Home LiteratureArticle Details
PMID: 6546418 Published · ppublish English Journal Article

A program for prediction of protein secondary structure from nucleotide sequence data: application to histocompatibility antigens.

Nucleic acids research ·Vol. 12 ·No. 1 Pt 1 ·1984-01-11 ·Pages 243-55

Novotný J, Auffray C

Abstract

A computer program is described which, given a nucleotide or an amino acid sequence, outputs protein secondary structure prediction curves as well as hydrophobicity and charged-residue profiles. The program allows for cumulative averaging of properties (secondary structure propensities, hydrophobicity and charge profiles) from several homologous primary structures, a novel concept shown to improve the predictive accuracy. The use of the program is demonstrated on a set of nucleotide and amino acid sequences from human and murine histocompatibility antigens of class I and II. The last extracellular domains of both class I and II antigens (alpha 3 of class I, alpha 2 and beta 2 of class II) and the beta 2-microglobulin domain are predicted to consist of seven anti-parallel beta-strands, in accord with previous claims of homology between these domains and the constant domains of immunoglobulin chains. The remaining extracellular domains are all proposed to form an anti-parallel, four-stranded beta-sheet with one of its faces being covered by alpha-helices and/or structureless segments ("open face sandwiches").

MeSH Terms
Animals Base Sequence Genes Histocompatibility Antigens Humans Hydrogen Bonding Mice Protein Conformation Software Solubility
Chemicals
Histocompatibility Antigens
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Novotný J
Auffray C
References (59)
59 references, click to expand
  1. Sequence data handling by computer.
    Nucleic Acids Res. 1977 Nov;4(11):4037-51 PMID: 593900
  2. The covalent structure of beef heart myoglobin.
    Eur J Biochem. 1970 Nov;16(3):465-71 PMID: 5477290
  3. Conformational preferences of amino acids in globular proteins.
    Biochemistry. 1978 Oct 3;17(20):4277-85 PMID: 708713
  4. Prediction of the secondary structure of proteins from their amino acid sequence.
    Adv Enzymol Relat Areas Mol Biol. 1978;47:45-148 PMID: 364941
  5. The major histocompatibility complex of the mouse.
    Science. 1979 Feb 9;203(4380):516-21 PMID: 104386
  6. Chemical, physical-chemical, and immunological properties of papain-solubilized human transplatation antigens.
    Biochemistry. 1979 May 29;18(11):2218-26 PMID: 444449
  7. Complete amino acid sequence of rabbit beta 2-microglobulin.
    Biochemistry. 1979 May 29;18(11):2267-72 PMID: 87220
  8. Heavy chain of HLA-A and HLA-B antigens is conformationally labile: a possible role for beta 2-microglobulin.
    Proc Natl Acad Sci U S A. 1979 Aug;76(8):3844-8 PMID: 91170
  9. Immunoglobulins and histocompatibility antigens.
    Nature. 1979 Nov 15;282(5736):230 PMID: 503199
  10. The heavy chain of human histocompatibility antigen HLA-B7 contains an immunoglobulin-like region.
    Nature. 1979 Nov 15;282(5736):266-70 PMID: 388231
  11. Complete amino acid sequence of a papain-solubilized human histocompatibility antigen, HLA-B7. 2. Sequence determination and search for homologies.
    Biochemistry. 1979 Dec 11;18(25):5711-20 PMID: 518865
  12. Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins.
    Biochim Biophys Acta. 1980 Jun 26;623(2):301-16 PMID: 7397216
  13. A theoretical study of the structure of parathyroid hormone.
    Proc Natl Acad Sci U S A. 1980 Jul;77(7):3791-5 PMID: 6933435
  14. Hydrophobic basis of packing in globular proteins.
    Proc Natl Acad Sci U S A. 1980 Aug;77(8):4643-7 PMID: 6933513
  15. Packing of alpha-helices onto beta-pleated sheets and the anatomy of alpha/beta proteins.
