Isolation of a new antibacterial peptide actinokineosin from Actinokineospora spheciospongiae based on genome mining.

Based on genome mining, a new antibacterial peptide named actinokineosin was isolated from a rare actinomycete Actinokineospora spheciospongiae. The amino acid sequence of the C-terminus of actinokineosin was established by TOF-MS/MS experiments. The amino acid sequence in the macrolactam ring was determined by TOF-MS/MS analyses after cleavage with BNPS-skatole and successive trypsin treatment. As a result of an antibacterial assay using a paper disk, actinokineosin showed antibacterial activity against Micrococcus luteus at a dosage of 50 µg per disk. From the genome sequence data of A. spheciospongiae, the biosynthetic gene cluster of actinokineosin was found and was indicated to consist of 10 genes. Among the genes, the gene aknA encoded the precursor of actinokineosin and the genes including aknC, aknB1 and aknB2 were proposed as modification enzymes to give mature actinokineosin. SIGNIFICANCE AND IMPACT OF THE STUDY: Genome mining is a powerful tool to find new bioactive compounds from the genome database. In this report, we succeeded in isolation and structure determination of a new antibacterial peptide named actinokineosin based on genome mining.

Quantification of binding affinities of essential sugars with a tryptophan analogue and the ubiquitous role of C-H···π interactions.

The role of noncovalent interactions in carbohydrate recognition by aromatic amino acids has long been reported. To develop a molecular understanding of noncovalent interactions in the recognition process, we have examined a series of binary complexes between 3-methylindole (3-MeIn) and sugars. In particular, the geometries and binding affinities of 3-MeIn with α/ß-D-glucose, ß-D-galactose, α-D-mannose and α/ß-L-fucose are obtained using the MP2(full)/6-31G(d,p) and the M06/TZV2D//MP2/6-31G(d,p) level of theories. The conventional hydrogen bonding such as N-H···O and C-H···O as well as nonconventional O-H···π and C-H···π type of interactions is, in general, identified as responsible for the moderately strong interaction energies. Large variations in the position-orientations of 3-MeIn with respect to saccharide are noticed, within the same sugar family, as well as across different sugar series. Furthermore, complexes with large differences in their geometries are recognized as capable of exhibiting very similar interaction energies, underscoring the significance of exhaustive conformation sampling, as carried out in the present study. These observations are readily attributed to the differences in the efficiency of the type of interactions enlisted above. The highest and lowest interaction energies, upon inclusion of 50% BSSE correction, are found to be -16.02 and -6.22 kcal mol(-1), respectively, for α-D-glucose (1a) and α-L-fucose (5j). While more number of prominent conventional hydrogen bonding contacts remains as a characteristic feature of the strongly bound complexes, the lower end of the interaction energy spectrum is dominated by multiple C-H···π interactions. The complexes exhibiting as many as four C-H···π contacts are identified in the case of α/ß-D-glucose, ß-D-galactose, and α/ß-L-fucose with an interaction energy hovering around -8 kcal mol(-1). The presence of effective C-H···π interactions is found to be dependent on the saccharide configuration as well as the area of the apolar patch constituted by the C-H groups. The study offers a comprehensive set of binary complexes, across different saccharides, which serves as an illustration of the significance and ubiquitous nature of C-H···π interactions in carbohydrate binding in saccharide-protein complexes.

Analysis of measured and calculated Raman spectra of indole, 3-methylindole, and tryptophan on the basis of observed and predicted isotope shifts.

