Protein Structure and Dynamics

Proteins are the building blocks of biology. They are nanometer-scale tangles of atoms that can perform a bewildering range of molecular feats. Just to name a few:

• Ion channels allow charged ions to pass through greasy membranes, and can selectively prefer one ionic species and over another.
• Antibodies can evolve to bind the molecular surface of pretty much any pathogen that invades our bodies.
• The water-splitting complex harnesses the energy of light to yank electrons off water molecules. Oxidizing water is not easy!
• Actin and myosin can exert pushing and pulling forces; they convert the chemical potential of ATP into mechanical work.
• Antifreeze proteins can lower the freezing point of water to allow organisms to survive in cold temperatures.
• Luciferase catalyzes the chemical reaction that emits light and makes fireflies glow.

Of course, proteins are also central to life: they replicate genetic material, catalyze chemical transformations, serve as scaffolding for cellular structures, transduce signals, and more.

In this section, we'll study how proteins work -- what they're made out of, how they're structured, and how they wiggle and jiggle around. Along the way, we'll run into some fun philosophical questions about thermodynamics. Finally, we'll dabble in the dark art of X-ray crystallography -- our greatest friend, but also our greatest enemy. Beware!

Outline of Protein Structure and Dynamics

• Amino acid chemistry
• 1,2,3,4 structure and “the folding question”
• Lengthscales and timescales. Dynamics, energetics, etc.
• Experimental techniques. X-ray crystallography