In this lesson, KP takes you on a deeper analysis of secondary structure. Building on the measurement techniques from Lesson 6, we’ll model an alpha helix, an antiparallel beta sheet, and a parallel beta sheet. We’ll analyze all three secondary structures to find out about the hydrogen bonding patterns that characterize each.

00:00 Intro
00:24 Setting up your workspace
00:52 Alpha helix modeling
01:34 The i+4 rule for alpha helices
03:32 Alpha helix backbone interactions with the measurement wizard
04:00 Grouping measurements
04:39 Measurement wizard – merge measurements
05:36 Antiparallel vs. parallel beta sheets
06:24 Modeling the antiparallel beta sheet
07:24 Modeling the parallel beta sheet
08:15 Parallel and antiparallel beta sheet structure comparison

REFERENCES:
• PDB ID: 1a0o
• Welch, M., Chinardet, N., Mourey, L. et al. Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY. Nat Struct Mol Biol 5, 25–29 (1998). https://doi.org/10.1038/nsb0198-25