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2.  Involvement of the β3-α3 loop of the Proline Dehydrogenase Domain in Allosteric Regulation of Membrane Association of Proline Utilization A†,‡ 
Biochemistry  2013;52(26):4482-4491.
Proline utilization A (PutA) from Escherichia coli is a membrane-associated trifunctional flavoenzyme that catalyzes the oxidation of proline to glutamate and moonlights as a transcriptional regulator. As a regulatory protein, PutA represses transcription of the put regulon, which contains the genes encoding PutA and the proline transporter PutP. The binding of proline to the proline dehydrogenase active site and the subsequent reduction of the flavin induces high affinity membrane association of PutA and relieves repression of the put regulon, thereby causing PutA to switch from its regulatory to its enzymatic role. Here, we present evidence suggesting that residues of the β3-α3 loop of the proline dehydrogenase domain (βα)8 barrel are involved in proline-mediated allosteric regulation of PutA-membrane binding. Mutation of the conserved residues Asp370 and Glu372 in the β3-α3 loop abrogates the ability of proline to induce functional membrane association. Both in vitro lipid/membrane binding assays and in vivo cell-based assays demonstrate that mutagenesis of Asp370 (D370N/A) or Glu372 (E372A) dramatically impedes PutA functional switching. The crystal structures of the proline dehydrogenase domain mutants PutA86-630D370N and PutA86-630D370A complexed with the proline analog L-tetrahydro-2-furoic acid show that the mutations cause only minor perturbations to the active site but no major structural changes, suggesting that the lack of proline response is not due to a failure of the mutated active sites to correctly bind the substrate. Rather, these results suggest that the β3-α3 loop may be involved in transmitting the status of the proline dehydrogenase active site and flavin redox state to the distal membrane association domain.
doi:10.1021/bi400396g
PMCID: PMC3731750  PMID: 23713611
3.  Kinetics of Reversible Reductive Carbonylation of Heme in Human Cystathionine β-synthase† 
Biochemistry  2013;52(26):4553-4562.
Cystathionine β-synthase (CBS) catalyzes the condensation of homocysteine with serine or cysteine to form cystathionine and water or hydrogen sulfide (H2S), respectively. In addition to pyridoxal phosphate, human CBS has a heme cofactor with cysteine and histidine as ligands. While Fe(III)-CBS is inert to exogenous ligands, Fe(II)-CBS can be reversibly inhibited by carbon monoxide (CO) and reoxidized by O2 to yield superoxide radical. In this study, we have examined the kinetics of Fe(II)CO-CBS formation and reoxidation. Reduction of Fe(III)-CBS by dithionite showed square root dependence on concentration, indicating that the reductant species was the sulfur dioxide radical anion (SO2•−) that exists in rapid equilibrium with S2O42−. Formation of Fe(II)CO-CBS from Fe(II)-CBS and 1 mM CO occurred at (3.1 ± 0.4) × 10−3 s−1 (pH 7.4, 25 °C). The reaction of Fe(III)-CBS with the reduced form of the flavoprotein methionine synthase reductase in the presence of CO and NADPH resulted in its reduction and carbonylation to form Fe(II)CO-CBS. Fe(II)-CBS was formed as intermediate with a rate constant of (9.3 ± 2.5) × 102 M−1 s−1. Reoxidation of Fe(II)CO-CBS by O2 was multiphasic. The major phase showed hyperbolic dependence on O2 concentration. Although H2S is a product of the CBS reaction and a potential heme ligand, we did not find evidence for exogenous H2S effect on activity or heme binding. Reversible reduction of CBS by a physiologically relevant oxidoreductase is consistent with a regulatory role for the heme and could constitute a mechanism for crosstalk between the CO, H2S and superoxide signaling pathways.
doi:10.1021/bi4004556
PMCID: PMC3741107  PMID: 23790103
Cystathionine β synthase; heme; carbon monoxide; hydrogen sulfide; heme autooxidation; methionine synthase reductase; kinetics; dithionite
4.  Structural and Functional Characterization of MppR, an Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus: Functional Diversity in the Acetoacetate Decarboxylase-Like Superfamily 
Biochemistry  2013;52(26):4492-4506.
The non-proteinogenic amino acid enduracididine is a critical component of the mannopeptimycins, cyclic glycopeptide antibiotics with activity against drug-resistant pathogens including methicillin-resistant Staphylococcus aureus. Enduracididine is produced in Streptomyces hygroscopicus by three enzymes, MppP, MppQ, and MppR. Based on primary sequence analysis, MppP and Q are pyridoxal-5'-phosphate-dependent aminotransferases; MppR shares low, but significant, sequence identity with acetoacetate decarboxylase. The exact reactions catalyzed by each enzyme, and the intermediates involved in the route to enduracididine are currently unknown. Herein we present biochemical and structural characterization of MppR that demonstrates a catalytic activity for this enzyme and provides clues about its role in enduracididine biosynthesis. Bioinformatic analysis shows that MppR belongs to a previously uncharacterized family within the acetoacetate decarboxylase-like superfamily (ADCSF) and suggests that MppR-like enzymes may catalyze reactions diverging from the well-characterized, prototypical ADCSF decarboxylase activity. MppR shares a high degree of structural similarity with acetoacetate decarboxylase, though the respective quaternary structures differ markedly and structural differences in the active site explain the observed loss of decarboxylase activity. The crystal structure of MppR in the presence of a mixture of pyruvate and 4-imidazolecarboxaldehyde shows that MppR catalyzes the aldol condensation of these compounds and subsequent dehydration. Surprisingly, the structure of MppR in the presence of a mixture of "4-hydroxy-2-ketoarginine" and "2-ketoenduracididine" shows only the correct 4R-enantiomer of "2-ketoenduracididine" bound to the enzyme. These data, together with bioinformatic analysis of MppR homologs, identifies a novel family within the acetoacetate decarboxylase-like superfamily with divergent active site structure and, consequently, biochemical function.
