Lecture10

Lecture10 - of Proteins Determines Their Tertiary Structure...

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Chapter 2 P ROTEIN C OMPOSITION AND S TRUCTURE Chapter 4 DNA, RNA, F LOW OF G ENETIC I NFORMATION Lecture 10 09/17/08 1
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Exam I Tues, Sept 23 8:00-10:00 PM Lily 1-105 OPTIONAL REVIEW SESSION Thursday, September 18th, 6-8 PM SMTH 108 Efrain Sanchez, TA 09/17/08 2
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Exam I coverage: Chapter 1: All sections Chapter 2: All sections Chapter 4: Through lecture Fri. 09/19 09/17/08 3
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Forces Stabilizing Proteins 1. Hydrophobic Effect (major) 2. van der Waals interactions (substantial) minor or no contribution 3. H-bonding 4. Electrostatic - ion pair ( Asp ··· + Lys ) G folded -G unfolded ~ 42 kJ mol -1 (10 kcal mol -1 ) for each residue 0.4 kJ mol -1 (0.1 kcal mol -1 ) 100 residue protein 09/17/08 4
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Domains Ca 2+ -binding domain Troponin C Cleaved by limited proteolysis Ca 2+ -binding domain 09/17/08 5
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SHP2 Phosphatase with two “built-in” regulatory domains SH2 domain ~ 90 res. 09/17/08 6
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Modular Proteins domains are found within multiple proteins 09/17/08 7
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supersecondary structures motifs folds T ERMINOLOGY 09/17/08 8
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09/17/08 9
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Domain of Pyruvate Kinase multiple β - α - β loops assembled together 09/17/08 10
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Transient Protein-Protein Interaction + + Heterotrimer 09/17/08 11
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Denaturation (unfolding) Temperature Urea Guanidine Hydrochloride pH Detergents 09/17/08 12
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Detergent Sodium dodecyl sulfate (SDS) Triton X-100 09/17/08 13
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The Amino Acid Sequence
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Unformatted text preview: of Proteins Determines Their Tertiary Structure 09/17/08 14 Amino Acid sequence of Ribonuclease A 09/17/08 15 Denaturants Reducing agent 09/17/08 16 Reduction of Protein Disulfide bonds by -mercaptoethanol 09/17/08 17 Denaturation and renaturation of Ribonuclease A 8M Urea -ME Slowly remove Urea & -ME 09/17/08 18 Probability of random reformation of correct disulfide bonds is 1/105 ~1% correctly folded 09/17/08 19 ~ 1% active 8M Urea Remove only -ME 8M Urea -ME Remove Urea Trace amounts of -ME Denaturation and renaturation of Ribonuclease A 09/17/08 20 Proteins do not fold by a random search of all possible conformations to find the lowest energy state Levinthals paradox 3 100 = 5 " 10 47 10 # 13 s 5 " 10 47 ( ) " 10 # 13 s = 1.6 " 10 27 yr 100-residue protein 3 conformations /residue conformations time to inter-convert conformations 09/17/08 21 Potential Protein folding pathway time scale in seconds Folding is hierarchal stable local structures form first complexity (organization) increases with time Partly correct intermediates are retained 09/17/08 22 Protein folding pathway entropy energy 09/17/08 23...
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Lecture10 - of Proteins Determines Their Tertiary Structure...

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