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PAAD domain-containing polypeptides, encoding nucleic acids, and methods of use

a technology of encoding nucleic acids and polypeptides, applied in the field of molecular biology and molecular medicine, can solve problems such as interfering with apoptosis-inducing activity of polypeptides

Inactive Publication Date: 2004-01-01
BURNHAM INST THE
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

For example, a PAAD domain-containing polypeptide which does not induce apoptosis may form hetero-oligomers with a PAAD domain-containing polypeptide which is apoptotic, thus interfering with its apoptosis-inducing activity.

Method used

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  • PAAD domain-containing polypeptides, encoding nucleic acids, and methods of use
  • PAAD domain-containing polypeptides, encoding nucleic acids, and methods of use
  • PAAD domain-containing polypeptides, encoding nucleic acids, and methods of use

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Embodiment Construction

[0263] 1.0 Identification of PAAD Domain-containing Polypeptides

[0264] The sequence of the N-terminal 100 amino acid fragment of the pyrin protein (Genbank Accession # NP00234; Pras, 1998, Scand. J. Rheumatol., 27:92-97) was used to perform a cascade of PSI-BLAST searches until no new hits were found. Lower significance hits from this procedure (called Saturated BLAST) were confirmed using the profile-to-profile alignment algorithm FFAS (Rychlewski et al., 2000, Protein Science 9:232-241) against a library of apoptosis-related domains. Proteins suspected of having a PAAD domain were added to the Saturated BLAST and FFAS databases and the FFAS similarity score was used to accept or reject the putative PAAD domains. Most of the proteins identified in FIGS. 1 and 2 could be connected with each other with PSI-BLAST significance better than 0.001 and / or the FFAS Z-score better than 10. The weakest link in the chain is the connection between the AIM2 / IFI16 branch and the rest of the famil...

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Abstract

The invention provides isolated nucleic acid molecules encoding PAAD-domain containing polypeptides and functional fragments thereof, including fragments containing PAAD domains, NACHT domains and ARED domains, encoded polypeptides, and antibodies. Also provided are methods of identifying polypeptides and agents that associate with a PAAD-domain containing polypeptide or fragment thereof, or that alter an association of a PAAD domain-containing polypeptides. Further provided are methods of identifying agents that modulate PAAD domain-mediated inhibition of NFkappaB activity, or modulate an activity of a NACHT domain of a PAAD domain-containing polypeptide. Also provided are methods of modulating NFkappaB transcriptional activity in a cell, and methods of altering expression of a PAAD domain-containing polypeptide in a cell

Description

[0001] This application claims benefit of the filing date of U.S. Provisional Application No. 60 / 370,538, filed Apr. 4, 2002, which is incorporated herein by reference.FIELD OF THE INVENTION[0003] This invention relates generally to the fields of molecular biology and molecular medicine and more specifically to the identification of proteins involved in innate immunity, programmed cell death, NF.kappa.B induction, cytokine processing and inflammation, and associations of these proteins.BACKGROUND INFORMATION[0004] Proteins containing the death domain fold (DDF) play pivotal roles in programmed cell death (apoptosis) and inflammatory responses. The DDF represents a protein interaction motif consisting of a bundle of (usually) six antiparallel .alpha.-helices. This core structure is found in at least three families of evolutionarily conserved and closely related domain families, including Death Domain (DD), Death Effector Domain (DED) and Caspase Recruitment Domain (CARD) families.[00...

Claims

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Application Information

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IPC IPC(8): C07H21/04C07K14/47
CPCC07H21/04Y10T436/143333C07K14/4747
Inventor REED, JOHN C.GODZIK, ADAM
Owner BURNHAM INST THE