Chem Lecture 2 Protein Structure Part 3
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1 Chem Lecture 2 Protein Structure Part 3 Question of the Day: Most proteins are made from a repertoire of 20 different amino acids. A small protein contains around 100 amino acids strung together in a polypeptide chain. How many different possible chains, containing 100 amino acids each, can be made when there are 20 different options for each of the amino acid in a chain? Protein Primary Structure The amino acids combine to form polymers of amino acids. Polymers of amino acids are called polypeptides 2 Question Based on the number of amino acid residues it contains A) how would you classify the oligopeptide shown below? B) What is the predicted mass for this oligopeptide? 3 Question Based on the number of amino acid residues it contains A) how would you classify the oligopeptide shown below? B) What is the predicted mass for this oligopeptide? Leu-Enkephalin 3
2 Protein Primary Structure While polypeptides are linear polymers, they can form cross links. 4 Protein Primary Structure Protein Sequencing The first protein to be sequenced was insulin Frederick Sanger (1953) Nobel Prize in Chemistry, 1958 Human Insulin 5 Protein Primary Structure Edman Degradation Protein Sequencing The first protein to be sequenced was insulin Frederick Sanger (1953) Nobel Prize in Chemistry, 1958 Human Insulin 5 Protein Primary Structure Edman Degradation Protein Sequencing The first protein to be sequenced was insulin Frederick Sanger (1953) Nobel Prize in Chemistry, 1958 Human Insulin 5
3 Protein Primary Structure Edman Degradation Protein Sequencing The first protein to be sequenced was insulin Frederick Sanger phenyl isothiocyanate (1953) Nobel Prize in Chemistry, 1958 Human Insulin 5 Protein Primary Structure Edman Degradation Protein Sequencing The first protein to be sequenced was insulin Frederick Sanger phenyl isothiocyanate (1953) Nobel Prize in Chemistry, 1958 Human Insulin phenyl thiohydantoin (PTH) derivative 5 Protein Primary Structure Edman Degradation Protein Sequencing The first protein to be sequenced was insulin Frederick Sanger phenyl isothiocyanate (1953) Nobel Prize in Chemistry, 1958 Read all about it in Chapter 3 Human Insulin phenyl thiohydantoin (PTH) derivative 5 Protein Primary Structure Edman Degradation Protein Sequencing The first protein to be sequenced was insulin Frederick Sanger phenyl isothiocyanate (1953) Nobel Prize in Chemistry, 1958 Human Insulin phenyl thiohydantoin (PTH) derivative 5
4 Protein Primary Structure Protein Sequencing The first protein to be sequenced was insulin Frederick Sanger (1953) Nobel Prize in Chemistry, 1958 Human Insulin 5 Polypeptide Conformations Polypeptides are conformationally flexible. Rotation is possible about the and bonds. 6 Polypeptide Conformations Rotation about the peptide () bond is restricted to 0 and 180. The bond behaves like a double bond cis (0 ) or trans (180 ) 7 Polypeptide Conformations Rotation about the peptide () bond is restricted to 0 and 180. The bond behaves like a double bond cis (0 ) or trans (180 ) 7
5 Polypeptide Conformations Rotation about the peptide () bond is restricted to 0 and 180. The bond behaves like a double bond cis (0 ) or trans (180 ) 7 Polypeptide Conformations Rotation about the peptide () bond is restricted to 0 and 180. The bond behaves like a double bond cis (0 ) or trans (180 ) 7 Polypeptide Conformations Rotation about the peptide () bond is restricted to 0 and 180. The bond behaves like a double bond cis (0 ) or trans (180 ) 7 Polypeptide Conformations Rotation about the peptide () bond is restricted to 0 and 180. The bond behaves like a double bond cis (0 ) or trans (180 ) trans is the sterically more favorable configuration 8
6 Polypeptide Conformations Rotation about the peptide () bond is restricted to 0 and 180. The bond behaves like a double bond cis (0 ) or trans (180 ) For peptide bonds involving proline, both cis and trans configurations are possible. 9 Polypeptide Conformations Rotation about the peptide () bond is restricted to 0 and 180. The bond behaves like a double bond cis (0 ) or trans (180 ) 10 Polypeptide Conformations Rotation about the peptide () bond is restricted to 0 and 180. The bond behaves like a double bond cis (0 ) or trans (180 ) 10 Polypeptide Conformations Rotation about the peptide () bond is restricted to 0 and 180. The bond behaves like a double bond cis (0 ) or trans (180 ) 10
7 Polypeptide Conformations Ramachandran determined the sterically most favorable combinations of and angles. 11 Primary -> Secondary -> Tertiary We will consider proteins structure hierarchically: 12 Primary -> Secondary -> Tertiary We will consider proteins structure hierarchically: 12 Question The functional diversity of proteins results from the large number of possible polypeptides that can be built using the 20 different amino acids Question: What is the minimum mass it would take to construct one molecule each of all of the possible polypeptides that contain 100 amino acids? 13
