Recursive domains in proteins

The domain is a fundamental unit of protein structure. Numerous studies have analyzed folding patterns in protein domains of known structure to gain insight into the underlying protein folding process. Are such patterns a haphazard assortment or are they similar to sentences in a language, which can be generated by an underlying grammar? Specifically, can a small number of intuitively sensible rules generate a large class of folds, including feasible new folds? In this paper, we explore the extent to which four simple rules can generate the known all‐β folds, using tools from graph theory. As a control, an exhaustive set of β‐sandwiches was tested and found to be largely incompatible with such a grammar. The existence of a protein grammar has potential implications for both the mechanism of folding and the evolution of domains.

[1]  G. Rose,et al.  A new algorithm for finding the peptide chain turns in a globular protein. , 1977, Journal of molecular biology.

[2]  A. Efimov.  Standard structures in proteins. , 1993, Progress in biophysics and molecular biology.

[3]  E G Hutchinson,et al.  The Greek key motif: extraction, classification and analysis. , 1993, Protein engineering.

[4]  R. Doolittle.  The multiplicity of domains in proteins. , 1995, Annual review of biochemistry.

[5]  A. Efimov.  A structural tree for proteins containing 3β‐corners , 1997 .

[6]  Patrice Koehl,et al.  The ASTRAL compendium for protein structure and sequence analysis , 2000, Nucleic Acids Res..

[7]  C. Chothia,et al.  Structural patterns in globular proteins , 1976, Nature.

[8]  G M Crippen,et al.  The tree structural organization of proteins. , 1978, Journal of molecular biology.

[9]  J. Hailman.  Wonderful Life: The Burgess Shale and the Nature of History, Stephen Jay Gould. W. W. Norton, New York (1989), 347, Price $19.95 (U.S.A.), $27.95 (Canada) , 1991 .

[10]  G. Rose,et al.  Hierarchic organization of domains in globular proteins. , 1979, Journal of molecular biology.

[11]  K. Dill,et al.  Hydrogen bonding in globular proteins. , 1992, Journal of molecular biology.

[12]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[13]  Antonio Trovato,et al.  Geometry and physics of proteins , 2002, Proteins.

[14]  A. Efimov,et al.  A structural tree for α‐helical proteins containing α‐α‐corners and its application to protein classification , 1996 .

[15]  Janet M. Thornton,et al.  Topological and stereochemical restrictions in β-sandwich protein structures , 1993 .

[16]  R. Srinivasan,et al.  The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[17]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[18]  Alexander V. Efimov,et al.  Super‐secondary structures involving triple‐strand β‐sheets , 1993 .

[19]  J. Richardson,et al.  β-Sheet topology and the relatedness of proteins , 1977, Nature.

[20]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[21]  P. Beachy,et al.  A potential catalytic site revealed by the 1.7-Å crystal structure of the amino-terminal signalling domain of Sonic hedgehog , 1995, Nature.

[22]  A M Lesk,et al.  Systematic representation of protein folding patterns. , 1995, Journal of molecular graphics.

[23]  R. Srinivasan,et al.  A physical basis for protein secondary structure. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[24]  E. Baker,et al.  Hydrogen bonding in globular proteins. , 1984, Progress in biophysics and molecular biology.

[25]  J. Thornton,et al.  Depicting topology and handedness in jellyroll structures , 1992, FEBS letters.

[26]  S H Kim,et al.  The anatomy of protein beta-sheet topology. , 2000, Journal of molecular biology.