help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS

Biophysical Journal 26: 367-373 (1979)
© 1979 the Biophysical Society

This Article
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Chou, P Y
Right arrow Articles by Fasman, G D
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chou, P Y
Right arrow Articles by Fasman, G D

Prediction of beta-turns.

P Y Chou and G D Fasman

ABSTRACT

An automated computer prediction of the chain reversal regions of globular proteins is described herein using bend frequencies and beta-turn conformational parameters (Pt) determined from 408 beta-turns in 29 proteins calculated from x-ray atomic coordinates. The probability of bend occurrence at residue i is pt = fi X fi+1 X fi+2 X fi+3 with the average bend probability less than Pt greater than = 0.55 X 10(-4). Tetrapeptides with pt greater than 0.75 X 10(-4) ( approximately to 1.5 X less than pt greater than) as well as less than Pt greater than 1.00 and less than Pa greater than less than less than Pt greater than greater than less than P beta greater than are selected by the computer as probable bends. Adjacent probable bends (i.e., 11-14, 12-15, 13-16) are compared pairwise by the computer, and the tetrapeptide with the higher pt value is predicted as a beta-turn. The percentage of bend and nonbend residues predicted correctly for 29 proteins by this computer algorithm is %t+nt = 70%, whereas 78% of the beta-turns were localized correctly within +/- 2 residues. The average beta-turn content in the 29 proteins is 32%, with helical proteins having fewer bends (17%) than beta-sheet proteins (41%). Three proteins having iron-sulfur clusters were found with the highest percentages of beta-turns: Chromatium high potential iron protein (65%), ferredoxin (57%), and rubredoxin (65%). Finally, the bend frequencies at all 12 positions from 457 beta-turns in 29 proteins (Chou and Fasman, 1977) were used to test the effectiveness of predicting bends using 2, 4, 8, and 12 residues as well as different cut-off pt values. The computer analysis showed that 1.25 less than pt greater than to be the best cut-off yielding 70% accuracy in %t+nt for 4 residues and %t+nt = 73% for 12 residues in predicting the bend and nonbend regions of proteins.




This article has been cited by other articles:


Home page
 J. Biol. Chem.Home page
Q. Chen, Y. Yang, L. Li, and J.-T. Zhang
The Amino Terminus of the Human Multidrug Resistance Transporter ABCC1 Has a U-shaped Folding with a Gating Function
J. Biol. Chem., October 13, 2006; 281(41): 31152 - 31163.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
W. Maccheroni, M. C. Alegria, C. C. Greggio, J. P. Piazza, R. F. Kamla, P. R. A. Zacharias, M. Bar-Joseph, E. W. Kitajima, L. C. Assumpcao, G. Camarotte, et al.
Identification and Genomic Characterization of a New Virus (Tymoviridae Family) Associated with Citrus Sudden Death Disease
J. Virol., March 1, 2005; 79(5): 3028 - 3037.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
S. M. Mitchell, E. Lee, M. L. Garcia, and M. M. Stephan
Structure and Function of Extracellular Loop 4 of the Serotonin Transporter as Revealed by Cysteine-scanning Mutagenesis
J. Biol. Chem., June 4, 2004; 279(23): 24089 - 24099.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
N. K. Surana, D. Cutter, S. J. Barenkamp, and J. W. St. Geme III
The Haemophilus influenzae Hia Autotransporter Contains an Unusually Short Trimeric Translocator Domain
J. Biol. Chem., April 9, 2004; 279(15): 14679 - 14685.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. W. Murcha, R. Lister, A. Y. Y. Ho, and J. Whelan
Identification, Expression, and Import of Components 17 and 23 of the Inner Mitochondrial Membrane Translocase from Arabidopsis
Plant Physiology, April 1, 2003; 131(4): 1737 - 1747.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
H. Kaur and G. P. S. Raghava
Prediction of {beta}-turns in proteins from multiple alignment using neural network
Protein Sci., March 1, 2003; 12(3): 627 - 634.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. V. Kajava, S. N. Zolov, K. I. Pyatkov, A. E. Kalinin, and M. A. Nesmeyanova
Processing of Escherichia coli Alkaline Phosphatase. SEQUENCE REQUIREMENTS AND POSSIBLE CONFORMATIONS OF THE -6 TO -4 REGION OF THE SIGNAL PEPTIDE
J. Biol. Chem., December 20, 2002; 277(52): 50396 - 50402.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
J. W. St. Geme III and D. Cutter
The Haemophilus influenzae Hia Adhesin Is an Autotransporter Protein That Remains Uncleaved at the C Terminus and Fully Cell Associated
J. Bacteriol., November 1, 2000; 182(21): 6005 - 6013.
[Abstract] [Full Text]

Home page
 J. Virol.Home page
H. Sato, Y. Tomita, K. Shibamura, T. Shiino, T. Miyakuni, and Y. Takebe
Convergent Evolution of Reverse Transcriptase (RT) Genes of Human Immunodeficiency Virus Type 1 Subtypes E and B following Nucleoside Analogue RT Inhibitor Therapies
J. Virol., June 1, 2000; 74(11): 5357 - 5362.
[Abstract] [Full Text]

Home page
 Proc. Natl. Acad. Sci. USAHome page
R. Srinivasan and G. D. Rose
A physical basis for protein secondary structure
PNAS, December 7, 1999; 96(25): 14258 - 14263.
[Abstract] [Full Text] [PDF]

Home page
 Mol Hum ReprodHome page
L. O. Goodwin, N. B. Leeds, D. Guzowski, I. R. Hurley, R. G. Pergolizzi, and S. Benoff
Identification of structural elements of the testis-specific voltage dependent calcium channel that potentially regulate its biophysical properties
Mol. Hum. Reprod., April 1, 1999; 5(4): 311 - 322.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
A. Van Dommelen, V. Keijers, J. Vanderleyden, and M. de Zamaroczy
(Methyl)ammonium Transport in the Nitrogen-Fixing Bacterium Azospirillum brasilense
J. Bacteriol., May 15, 1998; 180(10): 2652 - 2659.
[Abstract] [Full Text]

Home page
 Proc. Natl. Acad. Sci. USAHome page
E. N. Bogacheva, V. I. Gol'danskii, A. V. Shishkov, A. V. Galkin, and L. A. Baratova
Tritium planigraphy: From the accessible surface to the spatial structure of a protein
PNAS, March 17, 1998; 95(6): 2790 - 2794.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
E. F.S. Wong, S. K. Brar, H. Sesaki, C. Yang, and C.-H. Siu
Molecular Cloning and Characterization of DdCAD-1, a Ca2+-dependent Cell-Cell Adhesion Molecule, in Dictyostelium discoideum
J. Biol. Chem., July 5, 1996; 271(27): 16399 - 16408.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
B. Pytowski, T. W. Judge, and T. E. McGraw
An Internalization Motif Is Created in the Cytoplasmic Domain of the Transferrin Receptor by Substitution of a Tyrosine at the First Position of a Predicted Tight Turn
J. Biol. Chem., April 21, 1995; 270(16): 9067 - 9073.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
E. Díaz and K. N. Timmis
Identification of Functional Residues in a 2-Hydroxymuconic Semialdehyde Hydrolase
J. Biol. Chem., March 17, 1995; 270(11): 6403 - 6411.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 1979 by the Biophysical Society.