| 14454374 |
Role of valine and isoleucine as regulators of actinomycin peptide formation by Streptomyces chrysomallus |
10.1128/jb.82.4.600-608.1961. |
J Bacteriol |
Role of valine and isoleucine as regulators of actinomycin peptide formation by Streptomyces chrysomallus
Abstract
- Katz, Edward (Rutgers, The State University, New Brunswick, N. J.), Clarence R. Waldron, and Mary Lou Meloni. Role of valine and isoleucine as regulators of actinomycin peptide formation by Streptomyces chrysomallus. J. Bacteriol. 82:600-608. 1961-d-Valine is an effective inhibitor of actinomycin synthesis by Streptomyces chrysomallus; l-valine stimulates actinomycin production and reverses the inhibition due to the d-enantiomorph. The incorporation of l-valine into the medium results, particularly, in a marked increase in actinomycin IV formation. In studies with various isoleucine isomers it was shown that l-isoleucine enhances actinomycin VII production; the principal effect of d-alloisoleucine and, especially, d-isoleucine, is to bring about synthesis of two new actinomycins which contain N-methylisoleucine. Both l- and d-threonine were observed to have an effect similar to that obtained with l-isoleucine. An interpretation of these findings has been discussed.
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| 14501110 |
Structure of apo, unactivated insulin-like growth factor-1 receptor kinase at 1.5 A resolution |
10.1107/s0907444903015415. |
Acta Crystallogr D Biol Crystallogr |
Structure of apo, unactivated insulin-like growth factor-1 receptor kinase at 1.5 A resolution
Abstract
- The crystal structure of the wild-type unactivated kinase domain (IGFRK-0P) of insulin-like growth factor-1 receptor has been reported previously at 2.7 A resolution [Munshi et al. (2002), J. Biol. Chem. 277, 38797-38802]. In order to obtain a high-resolution structure, a number of variants of IGFRK-0P were prepared and screened for crystallization. A double mutant with E1067A and E1069A substitutions within the kinase-insert region resulted in crystals that diffracted to 1.5 A resolution. Overall, the structure of the mutant IGFRK-0P is similar to that of the wild-type IGFRK-0P structure, with the exception of the previously disordered kinase-insert region in the wild type having become fixed. In addition, amino-acid residues 947-952 at the N-terminus are well defined in the mutant structure. The monomeric protein structure is folded into two lobes connected by a hinge region, with the catalytic center situated at the interface of the two lobes. Two molecules of IGFRK-0P in the asymmetric unit are associated as a dimer and two different types of dimers with their ATP-binding clefts either facing towards or away from each other are observed. The current refined model consists of a dimer and 635 water molecules.
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| 14507218 |
A new cytotoxic and tubulin-interactive milnamide derivative from a marine sponge Cymbastela sp |
10.1021/ol035476c. |
Org Lett |
A new cytotoxic and tubulin-interactive milnamide derivative from a marine sponge Cymbastela sp
Abstract
- [structure: see text] The crude methanol extract of a marine sponge Cymbastela sp. collected in Papua New Guinea was selected for chemical investigation due to its significant cytotoxicity. Fractionation of the extract led to the isolation of jaspamide (1), hemiasterlin (2), milnamide A (3), and a new metabolite, milnamide D (4). The structure was solved by interpretation of NMR and mass spectra data. The cytotoxic and antitubulin activities of milnamide D (4) were evaluated.
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| 14525994 |
Spheniscins, avian beta-defensins in preserved stomach contents of the king penguin, Aptenodytes patagonicus |
10.1074/jbc.M306839200. |
J Biol Chem |
Spheniscins, avian beta-defensins in preserved stomach contents of the king penguin, Aptenodytes patagonicus
Abstract
- During the last part of egg incubation in king penguins, the male can preserve undigested food in the stomach for several weeks. This ensures survival of the newly hatched chick, in cases where the return of the foraging female from the sea is delayed. In accordance with the characterization of stress-induced bacteria, we demonstrate the occurrence of strong antimicrobial activities in preserved stomach contents. We isolated and fully characterized two isoforms of a novel 38-residue antimicrobial peptide (AMP), spheniscin, belonging to the beta-defensin subfamily. Spheniscin concentration was found to strongly increase during the period of food storage. Using a synthetic version of one of two spheniscin isoforms, we established that this peptide has a broad activity spectrum, affecting the growth of both pathogenic bacteria and fungi. Altogether, our data suggest that spheniscins and other, not yet identified, antimicrobial substances may play a role in the long term preservation of stored food in the stomach of king penguins.
