791_my_lecture6

791_my_lecture6 - 7.91 Lecture #6 Michael Yaffe Protein...

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7.9 1 – Lecture # 6 Protein Secondary Structure Prediction Michael Yaffe
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7.93 – Lecture #9 Protein Secondary Structure Prediciton -and- Motif Searching with Scansite
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Outline • Brief review of protein structure • Chou-Fasman predictions • Garnier, Osguthorpe and Robson • Helical wheels and hydrophobic moments • Neural networks • Nearest neighbor methods • Consensus prediction approaches
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Hierarchy of protein structure
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implies planarity Reasonance of peptide bond
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Dihedral angles define secondary structure Please refer to Branden, Carl, and John Tooze. Introduction to Protein Structure . 2nd ed. Garland Publishing, Inc. , 1999. ISBN: 0815323042.
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Structure of α -helices Please refer to Branden, Carl, and John Tooze. Introduction to Protein Structure . 2nd ed. Garland Publishing, Inc., 1999. ISBN: 0815323042.
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α -helix dipole moment Please refer to Branden, Carl, and John Tooze. Introduction to Protein Structure . 2nd ed. Garland Publishing, Inc., 1999. ISBN: 0815323042.
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Anti-parallel β -sheets Please refer to Branden, Carl, and John Tooze. Introduction to Protein Structure . 2nd ed. Garland Publishing, Inc., 1999. ISBN: 0815323042.
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The “pleat”- a function of the tetrahedral C α carbon Please refer to Branden, Carl, and John Tooze. Introduction to Protein Structure . 2nd ed. Garland Publishing, Inc., 1999. ISBN: 0815323042.
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The parallel β -sheet Please refer to Branden, Carl, and John Tooze. Introduction to Protein Structure . 2nd ed. Garland Publishing, Inc., 1999. ISBN: 0815323042.
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All α -helical All β -sheet Protein Classes – defined by secondary structural elements
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α/β -protein
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Chou-Fasman Biochemistry, 13 : 222-245, 1974 •Statistical Method Based on 15 proteins of known conformation, 2473 total amino acids Determined “protein conformational parameters” P α , P β , based on f i s /( Σ f j s /20) 0.5-1.5
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Helical residues P α Glu Ala Leu His Met Gln Val Phe Trp 1.53 Strong 1.45 Ηα 1.34 helix former 1.24 1.20 1.17 h α Helix former 1.14 1.14 1.12 Lys Ile Asp Thr Ser Arg Cys Asn Tyr Pro Gly 1.07 1.00 0.98 0.82 0.79 0.79 0.77 0.73 0.61 0.59 0.53 I α Weak helix former i α Helix indifferent b α Helix breaker Strong B α helix breaker
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β -Sheet residues Met Val Ile Cys Tyr Phe Gln Leu Thr Trp P β 1.67 1.65 1.60 Ala Arg 0.90 Gly 0.81 Asp 0.80 Lys 0.74 Ser 0.73 His 0.71 Asn 0.65 Pro 0.62 Glu 0.26 0.97 Strong Ηβ sheet former 1.30 1.29 1.28 Sheet former h β 1.23 1.22 1.20 1.19 Weak sheet former I β i α Sheet indifferent b β Sheet breaker Strong B β sheet breaker
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α -helical β -sheet Glu Met Ala Val Leu Ile His Cys Met Tyr Gln Phe Trp Gln Val Leu Phe Thr Lys Trp Ile Ala Asp Arg Thr Gly Ser Asp Arg Lys Cys Ser Asn His Tyr Asn Pro Pro Gly Glu
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Chou-Fasman Empirical rule set for secondary structure nucleation using <P α >, <P
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This note was uploaded on 11/11/2011 for the course BIO 20.410j taught by Professor Rogerd.kamm during the Spring '03 term at MIT.

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791_my_lecture6 - 7.91 Lecture #6 Michael Yaffe Protein...

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