doi:10.1021/bi400397k
PMCID: PMC3743547  PMID: 23758195
Nonribosomal peptide antibiotics; mannopeptimycin; acetoacetate decarboxylase; pyruvate aldolase
5.  Structural Basis of Multisite Single-Stranded DNA Recognition and ACTA2 Repression by Purine-Rich Element Binding Protein B (Purβ)† 
Biochemistry  2013;52(26):4439-4450.
A hallmark of dysfunctional fibroblast to myofibroblast differentiation associated with fibrotic disorders is persistent expression of ACTA2, the gene encoding the cyto-contractile protein smooth muscle α-actin. In this study, a PURB-specific gene knockdown approach was used in conjunction with biochemical analyses of protein subdomain structure and function to reveal the mechanism by which purine-rich element binding protein B (Purβ) restricts ACTA2 expression in mouse embryo fibroblasts (MEFs). Consistent with the hypothesized role of Purβ as a suppressor of myofibroblast differentiation, stable short hairpin RNA-mediated knockdown of Purβ in cultured MEFs promoted changes in cell morphology, actin isoform expression, and cell migration indicative of conversion to a myofibroblast-like phenotype. Promoter-reporter assays in transfected Purβ knockdown MEFs confirmed that these changes were attributable, in part, to de-repression of ACTA2 transcription. To map the domains in Purβ responsible for ACTA2 repression, several recombinant truncation mutants were generated and analyzed based on hypothetical, computationally-derived models of the tertiary and quaternary structure of Purβ. Discrete subdomains mediating sequence- and strand-specific cis-element binding, protein-protein interaction, and inhibition of a composite ACTA2 enhancer were identified using a combination of biochemical, biophysical, and cell-based assays. Our results indicate that the Purβ homodimer possesses three separate but unequal single-stranded DNA-binding modules formed by subdomain-specific inter- and intramolecular interactions. This structural arrangement suggests that the cooperative assembly of the dimeric Purβ repressor on the sense strand of the ACTA2 enhancer is dictated by the association of each subdomain with distinct purine-rich binding sites within the enhancer.
doi:10.1021/bi400283r
PMCID: PMC3750979  PMID: 23724822
6.  Straight-Chain Alkyl Isocyanides Open the Distal Histidine Gate in Crystal Structures of Myoglobin† 
Biochemistry  2010;49(24):4977-4986.
Crystal structures of methyl, ethyl, propyl and butyl isocyanide bound to sperm whale myoglobin (Mb) reveal two major conformations. In the in conformer, His(E7) is in a “closed” position, forcing the ligand alkyl chain to point inward. In the out conformer, His(E7) is in an “open” position, allowing the ligand side chain to point outward. A progressive increase in the population of the out conformer is observed with increasing ligand length in P21 crystals of native Mb at pH 7.0. This switch from in to out with increasing ligand size also occurs in solution as measured by the decrease in the relative intensity of the low (~2075 cm 1) versus high frequency (~2125 cm 1) isocyano bands. In contrast, all four isocyanides in P6 crystals of wild type recombinant Mb occupy the in conformation. However, mutating either His64 to Ala, creating a “hole” to solvent, or Phe46 to Val, freeing rotation of His64, causes bound butyl isocyanide to point completely outward in P6 crystals. Thus, the unfavorable hindrance caused with crowding a large alkyl side chain into the distal pocket appears to be roughly equal to that for pushing open the His(E7) gate and is easily affected by crystal packing. This structural conclusion supports the “side path” kinetic mechanism for O2 release, in which the dissociated ligand first moves toward the protein interior and then encounters steric resistance, which is roughly equal to that for escaping to solvent through the His(E7) channel.
doi:10.1021/bi1001739
PMCID: PMC4074459  PMID: 20481504
myoglobin; alkyl isocyanide; isonitrile; X-ray crystallography; FTIR; infrared; vibrational spectroscopy; iron coordination
7.  Intermediate P* from Soluble Methane Monooxygenase Contains a Diferrous Cluster 
Biochemistry  2013;52(25):4331-4342.
