Table of Contents
Molecular Simulations of Proteins and Peptides
Types of simulations
Lattice model for folding Monte Carlo simulations
Hard sphere models
Hard sphere models
Atomistic models
Atomistic forcefields
Protein Folding
Overview of Folding Inside a Cell
Early work
The Anfinsen experiment: spontaneous folding
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Why study protein folding?
Protein misfolding
Aggregation
P22 tailspike protein
Protein folding diseases
Familial Amyloidic Polyneuropathy
Alzheimer’s disease
Aggregation and off-pathway events
Non-covalent forces in proteins What holds them together?
Protein stabilization energy is small
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Hydrophobic interactions
Contributions to DG
Zimm-Bragg Formalism
Models of protein folding
The Levinthal Paradox
Two-state folding mechanism
The Pathway Model
BPTI folding pathways
BPTI: evidence for folding pathways
BPTI folding pathways
The molten globule
a-lactalbumin
Is hydrophobic collapse the same as the molten globule state?
Formation of tertiary structure
The Folding Funnel
Barnase mechanism
Barnase substrate specificity
Barnase
Barnase
Barnase folding pathway
Barnase
Folding of a heptapeptide in methanol
Folding of a heptapeptide in methanol
Time course of the simulation
Betanova
Complete unfolding pathways for b-sheet forming peptides
Clusters of unfolded DPG b-sheet forming peptides
Comparison of energy and free energy surfaces for b-sheet folding
Differences between b-sheet and a-helix folding
a-helix folding
Barriers and misfolding
Lattice model
Lattice model for folding Monte Carlo dynamics
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Lattice model for complex folding
The folding of apomyoglobin
The energy landscape
Diffusion on the energy landscape
The energy/entropy tradeoff
Bryngelson/Wolynes Theory
The folding time
The free energy barrier
The temperature dependent diffusion coefficient
The temperature dependence of the folding time
Aggregation Studies
Hard sphere model test: Polyalanine helices
Amphipathic helices with heptad repeats
Assembly of a four-helix bundle
Assembly of a four-helix bundle
Studies of peptides
EPO
EPO complexed with the erythropoietin receptor
Anti-microbial peptides
Folding and membrane insertion
Mean-field and all-atom simulations
Mean-field simulations
Protease inhibitors
HIV protease inhibitors
HIV protease inhibitor saquinavir
Zimm-Bragg Formalism
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Secondary Structure Prediction
Protein Sequence Analysis
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Chou-Fasman (a-helix assignment)
Chou-Fasman (b-sheet assignment)
Chou-Fasman (bend assignment)
CASP
HDEA
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