1. Biochemistry Sixth Edition Chapter 2 Protein Composition and Structure Copyright © 2007 by W. H. Freeman and Company Berg Tymoczko Stryer

3. Protein composition and structure Linear polymer of amino acids – folding – 3D structure Chapter 2. Proteins contain various functional groups Proteins interact with one another and with other macromolecules to form complex assemblies Some rigid, some flexible The most versatile macromolecules

4. Structure dictates function.

5. Insect flight tissue

6. Flexibility & function: lactoferrin

7. 2.1 Proteins are built from a repertoire of 20 amino acids  -carbon, side chain, chiral only L isomers, S absolute configuration Zwitterions (dipolar ions) at neutral pH 20 amino acids with different size, charge, shape, hydrogen bonding capacity, hydrophobic character, chemical reactivity

11. Isomers of amino acids

12. S absolute configuration

13. Ionization of amino acids

16. achiral

17. Aliphatic side chains thioether2 chiral centers

21. Proline has a ring structure.

24. Aromatic side chains

25. hydroxyl group indole ring

28. chiral carbon

29. carboxamide

30. Thiol or sulfhydryl

34. Positively charged, basic

37. Histidine ionization

39. acidic

41. Asn, Gln, Ile, Trp R, N, D, Q, E, K, F, W, Y

42. Reason for selection of 20 aa 1.Diverse 2.Available from prebiotic reactions 3.Not very reactive

43. 2.2 Primary structure: amino acids are linked by peptide bonds to form polypeptide chains Peptide bond Oligopeptide, polypeptide, protein, residue, polarity YGGFL vs. LFGGY Main chain or backbone vs. Side chain disulfide bonds

44. Amide bond Kinetically stable

46. rich in hydrogen-bonding potential 50-2,000 aa Average MW; 110

47. Disulfide bond Less disulfide bonds in intracellular proteins, Reason to add DTT,  -ME, etc

48. Proteins have unique amino acid sequences that are specified by genes Each protein has a unique, precisely defined amino acid sequence Sequence information: mechanism of action, three dimensional structure, molecular pathology, evolutionary history

49. Bovine insulin

50. Polypeptide chains are flexible yet conformationally restricted peptide bond is planar and has double bond character

52. Peptide bonds are planar.

53. Typical bond lengths

54. Almost all peptide bonds are trans

55. X-Pro: cis and trans

56. Angle of rotation about the bond between N and C  : phi,  Angle of rotation about the bond between C  and carbonyl carbon: psi,  Limited freedom of rotation by steric exclusion

59. Ramachandran diagram Rigidity and restricted set of allowed angles limit the number of structures accessible to unfolded form sufficiently to allow proteins to fold

60. 2.3 Secondary structure: polypeptide chains can fold into regular structures such as the alpha helix, the beta sheet, and turns and loops Folding into a regularly repeating structure Linus Pauling and Robert Corey in 1951

61. The alpha helix is a coiled structure stabilized by intrachain hydrogen bonds only main chain Almost all the main chain CO and NH groups are H-bonded. rodlike shape

62. alpha helix rise of 1.5A, 3.6 aa per turn, pitch=1.5A*3.6=5.4A

67. hydrogen bonds between NH and CO

68. Right-handed helices are energetically more favorable

70. Ferritin Less than 10 helical turns (~45A)

71. Beta sheets are stabilized by hydrogen bonding between polypeptide strands Beta strand is almost fully extended Beta sheet: H bond between strands rise of 3.5A Parallel or antiparallel

73. Almost fully extended side chain

74. antiparallel beta sheet

75. parallel beta sheet

76. mixed

78. Fatty acid binding protein

79. Polypeptide chains can change direction by making reverse turns and loops Beta turn and omega loop Loops do not have periodic structure but usually well defined on the surface of proteins

80. Beta turn: CO of residue i H-bonded to NH of residue i+3

81. Loops on a protein surface

82. Fibrous proteins provide structural support for cells and tissues  -Keratin (hair):  coiled coil, left-handed superhelix Heptad repeats  3.5 residues/turn  7 residues/2 turns Stability: hydrophobic and ionic interactions, disulfide bonds Collagen: three helical chains, Gly-Pro-Hyp Stability: hydrogen bonds, steric repulsion of pyrrolidine rings

89. 2.4 Tertiary structure: water-soluble proteins fold into compact structure with nonpolar cores Main chain NH and CO groups are maximally H-bonded in the core Thermodynamically most stable Side chain and main chain Tertiary structure

90. Myoglobin: compact

93. Distribution of side chains surfacecross-section The interior consists almost entirely of nonpolar residues The outside consists of both polar and nonpolar residues

96. membrane proteins like porins

97. Motif or supersecondary structure

98. Domain: compact globular unit CD4

99. 2.5 Quaternary structure: polypeptide chains can assemble into mutisubunit structures Quaternary structure: the spatial arrangement of subunits and the nature of their interactions

100. Cro protein of bacteriophage lambda

101. hemoglobin

104. rhinovirus particle

105. 2.6 The amino acid sequence of a protein determines its three dimensional structure Refolding of ribonuclease Christian Anfisen After denaturation, what conditions were required to restore the structure Sequence specifies conformatiom and function

106. Chaotropic agent (urea, gunidinium chloride): non-covalent bond breaker Reducing agent

107. Bovine ribonuclease

108. Reducing agent (beta-mercaptoethanol): S-S to SH

110. Oxidation in 8M urea And dialysis Thermodynamically preferred structure

111. Amino acids have different propensities for forming alpha helices, beta sheets, and beta turns Secondary structure: only main chain Effects of side chains on secondary structure Branching at  -carbon as in Val, Thr, Ile:  sheet H-bonding capability of Ser, Asp, Asn: turn Pro, Gly: turn

113. Tertiary interactions may be decisive in determining the secondary structure Alternative conformation of VDLLKN

114. Protein misfolding and aggregation are associated with some neurological diseases Bovine spongiform encephalopathy (mad cow disease) Creutzfeldt-Jakob disease (CJD) scrapie Prions 1.The transmissible agent consists of aggregated forms of a protein 2.Resistant to treatments with agents that degrade most proteins 3.Derived from PrP that is normally present in the brain Some parts of PrP in  -helix or turn are converted to  -strand   sheets Protein-only model for prion disease transmission Alzheimer disease – amyloid precursor protein(APP)  A    amyloid plaque

117. Protein folding is a highly cooperative process All or none process from a cooperative transition

118. Transition from foled to unfolded state

119. Partially denatured protein solution

120. Proteins fold by progressive stabilization of intermediates rather than by random search Levinthal’s paradox: enormous difference between calculated and actual folding times Typing monkey Retention of partly correct intermediates

121. Typing monkey analogy

123. Prediction of three-dimensional structure from sequence remains a great challenge ab initio prediction knowledge-based methods

124. Protein modification and cleavage confer new capability Acetylation of N-termini, Hydroxylation of proline, Carboxylation of glutamate, Glycosylation, Phosphoryation of Ser, Thr, Tyr, Green fluorescent protein (GFP) Cleavage

128. Space-filling model

129. Ball-and-stick model

130. Backbone model

131. Ribbon diagram