PPS '96 Syllabus

Course Index Syllabus Index Term 1

Term 2

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Section 7

• Overview of Molecular Forces
  • Preliminary considerations -
    • Interactions, forces and energies
    • Electromagnetic interactions dominate on the molecular scale
    • The Born-Oppenheimer approximation
    • Quantum chemistry can (theoretically) deal with all molecular interactions
    • Advanced topic: A brief introduction to quantum chemistry.
    • Advanced topic: The application of quantum chemistry to protein simulation.
  • Covalent Interactions
    • Simplified models of interaction
    • Covalent Bonds
    • Bond Angles
    • Dihedral Angles
  • Non-bonded Interactions
    • Electrostatic interactions
    • Induction and Dispersion
    • Repulsion terms
    • Hydrogen bonding
  • The effect of solvent and hydrophobic interactions
    • Dielectric effects
    • The hydrophobic effect
    • Advanced topic: The hydrophobic effect and protein unfolding
  • Potential energy functions and simulation methods
    • Potential energy functions
    • Energy minimization
    • Molecular Dynamics
    • Other simulation methods

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  Section 8

• Secondary Structure In Detail
  • Background and History
  • Introduction to Terminology
  • Types of Secondary Structure
    • Helices
      • alpha
      • 3.10
      • pi
    • Sheets
      • Antiparallel
      • Parallel
      • Twists
      • Bulges
      • Strand connections
    • Turns
      • gamma
      • I, I'
      • II, II'
      • III, III'
    • Other
      • Loops
      • Paperclips
  • Identification of Secondary Structure
    • Identification in 3D Structures
    • Identification without 3D Structure
      • CD
      • NMR
      • FT-infrared
    • Prediction of Secondary Structure
      • homology
      • statistical
      • stereochemical

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  Section 9

• Tertiary Structure, Part I
  • Overview of Terminology

  • Prinicples of Packing of Secondary Structures
    • Helix-helix
    • Sheet-sheet - sandwiches and barrels
    • Helix-sheet

  • Supersecondary Structure
    • Beta hairpins
      • 2-residue
      • 3-residue
      • 4-residue
      • longer loops
    • Beta corners
    • Helix hairpins
    • Alpha corners
    • Helix-turn-Helix motifs; EF-Hand
    • Beta-Alpha-Beta motifs
    • Coiled coils

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  Section 10

• Tertiary Structure, Part II
  • Domains

  • Domain Folds
    • All-Alpha
      • The Lone Helix
      • Helix-turn-helix
      • The Four-helix Bundle
      • DNA-binding domains
      • Globins
    • All-Beta
      • Up-and-down Antiparallel Beta Sheets
      • Greek Key
      • Jellyroll
      • Beta Propellors
      • Beta Trefoils
      • Beta Helix
    • Alpha/Beta
      • Rossman Fold
      • alpha/beta horseshoe
      • alpha/beta barrels
        • singly wound
        • doubly wound; variations
    • Alpha+Beta
    • Small disulphide rich proteins

  • Types of proteins
    • Introduction
    • Globular (Water-Soluble) Proteins
    • Membrane Proteins
    • Fibrous and Structural Proteins
    • Mosaic Proteins

  • Protein Structure Databases
    • PDB
    • SCOP
    • CATH

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  Section 11

• Quaternary Structure
  • Introduction
  • Symmetry
  • Enzyme & Other Multimers
  • Multi-Enzyme Complexes
  • Larger Assemblies and Aggregations

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  Section 12

• Protein Interactions overview
  • Binding
    • inhibitor proteins
    • messaging; Signal Transduction Pathways
    • adhesion
  • Enzymes
    • Enzyme nomenclature databases
      • ENZYME
      • UCL Enzyme Structures Database
  • Lysis
    • proteolysis: the 4 families of proteases
    • of polysaccharides
    • of Lipids
  • Conformational changes
    • allostery: haemoglobin
    • larger scale movements: muscle fibres
    • Protein Motions database

Course Index

Syllabus Index

Term 1

Last updated 15th Aug '96