The aromatic amino acid tryptophan plays an important role in protein electron-transfer and in enzyme catalysis. Tryptophan is also used as a probe of its local protein environment and of dynamic changes in this environment. Raman spectroscopy of tryptophan has been an important tool to monitor tryptophan, its radicals, and its protein environment. The proper interpretation of the Raman spectra requires not only the correct assignment of Raman bands to vibrational normal modes but also the correct identification of the Raman bands in the spectrum. A significant amount of experimental and computational work has been devoted to this problem, but inconsistencies still persist. In this work, the Raman spectra of indole, 3-methylindole (3MI), tryptophan, and several of their isotopomers have been measured to determine the isotope shifts of the Raman bands. Density functional theory calculations with the B3LYP functional and the 6-311+G(d,p) basis set have been performed on indole, 3MI, 3-ethylindole (3EI), and several of their isotopomers to predict isotope shifts of the vibrational normal modes. Comparison of the observed and predicted isotope shifts results in a consistent assignment of Raman bands to vibrational normal modes that can be used for both assignment and identification of the Raman bands. For correct assignments, it is important to determine force field scaling factors for each molecule separately, and scaling factors of 0.9824, 0.9843, and 0.9857 are determined for indole, 3MI, and 3EI, respectively. It is also important to use more than one parameter to assign vibrational normal modes to Raman bands, for example, the inclusion of isotope shifts other than those obtained from H/D-exchange. Finally, the results indicate that the Fermi doublet of indole may consist of just two fundamentals, whereas one fundamental and one combination band are identified for the Fermi resonance that gives rise to the doublet in 3MI and tryptophan.

A novel approach to 3-methylindoles by a Heck/cyclization/isomerization process.

A novel synthesis of 3-methylindoles from chlorotriflates through a Heck reaction, carbamate/aryl chloride coupling, and isomerization sequence is presented. The three-step sequence is highly efficient and general, enabling the regiocontrolled synthesis of substituted indoles in short order.

Metabolic activation of a novel 3-substituted indole-containing TNF-alpha inhibitor: dehydrogenation and inactivation of CYP3A4.

SPD-304 is a recently discovered small-molecule TNF-alpha antagonist. However, SPD-304 contains a potentially toxic 3-alkylindole moiety. Previous studies on 3-methylindole and the 3-alkylindole-containing drugs zafirlukast and MK-0524 structural analogues found that they were bioactivated by cytochrome P450s through a dehydrogenation process to form 3-methyleneindolenine intermediates that are electrophilic alpha,beta-unsaturated iminium species. These electrophiles could react with protein and/or DNA nucleophilic residues to cause toxicities. In the present study, we found that SPD-304 was bioactivated through a similar dehydrogenation mechanism to produce a similar electrophilic 3-methyleneindolenine intermediate. The electrophile was trapped with nucleophilic glutathione and identified by LC/MS/MS. The iminium or another reactive intermediate also was a mechanism-based inactivator of CYP3A4. The inactivation parameters were K I = 29 microM and k inact = 0.047 min (-1). In addition, SPD-304 was metabolized through hydroxylation, N-dealkylation, and epoxidation pathways, and several metabolites and glutathione adducts were characterized by tandem mass spectrometry. The metabolism profile was also evaluated by in silico molecular docking of SPD-304 into the active site of CYP3A4, which predicted that the dehydrogenation reaction was initiated by 3-methylene C-H atom abstraction at the trifluoromethylphenyl-1 H-indol-3-ylmethyl portion of SPD-304. Hydroxylation of the 6'-methyl of the dimethylchromone portion of SPD-304 was the other major predicted metabolic pathway. The molecular models correlated precisely with experimental metabolic results. In summary, dehydrogenation of SPD-304 may cause toxicities through the formation of electrophilic intermediates and cause drug-drug interactions through CYP3A4 inactivation.

Effect of dietary melengestrol acetate on the incidence of acute interstitial pneumonia in feedlot heifers.

