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BEL110 presentation


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This presentation is on protiens.

This presentation is on protiens.

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  • 1. Protein tertiary and quaternary structure determination using Bio informatics tools Dipankar Sarkar 2003CS10161 Group #1
  • 2. Introduction
    • What is a protein?
      • A protein (from the Greek protas meaning of primary importance) is a complex, high-molecular-weight, organic compound that consists of amino acids joined by peptide bonds.
    • Proteins are essential to the structure and function of all living cells and viruses.
  • 3. Protein – Component & synthesis
    • Proteins are polymers built from 20 different L-alpha-amino acids. Proteins are assembled from amino acids using information present in genes. Genes are transcribed into RNA, RNA is then subject to post-transcriptional modification and control, resulting in a mature mRNA that undergoes translation into a protein. mRNA is translated by ribosomes that match the three-base codons of the mRNA to the three-base anti-codons of the appropriate tRNA. The enzyme aminoacyl tRNA synthetase catalyzes the formation of covalent peptide bonds between amino acids forming the protein.
    • The two ends of the amino acid chain are referred to as the carboxy terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity.
  • 4. Protein - structure
    • Primary - amino acid sequence
    • Secondary - highly patterned sub-structures
    • Tertiary - the overall shape of a single protein molecule
    • Quaternary - the shape or structure that results from the union of more than one protein molecule
  • 5. Tertiary structure prediction
    • Aim is of determining the three-dimensional structure of proteins from their amino acid sequences
    • There are two methods of structure prediction
      • De novo protein modeling – Brute force method of predicting the 3D structure of the protein. Needs a lot of computational power. Example – Rosetta.
  • 6. Tertiary - Continued
      • Comparative protein modeling – It uses previously solved structures as starting points, or templates. This is effective because it appears that although the number of actual proteins is vast, there is a limited set of tertiary structural motifs to which most proteins belong. Into 2 more types of modeling :
        • Homology modelling
        • Protein threading
  • 7. Quaternary structure prediction
    • In addition to the tertiary structure of the subunits, multiple-subunit proteins possess a quaternary structure, which is the arrangement into which the subunits assemble
    • There are 3 primary methods of predicting protein-protein interaction
      • Phylogenetic distance and co-evolution of interacting domains – Example – ADVICE
  • 8. Quaternary - Continued
      • Identification of homologous interacting pairs – This method consists of searching whether the two sequences have homologues which form a complex in a database of known structures of complexes. Example :- InterPreTS (Interaction Prediction through Tertiary Structure)
      • Identification of structural patterns (target must be a structure) – The third method builds a library of known protein-protein interfaces from the Protein Data Bank. The sequences in the library are then clustered based on structural alignment and redundant sequences are eliminated. Example :- PRISM
  • 9. Conclusion
    • Methods used by bioinformatics tools are heavily based on algorithmic research, a key area of computer science research.
    • As structure prediction is composed of NP hard sub-problems, techniques like neural networks and approximation algorithms are heavily used in the bioinformatics tools.
  • 10. Bibliography
    • Simons, K. T., Bonneau, R., Ruczinski, I., Baker, D.,(1999) Ab initio protein structure prediction of CASP III targets using ROSETTA, Proteins Suppl 3, 171-6.
    • Bates, P.A., Kelley, L.A., MacCallum, R.M. and Sternberg, M.J.E., (2001) Enhancement of Protein Modelling by Human Intervention in Applying the Automatic Programs 3D-JIGSAW and 3D-PSSM., Proteins: Structure, Function and Genetics, Suppl 5:39-46.
    • Tan S.H., Zhang Z., Ng S.K.,(2004) ADVICE: Automated Detection and Validation of Interaction by Co-Evolution.. Nucl. Ac. Res., 32 (Web Server issue):W69-72.
    • Aloy P.,Russell R.B, InterPreTS: Protein Interaction Prediction through Tertiary Structure., Bioinformatics, 19 (1), 161-162.
    • Ogmen U., Keskin O., Aytuna A.S., Nussinov R. and Gursoy A,(2005) PRISM: protein interactions by structural matching., Nucl. Ac. Res.,33 (Web Server issue):W331-336.
    • Wikipedia,