Structure and function prediction of the Brucella abortus P39 protein by comparative modeling with marginal sequence similarities

K. De Fays, A. Tibor, C. Lambert, C. Vinals, P. Denoël, X. De Bolle, J. Wouters, J. J. Letesson, E. Depiereux

Research output: Contribution to journalArticle

Abstract

A methodology is proposed to solve a difficult modeling problem related to the recently sequenced P39 protein. This sequence shares no similarity with any known 3D structure, but a fold is proposed by several threading tools. The difficulty in aligning the target sequence on one of the proposed template structures is overcome by combining the results of several available prediction methods and by refining a rational consensus between them. In silico validation of the obtained model and a preliminary crosscheck with experimental features allow us to state that this borderline prediction is at least reasonable. This model raises relevant hypotheses on the main structural features of the protein and allows the design of site-directed mutations. Knowing the genetic context of the P39 reading frame, we are now able to suggest a function for the P39 protein: it would act as a periplasmic substrate-binding protein.

Original languageEnglish
Pages (from-to)217-223
Number of pages7
JournalProtein Engineering
Volume12
Issue number3
Publication statusPublished - 15 Apr 1999

Fingerprint

Brucella abortus
Periplasmic Binding Proteins
Reading Frames
Proteins
Computer Simulation
Refining
Carrier Proteins
Mutation
Substrates
Brucella p39 protein

Keywords

  • Consensus
  • Fold recognition
  • Periplasmic sugar-binding proteins
  • Protein modeling
  • Secondary structure prediction

Cite this

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title = "Structure and function prediction of the Brucella abortus P39 protein by comparative modeling with marginal sequence similarities",
abstract = "A methodology is proposed to solve a difficult modeling problem related to the recently sequenced P39 protein. This sequence shares no similarity with any known 3D structure, but a fold is proposed by several threading tools. The difficulty in aligning the target sequence on one of the proposed template structures is overcome by combining the results of several available prediction methods and by refining a rational consensus between them. In silico validation of the obtained model and a preliminary crosscheck with experimental features allow us to state that this borderline prediction is at least reasonable. This model raises relevant hypotheses on the main structural features of the protein and allows the design of site-directed mutations. Knowing the genetic context of the P39 reading frame, we are now able to suggest a function for the P39 protein: it would act as a periplasmic substrate-binding protein.",
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Structure and function prediction of the Brucella abortus P39 protein by comparative modeling with marginal sequence similarities. / De Fays, K.; Tibor, A.; Lambert, C.; Vinals, C.; Denoël, P.; De Bolle, X.; Wouters, J.; Letesson, J. J.; Depiereux, E.

In: Protein Engineering, Vol. 12, No. 3, 15.04.1999, p. 217-223.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Structure and function prediction of the Brucella abortus P39 protein by comparative modeling with marginal sequence similarities

AU - De Fays, K.

AU - Tibor, A.

AU - Lambert, C.

AU - Vinals, C.

AU - Denoël, P.

AU - De Bolle, X.

AU - Wouters, J.

AU - Letesson, J. J.

AU - Depiereux, E.

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AB - A methodology is proposed to solve a difficult modeling problem related to the recently sequenced P39 protein. This sequence shares no similarity with any known 3D structure, but a fold is proposed by several threading tools. The difficulty in aligning the target sequence on one of the proposed template structures is overcome by combining the results of several available prediction methods and by refining a rational consensus between them. In silico validation of the obtained model and a preliminary crosscheck with experimental features allow us to state that this borderline prediction is at least reasonable. This model raises relevant hypotheses on the main structural features of the protein and allows the design of site-directed mutations. Knowing the genetic context of the P39 reading frame, we are now able to suggest a function for the P39 protein: it would act as a periplasmic substrate-binding protein.

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KW - Periplasmic sugar-binding proteins

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