Geometry Selects Highly Designable Structures

By enumerating all sequences of length 20, we study the designability of structures in a two-dimensional hydrophobic-polar (HP) lattice model in a wide range of intermonomer interaction parameters. We find that although the histogram of designability depends on interaction parameters, the set of highly designable structures is invariant. So in the HP lattice model the high designability should be a purely geometrical feature. Our results suggest two geometrical properties for highly designable structures; they have the maximum number of contacts and a unique neighborhood vector representation. Also we show that the contribution of perfectly stable sequences in the designability of structures plays a major role in making them highly designable.

[1]  R A Goldstein,et al.  Why are some proteins structures so common? , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[2]  K. Dill,et al.  ‘‘Sequence space soup’’ of proteins and copolymers , 1991 .

[3]  K. Dill,et al.  Intrachain loops in polymers: Effects of excluded volume , 1989 .

[4]  C. Chothia.  One thousand families for the molecular biologist , 1992, Nature.

[5]  Richard A. Goldstein,et al.  Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus , 2000 .

[6]  William Bialek,et al.  Princeton Lectures on Biophysics , 1993 .

[7]  V. Shahrezaei,et al.  Geometrically Reduced Number of Protein Ground State Candidates , 1998, cond-mat/9811127.

[8]  E. Bornberg-Bauer,et al.  How are model protein structures distributed in sequence space? , 1997, Biophysical journal.

[9]  David T. Jones,et al.  Protein superfamilles and domain superfolds , 1994, Nature.

[10]  C T Shih,et al.  Mean-field HP model, designability and alpha-helices in protein structures. , 2000, Physical review letters.

[11]  N. Wingreen,et al.  NATURE OF DRIVING FORCE FOR PROTEIN FOLDING : A RESULT FROM ANALYZING THE STATISTICAL POTENTIAL , 1995, cond-mat/9512111.

[12]  Analytical approach to the protein design problem , 1999, cond-mat/9904377.

[13]  V. Shahrezaei,et al.  Highly designable protein structures and inter-monomer interactions , 1997, cond-mat/9710028.

[14]  Vijay S. Pande,et al.  How accurate must potentials be for successful modeling of protein folding , 1995, cond-mat/9510123.

[15]  N. Wingreen,et al.  Emergence of Preferred Structures in a Simple Model of Protein Folding , 1996, Science.

[16]  Ned S. Wingreen,et al.  Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study , 1998, cond-mat/9806197.

[17]  Ruben Recabarren,et al.  Estimating the total number of protein folds , 1999, Proteins.

[18]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[19]  H W Hellinga,et al.  Rational protein design: combining theory and experiment. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[20]  V. Shahrezaei,et al.  Protein ground state candidates in a simple model: an enumeration study. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[21]  N S Wingreen,et al.  Are protein folds atypical? , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Nicolas E. Buchler,et al.  Effect of alphabet size and foldability requirements on protein structure designability , 1999, Proteins.

[23]  Origin of the designability of protein structures. , 1998, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.