During a single turnover of the hydroxylase component (MMOH) of soluble methane monooxygenase from Methylosinus trichosporium OB3b, several discrete intermediates are formed. The diiron cluster of MMOH is first reduced to the FeIIFeII state (Hred). O2 binds rapidly at a site away from the cluster to form the FeIIFeII intermediate O, which converts to an FeIIIFeIII-peroxo intermediate P and finally to the FeIVFeIV intermediate Q. Q binds and reacts with methane to yield methanol and water. The rate constants for these steps are increased by a regulatory protein, MMOB. Previously reported transient kinetic studies have suggested that an intermediate P* forms between O and P in which the g = 16 EPR signal characteristic of the reduced diiron cluster of Hred and O is lost. This was interpreted as signaling oxidation of the cluster, but low accumulation of P* prevented further characterization. In this study, three methods to directly detect and trap P* are applied together to allow its spectroscopic and kinetic characterization. First, the MMOB mutant His33Ala is used to specifically slow the decay of P* without affecting its formation rate, leading to its nearly quantitative accumulation. Second, spectra-kinetic data collection is used to provide a sensitive measure of the formation and decay rate constants of intermediates as well as their optical spectra. Finally, the substrate furan is included to react with Q and quench its strong chromophore. The optical spectrum of P* closely mimics those of Hred and O, but it is distinctly different from that of P. The reaction cycle rate constants allowed prediction of the times for maximal accumulation of the intermediates. Mössbauer spectra of rapid freeze quench samples at these times show that the intermediates are formed at almost exactly the predicted levels. The Mössbauer spectra show that the diiron cluster of P*, quite unexpectedly, is in the FeIIFeII state. Thus, the loss of the g = 16 EPR results from a change of the electronic structure of the FeIIFeII center rather than oxidation. The similarity of the optical and Mössbauer spectra of Hred, O, and P* suggest that only subtle changes occur in the electronic and physical structure of the diiron cluster as P* forms. Nevertheless, the changes that do occur are necessary for O2 to be activated for hydrocarbon oxidation.
doi:10.1021/bi400182y
PMCID: PMC3712755  PMID: 23718184
8.  Membrane depth-dependent energetic contribution of tryptophan side-chain to the stability of integral membrane proteins+ 
Biochemistry  2013;52(25):4413-4421.
Lipid solvation provides the primary driving force for the insertion and folding of integral membrane proteins. Although the structure of the lipid bilayer is often simplified as a central hydrophobic core sandwiched between two hydrophilic interfacial regions, the complexity of the liquid-crystalline bilayer structure and the gradient of water molecules across the bilayer finetune the energetic contributions of individual amino acid residues to the stability of membrane proteins at different depths of the bilayer. The tryptophan side-chain is particularly interesting because despite its widely recognized role in anchoring membrane proteins in lipid bilayers, there is little consensus on its hydrophobicity among various experimentally determined hydrophobicity scales. Here we investigated how lipid-facing tryptophan residues located at different depths in the bilayer contribute to the stability of integral membrane proteins using the outer membrane protein A (OmpA) as a model. We replaced all lipid-contacting residues of the first transmembrane β-strand of OmpA with alanines and individually incorporated tryptophans in these positions along the strand. By measuring the thermodynamic stability of these proteins, we found that OmpA is slightly more stable when tryptophans are placed in the center of the bilayer and that it is somewhat destabilized as tryptophans approach the interfacial region. However, this trend may be partially reversed when a moderate concentration of urea rather than water is taken as the reference state. The measured stability profiles are driven by similar profiles of the m-value, a parameter that reflects the shielding of hydrophobic surface area from water. Our results indicate that knowledge of the free energy level of the protein’s unfolded reference state is important for quantitatively assessing the stability of membrane proteins, which may explain differences in observed profiles between in vivo and in vitro scales.
doi:10.1021/bi400344b
PMCID: PMC3731455  PMID: 23763479
9.  Quantitation of Recombinant Protein in Whole Cells and Cell Extracts with Solid-State NMR Spectroscopy 
Biochemistry  2013;52(25):4285-4287.
Recombinant proteins (RPs) are commonly expressed in bacteria followed by solubilization and chromatography. Purified RP yield can be diminished by losses at any step with very different changes in methods needed to try to improve yield. Time and labor can therefore be saved by first identifying the specific reason for low yield. The present study describes a new solid-state NMR approach to RP quantitation in whole cells or cell pellets without solubilization or purification. The approach is straightforward and inexpensive and only requires ~50 mL culture and a low-field spectrometer.
doi:10.1021/bi4007034
PMCID: PMC3734946  PMID: 23742073
10.  Multiple Pathways Promote Dynamical Coupling between Catalytic Domains in Escherichia coli Prolyl-tRNA Synthetase 
Biochemistry  2013;52(25):4399-4412.
Aminoacyl-tRNA synthetases are multi-domain enzymes that catalyze covalent attachment of amino acids to their cognate tRNA. Cross-talk between functional domains is a prerequisite for this process. In the present study, we investigate the molecular mechanism of site-to-site communication in Escherichia coli prolyl-tRNA synthetase (Ec ProRS). Earlier studies have demonstrated that evolutionarily conserved/co-evolved residues that are engaged in correlated motion are critical for the propagation of functional conformational changes from one site to another in modular proteins. Here, molecular simulation and bioinformatics-based analysis was performed to identify dynamically coupled and evolutionarily constrained residues that form contiguous pathways of residue-residue interactions between the aminoacylation and editing domains of Ec ProRS. The results of this study suggest that multiple pathways exist between these two domains to maintain the dynamic coupling essential for enzyme function. Moreover, residues in these interaction networks are generally highly conserved. Site-directed changes of on-pathway residues have a significant impact on enzyme function and dynamics suggesting that any perturbation along these pathways disrupts the native residue-residue interactions that are required for effective communication between the two functional domains. Free energy analysis revealed that communication between residues within a pathway, as well as cross-talk between pathways are important to coordinate functions of different domains of Ec ProRS for efficient catalysis.
doi:10.1021/bi400079h
PMCID: PMC3749879  PMID: 23731272
11.  Prenylation and membrane localization of Cdc42 are essential for activation by DOCK7 
Biochemistry  2013;52(25):4354-4363.
