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Lecture Biochemistry (2/e): Chapter 6 - Reginald Garrett, Charles Grisham

This chapter reveals and elaborates upon the exquisite beauty of protein structures. What will become apparent in this discussion is that the three-dimensional structure of proteins and their biological function are linked by several overarching principles: Function depends on structure, structure depends both on amino acid sequence and on weak, noncovalent forces, the number of protein folding patterns is very large but finite,. | Chapter 6 Proteins: Secondary, Tertiary, and Quaternary Structure to accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham All rights reserved. Requests for permission to make copies of any part of the work should be mailed to: Permissions Department, Harcourt Brace & Company, 6277 Sea Harbor Drive, Orlando, Florida 32887-6777 Outline 6.1 Forces Influencing Protein Structure 6.2 Role of the Amino Acid Sequence in Protein Structure 6.3 Secondary Structure of Proteins 6.4 Protein Folding and Tertiary Structure 6.5 Subunit Interactions and Quaternary Structure 6.1 The Weak Forces What are they? What are the relevant numbers? van der Waals: 0.4 - 4 kJ/mol hydrogen bonds: 12-30 kJ/mol ionic bonds: 20 kJ/mol hydrophobic interactions: <40 kJ/mol 6.2 The Role of the Sequence in Protein Structure All of the information necessary for folding the peptide chain into its "native” structure is contained in the primary amino acid structure of the peptide. How do proteins recognize and interpret the folding information? Certain loci along the chain may act as nucleation points Protein chain must avoid local energy minima Chaperones may help 6.3 Secondary Structure The atoms of the peptide bond lie in a plane The resonance stabilization energy of the planar structure is 88 kJ/mol A twist about the C-N bond involves a twist energy of 88 kJ/mol times the square of the twist angle. Twists can occur about either of the bonds linking the alpha carbon to the other atoms of the peptide backbone Consequences of the Amide Plane Two degrees of freedom per residue for the peptide chain Angle about the C(alpha)-N bond is denoted phi Angle about the C(alpha)-C bond is denoted psi The entire path of the peptide backbone is known if all phi and psi angles are specified Some values of phi and psi are more likely than others. The angles phi and psi are shown here Steric Constraints on phi & psi Unfavorable orbital overlap precludes some combinations of phi and psi phi = 0, psi = 180 . | Chapter 6 Proteins: Secondary, Tertiary, and Quaternary Structure to accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham All rights reserved. Requests for permission to make copies of any part of the work should be mailed to: Permissions Department, Harcourt Brace & Company, 6277 Sea Harbor Drive, Orlando, Florida 32887-6777 Outline 6.1 Forces Influencing Protein Structure 6.2 Role of the Amino Acid Sequence in Protein Structure 6.3 Secondary Structure of Proteins 6.4 Protein Folding and Tertiary Structure 6.5 Subunit Interactions and Quaternary Structure 6.1 The Weak Forces What are they? What are the relevant numbers? van der Waals: 0.4 - 4 kJ/mol hydrogen bonds: 12-30 kJ/mol ionic bonds: 20 kJ/mol hydrophobic interactions: <40 kJ/mol 6.2 The Role of the Sequence in Protein Structure All of the information necessary for folding the peptide chain into its "native” structure is contained in the primary amino acid structure of the peptide. How do proteins recognize and