3. … ..AATGCCGCGTAGTCGGGTAAGGGTCTGAAGCTGAAATCTTTTCACACCGAGTCGATGGG… … .APTCHYLDELAKGGRLDATIKRDGLGVLVWAQND…. Hierarchy in Understanding Function “ We may, I believe, anticipate that the chemist of the future who is interested in the structures of proteins, nucleic acids, polysaccharides, and other complex substances with higher molecular weights will come to rely upon a new structural chemistry, involving precise geometrical relationships among the atoms in the molecules and the rigorous application of the new structural principles, and that great progress will be made, through this technique, in the attack, by chemical methods, on the problems of biology and medicine.” -Linus Pauling, Nobel Lecture, 1954 … ..GCCGCGTAGTCGGGTAAGGGTCACACCGAGTCGATGG…
4. Paradigm: Function of biological macromolecules is intricately related to their three-dimensional shape and structure. Structural knowledge is therefore an important step in understanding function. Techniques available: X-ray crystallography, NMR, CD, Fluorescence spectroscopy, Mass spectrometry…..
5. Some Landmarks in Macromolecular Structure Determination Watson and Crick Perutz and Kendrew Hodgkin Pauling Great ideas have always faced violent opposition from mediocre minds -Albert Einstein
6. Some Landmarks in Macromolecular Structure Determination……..contd. Photosynthetic reaction centre Potassium channel Virus
7. Experimental Methods of Structure Determination X-ray crystallography Solubilization of the over-expressed protein Obtaining crystals that diffract Structure determination by diffraction of protein crystals Size of a molecule: no theoretical limit Nuclear Magnetic Resonance spectroscopy Solubilization of the over-expressed protein Structure determination of a molecule as it exists in solution Size-limit is a major factor
19. The Protein Folding Problem Amino acid sequence of a polypeptide has all the information required to determine its three-dimensional topology
20. If a polypeptide sequence corresponds to a unique conformation of the protein, how does nature take care of point mutations in the primary sequences?
21. Triosephosphate Isomerase Structures of E. coli, B. stearothermophilus, P. falciparum, T. brucei, S. cerevesiae , chicken, human TIMS are identical though amino acid sequences differ by >50%
22. Chicken Human Leishmania Pyrococcus Thermotoga Vibrio Three-dimensional structures of homologous proteins are very similar
23. The relation between the divergence of sequence and structure in proteins. Chothia C, Lesk AM. EMBO J. 1986 Apr;5(4):823-6. The sequence- structure relationship
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25. Predicting Protein Structure: Comparative (Homology) Modeling ? KQFTKCELSQNLYDIDGYGRIALPELICTMFHTSGYDTQAIVENDESTEYGLFQISNALWCKSSQSPQSRNICDITCDKFLDDDITDDIMCAKKILDIKGIDYWIAHKALCTEKLEQWLCEKE Use as template & model 8lyz 1alc KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL Share Similar Sequence Homologous
26. How have the protein structures enhanced our understanding of Biology?
31. “ Throughout our endeavors we have been motivated by the expectation that the detailed knowledge of its (F 0 F 1 ATP synthase) structure would lead to a better understanding of how ATP is made.” -John Walker Mechanism of F 0 F 1 ATP Synthase
38. Challenges for Structural Biology How can the process of structure determination be expedited? Can we predict the structures of proteins accurately? How can we use the structures in designing novel therapies? Thank You !
