U.S. Department of Health and Human Services
 

 Contact Info

 
Tel: 301-594-3122
Email: johnl@niddk.nih.gov
 

 Select Experience

 
  • HeadProtein Engineering and Chemistry Group, Laboratory of Chemical Physics, NIDDK, NIH 2005-present
  • Research Biologist, Laboratory of Chemical Physics, NIDDK, NIH 1996-2005
  • Staff FellowLaboratory of Cellular and Developmental Biology, NIDDK, NIH 1990-1996
  • FellowDivision of Cancer Biology and Diagnosis, NCI, NIH 1986-1989
 

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    John Louis Medabalimi, Ph.D. (alias: John M. Louis)

    Research Biologist, Office of the Chief, Laboratory of Chemical Physics
    Specialties
    • Chemistry/Chemical Biology
    • Molecular Biology/Biochemistry

    ​Research Images

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    TitleDescriptionImage
    Dissociative inhibition of PR autoprocessingA possible approach to inhibition of PR autoprocessing from its Gag-Pol precursor involves disruption of the PR dimer interface. Binding of a monoclonal antibody that recognizes the N-terminal sequence of the mature PR, resulting in its dissociative inhibition, constitutes a proof of this principle. The antibody inhibits cleavage between the PR and RT domains after N-terminal autoprocessing.Dissociative inhibition of PR autoprocessingEnlarge
    Terminal β-sheet dimer interface of PR precursor analogueThe first crystal structures of a precursor mimetic (SFNFPR; four residues derived from the TFR are appended to its N-terminus) reveal several novel conformations, including disengagement of the four N-terminal residues (P1QIT4) from the β-sheet interface, accounting for its markedly lower dimer stability.Terminal β-sheet dimer interface of PR precursor analogueEnlarge
    Clinical inhibitors bind very weakly to PR precursor and to active site mutant.Active site D25N mutation decreases darunavir (DRV) binding by ~6 orders of magnitude.  PRD25N dimer/DRV complex exhibitsa 3°C increase in Tm on DRV binding, compared with 22 °C for wild type PR.  The precursor TFR-PR exhibits a similar low Tm because of decreased dimer stability and inhibitor affinity.Clinical inhibitors bind very weakly to PR precursor and to active site mutant.Enlarge
    Monomer fold and hydrophilic inhibitor of active PR dimerEach of the two identical 99-amino acid subunits of PR contributes one of the catalytic Asp25 residues.  Interactions that hold the dimer together involve the active site (Asp25 residues shown) and flaps, and the β-sheet comprising the four N-terminal and four C-terminal residues of each monomer. Deletion of the C-terminal residues results in a stable but inactive PR monomer whose residues 10-90 adopt a fold similar to that of the dimer, as revealed by its NMR structure. Precursor with PR flanked by the TFR adopts a similar monomer fold.  The N-terminal transframe octapeptide shown in surface representation (cleaved from the TFR at pH < 5; site 2 in figure 1) and its Glu-Asp-Leu sequence are competitive inhibitors of PR. Polar interactions with these residues enable a pH-dependent regulatory mechanism for PR maturation.Monomer fold and hydrophilic inhibitor of active PR dimerEnlarge
    Genotyping, chemical synthesis, and elucidation of self-cleavage of HIV-1 protease (PR) from its precursor, Gag-PolThe HIV-1 Gag-Pol polyprotein comprises the matrix, capsid, spacer peptide 1, nucleocapsid, protease, reverse transcriptase, ribonuclease, and integrase proteins (MA, CA, sp1, NC, PR, RT, RN, and IN). PR catalyzes its own release by sequential cleavages 1, 2, and 3 (upward red arrows) enabling controlled proteolysis of the Gag and Gag-Pol, indispensable for virus maturation. Cleavage 3 between the transframe region (TFR) and PR occurs intramolecularly to release a stable dimer with full catalytic activity.  Subsequent cleavage at the C-terminus of PR occurs intermolecularly.Genotyping, chemical synthesis, and elucidation of self-cleavage of HIV-1 protease (PR) from its precursor, Gag-PolEnlarge