Distribution of the amino acids in ature Amino Acid Frequency in proteins (%) Leucine Alanine Glycine erine Valine Glutamic acid Threonine Arginine Lysine Aspartic acid Isoleucine Proline Asparagine Glutamine Phenylalanine Tyrosine Methionine istidine Cysteine Tryptophan 9.0 8.3 7.2 6.9 6.6 6.2 5.8 5.7 5.7 5.3 5.2 5.1 4.4 4.0 3.9 3.2 2.4 2.2 1.7 1.3 Increasing Frequency Four special amino acids 2 C 2 2 glycine proline cysteine histidine 1
Glycine: The mallest Amino Acid 2 First amino acid discovered in 1820 from gelatin. = hydrogen educed steric hindrance: can adopt a wider range of peptide conformations compared to other amino acids. Trans Proline Cis eavily favored C lightly favored In proline, the trans isomer is only slightly favored over the cis isomer. Thus, proline can readily adopt the cis conformation. C 2
Cysteine and Cystine cysteine cystine Disulfide bonds constrain protein conformation Disulfide Bonds and Perms educe Curl xidize 3
What is pk a? + K a = pk a = - log K a K a = p 7.5 6.5 5.5 4.5 pk a = - log [ + ] = p 7 6 5 Titration Curve of istidine 4 1 1.2 1.4 1.6 1.8 2 Volume of Base (ml) istidine can shuffle between forms 2 slight increase in physiological p (more basic) slight decrease in physiological p (more acidic) 2 4
ydrolysis of a peptide bond chymotrypsin acrosin Factor X ' Uncatalyzed rate 7-400 years + 2 + 2 ' Enzymes make the rate of reactions go faster. Amino acids cooperate in catalysis Asp 102 er is chymotrypsin er 195 is 57 The catalytic triad: serine, histidine, and aspartic acid work together to cleave amide bonds Asp The aspartate -bonds to the histidine side chain, perturbing its pka and making it more basic. This makes it easier for histidine to remove a proton from serine during the reaction. 5
Take home messages Proteins are polymers of amino acids. Amino acids are connected through peptide bonds. The nature of the peptide bond constrains the shape of the polymer. onbonded interactions between side chains also constrain the shape of the peptide backbone. There are twenty amino acids, each containing unique side chains. Amino acids can work in concert in a polypeptide chain to generate new functions. Question: ow does a straight chain polymer of amino acids fold?? Protein tructure and Folding UMPTY DUMPTY AT A WALL. UMPTY DUMPTY AD A GEAT FALL. ALL TE KIG E AD ALL TE KIG ME, CULD T PUT UMPTY TGETE AGAI. Life ciences 1a Lecture otes et 5 Fall 2006 Prof. Daniel Kahne 6
Lectures 7-8: The Molecular Basis of Translation: Proteins: The Workhorses of Biology a. A chemical look at proteins i. Introduction to proteins and amino acids ii. Conformational peculiarities of peptide bonds iii. tructures and properties of the twenty natural amino acids iv. A closer look at four special amino acids -- Gly, Pro, Cys, and is. v. Collaborations between amino acids in proteins b. Protein structure i. The four levels of structure ii. A closer look at secondary structure c. Protein folding: i. Anfinsen s experiment ii. Thermodynamic forces involved in protein structures. iii. Thermodynamics of protein folding iv. The Levinthal paradox (the kinetics of protein folding) v. Molecular chaperones Lecture eadings Alberts pp. 119-128; McMurry: pp. 182-192, 233-238 Four Levels of Protein tructure 7
Different Proteins Contain Different econdary tructural Elements Cytochrome b562 LD Antibody ierarchical rganization of Protein tructure Protein Molecule ingle Polypeptide Domain econdary tructure 8
phi 3 psi 3 nly some peptide backbone conformations are sterically allowed psi 2 phi 2 psi 1 phi 1 C α peptide plane C phi C α A amachandran plot shows the allowed combinations of the dihedral angles. econdary tructure: α-helices 2 acetamide Linus Pauling and obert B. Corey, Proc at Acad ci, 1951, 37, 235. 9
Details about α-helices 9 Cα 8 C 8 8 7 C 7 C 6 Cα 7 6 Cα 6 5 C 5 Cα 5 C 4 Cα 3 Cα 4 C 3 4 C 1 Cα 1 3 Cα 2 2 C 2 econdary tructure: β-sheets Cα Cα C C C 10
Does primary sequence determine protein conformation? Thermodynamic ypothesis: The information contained in the primary amino acid sequence leads to the correct protein fold. (or in other words... Could you put umpty Dumpty back together again?) Christian Anfinsen, obel Prize in Chemistry 1972 Test: Will a denatured protein (ibonucleasea) refold to its native conformation? Anfinsen s protein folding experiment Conclusion: The information required to fold a protein is contained within its sequence. 11