringing the right amino acid to polypeptide chain. Later on the chain will become a protein. TRNA consists of 74-93 nucleotides and has sites for codon recognition and amino acid. It belongs to non-coding RNAs. TRNA attaches to the mRNAs codon by hydrogen bond and leaves the right amino acid to its place. 2.4.3 rRNA Ribosomal RNA is one part of the ribosomes, which are the producers of proteins. There are four different kinds of rRNA (18S, 5,8S, 28S and 5S rRNA) in eucaryotic cell. Nucleolus synthesizes three of those. 80% of cells RNA molecules are ribosomal RNA. Ribosome has also some protein, so belongs to nucleoprotein group. 2.4.4 5S rRNA in VMD Catalytic RNA Some RNA molecules are able to catalyze chemical reactions, for example, ligation of other RNA molecules and forming peptide bond in the ribosome. 5 2.4.5 Double stranded RNA In some viruses RNA is double stranded (dsRNA) and contains the genetic information. 2.4.6 RNA genes RNA genes (non-coding RNA) encode RNA and wont go to the cytoplasm for protein synthesis. Also small fractions of RNA, micro RNA, can regulate genes. 3 VMD VMD (abbrev. Visual Molecular Dynamics) is a molecule visualisation and analysing tool for large biological macromolecules: proteins, lipids, nucleic acids and membrane structures. It runs on most Unix systems, Apple Mac OS X and MS Windows. In addition to visualisation VMD's key features are visualisation of dynamic molecular data, visualisation of volumetric data, interactive molecular dynamics simulations, molecular analysis commands, Tcl and Python scripting languages, extendability and support for multimodal input and various display systems. VMD is written in C++. 3.1 3.1.1 Visualisation in VMD Loading a molecule VMD supports most standard file formats used in biological modeling software: PDB, PSF, and Gromacs and AMBER files. More than one molecule can be loaded on screen simultaneously, allowing the user to compare between different molecules. Upon loading a file, VMD receives information on each atom of the molecule and their relative distances 6 and sizes, of which it is able to calculate where bonds are formed between atoms. 3.1.2 Observing the molecule in the Graphics window Once loaded the molecule is displayed in the Graphics window. It can be rotated, scaled and moved with mouse commands. The window contains arrows in three (X,Y,Z) dimensions to facilitate coordination. In addition, the lights of the displayed space can be moved and bonds can be added to or removed from between molecules. 3.1.3 Changing the molecule's representation on screen VMD offers numerous ways to change the way a molecule is displayed. Both the colouring and the surface of the molecule can be altered to highlight certain areas or sections of the molecule. Using a specific naming system the user can select anything from a certain hydrogen bond to larger sections of a molecule, say, a nucleotide or a base, and edit the way they appear on screen. This way the user is able to easily present the wanted molecule structure. The colours and surface materials can also be changed to suit the user's purpose better by, for example, changing the hue of a colour or switching between different surface materials. 3.1.4 Descriptions of molecule representation styles in VMD Extensions VMD is easily expandable and comes with several built-in extensions which add a great deal to the properties of the software. The extensions add more features to modeling, analyzing, simulation and, for example, provides a possibility to browse through PDB and STING databases. 3rd party extensions can easily be installed in some extention windows 7 addition to built-in software. This also concerns 3rd party raytracing software; although VMD comes with a basic rendering tool the resolution is rather poor and the emphasis is clearly on fast rather than high quality performance. 3.1.5 Rendering Whether the user chooses the built-in or a 3rd party raytracer program, VMD can render both snapshot images as well as animations through Python and Tcl scripts. The renderer produces a sequence of rendered snapshot images which can easily be transformed to an animation using popular movie encoding systems. 3.1.6 Text interfaces VMD can be extended beyond it's GUI features using it's text-based input systems, the Tcl text interface and the Python interface. Tcl ( Tool command language) is a script language featuring loops, variationals and conditionals. Tcl can be used to execute everything the GUI offers, but it can also be used for more complex operations. VMD also has a Python (an extensively used programming language in bio- as well as other sciences) interface which can be used as an alternative to Tcl. Python interface running in OSX terminal 8 4 References http://en.wikipedia.org/wiki/Image:NA-comparedto-DNA_thymineAndUracilCorrected.png http://fi.wikipedia.org/wiki/RNA http://en.wikipedia.org/wiki/RNA http://www.stanford.edu/~esorin http://www.rnabase.org http://www.ks.uiuc.edu/Research/vmd/ http://www.rcsb.org/ http://www.lbl.gov/Science-Articles/Archive/busta-rna.html Humphrey, W., Dalke, A. and Schulten, K., ”VMD-Visular Molecular Dynamics” J. Molec. Graphics 1996, 14.1, 33-38 Hiltunen et al.: Galenos IV 4th edition 9