Starting with the second lecture, we will spend the first 10-15 min to discuss the study questions from last lecture. Unfortunately this part might not work very well to watch in the recording since you can only hear Erik's voice, but not the discussion of the students. Still, just in case you want to hear anything I said, I've left this part in the lecture recording.

For lecture 2, we start by repeating Anfinsens observation that proteins assume the global free energy minimum structure, and Levinthal's paradox that it seems impossible to find this structure by plain searching.

We will discuss the different approximations we use with quantum mechanics vs. classica models, and why the latter is frequently a better choice for proteins. We introduce partial charges, and dig deeper into the fundamental properties of proteins.

After this, we introduce the energy (or potential) of a complex molecule, and the concept of simplified (model) "energy landscapes". This turns out to be intimately related to another very important concept: The Boltzmann distribution that tells you what states of a molecule will be occupied depending on their energy and the current temperature.

Armed with this, we are able to introduce the concepts of free energy and entropy, which are important when there are many "microscopic" states sharing the same absolute value of energy - since on the macroscopic scale we think of all these collected state as a single state, but with more freedom - or entropy.

One of the key results here is that entropy is actually pretty simple: it's merely a way to count that some states have more internal states, and then we introduce a convenience notation for it.

Reading instructions

Chapters 3-4 in the Protein Physics book

Study questions

Why do chemical bonds form? Why are e.g. noble gases inert?
What are the interactions related to bonds between atoms in a protein?
What are the non-bonded interactions in a protein?
What interactions are strongest? Weakest?
What interactions do you have most of?
Compare electrostatics with dispersion. Strength? Sign?
What happens with hydrogen bonds when ice melts to water? Do some bonds
break completely while others are maintained, or is it something else?
What is the hydrophobic effect? What interactions cause the hydrophobic effect?
What is an energy landscape?
For what can you use the Boltzmann distribution? Give concrete examples!
How does volume, or microstates, complicate the Boltzmann distribution?
What is the difference between energy and free energy?
Can you give examples of systems with (a) low, and (b) high entropy?
Entropy is closely related to h-bonds and hydrophobic effect. How?

Other videos

Cyrus Levinthal's Myoglobin visualization movie

Cyrus Levinthal's Lysozyme visualization movie

Slides

Handout-format slides for lecture 2

Full-format slides for lecture 2

Scientific articles

Cyrus Levinthal's Scientific American article on the first visualizations of proteins