Biochem I MastheadBA

Protein Structures List

The following links are to Chime displays of the structures shown in Chapter 4 of Campbell. The corresponding figure (or page) numbers are shown at left [in brackets].
Each page illustrates an important structural feature or general principle found in other proteins. The emphasis here is on the overall architecture of proteins rather than specific functions of individual amino acid residues (more on this topic later!). Mastery of the key principles is required for the course. These are covered in the Protein Architecture Tutorial using Chime-generated images of Protein G.

Suggested plan of study:

  1. Read Chapter 4 of Campbell.
  2. See how the general principles apply to the specific example of Protein G (as shown in the tutorial).
  3. Examine the structures linked here to appreciate the many similarities and the key differences found in these representative protein structures.
  4. Test your general understanding of protein architecture with the Protein Structure Quiz. It uses GIF images that are taken from the Protein Architecture Tutorial.

Structures shown in Campbell, Chapter 4, unless noted (coordinate file size):
[9a.]   Rubredoxin: a small protein consisting mostly of b-meanders. (12K)
[9b.]   Prealbumin: (a.k.a. transerythrin), an antiparallel b-barrel. (24K)
[9c & d.]   Triose Phosphate Isomerase: a parallel b-barrel with alternating bab motifs. (84K)
[10.]   Collagen: a theoretical model of the triple helix. (20K)
[13.]   a-lactalbumin: a human plasma transport protein. (32K)
[14.]   Myoglobin (oxy): a monomeric O2 carrier. (40K)
[20 & 22.]   Hemoglobin (oxy): the red blood cell O2 carrier. (96K)
[26.]   Hemoglobin (deoxy): with bound 2,3-bisphosphoglycerate (BPG). (104K)

[Fig. 6.3]   Aspartate Transcarbamoylase: T & R-State Architecture. (392K)
[Ch. 6, p. 181]   Serine Protease Structures: Trypsin, Chymotrypsin, & Elastase Superimposed. (84K)
[Fig. 8.16]   Nucleosome: Repeating unit of eukaryotic chromatin. (308K)
[Fig. 10.1(?)]   RNA Polymerase-Promoter Complex: Bacterial Enzyme Architecture. (188K)
[Fig. 10.16]   RNA Polymerase Elongation Complex: Yeast Enzyme Architecture. (80K)
[Fig. 10.29]   CREB-DNA Complex: Human bZIP Activator Protein. (44K)
[Fig. 10.29]   Fos-Jun & NFAT-DNA Complex: Another human bZIP Activator Protein. (88K)
[Fig. 10.11]   CAP-cAMP-DNA Complex: Helix-turn-Helix Activator. (120K)
[Fig. 10.26]   Zif268-DNA Complex: Human Zinc-Finger Protein. (32K)
[Fig. 14.4]   Hexokinase: Induced Fit by Glucose Binding. (112K)
[Fig. 17.11]   ATP Synthase: Structures of the F1Fo Complexes. (280K)
Structures not in Campbell:
Tropomyosin: a fibrous coiled-coil protein. (16K)
Rop Protein Dimer: a globular coiled-coil protein. (16K)
Immunoglobulin G: an all-b antibody protein. (248K)
Antibody-Lysozyme Complexes: Three different complexes between Fab's and the enzyme. (244K)
Concanavalin A: an antiparallel b-barrel. (44K)
Carbonic Anhydrase: Catalyzes the hydration of CO2. (56K)
Pyruvate Kinase: a multi-domain protein with three discrete b-structures. (92K)
Lactate Dehydrogenase: a two-domain protein with a nucleotide-binding motif. (52K)
Silk Protein: a theoretical model of the fibrous b-sheet protein. (24K)
Glycogen Phosphorylase: the allosteric enzyme from muscle. (72K)
Several b-Stranded, Super Secondary Structural Motifs:
     b-Helices: are formed from repeated layers of three b-strands.
     b-Propellers: differ in the number of "blades".
     b-Sandwiches: include several other "named motifs".
Membrane Protein Structures (not in Campbell):
Bacteriorhodopsin: a light-driven proton pump. (152K)
K+-Channel (KcsA): an ion-selective pore. (60K)
Maltoporin: a trimeric sugar transporter in bacteria. (228K)
Hemolysin: a heptameric channel-forming toxin. (292K)
Photosynthetic Reaction Center: the bacterial electron pumping complex. (160K)
Membrane Channel & Pump Structures: Index page with links to Chime pages showing several more specialized membrane proteins.

ropIcon Classes of Protein Structures organizes the above links by their protein structural class, shown as "rainbow diagrams".

Protein Structures Vital Statistics, tabulates the molecular weights and other information about the proteins in the above list.
Molecular Mass Scales, shows a selection of eight superimposed structures ranging in molecular weight from 18 Da (H2O) to 2.6*106 Da (70S Ribosome).

Chime Routines and Animations for a biochemistry course at the University of Arizona. About 60 structures that relate to topics in biochemistry are indexed.

The images displayed on the linked pages require the Chemscape Chime plug-in. For optimal interactive viewing, Chime v2.6 is recommended. The CMU Chime Tutorial provides an introduction and overview of how to manipulate the structural models. The Chime 2.6 Viewer's Guide is a PDF document that summarizes the Chime 2.6 menu choices in capsule form.

Additional information on these and related structures can be found at the RCSB Protein Data Bank of proteins and nucleic acids. This site also permits you to search the Protein Data Bank using ID codes, keywords, etc.
Molecule of the Month Also at the Protein Data Bank, David Goodsell has posted GIF images and a concise description of a macromolecule each month for the past three years. It is an excellent starting point for a more detailed study of any of the 60+ structures listed.

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