The unconventional Guanine Nucleotide Exchange Factor (GEF) family comprising 11 DOCK180 related proteins is classified into four subfamilies, A through D, based on their relative GEF activity towards the closely related Rac and Cdc42 GTPases. DOCK proteins participate in the remodeling of the actin cytoskeleton and are key regulators of cell motility, phagocytosis and adhesion. Here we show that the guanine nucleotide exchange domain of DOCK7, DHR2 (for DOCK homology region 2), is a potent GEF for prenylated Cdc42 and Rac1 in a model liposome system, demonstrating that the prenylation and membrane localization of Cdc42 or Rac1 are necessary for their activation by DOCK7. Additionally, we identify DOCK7 residues that confer GTPase GEF specificity. Finally, using our liposome reconstitution assay, we show that a more narrowly defined GEF domain of DHR2 (designated DHR2s) harbors an N-terminal site distinct from the GEF active site that binds preferentially to the active, GTP-bound forms of Cdc42 and Rac1 and thereby recruits free DHR2s from solution to the membrane surface. This recruitment results in a progressive increase in the effective concentration of DHR2s at the membrane surface that in turn provides for an accelerated rate of guanine nucleotide exchange on Cdc42. The positive cooperativity observed in our reconstituted system suggests that the action of DOCK7 in vivo may involve the coordinated integration of Cdc42/Rac signaling in the context of the membrane recruitment of a DOCK7 GEF complex.
doi:10.1021/bi301688g
PMCID: PMC3752685  PMID: 23718289
12.  UDP-Galactopyranose Mutase in Nematodes 
Biochemistry  2013;52(25):4391-4398.
Nematodes represent a diverse phylum of both free living and parasitic species. While the species Caenorhabditis elegans (C. elegans) is a valuable model organism, parasitic nematodes or helminths pose a serious threat to human health. Indeed, helminths cause many neglected tropical diseases that afflict humans. Nematode glycoconjugates have been implicated in evasive immunomodulation, a hallmark of nematode infections. One monosaccharide residue present in the glycoconjugates of several human pathogens is galactofuranose (Galf). This five-membered ring isomer of galactose has not been detected in mammals, making Galf metabolic enzymes attractive therapeutic targets. The only known pathway for biosynthetic incorporation of Galf into glycoconjugates depends upon generation of the glycosyl donor UDP-Galf by the flavoenzyme uridine 5’-diphosphate (UDP) galactopyranose mutase (UGM or Glf). A putative UGM encoding gene (glf-1) was recently identified in C. elegans. Because Galf has yet to be identified in any nematode glycan, we sought to assess the catalytic activity of the C. elegans glf-1 gene product (CeUGM). We found that CeUGM catalyzes the isomerization of UDP-Galf and UDP-galactopyranose (UDP-Galp). In the presence of enzyme, substrate, and a hydride source, a galactose–N5-FAD adduct was isolated, suggesting the CeUGM flavin adenine dinucleotide (FAD) cofactor serves as a nucleophile in covalent catalysis. Homology modeling and protein variants indicate that CeUGM possesses an active site similar to that of prokaryotic enzymes, despite the low sequence identity (~15%) between eukaryotic and prokaryotic UGM proteins. Even with the primary sequence differences, heterocyclic UGM inhibitors developed against prokaryotic proteins also inhibit CeUGM activity. We postulate that these inhibitors can serve as chemical probes of Galf in nematodes and as anthelmintic leads. Together, our data suggest that CeUGM facilitates the biosynthetic incorporation of Galf into nematode glycoconjugates through generation of the glycosyl donor UDP-Galf.
doi:10.1021/bi400264d
PMCID: PMC3779688  PMID: 23697711
glycobiology; UDP-galactopyranose mutase (UGM); UDP-galactofuranose; flavoprotein; nematode; C. elegans; parasitic; helminth; neglected tropical diseases; small molecule inhibition; anthelmintic
13.  Free Cholesterol Determines rHDL Phospholipid Phase Structure and Stability 
Biochemistry  2013;52(25):4324-4330.
