Mandar T Naik

Academia Sinica, T’ai-pei, Taipei, Taiwan

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Publications (9)44.87 Total impact

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    ABSTRACT: The E3 ubiquitin-protein ligase RNF4 contains four tandem SUMO interacting motif (SIM) repeats for selective interaction with poly-SUMO modified proteins, which it targets for degradation. We employed a multifaceted approach to characterise structures of the RNF4-SIMs domain and tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIMs domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of RNF4-SIMs domains bind to SUMO2 in the groove between the β2 strand and the α1-helix parallel to the β2 strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable to that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2/RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.
    The Biochemical journal. 05/2014;
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    ABSTRACT: While numerous small ubiquitin-like modifier (SUMO) conjugated substrates have been identified, very little is known about the cellular signalling mechanisms that differentially regulate substrate sumoylation. Here, we show that acetylation of SUMO E2 conjugase Ubc9 selectively downregulates the sumoylation of substrates with negatively charged amino acid-dependent sumoylation motif (NDSM) consisting of clustered acidic residues located downstream from the core ψ-K-X-E/D consensus motif, such as CBP and Elk-1, but not substrates with core ψ-K-X-E/D motif alone or SUMO-interacting motif. Ubc9 is acetylated at residue K65 and K65 acetylation attenuates Ubc9 binding to NDSM substrates, causing a reduction in NDSM substrate sumoylation. Furthermore, Ubc9 K65 acetylation can be downregulated by hypoxia via SIRT1, and is correlated with hypoxia-elicited modulation of sumoylation and target gene expression of CBP and Elk-1 and cell survival. Our data suggest that Ubc9 acetylation/deacetylation serves as a dynamic switch for NDSM substrate sumoylation and we report a previously undescribed SIRT1/Ubc9 regulatory axis in the modulation of protein sumoylation and the hypoxia response.
    The EMBO Journal 02/2013; · 9.82 Impact Factor
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    ABSTRACT: The purified mammalian branched-chain α-ketoacid dehydrogenase complex (BCKDC), which catalyzes the oxidative decarboxylation of branched-chain α-keto acids, is essentially devoid of the constituent dihydrolipoamide dehydrogenase component (E3). The absence of E3 is associated with the low affinity of the subunit-binding domain of human BCKDC (hSBDb) for hE3. In this work, sequence alignments of hSBDb with the E3-binding domain (E3BD) of the mammalian pyruvate dehydrogenase complex show that hSBDb has an arginine at position 118, where E3BD features an asparagine. Substitution of Arg-118 with an asparagine increases the binding affinity of the R118N hSBDb variant (designated hSBDb*) for hE3 by nearly 2 orders of magnitude. The enthalpy of the binding reaction changes from endothermic with the wild-type hSBDb to exothermic with the hSBDb* variant. This higher affinity interaction allowed the determination of the crystal structure of the hE3/hSBDb* complex to 2.4-Å resolution. The structure showed that the presence of Arg-118 poses a unique, possibly steric and/or electrostatic incompatibility that could impede E3 interactions with the wild-type hSBDb. Compared with the E3/E3BD structure, the hE3/hSBDb* structure has a smaller interfacial area. Solution NMR data corroborated the interactions of hE3 with Arg-118 and Asn-118 in wild-type hSBDb and mutant hSBDb*, respectively. The NMR results also showed that the interface between hSBDb and hE3 does not change significantly from hSBDb to hSBDb*. Taken together, our results represent a starting point for explaining the long standing enigma that the E2b core of the BCKDC binds E3 far more weakly relative to other α-ketoacid dehydrogenase complexes.
    Journal of Biological Chemistry 05/2011; 286(26):23476-88. · 4.65 Impact Factor
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    ABSTRACT: Small ubiquitin-like modifier (SUMO) conjugation and interaction are increasingly associated with various cellular processes. However, little is known about the cellular signaling mechanisms that regulate proteins for distinct SUMO paralog conjugation and interactions. Using the transcriptional coregulator Daxx as a model, we show that SUMO paralog-selective binding and conjugation are regulated by phosphorylation of the Daxx SUMO-interacting motif (SIM). NMR structural studies show that Daxx (732)E-I-I-V-L-S-D-S-D(740) is a bona fide SIM that binds to SUMO-1 in a parallel orientation. Daxx-SIM is phosphorylated by CK2 kinase at residues S737 and S739. Phosphorylation promotes Daxx-SIM binding affinity toward SUMO-1 over SUMO-2/3, causing Daxx preference for SUMO-1 conjugation and interaction with SUMO-1-modified factors. Furthermore, Daxx-SIM phosphorylation enhances Daxx to sensitize stress-induced cell apoptosis via antiapoptotic gene repression. Our findings provide structural insights into the Daxx-SIM:SUMO-1 complex, a model of SIM phosphorylation-enhanced SUMO paralog-selective modification and interaction, and phosphorylation-regulated Daxx function in apoptosis.
