RNA in 3D? Poles leave competition behind!
Already a million times researchers and people from all over the world have used RNAComposer – a publicly available, successful Poznan-based system for modeling the 3D structure of RNA. And this is not the only Polish success in RNA structure determination research.
RNAs are ribonucleic acid molecules. Without them, the comorka could not produce proteins – molecules thatore important for the structure and function of a cellorek. Typeoin RNA is plentiful, and they serve in the cell’sorce rodifferent functions.
Thus, for example. Matrix RNAs are intermediates, thanks to which ktorym information can be extracted from DNA – the recipe for proteins. Ribosome RNAs are made of ribosomes – a comork protein production centers. And transfer RNAs are expected to bring to these centraoin the relevant amino acids – the building blocks of proteins.
RNA functions are so important that scientists from around the world are studying the properties of roof its different molecules. However, to more effectively predict the function of a given RNA and moc to design fully functional molecules in laboratories, it is necessary to know what 3D structure a particular RNA has, i.e. how it is curled up in space.
– RNA’s spatial structure determines its functions, says Dr. hab in an interview with PAP. Eng. Marta Szachniuk of the European Center for Bioinformatics and Genomics (a consortium of Poznan University of Technology and the Institute of Bioorganic Chemistry of the Polish Academy of Sciences).
In the meantime, however, it is not at all that easy to study by experimental methods how a particular RNA is coiled upolne molecules.
RNA molecule is usually formed by a strand consisting of interconnected nucleotide residues (in skrocie: A, C, G, U). Even if one deciphers their order in the RNA chain, i.e. determines the sequence, it is not certain how the whole molecule arranges itself in space. Because RNA molecules – unlike a headphone cable thrown into a backpack – do not coil into random knots. There are certain rules thatore allow to predict what shape a given molecule will take. In unraveling this issue, computer methods for predicting 3D RNA structures are proving helpful.
Dr. hab. Marta Szachniuk wspoln conjunction with the team of Prof. Ryszard Adamiak from the Institute of Bioorganic Chemistry of the Polish Academy of Sciences in Poznań has developed a free, publicly available system called RNAComposer. The RNA sequence (or information about the interactions between nucleotide residues, the so-called. secondary structure), and it calculates and presents trojdimensional model of the molecule. The program efficiently handles zarotion with krotic, as well as very long chains of RNA molecules with complex architecture.
– Many scientistsoD., of the Institute of Bioorganic Chemistry of the Polish Academy of Sciences, uses RNAComposer to get a first idea of what a molecule may look like in 3D, whichorna are studied by. Our system since 2012. has already performed 1 million predictions,” says Dr. hab. Marta Szachniuk.
This is not the only computer system for predicting the 3D structure of RNA. Such automated systemow is several. In addition, the prediction of RNA structures is handled by research teams assisted by experimental studies.
In order to cfoknow the effectiveness of rohe RNA-Puzzles competition has been organized since 2010, in order to find new methods for determining the shape of RNA in 3D space. The idea is that, given a given RNA sequence, to determine the structure of the molecule as accurately as possible. Models provided by the participantoin the competition poroare then compared with the results of experimentsoIn chemical and biological studies leading to structure determination. The competition is currently being organized in twooch categories: serverow, whichore automatically generate results, and in the category of human prediction, where models are created by integrating computer calculations and experimentationoin the laboratory. – We are the best in the category of automated systemsow for 3D RNA prediction,” emphasizes Dr. Szachniuk.