Reassembled high density lipoproteins (rHDL) of various sizes and compositions containing apo A-I or apo A-II as their sole protein, dimyristoyl phosphatidylcholine (DMPC), and various amounts of free cholesterol (FC) have been isolated and analyzed by differential scanning calorimetry (DSC) and by circular dichroism to determine their stability and the temperature dependence of their helical content. Our data show that the multiple rHDL species obtained at each mol% FC usually do not have the same mole% FC as the starting mixture and that the size of the multiple species increases in a quantized way with their respective mol% FC. DSC studies reveal multiple phases or domains that can be classified as virtual DMPC, which contains a small amount of DMPC that slightly reduces the melting temperature Tm, a boundary phase that is adjacent to the apo A-I or apo A-II that circumscribes the discoidal rHDL, and a mixed FC + DMPC phase that has a Tm that increases with mol% FC. Only the large rHDL contain virtual DMPC whereas all contain boundary phase and various amounts of mixed FC + DMPC according to increasing size and mol% FC. As reported by others, FC stabilizes the rHDL. For rHDL (apo A-II) compared to rHDL (apo A-I), this occurs in spite of the reduced number of helical regions that mediate binding to the DMPC surface. This effect is attributed to the very high lipophilicity of apo A-II and the reduction in the polarity of the interface between DMPC and the aqueous phase with increasing mol% FC, an effect that is expected to increase the hydrophobic associations with the non polar face of the amphipathic helices of apo A-II. These data are relevant to the differential effects of FC and apolipoprotein species on intracellular and plasma membrane nascent HDL assembly and subsequent remodeling by plasma proteins.
doi:10.1021/bi4006732
PMCID: PMC3959168  PMID: 23721456
Cholesterol; Apolipoprotein A-I; Apolipoprotein A-II; Size Exclusion Chromatography; Circular Dichroism; Fluorescence; Differential Scanning Calorimetry
14.  The Roles of Four Conserved Basic Amino Acids in a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase 
Biochemistry  2013;52(25):4343-4353.
The roles of four conserved basic amino acids in the reaction catalyzed by the ferredoxin-dependent nitrate reductase from the cyanobacterium Synechococcus sp. PCC 7942 have been investigated using site-directed mutagenesis in combination with measurements of steady-state kinetics, substrate-binding affinities and spectroscopic properties of the enzyme’s two prosthetic groups. Replacement of either Lys58 or Arg70 by glutamine leads to a complete loss of activity, with both the physiological electron donor, reduced ferredoxin and with a non-physiological electron donor, reduced methyl viologen. More conservative, charge-maintaining K58R and R70K variants were also completely inactive. Replacement of Lys130 by glutamine produced a variant that retained 26% of the wild-type activity with methyl viologen as the electron donor and 22% of the wild-type activity with ferredoxin as the electron donor, while replacement by arginine produces a variant that retains a significantly higher percentage of the wild-type activity with both electron donors. In contrast, replacement of Arg146 by glutamine had minimal effect on the activity of the enzyme. These results, along with substrate-binding and spectroscopic measurements, are discussed in terms of an in silico structural model for the enzyme.
doi:10.1021/bi400354n
PMCID: PMC3741069  PMID: 23692082
15.  Nitric Oxide Effect on Naphthoquinone Toxicity in Endothelial Cells: Role of Bioenergetic Dysfunction and PARP Activation 
Biochemistry  2013;52(25):4364-4372.
When produced at physiological levels reactive oxygen species (ROS) can act as signaling molecules to regulate normal vascular function. Produced under pathological conditions, ROS can contribute to oxidative damage of cellular components (e.g., DNA and proteins) and trigger cell death. Moreover, the reaction of superoxide with nitric oxide (NO) produces the strong oxidant peroxynitrite and decreases NO bioavailability, both of which may contribute to activation of cell death pathways. The effects of ROS generated from the 1,4-naphthoquinones alone and in combination with NO on the activation status of poly(ADP-ribose) polymerase (PARP) and cell viability were examined. Treatment with redox cycling quinones activates PARP, and this stimulatory effect is attenuated in the presence of NO. Mitochondria play a central role in cell death signaling pathways and are a target of oxidants. We show that simultaneous exposure of endothelial cells to NO and ROS results in mitochondrial dysfunction, ATP and NAD+ depletion, and cell death. Alone, NO and ROS have only minor effects on cellular bioenergetics. Further, PARP inhibition does not attenuate reduced cell viability or mitochondrial dysfunction. These results show that concomitant exposure to NO and ROS impairs energy metabolism and triggers PARP-independent cell death. While superoxide-mediated PARP activation is attenuated in the presence of NO, PARP inhibition does not modify the loss of mitochondrial function or adenine and pyridine nucleotide pools and subsequent bioenergetic dysfunction. These findings suggest that the mechanisms by which ROS and NO induce endothelial cell death is closely linked to maintenance of mitochondrial function and not overactivation of PARP.
doi:10.1021/bi400342t
PMCID: PMC4028014  PMID: 23718265
Mitochondria; oxidative stress; mitochondrial bioenergetics
16.  EVB Simulations of the Chemical Mechanism of ATP to cAMP Conversion by Anthrax Edema Factor$ 
Biochemistry  2013;52(15):2672-2682.
The two-metal catalysis by the adenylyl cyclase domain of the anthrax edema factor toxin was simulated using the empirical valence bond (EVB) quantum mechanical/molecular mechanical approach. These calculations considered the energetics of the nucleophile deprotonation and a new PO bond formation in the aqueous solution and in the enzyme-substrate complex present in the crystal structure models of the reactant and product state of the reaction. Our calculations support reaction pathway that involves metal-assisted proton transfer from the nucleophile to bulk aqueous solution followed by subsequent formation of an unstable pentavalent intermediate that decomposes into cAMP and pyrophosphate (PPi). This pathway involves ligand exchange in the first solvation sphere of the catalytic metal. The last step of the reaction – the cleavage of the PO bond to PPi – has the highest activation barrier of 13.9 kcal/mol but this barrier height is too close to 12.5 kcal/mol calculated for the nucleophilic attack step to make a definitive conclusion about the rate-limiting step. The calculated reaction mechanism is supported by reasonable agreement between the experimental and calculated catalytic rate constant decrease due to the mutation of the active site lysine 346 to arginine.
doi:10.1021/bi400088y
PMCID: PMC4069339  PMID: 23480863
17.  Facilitating RNA Structure Prediction with Microarrays† 
Biochemistry  2006;45(2):581-593.