8 13 Question The functional diversity of proteins results from the large number of possible polypeptides that can be built using the 20 different amino acids Question: What is the minimum mass it would take to construct one molecule each of all of the possible polypeptides that contain 100 amino acids? View the polypeptides as beads on a string, with one of 20 possible types of beads at each position Question The functional diversity of proteins results from the large number of possible polypeptides that can be built using the 20 different amino acids Question: What is the minimum mass it would take to construct one molecule each of all of the possible polypeptides that contain 100 amino acids? View the polypeptides as beads on a string, with one of 20 possible types of beads at each position o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o 13 Thinking of the Possibilities The Earth weighs 6.0 x g, how many Earths would it take? 14 Thinking of the Possibilities The Sun weighs 2.0 x g, how many Suns would it take? 15
9 Thinking of the Possibilities The Milky Way galaxy weighs 1.2 x times the mass of the sun A) (1.2 x suns)(2.0 x g/sun) = 2.4 x g B) How may galaxies would it take? 16 Thinking of the Possibilities The Coma galaxy cluster contains several thousand galaxies, how many...? 17 Thinking of the Possibilities Number of polypeptides ( ) 1.26 x Avg. Mass of each polypeptide Total mass needed 1.83 x g 2.32 x g Number of Earths 3.9 x Number of Suns 1.2 x Number of Galaxies 9.7 x The amino acid residues in a folded, globular protein, generally adopt these favorable combinations of and angles. Ribonuclease A 19
10 The first 3-dimensional structure of a protein were published in the late 1950 s by John Kendrew (myoglobin) and Max Perutz (hemoglobin). 20 The first 3-dimensional structure of a protein were published in the late 1950 s by John Kendrew (myoglobin) and Max Perutz (hemoglobin). 21 The first 3-dimensional structure of a protein were published in the late 1950 s by John Kendrew (myoglobin) and Max Perutz (hemoglobin). Interior or folded proteins is packed almost exclusively with non-polar amino acid side chains. 21 What effect does the polar backbone have on folding? 22
11 Looking at the sterically favorable and angles. 23 Looking at the sterically favorable and angles. 23 -helix region -helix 24 -helix region -helix 24
12 -helix region -helix 24 Looking at the sterically favorable and angles. 25 Looking at the sterically favorable and angles. 25 -sheet region 26
13 -sheet region Antiparallel -sheet Parallel -sheet 27 -sheet region Can also have mixed parallel and antiparallel -sheets 28 -sheet region 29 The amino acid residues in a folded, globular protein, generally adopt these favorable combinations of and angles. Ribonuclease A 30
14 Loops and β-turns 31 Proteins vary in their α-helix and β-sheet content. Ferritin (1aew) Antibody (7fab) 32 Fibrous Proteins Some fibrous proteins lack tertiary α-helical coiled coils 33 Fibrous Proteins Some fibrous proteins lack tertiary α-helical coiled coils 33
15 Fibrous Proteins Some fibrous proteins lack tertiary -helical coiled coils 33 Fibrous Proteins Some fibrous proteins lack tertiary Leucine zippers -helical coiled coils 33 Fibrous Proteins Some fibrous proteins lack tertiary Leucine zippers -helical coiled coils 33 Fibrous Proteins Some fibrous proteins lack tertiary Leucine zippers -helical coiled coils 33
16 Fibrous Proteins Some fibrous proteins lack tertiary Collagen (polyproline triple helix) 34 Fibrous Proteins Some fibrous proteins lack tertiary Collagen (polyproline triple helix) 34 Fibrous Proteins Some fibrous proteins lack tertiary Collagen (polyproline triple helix) 34 Fibrous Proteins Some fibrous proteins lack tertiary Collagen (polyproline triple helix) 35
17 Fibrous Proteins Some fibrous proteins lack tertiary polyproline II helix polyproline I helix Collagen (polyproline triple helix) 35 Fibrous Proteins Some fibrous proteins lack tertiary Collagen (polyproline triple helix) 35 The 3-dimensional fold of a single polypeptide 36 Polypeptides fold to remove hydrophobic amino acid side chains from exposure to water. surface interior 37
18 Polypeptides fold to remove hydrophobic amino acid side chains from exposure to water. yellow - hydrophobic blue - charged white - other surface interior 37 Formation of secondary structure allows for the polar backbone to be buried as well. Ubiquitin 38 Most of the amino acid residues have and angles in the sterically favorable regions Ribonuclease A 39 Disulfide bonds help cement the tertiary fold. Ribonuclease A 40
19 Some proteins are built inside out Porin, a membrane protein 41 Some proteins are built inside out Porin, a membrane protein 41 Some proteins are built inside out Porin, a membrane protein 41 Protein Quaternary Structure Some proteins have multiple polypeptides (subunits). Ubiquitin 42
20 Protein Quaternary Structure Quaternary structures are stabilized by the same interactions that stabilize tertiary structures. Non-covalent interactions involving primarily the amino acid side chains. 43 Protein Quaternary Structure Some tertiary structures have multiple folding domains, which give them the appearance of having quaternary structure CD4 protein 44 Hierarchy of Protein Structure Primary Secondary Tertiary Quaternary Phosphofructokinase I 45 Next up Protein folding and misfolding. Question of the Day: How is online video game-playing is being used to help find cures for diseases? 46
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