Prediction of protein secondary structure and active sites using the alignment of homologous sequences

Markéta J. Zvelebil, Geoffrey J. Barton, William R. Taylor, Michael J. E. Sternberg

Research output: Contribution to journalLetter

360 Citations (Scopus)

Abstract

The prediction of protein secondary structure (alpha-helices, beta-sheets and coil) is improved by 9% to 66% using the information available from a family of homologous sequences. The approach is based both on averaging the Garnier et al. (1978) secondary structure propensities for aligned residues and on the observation that insertions and high sequence variability tend to occur in loop regions between secondary structures. Accordingly, an algorithm first aligns a family of sequences and a value for the extent of sequence conservation at each position is obtained. This value modifies a Garnier et al. prediction on the averaged sequence to yield the improved prediction. In addition, from the sequence conservation and the predicted secondary structure, many active site regions of enzymes can be located (26 out of 43) with limited over-prediction (8 extra). The entire algorithm is fully automatic and is applicable to all structural classes of globular proteins.

Original languageEnglish
Pages (from-to)957-961
Number of pages5
JournalJournal of Molecular Biology
Volume195
Issue number4
DOIs
Publication statusPublished - 20 Jun 1987

Fingerprint

Secondary Protein Structure
Sequence Homology
Catalytic Domain
Insertional Mutagenesis
Enzymes
Proteins
beta-Strand Protein Conformation
alpha-Helical Protein Conformation

Keywords

  • Algorithms
  • Amino acid sequence
  • Binding sites
  • Protein conformation

Cite this

Zvelebil, Markéta J. ; Barton, Geoffrey J. ; Taylor, William R. ; Sternberg, Michael J. E. / Prediction of protein secondary structure and active sites using the alignment of homologous sequences. In: Journal of Molecular Biology. 1987 ; Vol. 195, No. 4. pp. 957-961.
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Prediction of protein secondary structure and active sites using the alignment of homologous sequences. / Zvelebil, Markéta J.; Barton, Geoffrey J.; Taylor, William R.; Sternberg, Michael J. E.

In: Journal of Molecular Biology, Vol. 195, No. 4, 20.06.1987, p. 957-961.

Research output: Contribution to journalLetter

TY - JOUR

T1 - Prediction of protein secondary structure and active sites using the alignment of homologous sequences

AU - Zvelebil, Markéta J.

AU - Barton, Geoffrey J.

AU - Taylor, William R.

AU - Sternberg, Michael J. E.

PY - 1987/6/20

Y1 - 1987/6/20

N2 - The prediction of protein secondary structure (alpha-helices, beta-sheets and coil) is improved by 9% to 66% using the information available from a family of homologous sequences. The approach is based both on averaging the Garnier et al. (1978) secondary structure propensities for aligned residues and on the observation that insertions and high sequence variability tend to occur in loop regions between secondary structures. Accordingly, an algorithm first aligns a family of sequences and a value for the extent of sequence conservation at each position is obtained. This value modifies a Garnier et al. prediction on the averaged sequence to yield the improved prediction. In addition, from the sequence conservation and the predicted secondary structure, many active site regions of enzymes can be located (26 out of 43) with limited over-prediction (8 extra). The entire algorithm is fully automatic and is applicable to all structural classes of globular proteins.

AB - The prediction of protein secondary structure (alpha-helices, beta-sheets and coil) is improved by 9% to 66% using the information available from a family of homologous sequences. The approach is based both on averaging the Garnier et al. (1978) secondary structure propensities for aligned residues and on the observation that insertions and high sequence variability tend to occur in loop regions between secondary structures. Accordingly, an algorithm first aligns a family of sequences and a value for the extent of sequence conservation at each position is obtained. This value modifies a Garnier et al. prediction on the averaged sequence to yield the improved prediction. In addition, from the sequence conservation and the predicted secondary structure, many active site regions of enzymes can be located (26 out of 43) with limited over-prediction (8 extra). The entire algorithm is fully automatic and is applicable to all structural classes of globular proteins.

KW - Algorithms

KW - Amino acid sequence

KW - Binding sites

KW - Protein conformation

U2 - 10.1016/0022-2836(87)90501-8

DO - 10.1016/0022-2836(87)90501-8

M3 - Letter

C2 - 3656439

VL - 195

SP - 957

EP - 961

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 4

ER -