5 February 2001

Biol 6312

Homework exercise due on Feb 21 (Link)

Motifs in Protein Structure

See the link for Chime Structures.

Motifs include:

1. helix-loop-helix

2. helix bundle

3. beta hairpin

4. beta-alpha-beta

5. Greek key beta

Motif Analysis by A.V. Efimov

FEBS Lett 463: 3-6 (1999) [20069434]

Complementary packing of alpha-helices in proteins.

Proteins 28: 241-260 (1997) [97332507]

Structural trees for protein superfamilies.

Protein Fold Databases:

See Cath and Scop

Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM:
CATH — a hierarchic classification of protein domain structures.
Structure 1997, 5: 1093–1108. MEDLINE

The CATH Database provides insights into protein structure/function relationships.
Orengo CA, Pearl FM, Bray JE, Todd AE, Martin AC, Lo Conte L, Thornton JM.
Nucleic Acids Res 1999 Jan 1;27(1):275-9 MEDLINE  Full text

Thornton JM, Orengo CA, Todd AE, Pearl FMG:
Proteins folds, functions and evolution.
J Mol Biol 1999, 293: 333–342. Full text MEDLINE

Examples of folds:

All Alpha-Helix Proteins

Primary examples:

1. 4-helix bundle

2. globin fold

Rop is a dimer that forms a 4-helix bundle. See link

Other examples:

myohemerythrin

leptin

Globin fold:

a) oxygen carriers: myoglobin See link

b) phycocyanins: light gathering proteins see link

New finding is a myoglobin in the brain, called neuroglobin

Evolutionary relationship between the 2 types of globins:

Proteins 1990;8(2):133-55

Comparison of the structures of globins and phycocyanins: evidence for evolutionary relationship.

Pastore A, Lesk AM

Coiled-Coils

See Chime link

Reviews:

Trends Biochem Sci 1996 Oct;21(10):375-82

Coiled coils: new structures and new functions.

Lupas A

Curr Opin Struct Biol 1997 Jun;7(3):388-93

Predicting coiled-coil regions in proteins.

Lupas A

Websites for prediction of coiled coils:

"Coils" Try this sequence(AMEAKRKAEEHISSSHGDVDYAQASAELAKAIAQLRVIELTKKAM) get this result

by Lupas "Coiled Coil"

"Paircoil"

Prediction of Coiled-Coil Partners

Journal of Molecular Biology, Vol. 307, No. 5, April 2001 Medline Full text
SOCKET: A Program for Identifying and Analysing Coiled-coil Motifs Within Protein Structures
pp. 1427-1450 (doi:10.1006/jmbi.2001.4545)
John Walshaw, Derek N. Woolfson

Website for Sockets

Crystal structure of a trimeric coiled-coil:

Protein Sci 1999 Jan;8(1):84-90

Crystal structure of a designed, thermostable, heterotrimeric coiled coil.

Nautiyal S, Alber T