Chapter !10 - Proteomics Code : KSI0019

<Index of Chapter 10>

 

Introduction

- The proteome is the complete set of proteins associated with a sample of living matter. Proteomics deals with the proteins that form the structures of living things, are active in living things, or are produced by living things. or are produced by living things. This includeds their nature, distrivution , activities , interactions , and evloution. Many fields contribute to proteomics.

 

Protein nature and types

Proteins are where the action is

1.  Proteins have a great variety of functions .

2. The amino acid sequences of proteins dictate their 3D structures and their folding pathways. (Folding pathway) 

3. Advances in protein science have spawned the biotechnology industry. 

 

Protein structure

 Backbone or mainchain / sidechain /

> Hydrogen bonding  / Hydrophobic interactions/ Disulphide bridges  ~ 

 

Different types of residues make different types of interactions , including hydrogen bonds, hydrophobic interactions, and disulphide bridges. Formation of the native structure allows optimal formation of favorable inter-residue and residue- solvent interactions 

 

> A protein is a message writeen in a 20 letter alphabets. 

Helices and sheets

> Helices and sheets are recurrent structures, stablized by mainchain hydrogen bonding, that appear in many protein structures. 

-The chemical structure of proteins 

-Conformation of the polypeptide chain

>Diheadral angles. 

-Protein folding patterns

> Folding patterns. 

1. Primary structure 

2. Sencondary structure.

3. Tertiary struture

4. quanteanry structure .

We describe protein folding patterns according to a hierachy of primarym secondary, tertiary and quaternaty sturctures

 

Post-translational modifications

-Why is there a common genetic code with 20 canorical amino acids?

Seperation and anylsis of proteins 

-Polyacrylamide gel electrophoresis (PAGE)

-Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE)

-Mass spectrometry

Classification of protein structures

-SCOP

-Changes in folding patterns in protein evolution

Many proteins change conformation as part of the mechanism of their function

-Conformational change during enzymatic catalysis

-Motor proteins

-Allosteric regulation of protein function

-Conformational states of serine protease inhibitors (serpins)

Protein structure prediction and modelling

-Homology modelling

-Available protocols for protein structure prediction

-Structural genomics

Directed evolution and protein design

-Directed evolution of subtilisin E

-Enzyme design

Protein complexes and aggregates

-Protein aggregation diseases

-Properties of protein-protein complexes

-Multisubinit proteins