Over a 3-y period, 906,000 cattle were monitored in 23 feedlots in southern Alberta for symptoms of acute interstitial pneumonia (AIP). Plasma, urine, and lung tissue were collected at slaughter from 299 animals clinically diagnosed with AIP and from 156 healthy penmates and analyzed for 3-methylindole (3MI) derivatives and reduced glutathione concentration. From each animal, the left lung was subsampled for histologic examination. Concentrations of glutathione in lung tissue were reduced (P < 0.001) in animals showing clinical symptoms of AIP as compared with their asymptomatic penmates. Animals histologically confirmed as having AIP had higher levels of 3MI protein adducts in blood and lung tissue (P < 0.05) than did emergency-slaughtered animals without AIP. Within feedlots, where pens of heifers were fed either a standard dosage of melengestrol acetate (MGA) or none, the rate of death attributable to AIP was similar between treatment groups, but emergency slaughter after clinical diagnosis of AIP was done 3.2 times more often (P < 0.001) in the MGA-fed heifers than in the group not fed MGA. Use of MGA did not influence glutathione concentration. As growth performance of heifers given steroidal implants may not be improved by feeding MGA, the most cost-effective method of reducing the incidence of AIP-related emergency slaughter in feedlot heifers may be to eliminate MGA from the diet.

Insulin-like growth factor binding protein-2: contributions of the C-terminal domain to insulin-like growth factor-1 binding.

Signaling by the insulin-like growth factor (IGF)-1 receptor (IGF-1R) has been implicated in the promotion and aggressiveness of breast, prostate, colorectal, and lung cancers. The IGF binding proteins (IGFBPs) represent a class of natural IGF antagonists that bind to and sequester IGF-1/2 from the IGF-1R, making them attractive candidates as therapeutics for cancer prevention and control. Recombinant human IGFBP-2 significantly attenuated IGF-1-stimulated MCF-7 cell proliferation with coaddition of 20 or 100 nM IGFBP-2 (50 or 80% inhibition, respectively). We previously identified IGF-1 contact sites both upstream and downstream of the CWCV motif (residues 247-250) in human IGFBP-2 (J Biol Chem 276:2880-2889, 2001). To further test their contributions to IGFBP-2 function, the single tryptophan in human IGFBP-2, Trp-248, was selectively cleaved with 2-(2'nitrophenylsulfenyl)-3-methyl-3 bromoindolenine (BNPS-skatole) and the BNPS-skatole products IGFBP-2(1-248) and IGFBP-2(249-289) as well as IGFBP-2(1-190) were expressed as glutathione S-transferase-fusion proteins and purified. Based on competition binding analysis, deletion of residues 249 to 289 caused an approximately 20-fold decrease in IGF-1 binding affinity (IGFBP-2 EC50 = 0.35 nM and IGFBP-2(1-248) = 7 nM). Removal of the remainder of the C-terminal domain had no further effect on affinity (IGFBP-2(1-190) EC50 = 9.2 nM). In kinetic assays, IGFBP-2(1-248) and IGFBP-2(1-190) exhibited more rapid association and dissociation rates than full-length IGFBP-2. These results confirm that regions upstream and downstream of the CWCV motif participate in IGF-1 binding. They further support the development of full-length IGFBP-2 as a cancer therapeutic.

Selective tryptophan modification with rhodium carbenoids in aqueous solution.

A new transition metal-based reaction has been developed for the selective modification of tryptophan residues on protein substrates. After activation of vinyl-substituted diazo compounds by Rh2(OAc)4, the resulting metallocarbenoid intermediates were found to modify indoles in aqueous media despite competing reactions with water. Both N- and 2-substituted indole products were observed in the reaction. Following initial small-molecule studies, the reaction was performed on two protein substrates. Both myoglobin and subtilisin Carlsberg were modified readily in aqueous solution, and the tryptophan selectivity of the reactions was confirmed through MS analyses of trypsin digest fragments. It was also demonstrated that myoblobin concentrations as low as 10 muM still led to appreciable levels of modification. Reconstitution experiments confirmed that myoglobin retained its ability to bind heme following modification.

Photoaffinity labeling identifies the substrate-binding site of mammalian squalene epoxidase.

