2009—2010
81817 Introduction to Protein
Structure and Function
Lecturer: Ora Schueler-Furman
oraf@ekmd.huji.ac.il 87094
Teaching assistants: Sivan
sivan.pearl@mail.huji.ac.il 85471 ; miriam.oxsman@mail.huji.ac.il 88337
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Date |
Lecture |
Exercise |
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Introduction to protein structure |
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1 |
19.10 |
·
The chemical nature of
polypeptides ·
Forces that determine protein
structure |
Ex1a: ·
databases (sw;
pdb) ·
DEEPVIEW1 |
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2 |
26.10 |
Structural properties of proteins ·
Secondary structure elements ·
Classification of tertiary structure; Protein families ·
Databases of protein families
(continued in last exercise of course) |
Ex1b: DEEPVIEW2 – HLA example |
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Sequence → structure |
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3 |
2.11 |
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Determinants of secondary
structure: context or propensity? Analysis of structural determinants: ·
Anfinsen’s principle |
Ex2: helices & sheets |
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4 |
9.11 |
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Conservation of structure during
evolution (globins) ·
Experimental evaluation of
structural stability (T4 lysozyme and others) |
Ex3: Evolutionary conservation of protein structure: the
hemoglobin family |
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5 |
16.11 |
Protein Folding ·
Theory and experimental analysis
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Ex4: Sensitivity to mutations: T4 lysozyme |
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Protein structure prediction |
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6 |
23.11 |
Protein structure prediction ·
Introduction ·
Comparative modeling |
Ex5: Comparative modeling (swissmodel) |
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7 |
30.11 |
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Secondary structure prediction ·
Fold recognition (threading) |
Ex6: Secondary structure prediction |
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8 |
7.12 |
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Ab initio modeling ·
Casp ·
Structural Genomics |
Ex7: Fold recognition |
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Structure →
function |
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9 |
14.12 |
Protein design ·
Paracelsus challenge ·
Switches (calmodulin) ·
New proteins: top7 ·
New enzymes: enzyme design |
Ex8: Adaptation to extremes |
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10 |
21.12 |
The structural basis of protein function ·
Evolution of new functions;
Moonlighting ·
Prediction of function |
Ex9: The structural basis of function ** Databases: EC numbers |
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Protein-DNA interactions |
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11 |
28.12 |
Structural motifs in regulatory proteins: DNA-protein
interactions (1) ·
DNA structure ·
Principles of protein - DNA
recognition |
Ex10: DNA; Zn
Finger |
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12 |
4.1 |
Structural motifs in regulatory proteins: DNA-protein
interactions cont.(2) ·
Zinc finger motif ·
Helix Turn Helix motif ·
Basic Leucine Zipper motif |
Ex11: HTH; Bzip |
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13 |
11.1 |
Structural motifs in regulatory proteins: DNA-protein
interactions cont. (3) |
Ex12: Protein Families Databases of protein families (scop
cath) (additions to lecture 2 – rounding up of
course) |
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14 |
18.1 |
Summary Lecture |
Summary
exercise |
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