    J Mol Biol. 1980 Oct 15;143(1):95-128 PMID: 7003165
  16. Primary structure of murine major histocompatibility complex alloantigens. Amino acid sequence of the NH2-terminal ninety-eight residues of the H-2Db glycoprotein.
    J Biol Chem. 1981 Mar 25;256(6):2863-72 PMID: 7225204
  17. Primary structure of a murine transplantation antigen.
    Nature. 1981 May 7;291(5810):35-9 PMID: 7231522
  18. Complete amino acid sequence of murine beta 2-microglobulin: structural evidence for strain-related polymorphism.
    Proc Natl Acad Sci U S A. 1981 Jan;78(1):554-8 PMID: 6165997
  19. Amino acid sequence of residues 1-98 of the K-2Kb murine major histocompatibility alloantigen: comparison with H-2Kb and H-2db reveals extensive localized differences.
    Biochemistry. 1981 May 26;20(11):3301-8 PMID: 7018573
  20. The anatomy and taxonomy of protein structure.
    Adv Protein Chem. 1981;34:167-339 PMID: 7020376
  21. A pseudogene homologous to mouse transplantation antigens: transplantation antigens are encoded by eight exons that correlate with protein domains.
    Cell. 1981 Sep;25(3):683-92 PMID: 6895187
  22. The primary structure of guinea pig beta 2-microglobulin.
    Mol Immunol. 1980 Dec;17(12):1493-505 PMID: 6170877
  23. [Primary structure of class II human histocompatibility antigens. 1st communication. Amino acid sequence of the N-terminal 198 residues of the beta chain of a HLA-Dw2,2;DR2,2-alloantigen (author's transl)].
    Hoppe Seylers Z Physiol Chem. 1981 Dec;362(12):1665-9 PMID: 6947956
  24. Exon/intron organization and complete nucleotide sequence of an HLA gene.
    Proc Natl Acad Sci U S A. 1982 Feb;79(3):893-7 PMID: 6461010
  25. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale.
    J Biol Chem. 1971 Apr 10;246(7):2211-7 PMID: 5555568
  26. Statistical analysis of the correlation among amino acid residues in helical, beta-structural and non-regular regions of globular proteins.
    J Mol Biol. 1971 Dec 28;62(3):613-24 PMID: 5167562
  27. [A semi-empirical method for predicting the helical regions of polypeptide chains according to their primary structure].
    Arch Int Physiol Biochim. 1972 Jan;80(1):185-7 PMID: 4111305
  28. Protein folding.
    J Am Chem Soc. 1972 May 31;94(11):4009-12 PMID: 5037986
  29. Logical analysis of the mechanism of protein folding. I. Predictions of helices, loops and beta-structures from primary structure.
    J Mol Biol. 1973 Apr 5;75(2):401-20 PMID: 4728695
  30. Amino acid sequence of the light chain of a mouse myeloma protein (MOPC-315).
    Biochemistry. 1973 Dec 18;12(26):5400-16 PMID: 4760498
  31. The complete amino acid sequence of beta 2-microglobulin.
    Biochemistry. 1973 Nov 20;12(24):4811-22 PMID: 4586824
  32. Prediction of protein conformation.
    Biochemistry. 1974 Jan 15;13(2):222-45 PMID: 4358940
  33. Amino acid sequence of the (lambda) light chain of a human myeloma immunoglobulin (IgG New).
    Biochemistry. 1974 Mar 12;13(6):1295-302 PMID: 4814727
  34. Logical analysis of the mechanism of protein folding II. The nucleation process.
    J Mol Biol. 1974 Apr 5;84(2):337-72 PMID: 4364589
  35. Algorithms for prediction of alpha-helical and beta-structural regions in globular proteins.
    J Mol Biol. 1974 Oct 5;88(4):873-94 PMID: 4427384
  36. Assessment of some problems associated with prediction of the three-dimensional structure of a protein from its amino-acid sequence.
    Proc Natl Acad Sci U S A. 1975 Apr;72(4):1221-5 PMID: 1055397
  37. The primary sequence of chicken myoglobin (Gallus gallus).
    Biochim Biophys Acta. 1975 Apr 29;386(2):567-75 PMID: 1169972
  38. Analysis of code relating sequences to conformation in globular prtoeins. Theory and application of expected information.
