Chapter 7RNA and Protein Structure:

Structure Prediction

Figure 7.1: Pleconaril (atoms shown as spheres) binds in a cleft within the rhinovirus capsid protein (ribbons), the same cleft where natural protective

antibodies bind the virusSource: Protein Data Bank 1NCR. Zhang, Y. et al., J.Virol. 78 (2004):11061-11069

Figure 7.2: The large subunit of the eukaryotic ribosome is a complex structure combining precisely folded proteins (dark regions) and RNA

molecules (light regions)Protein Data Bank 1FFK. Ban, N. et al., Science 289 (2000):905-920

Figure 7.3: Secondary structure of the 16S ribosomal RNA from corn

Data from European Molecular Biology Laboratory

Figure 7.4: An alpha-helix as seen from the top

Protein Data Bank 2ZNA. Wang, A.H.-J., Science 211(1981):171-176

Figure 7.5: Two strands of a beta-sheet structure

Figure 7.6: Folding of a protein: primary (1º), secondary (2º), tertiary (3º) and quaternary (4º) structure

Figure 7.7a: Protein secondary structure: (A) alpha-helix

Modified from Horton, H. Robert; Moran, Laurence A.; Ochs, Raymond S; Rawn, David J.; Scrimegeour, K. Gray, Principles of Biochemistry, Third edition, © 2002, p. 90. Reprinted with permission of Pearson Education, Inc., Upper Saddle River, NJ.

Figure 7.7b: Protein secondary structure: (B) beta-pleated sheet

Adapted from Nelson, D.C., and Cox, M.M. Lehninger Principles of Biochemistry, Fourth edition. W.H. Freeman & Company, 2004.

Figure 7.8a: Examples of protein structure: (A) a DNA-binding protein

Protein Data Bank ID: 1R4R. Luisi, B.F., et al., Nature 352 (1991): 497-505.

Figure 7.8b: Examples of protein structure: (B) a channel protein in the membrane

Figure 7.8c: Examples of protein structure: (C) silk protein

Adapted from W.I. Weiss, K. Drickamer, and W.A. Hendrickson, Nature 360 (1992): 127-134

Figure 7.9a: Structure of transfer RNA: (A) base-pairing (secondary structure)

Figure 7.9b: Structure of transfer RNA: (B) three-dimensional structure

Adapted from Arnez, J.G., and Moras, D., Trends Biochem. Sci. 22 (1997): 211-216.

Figure 7.10a: Examples of RNA secondary structure: (A) a hairpin, or stem-and-loop structure

Figure 7.10b: Examples of RNA secondary structure: (B) an internal loop and a bulge within a stem

Figure 7.11: Sample output from the PSIPRED program

Figure 7.12: Viewing a protein structure and sequence with Cn3D

Courtesy of Cn3D/National Center for Biotechnology Information

Figure 7.13: Possible positions for hairpin loops between nucleotide i and nucleotide j in an RNA molecule

Figure 7.14: Screenshot from a computer participating in the Folding@home project

Courtesy of Vijay Pande, Stanford University and Folding@home

Figure 7.T1: The Chou-Fasman parameters