Squalene epoxidase (SE) catalyzes the conversion of squalene to (3S)-2,3-oxidosqualene. Photolabeling and site-directed mutagenesis were performed on recombinant rat SE (rrSE) in order to identify the location of the substrate-binding site and the roles of key residues in catalysis. Truncated 50-kDa rrSE was purified and photoaffinity labeled by competitive SE inhibitor (Ki=18.4 microM), [(3)H]TNSA-Dza. An 8-kDa CNBr/BNPS-skatole peptide was purified and the first 24 amino acids were sequenced by Edman degradation. The sequence PASFLPPSSVNKRGVLLLGDAYNL corresponded to residues 388-411 of the full-length rat SE. Three nucleophilic residues (Lys-399, Arg-400, and Asp-407) were labeled by [(3)H]TNSA-Dza. Triple mutants were prepared in which bulky groups were used to replace the labeled charged residues. Purified mutant enzymes showed lower enzymatic activity and reduced photoaffinity labeling by [(3)H]TNSA-Dza. This constitutes the first evidence as to the identity of the substrate-binding site of SE.

Molecular modeling, affinity labeling, and site-directed mutagenesis define the key points of interaction between the ligand-binding domain of the vitamin D nuclear receptor and 1 alpha,25-dihydroxyvitamin D3.

We have combined molecular modeling and classical structure-function techniques to define the interactions between the ligand-binding domain (LBD) of the vitamin D nuclear receptor (VDR) and its natural ligand, 1alpha,25-dihydroxyvitamin D(3) [1alpha,25-(OH)(2)D(3)]. The affinity analogue 1alpha,25-(OH)(2)D(3)-3-bromoacetate exclusively labeled Cys-288 in the VDR-LBD. Mutation of C288 to glycine abolished this affinity labeling, whereas the VDR-LBD mutants C337G and C369G (other conserved cysteines in the VDR-LBD) were labeled similarly to the wild-type protein. These results revealed that the A-ring 3-OH group docks next to C288 in the binding pocket. We further mutated M284 and W286 (separately creating M284A, M284S, W286A, and W286F) and caused severe loss of ligand binding, indicating the crucial role played by the contiguous segment between M284 and C288. Alignment of the VDR-LBD sequence with the sequences of nuclear receptor LBDs of known 3-D structure positioned M284 and W286 in the presumed beta-hairpin of the molecule, thereby identifying it as the region contacting the A-ring of 1alpha, 25-(OH)(2)D(3). From the multiple sequence alignment, we developed a homologous extension model of the VDR-LBD. The model has a canonical nuclear receptor fold with helices H1-H12 and a single beta hairpin but lacks the long insert (residues 161-221) between H2 and H3. We docked the alpha-conformation of the A-ring into the binding pocket first so as to incorporate the above-noted interacting residues. The model predicts hydrogen bonding contacts between ligand and protein at S237 and D299 as well as at the site of the natural mutation R274L. Mutation of S237 or D299 to alanine largely abolished ligand binding, whereas changing K302, a nonligand-contacting residue, to alanine left binding unaffected. In the "activation" helix 12, the model places V418 closest to the ligand, and, consistent with this prediction, the mutation V418S abolished ligand binding. The studies together have enabled us to identify 1alpha,25-(OH)(2)D(3)-binding motifs in the ligand-binding pocket of VDR.

Emulsification of chemical and enzymatic hydrolysates of beta-lactoglobulin: characterization of the peptides adsorbed at the interface.

Bovine beta-Lactoglobulin (BLG) was cleaved by BNPS-skatole (2-(2'-nitrophenylsulfenyl)-3-methyl-3'-bromoindolenine), trypsin, or pepsin in 40% ethanol before emulsification with hexadecane in order to characterize the peptides active at the interfaces. The total digests and the different phases obtained after emulsification were analyzed by RP-HPLC to separate the peptides according to their gradual order on a hydrophilicity-to-hydrophobicity scale. In each case, hydrophobic peptides were recovered in the creamed phase and characterized by mass spectrometry and sequencing. After tryptic hydrolysis, short peptides were identified at the interfacial layer as fragments S21-L32, V41-L57, V41-K60, and W61-K70 linked to L149-I162 by a C66-C160 bond. It indicates that the hydrophilic/hydrophobic distribution of the amino acids in the sequence of the fragments is more relevant to adsorption than the length of the peptide. BNPS-skatole and peptic hydrolysis produced larger hydrophobic peptides which were also recovered in the creamed phase of the emulsion and characterized.