    Biochem J. 1974 Sep;141(3):853-67 PMID: 4463965
  39. The primary structure of the myoglobin of Didelphis marsupialis (Virginia opossum).
    Biochim Biophys Acta. 1975 Aug 19;400(2):387-98 PMID: 1164514
  40. Immunoglobulin allotypes of rabbit kappa chains: polymorphism of a control mechanism regulating closely linked duplicated genes?
    Proc Natl Acad Sci U S A. 1976 Apr;73(4):1293-6 PMID: 817288
  41. Handedness of crossover connections in beta sheets.
    Proc Natl Acad Sci U S A. 1976 Aug;73(8):2619-23 PMID: 183204
  42. Complete amino acid sequence of the myoglobin from the Atlantic bottlenosed dolphin, Tursiops truncatus.
    Biochemistry. 1976 Oct 5;15(20):4418-22 PMID: 974068
  43. On the conformation of proteins: the handedness of the connection between parallel beta-strands.
    J Mol Biol. 1977 Feb 25;110(2):269-83 PMID: 845952
  44. Amino acid sequence of normal (microheterogeneous) porcine immunoglobulin lambda chains.
    Biochemistry. 1977 Aug 23;16(17):3765-72 PMID: 409425
  45. Preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin new at 2.0 A resolution.
    J Biol Chem. 1978 Jan 25;253(2):585-97 PMID: 618887
  46. Complete amino acid sequence of an HLA-DR antigen-like beta chain as predicted from the nucleotide sequence: similarities with immunoglobulins and HLA-A, -B, and -C antigens.
    Proc Natl Acad Sci U S A. 1982 Jun;79(12):3687-91 PMID: 6954511
  47. Analysis and prediction of the packing of alpha-helices against a beta-sheet in the tertiary structure of globular proteins.
    J Mol Biol. 1982 Apr 25;156(4):821-62 PMID: 7120396
  48. Sequence of an HLA-DR alpha-chain cDNA clone and intron-exon organization of the corresponding gene.
    Nature. 1982 Oct 21;299(5885):750-2 PMID: 6811954
  49. HLA-DR antigens: structure, separation of subpopulations, gene cloning and function.
    Immunol Rev. 1982;66:133-87 PMID: 6813244
  50. cDNA clone for the heavy chain of the human B cell alloantigen DC1: strong sequence homology to the HLA-DR heavy chain.
    Proc Natl Acad Sci U S A. 1982 Oct;79(20):6337-41 PMID: 6815651
  51. DNA sequence of the gene encoding the E alpha Ia polypeptide of the BALB/c mouse.
    Science. 1982 Dec 17;218(4578):1229-32 PMID: 6815800
  52. Evolution of proteins formed by beta-sheets. II. The core of the immunoglobulin domains.
    J Mol Biol. 1982 Sep 15;160(2):325-42 PMID: 7175935
  53. The murine Ia alpha chains, E alpha and A alpha, show a surprising degree of sequence homology.
    Proc Natl Acad Sci U S A. 1983 Jan;80(2):534-8 PMID: 6300851
  54. The amino acid sequence and gene organization of the heavy chain of the HLA-DR antigen: homology to immunoglobulins.
    Proc Natl Acad Sci U S A. 1982 Oct;79(19):6013-7 PMID: 6821129
  55. The amino-acid sequence x-ray methods, and its correlation with chemical data.
    Nature. 1961 May 20;190:666-70 PMID: 13752474
  56. A CORRELATION BETWEEN AMINO ACID COMPOSITION AND PROTEIN STRUCTURE.
    J Mol Biol. 1964 Aug;9:605-9 PMID: 14202291
  57. The myoglobin of primates. I. Hylobates agilis (gibbon).
    Biochim Biophys Acta. 1971 Dec 28;251(3):482-8 PMID: 11452891
  58. Correlation of amino acid sequence and conformation in tobacco mosaic virus.
    Biophys J. 1968 Jan;8(1):29-39 PMID: 5641402
  59. Prediction of chain turns in globular proteins on a hydrophobic basis.
    Nature. 1978 Apr 13;272(5654):586-90 PMID: 643051
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/12.1part1.243
Published
1984-01-11
Pages
243-55
Language
English
Region
England
NLM ID
0411011
PMCID
PMC321001
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/12.1part1.243 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2