Table of Contents

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)