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| 14531661 |
Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot |
10.1021/ja036677e. |
J Am Chem Soc |
Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot
Abstract
- The antibacterial peptide microcin J25 (MccJ25) inhibits bacterial transcription by binding within, and obstructing, the nucleotide-uptake channel of bacterial RNA polymerase. Published covalent and three-dimensional structures indicate that MccJ25 is a 21-residue cycle. Here, we show that the published covalent and three-dimensional structures are incorrect, and that MccJ25 in fact is a 21-residue "lariat protoknot", consisting of an 8-residue cyclic segment followed by a 13-residue linear segment that loops back and threads through the cyclic segment. MccJ25 is the first example of a lariat protoknot involving a backbone-side chain amide linkage.
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| 14531690 |
Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone |
10.1021/ja0367703. |
J Am Chem Soc |
Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone
Abstract
- Microcin J25 is a 21 amino acid bacterial peptide that has potent antibacterial activity against Gram-negative bacteria, resulting from its interaction with RNA polymerase. The peptide was previously proposed to have a head-to-tail cyclized peptide backbone and a tight globular structure (Blond, A., Péduzzi, J., Goulard, C., Chiuchiolo, M. J., Barthélémy, M., Prigent, Y., Salomón, R. A., Farías, R. N., Moreno, F. & Rebuffat, S. Eur. J. Biochem. 1999, 259, 747-755). It exhibits remarkable thermal stability for a peptide of its size lacking disulfide bonds and in part this was previously proposed to derive from its macrocyclic structure. We show here that in fact the peptide does not have a head-to-tail cyclic structure but rather a side chain to backbone cyclization between Glu8 and the N-terminus. This creates an embedded ring that is threaded by the C-terminal tail of the molecule, forming a noose-like feature. The three-dimensional structure deduced from NMR data suggests that slippage of the noose is prevented by two aromatic residues flanking the embedded ring. Unthreading does not occur even when the molecule is enzymatically digested with thermolysin. The new structural interpretation fully accounts for previously reported NMR and biophysical data and is consistent with the remarkable stability of this potent antimicrobial peptide.
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| 14532033 |
Functional analysis of the gene cluster involved in production of the bacteriocin circularin A by Clostridium beijerinckii ATCC 25752 |
10.1128/AEM.69.10.5839-5848.2003. |
Appl Environ Microbiol |
Functional analysis of the gene cluster involved in production of the bacteriocin circularin A by Clostridium beijerinckii ATCC 25752
Abstract
- A region of 12 kb flanking the structural gene of the cyclic antibacterial peptide circularin A of Clostridium beijerinckii ATCC 25752 was sequenced, and the putative proteins involved in the production and secretion of circularin A were identified. The genes are tightly organized in overlapping open reading frames. Heterologous expression of circularin A in Enterococcus faecalis was achieved, and five genes were identified as minimally required for bacteriocin production and secretion. Two of the putative proteins, CirB and CirC, are predicted to contain membrane-spanning domains, while CirD contains a highly conserved ATP-binding domain. Together with CirB and CirC, this ATP-binding protein is involved in the production of circularin A. The fifth gene, cirE, confers immunity towards circularin A when expressed in either Lactococcus lactis or E. faecalis and is needed in order to allow the bacteria to produce bacteriocin. Additional resistance against circularin A is conferred by the activity of the putative transporter consisting of CirB and CirD.