Determining RNA secondary structure is important for understanding structure-function relationships and identifying potential drug targets. This paper reports the use of microarrays with heptamer 2′-O-methyl oligoribonucleotides to probe the secondary structure of an RNA and thereby improve prediction of that secondary structure. When experimental constraints from hybridization results are added to a free energy minimization algorithm, the prediction of the secondary structure of E. coli 5S rRNA improves from 27% to 92% of the known canonical base pairs. Optimization of buffer conditions for hybridization and application of 2′-O-methyl-2-thiouridine to enhance binding and improve discrimination between AU and GU pairs are also described. The results suggest that probing RNA with oligonucleotide microarrays can facilitate determination of secondary structure.
doi:10.1021/bi051409+
PMCID: PMC4070881  PMID: 16401087
18.  The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from its Structure in Crystals of 50S Ribosomal Subunits 
Biochemistry  2006;45(39):11776-11789.
Internal loops play an important role in structure and folding of RNA and in RNA recognition by other molecules such as proteins and ligands. An understanding of internal loops with propensities to form a particular structure will help predict RNA structure, recognition, and function. The structures of internal loops 5'1009CUAAG10133'3'1168GAAGC11645' and 5'998CUAAG10023'3'1157GAAGC11535' from helix 40 of the large subunit rRNA in Deinococcus radiodurans and Escherichia coli, respectively, are phylogenetically conserved, suggesting functional relevance. The energetics and NMR solution structure of the loop were determined in the duplex, 5'1GGCUAAGAC93'3'18CCGAAGCUG105' The internal loop forms a different structure in solution than in the crystal structures of the ribosomal subunits. In particular, the crystal structures have a bulged out adenine at the equivalent of position A15 and a reverse Hoogsteen UA pair (trans Watson-Crick/Hoogsteen UA) at the equivalent of U4 and A14, whereas the solution structure has a single hydrogen bond UA pair (cis Watson-Crick/sugar edge A15U4) between U4 and A15 and a sheared AA pair (trans Hoogsteen/sugar edge A14A5) between A5 and A14. There is cross-strand stacking between A6 and A14 (A6/A14/A15 stacking pattern) in the NMR structure. All three structures have a sheared GA pair (trans Hoogsteen/sugar edge A6G13) at the equivalent of A6 and G13. The internal loop has contacts with ribosomal protein L20 and other parts of the RNA in the crystal structures. These contacts presumably provide the free energy to rearrange the base pairing in the loop. Evidently, molecular recognition of this internal loop involves induced fit binding, which could confer several advantages. The predicted thermodynamic stability of the loop agrees with the experimental value, even though the thermodynamic model assumes a Watson–Crick UA pair.
doi:10.1021/bi0605787
PMCID: PMC4070884  PMID: 17002278
19.  Correlation of Structure and Function in the Human Hotdog-fold Enzyme hTHEM4† 
Biochemistry  2012;51(33):6490-6492.
Human THEM4 (hTHEM4) is comprised of a catalytically active hotdog-fold acyl-CoA thioesterase domain and an N-terminal domain of unknown fold and function. hTHEM4 has been linked to Akt1 regulation and cell apoptosis. Herein, we report the X-ray structure of hHTEM4 bound with undecan-2-one-CoA. Structure guided mutagenesis was carried out to confirm the catalytic residues. The N-terminal domain is shown to be partially comprised of irregular and flexible secondary structure, reminiscent of a protein-binding domain. We demonstrate direct hTHEM4-Akt1 binding by immunoprecipitation and by inhibition of Akt1 kinase activity, thus providing independent evidence that hTHEM4 is an Akt1 negative regulator.
doi:10.1021/bi300968n
PMCID: PMC4066673  PMID: 22871024
20.  Human Brown Fat Inducible Thioesterase Variant 2 (BFIT2) Cellular Localization and Catalytic Function# 
Biochemistry  2012;51(35):6990-6999.
The mammalian brown fat inducible thioesterase variant 2 (BFIT2), also known as ACOT11, is a multi-modular protein containing two consecutive hotdog-fold domains and a C-terminal steroidogenic acute regulatory protein related lipid transfer (START) domain (StarD14). In this study, we demonstrate that the N-terminal region of human BFIT2 (hBFIT2) constitutes a mitochondrial location signal sequence, which undergoes mitochondria-dependent posttranslational cleavage. The mature hBFIT2 is shown to be located in the mitochondrial matrix whereas the paralog “cytoplasmic acetyl-CoA hydrolase” (CACH, also known as ACOT12) was found in the cytoplam. In-vitro activity analysis of full-length hBFIT2 isolated from stably transfected HEK293 cells demonstrates selective thioesterase activity directed towards long chain fatty acyl-CoA thioesters, thus distinguishing BFIT2 catalytic function from that of CACH. The results from a protein-lipid overlay test indicate that the hBFIT2 StarD14 domain binds phosphatidylinositol 4-phosphate.
doi:10.1021/bi3008824
PMCID: PMC4066737  PMID: 22897136
thioesterase; mitochondria; START domain; hotdog-fold; thioester hydrolysis; lipid metabolism; ACOT11; ACOT12; BFIT; CACH; StarD14; StarD15; fatty acid
21.  Cholesterol’s Interfacial Interactions with Galactosylceramides† 
Biochemistry  1994;33(10):2900-2906.
