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Slide 1
Good afternoon ladies and gentlemen, my name is krystof and I am a student at ICT Prague,
fifth grade and…I'd like to present you a scientific project, on which I will be working during
my PhD studies. This project concerns the study of protein-nucleic acids interactions, forces
and rules governing these interactions and what are the structural changes on the proteinnucleic acid interfaces. However, before I will talk about the project in a bit more detail, I'll
present some basic facts about molecular biology - the science my project is based on.
The project falls into the realms of structural biology, and it concerns the investigation how
proteins interacts with nucleic acids, what are the forces and rules governing the interaction
and what are the structural changes on the protein-nucleic acid interfaces. However, before I
will talk about the project in a bit more detail, I'll present some basic facts about molecular
biology - the science my project is based on.
I'd like to present you a scientific project, which I will work on during my PhD studies. The
project falls into the realms of structural biology, and it concerns the investigation how
proteins interacts with nucleic acids, what are the forces and rules governing the interaction,
and what are the structural changes on the protein-nucleic acid interfaces imposed by their
interaction. However, before I will talk about the project in a bit more detail, I'll present some
basic facts about molecular biology - the science my project is based on.
Slide 2
This is as you all might know the very simple form of Central Dogma of Molecular Biology.
In fact mostly all of the processes and reactions inside human body are initialized and ruled
by proteins and this dogma is a pattern or framework showing the way how proteins are being
synthesized. The process of unwinding double-stranded DNA and its transcription into singlestranded RNA and afterwards the process of RNA translation into protein.
This process is generally known and called the gene expression.
Slide 3
As obvious from the previous slide, there are three major classes of biopolymers
Click – DNA – the nucleic acid in which the genetic information is coded, I mean all the
instructions for creating RNA and Proteins. For your amusement: In humane one cell there are
about 2 meters of DNA very well packed, because the average cell size is about 10
micrometers. But there are about 100 trillions of cells in human body, so some says if the
whole DNA of one man is stretched out it would reach from Earth to our Sun a hundred
times!
Click – RNA – is also a nucleic acid responsible for creation of proteins by the process of
RNA translation.
Click – Protein – the big organic macromolecules made of amino acids. Proteins participate in
every process within cells, they have catalytic, structural, mechanical and many other
functions. The word protein comes from Greek word “proteios” which means primary!
Slide 4
And in the bilogical world at the microbiological level, the biopolymer interactions play the
main role.
Click DNA+protein: It might be the interaction between DNA and Protein, where here is
DNA and here are the proteins. In this example these proteins are called transcription factors.
They regulate whole gene expression by binding to DNA.
Another example might be drugs. The interactions do not occur only in the CDMB but many
medical drugs interact with biopolymers as well. There are 2 major categories of drugs:
Click – Low-Molecular drugs called Ligands – This is the interaction between DNA and
distamycin, used to inhibit the cancer growth.
Click – Proteins drugs – well known Insulin. Used for treating diabetes.
Slide 5
And what was all this good for? In general, the structure of biopolymers determines their
function. By the structure we mean the knowledge of the positions of all atoms in space.
Very nice example of the importance of the structure was the award of a Nobel Price to
molecular biologists Watson, Crick and Wilkins in 1962 for revealing the DNA structure and
showing that genetic information is not coded in proteins but in DNA.
There are several methods for revealing the molecule structure, where the most efficient and
used is the X-Ray crystallography, but the NMR or cryo-EM are also used as well.
And structures obtained from these experimental methods are deposited into publicly
available database, protein data bank. It is called protein, but you can find here NA as well.
Slide 6
Because there exist clear link between structure and the function, better understanding of the
molecular structure would lead to better understanding of function of Biomacromolecules in
the organism (flow of the information, acting and the function of drugs).
Therefore we are going to study structures from the PDB data bank and we are going to look
for the patterns and regularities in their structure mainly concentrating on the NA/proteins
interaction with special regard to the interactions with drugs.
Slide 7
To perform this scientific research, we have “I would say” perfect conditions, because both
sides: our partner at French University Diderot Paris and the Czech side at ICT Prague with
the co-operation with the Institute of Biotechnology of Academy of Science have their own
original methods for the classification of Biomacromolecules.
Our French partner has developed a method for classification of proteins and we in Prague
have developed method for the DNA/RNA classification.
And by combining Czech and French research experiences and knowledge we are able to
perform a great research on Biomacromolecules and drug interactions.
This whole research is very difficult and it combines modern structural and molecular
biology, statistics, machine learning method and artificial intelligence as well as the raw
programming.
We hope that by our co-operation we can achieve better results in the field of
Biomacromolecules and drugs interactions.