    Molecular cell 04/2011; 42(1):62-74. · 14.61 Impact Factor
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    ABSTRACT: Small Ubiquitin-like MOdifiers (SUMOs) are ubiquitin-like proteins known to covalently modify large number of cellular proteins. The mammalian SUMO family includes four paralogues, SUMO-1 through SUMO-4. Death-associated protein-6, Daxx, is a 740 residue important transcription corepressor known to represses transcriptional potential of several sumolyted transcription factors. Daxx also plays important role in apoptosis. Both terminals of Daxx harbor separate SUMO Interaction Motifs (SIM), which mediate its interaction with SUMO and hence the sumolyted transcription factors. The C-terminal SIM of Daxx preferentially binds SUMO-1. Practically complete (1)H, (13)C and (15)N resonance assignments for the complex between SUMO-1 and 20 residue Daxx C-terminal SIM peptide are reported here.
    Biomolecular NMR Assignments 10/2010; 5(1):75-7. · 0.64 Impact Factor
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    ABSTRACT: Blo t 5 is the major allergen from Blomia tropicalis mites and shows strong IgE reactivity with up to 90% of asthmatic and rhinitis patients' sera. The NMR solution structure of Blo t 5 comprises three long alpha helices, forming a coiled-coil, triple-helical bundle with a left-handed twist. TROSY-NMR experiments were used to study Blo t 5 interaction with the Fab' of a specific monoclonal antibody, mAb 4A7. The mAb epitope comprises two closely spaced surfaces, I and II, connected by a sharp turn and bearing critical residues Asn46 and Lys47 on one surface, and Lys54 and Arg57 on the other. This discontinuous epitope overlaps with the human IgE epitope(s) of Blo t 5. Epitope surface II is further predicted to undergo conformational exchange in the millisecond to microsecond range. The results presented are critical for the design of a hypoallergenic Blo t 5 for efficacious immunotherapy of allergic diseases.
    Structure 02/2008; 16(1):125-36. · 5.99 Impact Factor
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    ABSTRACT: House dust mites are main source of indoor allergens triggering the development of allergic diseases such as atopic dermatitis, perennial rhinitis and asthma. Blomia tropicalis (Family: Echimyopodidae) is a predominant and clinically important mite species in tropical and subtropical countries. B. tropicalis allergens are shown to be distinct and have relatively low to moderate IgE cross-reactivity with Dermatophagoides pteronyssinus mite allergens. Group 5 allergen, Blo t 5 is the major allergen from this mite and shows up to 90% IgE reactivity with asthmatic sera (Kuo et al. 2003). 13 C and/or 15 N isotopically enriched Blo t 5 samples were prepared as described previously (Arruda et al. 1997). Practically complete backbone (99.4%) and side-chain (95%) assignments were achieved by standard triple resonance experiments using Bruker Avance spectrometers equipped with cryoprobe. The chemical shifts are deposited in the BioMagResBank with accession number 7276. Chemical shifts index analysis of the data predicts Blo t 5 as an all-helical protein comprising of three long a-helices.
    Journal of Biomolecular NMR 07/2007; 38(2):189. · 2.85 Impact Factor
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    Mandar T Naik, Tai-Huang Huang
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    ABSTRACT: The lipoic acid bearing domain (hbLBD) of human mitochondrial branched chain alpha-ketoacid dehydrogenase (BCKD) plays important role of substrate channeling in oxidative decarboxylation of the branched chain alpha-ketoacids. Recently hbLBD has been found to follow two-step folding mechanism without detectable presence of stable or kinetic intermediates. The present study describes the conformational stability underlying the folding of this small beta-barrel domain. Thermal denaturation in presence of urea and isothermal urea denaturation titrations are used to evaluate various thermodynamic parameters defining the equilibrium unfolding. The linear extrapolation model successfully describes the two-step; native state <-->denatured state unfolding transition of hbLBD. The average temperature of maximum stability of hbLBD is estimated as 295.6 +/- 0.9 K. Cold denaturation of hbLBD is also predicted and discussed.
    Protein Science 10/2004; 13(9):2483-92. · 2.74 Impact Factor
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    Mandar T Naik, Yu-Chu Chang, Tai-huang Huang
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    ABSTRACT: A reversible two-step (native state<-->denatured state) folding mechanism based on equilibrium and stopped flow experiments is proposed for urea denaturation of the lipoyl-bearing domain (hbLBD) of human mitochondrial branched chain alpha-ketoacid dehydrogenase (BCKD) complex. The results from this circular dichroism (CD) and fluorescence study have ruled out populated kinetic or equilibrium intermediates on folding pathway of this beta-barrel domain under experimental conditions. Both studies suggested mono-exponential kinetics without any burst phases. Moreover the thermodynamic parameters DeltaG(H(2)O) and m obtained from the kinetic analysis are consistent with the equilibrium measurements.
    FEBS Letters 10/2002; 530(1-3):133-8. · 3.58 Impact Factor