Protein motif analysis and optimization using neural algorithms
- 1. Protein motif analysis and optimization using neural algorithms SANKALPA CHOWDHURY INFORMATION TECHNOLOGY THE UNIVERSITY OF BURDWAN
- 2. What is protein sequence motif? In genetics, a sequence motif is a nucleotide or amino- acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. For proteins, a sequence motif is distinguished from a structural motif , a motif formed by the three-dimensional arrangement of amino acids which may not be adjacent.
- 3. Why protein motif is so important ? Proteins play countless roles through out the biological world. Some transport nutrients through out the body, some helps chemical reactions to happen at faster rates, others makeup structures that make up living things,
- 4. Building blocks of proteins Amino acids are made up of carbon , nitrogen , oxygen , hydrogen and sulphur atoms.
- 5. The protein structure Primary structure – the linear sequence of amino acids encoded by DNA ATG – Met , CAA – Gln , ACT – Ile , TTC- Phe , GTG – Val, AAG – Lys, ACC – Thr The amino acids in the protein are joined by peptide bonds , which link the one group of amino acid with carboxyl group of the other, and a water molecule is released each time when a peptide bond is formed. This links a series of carbon, nitrogen and oxygen atom bond sequence is the protein backbone.
- 6. Secondary structures – alpha helix and beta sheet Alpha helix – Coil like structure stabilised by hydrogen bonds between the amine and carboxyl groups of amino acids. Beta sheets – They are formed when hydrogen bonds are formed between two or more adjacent strands of amino acids of amino acids The tertiary structures – The combination of both the structures of alpha helix and beta sheets. Quaternary structures – Two or more poly peptide chains can come together to form a molecule with several sub-units.
- 7. Functions of proteins The functions of proteins lie upon their structures and sequence. The 3D shapes of proteins determine their functions. Defence – The flexible arms of antibodies bind with to pathogens and target them for destruction by the immune system. Transport – Glucose transporter insulin Storage – Alpha amylase enzyme begins digestion of starch inn our saliva Communication – Calcium pump Structure – Ferritin has channels that allows iron atoms to enter and exit, and it has inner hollow sphere which stores iron inn non toxic form Enzymes
- 8. Bioinformatics Its an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines Computer Science, Biology, Mathematics , Statistics , and Engineering to analyze and interpret biological data. Bioinformatics has been used for analyses of biological queries using mathematical and statistical techniques. More broadly, bioinformatics is applied statistics and computing to biological science.
- 9. Algorithm to analyse and better optimise the motif sequence
- 10. Application in diagnosis A disease can be easily eliminated permanently by using it to develop new patterns of motifs, which will eventually re-writing the antibody structures to better help immune system to target pathogens more accurately . Early detection of a disease, by storing the amino-acid structural motif from early detections case samples. Better analysis of protein , which will help in better understanding of the different motif causing different functions in a protein. Scientists will get a better tool to know more about a disease, and can instruct experts and doctors for better treatment and understanding. This algorithm will help to explore a new horizon of medical science.
- 11. Application in curing Alzheimer’s disease Jellyfish species Aequorea victoria has an amazing Bioluminescence protein called Green Fluorescent Protein or GFP. By extracting the protein motif and inserting the same into some other cell’s DNA and Genetically modifying the cell species with the ability of Bioluminescence. By doing so , we can insert the same to detect the exact blood flow route which is blocked or can illuminate the exact neuro-beta amyloid plaques or neuro tangles , and doctors can target immediate treatment at that region.
- 12. By optimization of alpha secretase enzyme which are responsible for processing a specific protein on the cell membrane of neurones , called Alpha Precarsor protein (APP) , and a second enzyme called Gamma secretase also snaps APP in another site. By restricting gamma secretase cut of APP which causes Plaques by producing Beta- Amyloid chains. Another protein called Tau gets modified to form neuro- fibrillary tangles which destroys a cluster of neurons by restricting microtubulary transportations. By analysis of what kink of motif of tau – modification happens which results in such destructions , neuroscientists can come up with new techniques with the help of the tool.
- 13. Other applications Applications in agriculture In neurosurgery In cancer treatment Food industry Diagnostic centres Research of new functions of proteins In genetic engineering Many more….
- 14. Thank you I acknowledge Sourav Samanta Sir, for his great help. I thank utkrisht for giving me a great stage