Recently, the influence of acyl structure on galactosylceramide’s (GalCer) interfacial phase behavior was studied [Ali, S., Smaby, J. M., & Brown, R. E. (1993) Biochemistry 32,11696–11703]. Here, we show that acyl structure is a key parameter controlling GalCer’s ability to interact with cholesterol. Different chain-pure GalCer species containing saturated (24:0, 18:0, or 10:0), or unsaturated (24:1Δ15, 22:1Δ13, or 18:2Δ9,12) acyl chains were synthesized. After measurement of the force–area behavior of mixed cholesterol/GalCer films at 24 °C, the average molecular area and average compressibility were determined as a function of film composition. Cholesterol exerts only a slight condensing effect when the GalCer species are ordered [liquid-condensed], with maximum condensation occurring near 0.25 mole fraction. However, cholesterol exerts a marked condensing effect on fluid phase (liquid-expanded) GalCer species regardless of whether the acyl chain is saturated or unsaturated. Maximum condensation occurs at cholesterol mole fractions between 0.3 and 0.4. We also compared cholesterol’s relative condensing effect on liquid-expanded GalCer versus sphingomyelin. Cholesterol’s condensation of either bovine brain or egg sphingomyelin is 25–30% greater than that observed with different liquid-expanded GalCer species. Aside from average area behavior, we assessed cholesterol’s interfacial interactions with the various sphingolipids by determining the average compressibility as a function of composition. The compressibility of condensed GalCer derivatives changes very little upon addition of cholesterol. In contrast, cholesterol causes dramatic changes when combined with liquid-expanded GalCer derivatives, which all have compressibilities 4–5-fold higher than bovine brain GalCer. The nature of the cholesterol-induced change in average compressibility for liquid-expanded GalCer derivatives depends on acyl structure and surface pressure.
PMCID: PMC4067055  PMID: 8130203
22.  Function of Resistance – Conferring Plasmodium falciparum Chloroquine Resistance Transporter (PfCRT) Isoforms 
Biochemistry  2013;52(24):4242-4249.
The function of P. falciparum chloroquine resistance transporter (PfCRT) can be quantified using a S. cerevisiae model system (Baro, N. K., Pooput C and Roepe P.D. Biochemistry. 50, 6701 – 6710). We further optimize this system to distinguish PfCRT isoforms found in P. falciparum strains and isolates from across the globe. We create and express 13 naturally occurring pfcrt alleles associated with a range of chloroquine resistant (CQR) phenotypes. Using galactose induction of PfCRT we quantify PfCRT and chloroquine (CQ) dependent yeast growth inhibition, and [3H]-CQ transport specifically due to a given PfCRT isoform. Surprisingly, we find poor correlation between these parameters vs CQ IC50 observed in strains of malaria harboring the same isoforms. This suggests that increased CQ transport due to PfCRT mutation is necessary, but not sufficient, for the range of CQ IC50 observed in globally distributed CQR P. falciparum isolates.
doi:10.1021/bi400557x
PMCID: PMC3703759  PMID: 23688277
malaria; drug resistance; chloroquine; PvCRT; PfCRT
23.  Mechanism-based Inhibition of iPLA2β Demonstrates a Highly Reactive Cysteine Residue (C651) That Interacts with the Active Site: Mass Spectrometric Elucidation of the Mechanisms of Underlying Inhibition 
Biochemistry  2013;52(24):4250-4263.
The multi-faceted roles of calcium-independent phospholipase A2β (iPLA2β) in numerous cellular processes have been extensively examined through utilization of the iPLA2-selective inhibitor (E)-6-(bromomethylene)-3-(1-naphthalenyl)-2H-tetrahydropyran-2-one (BEL). Herein, we employed accurate mass/high resolution mass spectrometry to demonstrate that the active site serine (S465) and C651 of iPLA2β are covalently cross-linked during incubations with BEL demonstrating their close spatial proximity. This crosslink results in macroscopic alterations in enzyme molecular geometry evidenced by anomalous migration of the cross-linked enzyme by SDS-PAGE. Molecular models of iPLA2β constructed from the crystal structure of iPLA2α (patatin) indicate that the distance between S465 and C651 is approximately 10 Å within the active site of iPLA2β. Kinetic analysis of the formation of the 75 kDa iPLA2β-BEL species with the (R) and (S) enantiomers of BEL demonstrated that the reaction of (S)-BEL with iPLA2β was more rapid than for (R)-BEL paralleling the enantioselectivity for the inhibition of catalysis by each inhibitor with iPLA2β. Moreover, we demonstrate that the previously identified selective acylation of iPLA2β by oleoyl-CoA occurs at C651 thereby indicating the importance of active site architecture for acylation of this enzyme. Collectively, these results identify C651 as a highly reactive nucleophilic residue within the active site of iPLA2β which is thioesterified by BEL, acylated by oleoyl-CoA and located in close spatial proximity to the catalytic serine thereby providing important chemical insights on the mechanisms through which BEL inhibits iPLA2β and the topology of the active site.
