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Chapter 4

CH250 - Midterm #2 Notes Chapter 4.docx

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James Gerlach

The ThreeDimensional Structure of ProteinsThe six themesoEverything that determines the structure taken up by a protein are amino acidsoThe function of the proteins depend on the structurefunction follows formoMost isolated proteins exist in one or a small number of stable structureal formsoWhat determines and maintains these shapes are noncovalent bonds while the covalent bonds just hold the primary amino acid sequence togetheroThere are some common structural patterns that help to organize out understanding of protein architectureoProtein structures are dynamic and changing They change shape flec undergo conformational changesPlanar peptide groupoEach peptide bond has some doublebond character due to resonance and cannot rotateoThree bonds separate sequential carbon in a polypeptide chain The NC and the COC bonds can rotate described by dihedral angles designatedandThe peptide CON bond is not able to rotate Other single bonds in the peptide may be hindered by the size and charge of the R groupthese determine to a large extent how the protein foldThis transarrangement is typically seen in all proteinsRamachandran PlotsoPeptide conformations are defined by the values ofandConformations deemed possible are those the involve little or no steric inference based on the calculation using know van der Waals radii and dihedral angles The areas that are darkly shaded represent conformations that involve no steric overlap medium represents conformations permitted if atoms are allowed to approach each other by a very modest flexibility a few degrees is allowed in thedihedral angle that describes the peptide bond itself generaly constrained to 180 The white regions are areas where the conformation is not allowed Protein Secondary Structure
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