Here is an image of a protein folding landscape. It’s a pretty complicated one to start with, but I found it looking through my archive and you have to start somewhere. The landscape itself is recognizable in the top middle of the diagram, with the topographic lines. The height of the landscape is colored from lowest — dark blue — to highest — bright red. The 3D landscape is projected onto the flat XY plane below. (Imagine taking a 3D topographic map of a mountain range and smushing it flat on a table.)
Arrayed alongside the energy landscape are pictures of what proteins at certain places in the landscape look like. These images are really composites. Imagine taking a long photographic exposure of someone dancing on a stage. You would see faint versions of their arms, legs, and body as they moved around all superimposed in the same image. In the places where they spent more time — either because they lingered there or came back multiple times — the image would be stronger and less transparent. In this case, we’re looking at the superposition of images of a single protein over time. The protein itself is just a thin cylinder colored red at one end and blue at the other, with white in the middle. But depending on how much the protein moves, we can either see one coherent pattern (Basin b3) or a big jumble (Basin b2, although notice the red part of the protein doesn’t move much). So the analogy with the photograph is close but not perfect, since every snapshot of the protein is drawn as opaque in the diagram in order to highlight the presence and absence of variation in its shape over time.
The energy landscape diagram therefore offers us a way of visualizing and imagining the relationship between a global property of the protein — its energy level — and what three dimensional structure it has. I’ll be surveying more images of protein landscapes to describe how the diagram functions as a way of imagining new hypotheses about how proteins fold as well as summarizing and testing these hypotheses.
From: Carlo Camilloni, Daniel Schaal, Kristian Schweimer, Stephan Schwarzinger, and Alfonso De Simone. “Energy Landscape of the Prion Protein Helix 1 Probed by Metadynamics and NMR.” Biophys J, 2012 vol. 102 (1) pp. 158-167.