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 Online Course
Introduction to proteins: structure, function, and motion 

This webpage includes freely downloadable videos and presentations based on the book.  
Please acknowledge the book when using the materials .

Chapter 1

Introduction

  • What are macromolecules?

  • Proteins' biological roles

  • The structural base of protein function

  • Non-covalent interactions

Chapter 2

Protein structure

  • Amino acids properties

  • The peptide bond

  • Secondary structures

  • Tertiary structure of globular proteins

  • Structural evolution

  • Quaternary structure

  • Post-translational modifications

  • Fibrous proteins

Chapter 3

Structure Prediction

  • Why predict protein structure?

  • General apporaches for structure prediction

  • The physical approach: explicit and mean-field models

  • The comparative approach: homology modeling and fold recognition

  • Integrative methods

  • Experimentally guided prediction

  • Prediction based on co-evolution

Chapter 4

Energetics & Stability

  • Proteins are marginally stable

  • Thermodynamics of protein structure stability

  • Physical forces and effects that stabilize or destabilize the folded structure

  • Protein denaturation and adaptation to extreme environments

  • Protein engineering for increased stability

Chapter 5

Dynamics

  • The importance of protein dynamics

  • Types of motions in proteins and their biological roles

  • Theoretical models of protein dynamics

  • Thermodynamic and kinetic effects

  • External effects on protein dynamics (e.g. ligand binding)

  • Protein folding and misfolding

Chapter 6
Disordered Proteins

  • Prevalence & degrees of disorder

  • Biological roles

  • Methods for studying these proteins

  • Specific functions and mechanisms

  • Example: the nuclear pore complex

  • Structure-function relationships

Chapter 7
Membrane Proteins

  • Biological roles

  • The lipid bilayer environment

  • Integral membrane proteins: structure, composition & energetics

  • Peripheral membrane proteins

  • Effects of membrane properties and lipids on bound proteins

  • G protein-coupled receptors: structure-function relationships

Chapter 8
Protein-Ligand Interactions

  • Biological importance

  • Binding affinity: measurements, calculations, and thermodynamics

  • Binding specificity: models, interactions, binding promiscuity

  • Case study: cholinesterase inhibition by toxins and drugs

  • Protein-ligand interactions in drug design

Tel-Aviv University course version (videos by lesson)

Chapter 9
Enzyme Catalysis

  • Why do organisms require enzymes?

  • The principles of catalysis

  • The six classes of enzymes (detailed)

  • Enzyme kinetics

  • Catalytic site and mechanisms

  • Enzyme cofactors

  • Enzyme inhibition

  • Industrial uses

Last updated: July 22 2022

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