doi:10.1021/bi4004233
PMCID: PMC3716383  PMID: 23701211
24.  A Mutational Analysis of the Active Site Loop Residues in cis-3-Chloroacrylic Acid Dehalogenase 
Biochemistry  2013;52(24):4204-4216.
cis -3-Chloroacrylic acid dehalogenase (cis-CaaD) from Pseudomonas pavonaceae 170 and a homologue from Corynebacterium glutamicum designated Cg10062 share 34% sequence identity (54% similarity). The former catalyzes a key step in a bacterial catabolic pathway for the nematocide 1,3-dichloropropene, whereas the latter has no known biological activity. Although Cg10062 has the six active site residues (Pro-1, His-28, Arg-70, Arg-73, Tyr-103, Glu-114) that are critical for cis-CaaD activity, it shows only a low level cis-CaaD activity and lacks the specificity of cis-CaaD: Cg10062 processes both isomers of 3-chloroacrylate with a preference for the cis-isomer. Although the basis for these differences is unknown, a comparison of the crystal structures of the enzymes covalently modified by an adduct resulting from their incubation with the same inhibitor offers a possible explanation. A 6-residue active site loop in cis-CaaD shows a strikingly different conformation from that observed in Cg10062: the loop closes down on the active site of cis-CaaD, but not on that of Cg10062. In order to examine what this loop might contribute to cis-CaaD catalysis and specificity, the residues were changed individually to those found in Cg10062. Subsequent kinetic and mechanistic analysis suggests that the T34A mutant of cis-CaaD is more Cg10062-like. The mutant enzyme shows a 4-fold increase in Km (using cis-3-bromoacrylate), but not to the degree observed for Cg10062 (687-fold). The mutation also causes a 4-fold decrease in the burst rate (compared to the wild type cis-CaaD), whereas Cg10062 shows no burst rate. More telling is the reaction of the T34A mutant of cis-CaaD with the alternate substrate, 2,3-butadienoate. In the presence of NaBH4 and the allene, cis-CaaD is completely inactivated after one turnover due to the covalent modification of Pro-1. The same experiment with Cg10062 does not result in the covalent modification of Pro-1. The different outcomes are attributed to covalent catalysis (using Pro-1) followed by hydrolysis of the enamine or imine tautomer in cis-CaaD vs direct hydration of the allene to yield acetoacetate in the case of Cg10062. The T34A mutant shows partial inactivation, requiring 5 turnovers of the substrate per monomer, which suggests that the direct hydration route is favored 80% of the time. However, the mutation does not alter the stereochemistry at C-2 of [2-D]acetoacetate when the reaction is carried out in D2O. Both cis-CaaD and the T34 mutant generate (2R)-[2-D]acetoacetate, whereas Cg10062 generates mostly the 2S-isomer. The combined observations are consistent with a role for the loop region in cis-CaaD specificity and catalysis, but the precise role remains to be determined.
doi:10.1021/bi4004414
PMCID: PMC3718188  PMID: 23692140
25.  PPAR δ agonist GW0742 interacts weakly with multiple nuclear receptors including the vitamin D receptor 
Biochemistry  2013;52(24):4193-4203.
A high throughput screening campaign was conducted to identify small molecules with the ability to inhibit the interaction between the vitamin D receptor (VDR) and steroid receptor coactivator 2. These inhibitors represent novel molecular probes to modulate gene regulation mediated by VDR. The peroxisome proliferator-activated receptor δ (PPARδ) agonist GW0742 was among the identified VDR-coactivator inhibitors and has been characterized herein as a pan nuclear receptor antagonist at concentrations higher than 12.1 µM. The highest antagonist activity for GW0742 was found for VDR and the androgen receptor (AR). Surprisingly, GW0742 behaved as PPAR agonist/antagonist activating transcription at lower concentration and inhibiting this effect at higher concentrations. A unique spectroscopic property of GW0742 was identified as well. In the presence of rhodamine-derived molecules, GW0742+ increased fluorescence intensity and fluorescence polarization at an excitation wavelength of 595 nm and emission wavelength of 615 nm in a dose dependent manner. The GW0742-inhibited NR-coactivator binding resulted in a reduced expression of five different NR target genes in LNCaP cells in the presence of agonist. Especially VDR target genes CYP24A1, IGFBP-3 and TRPV6 were negatively regulated by GW0742. GW0742 is the first VDR ligand inhibitor lacking the secosteroid structure of VDR ligand antagonists. Nevertheless, the VDR-meditated downstream process of cell differentiation was antagonized by GW0742 in HL-60 cells that were pretreated with the endogenous VDR agonist 1,25-dihydroxyvitamin D3.
doi:10.1021/bi400321p
PMCID: PMC3724348  PMID: 23713684
GW0742; vitamin D receptor; androgen receptor; peroxisome proliferator-activated receptor; steroid receptor coactivator 2; fluorescence polarization; high throughput screening; IGFBP-3; CYP24A1; TRPV6; UGT1A1; PSA; BTG2

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