Probing the vitamin D sterol-binding pocket of human vitamin D-binding protein with bromoacetate affinity labeling reagents containing the affinity probe at C-3, C-6, C-11, and C-19 positions of parent vitamin D sterols.

The multiple physiological properties of vitamin D-binding protein (DBP) include organ-specific transportation of vitamin D(3) and its metabolites, manifested by its ability to bind vitamin D sterols with high affinity. In the present investigation we probed the vitamin D sterol-binding pocket of human DBP with affinity labeling analogs of 25-hydroxyvitamin D(3) ¿25-OH-D(3) and 1, 25-dihydroxyvitamin D(3) ¿1,25(OH)(2)D(3) containing bromoacetate alkylating probe at C-3 (A-ring), C-6 (triene), C-11 (C-ring), and C-19 (exocyclic methylene) of the parent sterol. Competitive binding assays with DBP showed approximately 22-, 68-, and 2000-fold decrease in the binding of 1,25(OH)(2)-D(3)-11-BE, 25-OH-D(3)-3-BE, and 25-OH-D(3)-6-BE, respectively, compared to that seen with 25-OH-D(3), while there was no significant difference in the DBP-binding affinity of 25-OH-D(3)-19-BE and 25-OH-D(3). Surprisingly, ¿(14)C25-OH-D(3)-11-BE and ¿(14)C1, 25(OH)(2)-D(3)-19-BE failed to label DBP despite high-affinity DBP-binding, indicating the absence of any nucleophilic amino acid in the vicinity of their bromoacetate moiety to form a covalent bond, while these analogs are inside the binding pocket. In contrast, ¿(14)C25-OH-D(3)-6-BE and ¿(14)C25-OH-D(3)-3-BE specifically labeled DBP. BNPS-skatole digestion of DBP labeled with ¿(14)C25-OH-D(3)-3-BE or ¿(14)C25-OH-D(3)-6-BE produced two peptides (M(r) 17,400 and 33,840), with radioactivity associated with the N- and C-terminal peptides, respectively, raising the possibility that either different areas of the same vitamin D sterol-binding pocket, or different domains of DBP might be labeled by these analogs. Successful affinity labeling of recombinant domain I (1-203) of DBP with both reagents indicated that different areas of the same vitamin D-binding pocket (domain I) were labeled. These affinity analogs are potentially useful for "mapping" the vitamin D sterol-binding pocket and developing a functional model.

Identification of the factors affecting the rate of deactivation of hypochlorous acid by melatonin.

It has been found that melatonin reacts rapidly with hypochlorous acid in phosphate-buffered, ethanol-water solutions to produce 2-hydroxymelatonin. The rate law, d[2 - HOMel]/dt - kHOCl[Mel][HOCl] - kOCl-[Mel][OCl-], was obtained. At 37 degrees C and at a water concentration of 23.5 M, kOCl- = 6.0 x 10(2) L. mol-1. s-1, and kHOCl was found to be a function of the water concentration, kHOCl = 11 +/- 3 L3. mol-3. s-1. [H2O]2, indicating that the availability of water at the site of the reaction plays a significant role. The part that the structural components of melatonin play in determining the reaction pathway was examined by comparing the rate of deactivation of HOCl by melatonin to that of the model compounds indole, 5-methoxyindole, and 3-methylindole. The relative reactivity is explained in terms of steric and electronic effects, and it was found that the presence of the substituent at the 3-position influences the nature of the oxidation product. Melatonin and 3-methylindole yielded hydroxylated products, whereas indole and 5-methoxyindole produce chlorinated products.

Chemical cleavage of bovine beta-lactoglobulin by BNPS-skatole for preparative purposes: comparative study of hydrolytic procedures and peptide characterization.

