chapter4 RKW - Lecture Connections 4 | Proteins Structure...

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Lecture Connections 4 | Proteins: Structure, Function, Folding © 2009 W. H. Freeman and Company
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1920’s Proteins Crystallized Crystals only form when units are identical. Proteins must have unique structures. Proteins denatured no longer function. Structure is related to function.
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Structure lead to Function 1. Structure determined by AA sequence. 2. Function depends on structure. 3. Proteins exist in stable forms. 4. Non-covalent interactions stabilize proteins 5. Common structures organize proteins.
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CHAPTER 4 Proteins: Structure, Function, Folding Structure and properties of the peptide bond Structural hierarchy in proteins Structure and function of fibrous proteins Protein folding and denaturation Structure analysis of globular proteins Key topics :
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Structure of Proteins Unlike most organic polymers, protein molecules adopt a specific 3-dimensional conformation in the aqueous solution. This structure is able to fulfill a specific biological function This structure is called the native fold The native fold has a large number of favorable interactions within the protein There is a cost in conformational entropy of folding the protein into one specific native fold
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Conformation Spatial arrangement of AA is the conformation of the protein. Crystal structures suggest (represents) one conformation. In solution the protein has multiple conformations. Movement is important for function. DNA polymerase Think PacMan
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Favorable Interactions in Proteins Hydrophobic effect Release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy Hydrogen bonds Interaction of N- H and C= O of the peptide bond leads to local regular structures such as α -helixes and β -sheets London dispersion Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein Electrostatic interactions Long-range strong interactions between permanently charged groups Salt-bridges, esp. buried in the hydrophobic environment strongly stabilize the protein
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Structure of the Peptide Bond Structure of the protein is partially dictated by the properties of the peptide bond The peptide bond is a resonance hybrid of two canonical structures The resonance causes the peptide bonds to be less reactive compared to e.g. esters be quite rigid and nearly planar exhibit large dipole moment in the favored trans configuration
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The Rigid Peptide Plane and the Partially Free Rotations Rotation around the peptide bond is not permitted Rotation around bonds connected to the alpha carbon is permitted φ (phi): angle around the α -carbon— amide nitrogen bond ψ (psi): angle around the α -carbon— carbonyl carbon bond In a fully extended polypeptide, both ψ and φ are 180°
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3 Distribution of φ and ψ Dihedral Angles Some φ and ψ combinations are very unfavorable because of
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