Structure and Function of Proteins 2009: Syllabus
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I. Introduction
The chemical nature of polypeptides
The polypeptide chain
Amino acids and their side chains (see
figure of the side chain structure
,
table of the genetic code
, and
list of three letter and single letter abbreviations
).
Covalent modifications of the polypeptide chain
Forces that determine protein structure
Tools
Databank of protein sequences (
SWISS-PROT
)
Basics of protein sequence alignment
Databank of protein structures (
PDB
)
Protein structure visualization and analysis of 3D structures (Deep-View tutorial:
Exercise 1
)
II. Sequence - Structure
Structural properties of proteins
Regular conformations of polypeptides: α-helices and β-sheets (
Exercise 2
).
Secondary, tertiary and quaternary structure
Protein families
Definition of protein families
Motifs that characterize protein families
Data bases of protein families (
Exercise 12
)
Homology between molecules: Evolutionary relationship (
Exercise 3
,
Exercise 8
).
Example: the globin family
Alignment based on sequence information
Alignment based on structural information
Conservation of protein core and active site
Effect of mutations on structure and function of molecules (
Exercise 4
)
Examples: lac repressor of
E.Coli
, T4 lysozyme and lambda repressor
Characterization of the conserved residues
Sequence similarity versus structure similarity
What determines secondary structure: propensity or context?
Examples of identical sequences which adopt different structure
Structure similarity without sequence similarity
Structure prediction based on sequence information
Principles of protein folding
Protein Structure Prediction
Comparative modeling (
Exercise 5
).
Secondary structure prediction (
Exercise 6
).
Fold recognition (
Exercise 7
).
Ab initio modeling
CASP, the Structural Genomics Initiative
III. Sequence - structure - Function
Protein engineering and designs
Design of new proteins
Design of new enzymes
Structure - function relationship in proteins (
Exercise 9
).
Evolution of function; Moonlighting
Function prediction based on structural information
Structural motifs in regulatory proteins: DNA-binding proteins
DNA structure (
Exercise 10a
).
Principles of protein - DNA recognition (Hydrogen bonding potential:
Figure of DNA base pair
,
Figure of protein side chains
)
Structural motifs of specific binding: Zinc finger motif (
Exercise 10b
)
Helix Turn Helix motif (
Exercise 11a
)
Basic Leucine Zipper motif (
Exercise 11b
)
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