Ben-Tal Lab

Chapter 1: introduction

• What is structural biology?

• The importance of macromolecules

• The biological roles of proteins (overview):

  • Enzymatic catalysis

  • Energy transfer

  • Solute transport

  • Cellular communication

  • Defense

  • Viral infection

  • Building cell & tissues

• Structure-function relationship in proteins

• Non-covalent interactions:

  • Electrostatic interactions (ionic, hydrogen bonds, π-π/cation, others)

  • Van der Waals interactions

  • Nonpolar interactions and the hydrophobic effect

 

Chapter 2: the structure of proteins

• Representing molecules graphically in the course

• Protein structure – and overview (hierarchy, hetero-groups)

• Primary structure:

  • Physicochemical properties of proteogenic amino acids (groups, chirality, polarity, side chains’ chemistry)

  • Non-canonical derivates of amino acids in proteins

  • The peptide bond

• Secondary structure:

  • Steric limitations on secondary structures (the Ramachandran plot).

  • The α-helix structure: geometry, stabilization, dipole and hydrogen bonds, amphipathic helices, amino acid propensities to appear in helices

  • Non-α helices (310, π, PPII)

  • The β structure: strands, sheets, and barrels

  • Why helices and sheets? – the price of desolvating the peptide bond

  • Turns and loops

• Tertiary structure:

  • General characteristics of globular proteins (hierarchy, geometry, stabilizing interactions)

  • Simple α and β motifs: EF hand, bHLH, HTH, β-hairpin, β-sandwich, β-α-β, others.

  • Complex folds and superfolds (Ig, Rossmann, P-loop, TIM barrel, globin, etc.)

  • Domains: definition, modularity, classification and databases

  • Evolutionary aspects

  • Water molecule inside protein structures

• Quaternary structure:

  • Types of quaternary structures and terminology

  • Stabilizing interactions

  • Evolutionary advantages

• Post-translational modifications:

  • Types and biological roles

  • Examples: phosphorylation, glycosylation, ADP-ribosylation

• Fibrous proteins:

  • General characteristics and biological roles

  • Structure-function relationships: α-keratin and collagen

 

 

Chapter 3: computational methods for studying protein structure

• Why predict protein structure?

• The physical approach:

  • The explicit (full-atom) approach: force field-based calculations of the potential energy, configurational sampling via molecular dynamics simulations

  • The mean-field approach

• The comparative approach:

  • Overview

  • Homology modeling

  • Fold recognition

• Integrative methods

• Experimentally guided computational prediction

• Evolutionary methods (correlated mutations)

 

Chapter 4: the energetics and stability of protein structure

• Overview:

  • The marginal stability of proteins

  • Thermodynamic components of the protein’s stabilization free energy

• Interactions and physical effects on protein’s stability:

  • Overview: promoting and opposing contributions to folding

  • Nonpolar and van der Waals interactions

  • Electrostatic interactions

  • Entropy changes

• Protein denaturation and adaptations to extreme environments

• Protein engineering for increased stability

 

 

Chapter 5: the structural dynamics of proteins

• Overview:

  • The importance of protein dynamics

  • Types of dynamic motions in proteins and their correspondence to biological processes

• Theories on protein dynamics:

  • Induced fit

  • Pre-existing equilibrium

  • Conformational selection

• Thermodynamic and kinetic effects on protein dynamics

• The biological significance of thermally induced motions

• External influence on protein dynamics:

  • Ligand binding and allostery

  • Post-translational modifications

  • Environmental changes

  • Mutations

• Protein folding:

  • Levinthal’s paradox and its solution (the energy-entropy folding funnel)

  • Folding kinetics models and the molten globule state

  • Misfolding, amyloids, and related pathologies

  • In vivo folding: interfering effects, molecular chaperones

 

Chapter 7: membrane-bound proteins

• Biological roles of membrane proteins

• Properties of the lipid bilayer: structure, lipid types, asymmetry, amphipathicity

• Integral membrane proteins:

  • Overall structure

  • Transmembrane segments: polarity, size, dynamics, lipid interactions

  • Membrane insertion and assembly

  • Architectural themes (example: transport proteins)

• Peripheral membrane proteins

• Effects of the membrane on proteins:

  • General  effects: hydrophobic mismatch

  • Effects of specific lipids: steroids, phosphoinositides

• Structure-function relationships: G protein-coupled receptors (GPCRs)

  • Background: biological roles, medical importance, signaling, ligands and effectors

  • Classification

  • General structure and structural motifs

  • Structure-function relationship of GPCR activation and allostery: rhodopsin, β2 adrenergic receptor, M2 (muscarinic receptor)

 

Chapter 8: protein-ligand interactions

• Biological importance

• Binding affinity:

• Binding affinity of different protein-ligand complex types

• Measuring and calculating the binding affinity

• Thermodynamics of binding and enthalpy-entropy compensation

• Binding specificity:

• Theoretical models

• Binding site-ligand matching through non-covalent interactions

• Binding promiscuity

• Protein-protein binding: domains

• Protein-ligand interactions in cholinesterase inhibition by toxins and drugs:

• The biological importance of acetylcholine signaling

• Cholinesterase as a target of natural toxins: fasciculin-2

• Cholinesterase inhibition by synthetic inhibitors: organophosphate and chemical warfare, carbamates, oximes.

• Protein-ligand interactions in drug design:

• Proteins involvement in disease

• How drugs work, proteins as drug targets

• Mechanisms of protein inhibition/activation by drugs: competitive binding and molecular mimicry, non-competitive (allosteric) drug action

Drug design: the ligand-based and receptor-based approaches, lab and virtual screening of drugs, case study (ACE inhibitors)