A comparative study of various procedures for tryptophanyl peptide bond cleavage by BNPS-skatole [2-(2-nitrophenyl)-3-methyl-3-bromoindolenine] was carried out on native and on reduced and alkylated bovine beta-lactoglobulin (BLG). The reaction yield and the composition of the derived products were studied in acetic acid, trifluoroacetic acid (TFA), and ethanol/TFA. For BNPS-skatole removal, extraction by water or ethyl ether was compared with dialysis and gel filtration. The three expected peptides (1-19, 20-61, 62-162) and incomplete cleaved fragments (1-61, 20-162) were separated and characterized by electrophoresis, reverse-phase high-performance liquid chromatography, and mass spectrometry. The highest hydrolysis yield (67.4%) occurred with native BLG cleaved in 88% acetic acid at 47 degrees C for 60 min. Subsequent water extraction and gel filtration led to total recovery of the material, but reagent elimination was only quantitative after gel filtration. Cleavage specificity was ensured by mass spectrometry and the amino acid composition of peptides 1-19 and 62-162. The chemical side reactions identified are discussed.

Identification of skatolyl hydroperoxide and its role in the peroxidase-catalysed oxidation of indol-3-yl acetic acid.

Indol-3-yl acetic acid (IAA, auxin) is a plant hormone whose degradation is a key determinant of plant growth and development. The first evidence for skatolyl hydroperoxide formation during the plant peroxidase-catalysed degradation of IAA has been obtained by electrospray MS. Skatolyl hydroperoxide degrades predominantly non-enzymically to oxindol-3-yl carbinol but in part enzymically into indol-3-yl methanol via a peroxidase cycle in which IAA acts as an electron donor. Skatolyl hydroperoxide is degradable by catalase. Horseradish peroxidase isoenzyme C (HRP-C) and anionic tobacco peroxidase (TOP) exhibit differences in their mechanisms of reaction. The insensitivity of the HRP-C-catalysed reaction to catalase is ascribed to the formation of HRP-C Compound III at the initiation step and its subsequent role in radical propagation. This is in contrast with the TOP-catalysed process in which skatolyl hydroperoxide has a key role. Indol-3-yl aldehyde is produced not via the peroxidase cycle but by catalysis involving ferrous peroxidase. Because indol-3-yl aldehyde is one of the main IAA-derived products identified in planta, we conclude that ferrous peroxidases participate in IAA catalytic transformations in vivo. A general scheme for peroxidase-catalysed IAA oxidation is presented.

Relationship between oxidation and conjugation metabolism of skatole in pig liver and concentrations of skatole in fat.

High concentrations of skatole in fat of some intact male pigs are a major cause of boar taint. In this study, we investigated the effect of oxidative and conjugative metabolism of skatole in liver on the concentrations of skatole in the fat of intact male pigs. In Trial 1, 18 Yorkshire intact males were equally divided into two treatments with high (mean, .42; SD, .26 ppm) and low (mean, .06; SD, .02 ppm) fat skatole levels. There was an increased rate of skatole metabolism, an increased glucuronidation activity, and a decreased sulfation activity toward 2-naphthol in liver from pigs with high skatole levels (P < .05). In Trial 2, Swedish Yorkshire x F4 European Wild Pig intact males were used. Among skatole metabolites that were produced in incubations with liver microsomes, pro-MII was conjugated with glucuronic acid and sulfate, and metabolite F-1 was conjugated with glucuronic acid. The rates of formation of various skatole metabolites and conjugation of pro-MII were evaluated for 22 pigs with different levels of cytochrome P4502E1 in the liver. The formation of F-1 and sulfation of pro-MII were negatively correlated with fat skatole levels (r = -.59, and r = -.56, respectively) and were decreased in pigs with high fat skatole levels and low P4502E1 levels (P < .01). The results indicate that oxidation and conjugation reactions of skatole in pig liver have a dramatic effect on skatole levels in the fat. In particular, the formation of F-1 and formation and subsequent sulfation of pro-MII are related to low levels of skatole in the fat, presumably due to rapid metabolic clearance of skatole.

