10 February 2003

Biol 6312

a/b Structures

See Chime tutorial of examples here

These are protein folds in which there is a regular pattern of repeating a-helices and b-strands, which form a parallel sheet. There are 3 main classes:

1. a/b barrel

2. open twisted sheet

3. horseshoe fold

The first two can be distinguished by considering two different ways of linking 2 b-a-b units

(ba)₈ barrels

Core is a barrel of approx. 8 parallel b-strands

Outside are a-helices, making a second ring.

Evolution of (ba)₈ barrels:

Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways

Copley RR,Bork P.

J Mol Biol. 2000 Nov 3;303(4):627-41.

The Evolution of a/b barrel enzymes

G.K. Farber & G.A. Petsko

Trends in Biochemical Sciences 1990 15:228

The structure and evolution of alpha/beta barrel proteins.

Reardon D, Farber GK

FASEB J. 1995 9:497-503

Proteins 1991;9(4):280-95

Energetic approach to the folding of alpha/beta barrels.

Chou KC, Carlacci L

Mol Biol 1991 Sep 20;221(2):603-13

Beta-breakers: an aperiodic secondary structure

Colloc'h N, Cohen FE

Proceedings of the National Academy of Sciences, Vol 90, 1379-1383 (1993)

Three-Dimensional Profiles from Residue-Pair Preferences: Identification of Sequences with ß/a-Barrel Fold
M Wilmanns and D Eisenberg

Science 289: 1546-1550 (2000)

Structural Evidence for Evolution of the / Barrel Scaffold by Gene Duplication and Fusion

Dietmar Lang, Ralf Thoma, Martina Henn-Sax, Reinhard Sterner, Matthias Wilmanns

Science 2000 289: 1490 (2000)

PROTEIN EVOLUTION: On the Ancestry of Barrels

Edith Wilson Miles and David R. Davies

Nagano N, Orengo CA, Thornton JM.
One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
J Mol Biol. 2002 Aug 30;321(5):741-65.

Silverman JA, Balakrishnan R, Harbury PB.
Reverse engineering the (beta/alpha )8 barrel fold.
Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3092-7.

b-loop-a Horseshoe

Mechanism of Ribonuclease Inhibition by Ribonuclease Inhibitor Protein Based on the Crystal Structure of its Complex with Ribonuclease A

J. Mol. Biol.(1996) Vol. 264 pp. 1028-1043

Bostjan Kobe1, 2, Johann Deisenhofer

Kobe B, Deisenhofer J.
A structural basis of the interactions between leucine-rich repeats and protein ligands.
Nature. 1995 Mar 9;374(6518):183-6.

Kobe B, Deisenhofer J.
Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats.
Nature. 1993 Dec 23-30;366(6457):751-6.

Kobe B, Deisenhofer J.
The leucine-rich repeat: a versatile binding motif.
Trends Biochem Sci. 1994 Oct;19(10):415-21. Review.

Curr Opin Struct Biol 1995 Jun;5(3):409-16

Proteins with leucine-rich repeats.

Kobe B, Deisenhofer J

Kajava AV, Kobe B.
Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information.
Protein Sci. 2002 May;11(5):1082-90.

Open twisted sheet

Rossmann fold: See Chime link

Mol Biol 1973 May 15;76(2):241-56

Comparison of super-secondary structures in proteins

Rao ST, Rossmann MG

Mol Cell Biochem 1978 Nov 16;21(3):161-82

The taxonomy of binding sites in proteins

Rossmann MG, Argos P

Nature 1974 Jul 19;250(463):194-9

Chemical and biological evolution of nucleotide-binding protein

Rossmann MG, Moras D, Olsen KW

Kleiger G, Eisenberg D.
GXXXG and GXXXA motifs stabilize FAD and NAD(P)-binding Rossmann folds through C(alpha)-H... O hydrogen bonds and van der waals interactions.
J Mol Biol. 2002 Oct 11;323(1):69-76.

Bottoms CA, Smith PE, Tanner JJ.
A structurally conserved water molecule in Rossmann dinucleotide-binding domains.
Protein Sci. 2002 Sep;11(9):2125-37.