Katri Vilkman 67615RIlkka Koskela 77267R

Visualization of RNA molecules using VMD

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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

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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), MSD-

EBI (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.

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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 NucleotidesNucleotide 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 acidsNucleic 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 H-

bonds force the polynucleotide chain to form different structures hairpin loop

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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 RNAThere 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 mRNAMessenger 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 tRNATransfer 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. 5S rRNA in VMD

2.4.4 Catalytic RNASome RNA molecules are able to catalyze chemical reactions, for example, ligation of

other RNA molecules and forming peptide bond in the ribosome.

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2.4.5 Double stranded RNAIn some viruses RNA is double stranded (dsRNA) and contains the genetic information.

2.4.6 RNA genesRNA 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 Visualisation in VMD

3.1.1 Loading a moleculeVMD 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

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and sizes, of which it is able to calculate where bonds are formed between atoms.

3.1.2 Observing the molecule in the Graphics windowOnce 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 screenVMD 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. Descriptions of molecule representation styles in VMD

3.1.4 ExtensionsVMD 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

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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 RenderingWhether 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 interfacesVMD 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

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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

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