Hepatic metabolism of skatole in pigs by cytochrome P4502E1.

High concentrations of skatole in fat are a major cause of boar taint in intact male pigs. Skatole is metabolized in the liver, and this metabolism could affect concentrations of skatole in fat. In this study, we evaluated the involvement of cytochrome P450, in particular cytochrome P4502E1, in skatole metabolism in pig liver. Liver microsomes from F4 European Wild Pig x Swedish Yorkshire intact male pigs were incubated in a buffer containing NADPH, NADH, and skatole. Several skatole metabolites were detected by HPLC, including 6-hydroxyskatole (pro-MII), 3-hydroxy-3-methyloxyindole (MIII), and five others not identified in this study. Inhibitors of P450 were added to microsomal incubations, and their effect on the formation of skatole metabolites and skatole disappearance was evaluated. The general cytochrome P450 inhibitors SKF 525A, at a concentration of .2 mM and metyrapone, at a concentration of .1 mM decreased the formation of pro-MII (P = .001) to 38.2 and 11.6%, respectively, of that of controls. The SKF 525A also reduced the synthesis of MIII and three other metabolites, whereas metyrapone only reduced the disappearance of skatole and synthesis of pro-MII. Inhibitors specific for cytochrome P4502E1 were more effective in reducing the formation of skatole metabolites than SKF 525A and metyrapone. Chlorzoxazone and diallyl sulfide reduced (P = .001) the synthesis of pro-MII to 9.7 and 30.9% of the control rate. The formation of most of the other skatole metabolites and disappearance of skatole were also reduced with these inhibitors. These results indicate that skatole is metabolized in pig liver to pro-MII and other metabolites by cytochrome P4502E1.

Roles of the structure and orientation of ligands and ligand mimics inside the ligand-binding pocket of the vitamin D-binding protein.

1alpha,25-Dihydroxyvitamin D3, the vitamin D hormone, manifests its diverse biological properties by specifically binding to the vitamin D sterol-binding pockets of vitamin D-binding protein (DBP) and vitamin D receptor. In the past, several affinity, photoaffinity, and chemical modification studies have been carried out to probe the vitamin D sterol-binding pocket of DBP and to evaluate the relationship between the structure of this pocket and the functions of the protein. In the present study, we examined the steric requirements inside this pocket by considering conformational structures of various bromoacetate derivatives of 25-hydroxyvitamin D3 and 1alpha,25-dihydroxyvitamin D3 and their abilities to covalently and specifically modify this pocket. We observed that, although 25-hydroxyvitamin D3 3beta-bromoacetate (25-OH-D3-3-BE), 1alpha,25-dihydroxyvitamin D3 3beta-bromoacetate [1alpha,25(OH)2D3-3-BE], 1alpha,25-dihydroxyvitamin D3 1alpha-bromoacetate [1alpha,25(OH)2D3-1-BE], and 1alpha,25-dihydroxyvitamin D3 1alpha,3beta-dibromoacetate [1alpha,25(OH)2D3-1,3-di-BE] bound DBP in a specific manner, only [3H]-25-OH-D3-3-BE and [3H]-1alpha,25(OH)2D3-3-BE affinity labeled the protein. BNPS-skatole cleavages of [3H]-25-OH-D3-3-BE- and 3H-1alpha,25(OH)2D3-3-BE-labeled DBP samples produced the same labeled peptide (N-terminal), demonstrating the specificity of labeling by these analogs. Energy-minimized conformational structures of these bromoacetate derivatives indicated significant changes in the A-ring conformations of these analogs. These structural changes were invoked to explain the inability of [3H]-1alpha,25(OH)2D3-1-BE and [3H]-1alpha,25(OH)2D3-1,3-di-BE to affinity label DBP. Overall, these studies suggested that the vitamin D sterol-binding pocket in DBP is sterically quite restrictive. This information could be potentially important in designing future vitamin D-based drugs for several diseases.

