Lecture 1-Water and Basics

Process description of structure dissection of

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Process: Description of Structure Dissection of Function
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Protein Data Bank (PDB) http://www.rcsb.org/pdb/ • Where? – San Diego Super Computer (SDSC) • What? – Structures 69,510 as of 11/23/10 - “Molecule of the Month” - Tutorial - Interactive
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Nature Nature is: Selective And Conservative Unity and diversity
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Dogma - Proteins • [proteios] = of the first rank] • Function { Structure Energetics Dynamics Energy Interaction * Order {Protein – Protein} Living matter evades the decay to equilibrium
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The Uniqueness of Water as the biological solvent Influences all molecular interactions Why? – Polarity (charge) – Cohesiveness (order) – Hydro/dehydration reactions – Electron transfer reactions – Proton transfer reactions Origin of Cavities : Creation of water-free microenvironments
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Levels of Structure in Protein Architecture Sequence structure function Primary : amino acid sequence Secondary : Folding motifs ( α , β ) Tertiary : Packing of secondary structures domains Quaternary : Packing of several polypeptide chains
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Reversible Molecular Interactions in biology Electrostatic ~3Å 3-7 kcal/mole Hydrogen Bonds ~3Å 3-7 kcal/mole Van der Waals ~1 kcal/mole A covalent bond (e.g. C-C) 1.5Å ~80 kcal/mole A photon (green light) ~60 kcal/mole
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Sequence-Structure relation Amphipatic β - strand: Polar = P Non-polar = N Sequence: N P N P N P N P N P …. Alignment: Strand Sequence # 1- I S A R F S V C 2- L E M T A K G C PP P Motif suited to create hydrophobic cavities
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Process Description of Structure Dissection of Function...

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