A method for the prediction of surface “U”‐turns and transglobular connections in small proteins

A simple method for predicting the location of surface loops/turns that change the overall direction of the chain that is, “U” turns, and assigning the dominant secondary structure of the intervening transglobular blocks in small, single‐domain globular proteins has been developed. Since the emphasis of the method is on the prediction of the major topological elements that comprise the global structure of the protein rather than on a detailed local secondary structure description, this approach is complementary to standard secondary structure prediction schemes. Consequently, it may be useful in the early stages of tertiary structure prediction when establishment of the structural class and possible folding topologies is of interest. Application to a set of small proteins of known structure indicates a high level of accuracy. The prediction of the approximate location of the surface turns/loops that are responsible for the change in overall chain direction is correct in more than 95% of the cases. The accuracy for the dominant secondary structure assignment for the linear blocks between such surface turns/loops is in the range of 82%. © 1997 Wiley‐Liss, Inc.

[1]  I. Shimada,et al.  Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures. , 1992, Biochemistry.

[2]  A V Finkelstein,et al.  The classification and origins of protein folding patterns. , 1990, Annual review of biochemistry.

[3]  J. Guss,et al.  Structure of oxidized poplar plastocyanin at 1.6 A resolution. , 1983, Journal of molecular biology.

[4]  Shoshana J. Wodak,et al.  Generating and testing protein folds , 1993 .

[5]  P. Privalov,et al.  Stability of protein structure and hydrophobic interaction. , 1988, Advances in protein chemistry.

[6]  Harold A. Scheraga,et al.  MONTE CARLO SIMULATION OF A FIRST-ORDER TRANSITION FOR PROTEIN FOLDING , 1994 .

[7]  R Langridge,et al.  Improvements in protein secondary structure prediction by an enhanced neural network. , 1990, Journal of molecular biology.

[8]  D. T. Jones,et al.  A new approach to protein fold recognition , 1992, Nature.

[9]  S. Bryant,et al.  Threading a database of protein cores , 1995, Proteins.

[10]  Andrzej Kolinski,et al.  Computer design of idealized β‐motifs , 1995 .

[11]  E. W. Morris.  No , 1923, The Hospital and health review.

[12]  M. Hao,et al.  STATISTICAL THERMODYNAMICS OF PROTEIN FOLDING : SEQUENCE DEPENDENCE , 1994 .

[13]  B Rost,et al.  Progress of 1D protein structure prediction at last , 1995, Proteins.

[14]  M. Karplus,et al.  Protein secondary structure prediction with a neural network. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[15]  P Argos,et al.  Analysis of sequence-similar pentapeptides in unrelated protein tertiary structures. Strategies for protein folding and a guide for site-directed mutagenesis. , 1987, Journal of molecular biology.

[16]  J. Thornton,et al.  Analysis and prediction of the different types of beta-turn in proteins. , 1988, Journal of molecular biology.

[17]  J. Thornton,et al.  Analysis and prediction of the different types of β-turn in proteins , 1988 .

[18]  Michael Levitt,et al.  Protein folding: Current Opinion in Structural Biology 1991, 1:224–229 , 1991 .

[19]  C. Sander,et al.  Correlated mutations and residue contacts in proteins , 1994, Proteins.

[20]  R. M. Abarbanel,et al.  Turn prediction in proteins using a pattern-matching approach. , 1986, Biochemistry.

[21]  B. Rost,et al.  Combining evolutionary information and neural networks to predict protein secondary structure , 1994, Proteins.

[22]  H. Scheraga,et al.  Chain reversals in proteins. , 1973, Biochimica et biophysica acta.

[23]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[24]  M J Sippl,et al.  Progress in fold recognition , 1995, Proteins.

[25]  J. Garnier,et al.  Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. , 1978, Journal of molecular biology.

[26]  A. Godzik,et al.  Topology fingerprint approach to the inverse protein folding problem. , 1992, Journal of molecular biology.

[27]  M Karplus,et al.  Theoretical studies of protein folding and unfolding. , 1995, Current opinion in structural biology.

[28]  P. Y. Chou,et al.  Prediction of the secondary structure of proteins from their amino acid sequence. , 2006 .

[29]  J. Skolnick,et al.  A reduced model of short range interactions in polypeptide chains , 1995 .

[30]  P. Gennes.  Scaling Concepts in Polymer Physics , 1979 .

[31]  M. Karplus,et al.  How does a protein fold? , 1994, Nature.

[32]  A. Godzik,et al.  A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins , 1993 .

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

[34]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[35]  George D. Rose,et al.  Prediction of chain turns in globular proteins on a hydrophobic basis , 1978, Nature.

[36]  Andrzej Kolinski,et al.  Dynamic Monte Carlo Study of the Conformational Properties of Long Flexible Polymers . , 1987 .

[37]  J. Szulmajster.  Protein folding , 1988, Bioscience reports.

[38]  M J Rooman,et al.  Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power. , 1989, Protein engineering.

[39]  Adam Godzik,et al.  Lattice representations of globular proteins: How good are they? , 1993, J. Comput. Chem..

[40]  J. Mesirov,et al.  Hybrid system for protein secondary structure prediction. , 1992, Journal of molecular biology.

[41]  J. Skolnick,et al.  Monte carlo simulations of protein folding. I. Lattice model and interaction scheme , 1994, Proteins.

[42]  T. Creighton,et al.  Protein Folding , 1992 .

[43]  J. Skolnick,et al.  Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin , 1994, Proteins.

[44]  P. Y. Chou,et al.  Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. , 1974, Biochemistry.

[45]  A. Gronenborn,et al.  A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. , 1993, Science.

[46]  N. Go.  The consistency principle in protein structure and pathways of folding. , 1984, Advances in biophysics.

[47]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

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

[49]  C Sander,et al.  On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[50]  D. Eisenberg,et al.  A method to identify protein sequences that fold into a known three-dimensional structure. , 1991, Science.