Chemical modifications of Bacillus subtilis tryptophanyl-tRNA synthetase.

A concerted conformational change in Bacillus subtilis tryptophanyl-tRNA synthetase (TrpRS) was evident from previous fluorescence on the quenching of the single Trp residue Trp-92 in the 4FTrp-AMP complexed enzyme. In this study, chemical modifications of the B. subtilis TrpRS were employed to further characterize this conformational change, with the single Trp residue serving as a marker for monitoring the change. Modifications of the enzyme by means of the Trp-specific agent N-bromosuccinimide (NBS) or 3-bromo-3-methyl-2-(2-nitrophenylmercapto)-3H-indole (BNPS-skatole) inactivated the enzyme in accord with the essential role of Trp-92, as identified previously by site-directed mutagenesis. ATP sensitized TrpRS toward inactivation by NBS and BNPS-skatole, which suggested a conformational change that resulted in greater accessibility of Trp-92 toward modifications. In contrast, the cognate tRNATrp substrate exerted a specific protective effect against inactivation by both of the reagents, indicating that the TrpRS-tRNATrp interaction reduces the accessibility of Trp-92 under our experimental conditions. By comparison, modification of sulfhydryl groups by means of iodoacetamide did not reduce TrpRS activity. Observations on Trp-specific modification and substrate protection effects are discussed in the context of the Bacillus stearothermophilus TrpRS crystal structure.

Interaction sites of the COOH-terminal region of the gamma subunit of cGMP phosphodiesterase with the GTP-bound alpha subunit of transducin.

In photoreceptor cells, visual transduction occurs through photoexcitation of rhodopsin, GTP activation of the alpha subunit of transducin, and interaction between GTP-bound transducin alpha subunit and the inhibitory gamma subunit of phosphodiesterase. The gamma subunit of phosphodiesterase, in turn, accelerates the hydrolysis of GTP on the alpha subunit of transducin. Within the COOH-terminal residues (46-87) of the phosphodiesterase gamma subunit, Trp-70 has been implicated in phosphodiesterase activation, transducin alpha subunit-phosphodiesterase gamma subunit interaction, and the GTP hydrolysis accelerating activity. We have derivatized the phosphodiesterase gamma subunit with a reversible photoactivatable reagent, [125I]N-[(3-iodo-4-azidophenylpropionamido-S-(2-thiopyridyl) ]cysteine ([125I]ACTP), at cysteine (Cys-68). A light-dependent, cross-linked complex of guanosine 5'-(gamma-thio)triphosphate-bound transducin alpha subunit and ACTPderivatized phosphodiesterase gamma subunit formed after photolysis of a 1:1 stoichiometic complex of the two proteins. The specificity of complex formation between the transducin alpha subunit and the phosphodiesterase gamma subunit was demonstrated by specific protection by the C68A mutant of the phosphodiesterase gamma subunit. The cross-linked complex was treated with beta-mercaptoethanol to transfer the 125I photomoiety from the phosphodiesterase gamma subunit to the transducin alpha subunit. Combined techniques involving electrophoresis, chemical and enzymatic cleavage, and chemical and radiosequencing were used to identify photoinsertion sites on the alpha3 and alpha4/beta6 regions of the transducin alpha subunit. Three photo-labeled residues, His-244 (alpha3 helix), Met-308, and Arg-310 (alpha4/beta6 interface), were specifically identified as photoinsertion sites. Utilizing the crystal structure coordinates of the GTP-bound transducin alpha subunit and molecular modeling, we conclude that Cys-68 of the phosphodiesterase gamma subunit is located at a position between the exposed face of the alpha3 and alpha4 helices of the transducin alpha subunit. We propose that the phosphodiesterase gamma subunit interacts with GTP-bound transducin alpha subunit at multiple sites in which the cysteine 68 to tryptophan 70 sequence of the phosphodiesterase gamma subunit, which is critical for GTP hydrolysis accelerating activity, interacts in the alpha3/alpha4/beta6 region of GTP-bound transducin alpha subunit.