The document discusses protein sequence motifs and their importance. It describes how motifs are patterns in amino acid sequences that have biological significance. Motifs are important because proteins play many critical roles in biology. The document then covers protein structure from primary to quaternary levels and how structure determines function. It proposes using neural algorithms to better analyze and optimize motif sequences, which could help in applications like disease diagnosis, curing Alzheimer's, and more. Developing this tool could open new horizons in medical research.

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