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| 14561762 |
A comparison of the self-association behavior of the plant cyclotides kalata B1 and kalata B2 via analytical ultracentrifugation |
10.1074/jbc.M306826200. |
J Biol Chem |
A comparison of the self-association behavior of the plant cyclotides kalata B1 and kalata B2 via analytical ultracentrifugation
Abstract
- The recently discovered cyclotides kalata B1 and kalata B2 are miniproteins containing a head-to-tail cyclized backbone and a cystine knot motif, in which disulfide bonds and the connecting backbone segments form a ring that is penetrated by the third disulfide bond. This arrangement renders the cyclotides extremely stable against thermal and enzymatic decay, making them a possible template onto which functionalities can be grafted. We have compared the hydrodynamic properties of two prototypic cyclotides, kalata B1 and kalata B2, using analytical ultracentrifugation techniques. Direct evidence for oligomerization of kalata B2 was shown by sedimentation velocity experiments in which a method for determining size distribution of polydisperse molecules in solution was employed. The shape of the oligomers appears to be spherical. Both sedimentation velocity and equilibrium experiments indicate that in phosphate buffer kalata B1 exists mainly as a monomer, even at millimolar concentrations. In contrast, at 1.6 mm, kalata B2 exists as an equilibrium mixture of monomer (30%), tetramer (42%), octamer (25%), and possibly a small proportion of higher oligomers. The results from the sedimentation equilibrium experiments show that this self-association is concentration dependent and reversible. We link our findings to the three-dimensional structures of both cyclotides, and propose two putative interaction interfaces on opposite sides of the kalata B2 molecule, one involving a hydrophobic interaction with the Phe6, and the second involving a charge-charge interaction with the Asp25 residue. An understanding of the factors affecting solution aggregation is of vital importance for future pharmaceutical application of these molecules.
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| 14574404 |
The DNA sequence and analysis of human chromosome 6. |
10.1038/nature02055 |
Nature |
The DNA sequence and analysis of human chromosome 6.
Abstract
- Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.
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| 14575437 |
Isolation and structure determination of lyngbyastatin 3, a lyngbyastatin 1 homologue from the marine cyanobacterium Lyngbya majuscula. Determination of the configuration of the 4-amino-2,2-dimethyl-3-oxopentanoic acid unit in majusculamide C, dolastatin 12, lyngbyastatin 1, and lyngbyastatin 3 from cyanobacteria |
10.1021/np0302145. |
J Nat Prod |
Isolation and structure determination of lyngbyastatin 3, a lyngbyastatin 1 homologue from the marine cyanobacterium Lyngbya majuscula. Determination of the configuration of the 4-amino-2,2-dimethyl-3-oxopentanoic acid unit in majusculamide C, dolastatin 12, lyngbyastatin 1, and lyngbyastatin 3 from cyanobacteria
Abstract
- The structure of lyngbyastatin 3 (1), including the configurations of the two unusual amino acid residues, viz., the 3-amino-2-methylhexanoic acid (Amha) and 4-amino-2,2-dimethyl-3-oxopentanoic acid units (Ibu), has been established by chemical degradation. Analysis of the cyanobacterial samples of lyngbyastatin 3 (1), lyngbyastatin 1 (2), and dolastatin 12 (3) demonstrated that they are mixtures of Ibu epimers [R (major) and S (minor)], whereas the structurally related majusculamide C (4) is a single diastereomer having an S-Ibu unit.
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| 14584933 |
Dissociation of antibacterial and hemolytic activities of an amphipathic peptide antibiotic |
10.1021/jm0341352. |
J Med Chem |
Dissociation of antibacterial and hemolytic activities of an amphipathic peptide antibiotic
Abstract
- Using an alanine-scanning method, we have found that the antibacterial and hemolytic activities of the amphipathic cyclic decapeptide antibiotic tyrocidine A depend on different structural components. Single substitution of glutamine-6 of the natural product with a cationic amino acid results in a therapeutic index enhancement of up to 140-fold. Successful dissociation of the two intimately associated properties should enable discovery of novel analogues with both high bacterial selectivity and antibacterial potency to counter microbial resistance.
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| 14594107 |
Effects of cortistatin-14 and somatostatin-14 on the endocrine response to hexarelin in humans |
10.1007/BF03347014. |
J Endocrinol Invest |
Effects of cortistatin-14 and somatostatin-14 on the endocrine response to hexarelin in humans
Abstract
- Cortistatin (CST)-14, a neuropeptide with high structural homology with somatostatine (SS)-14, binds all SS receptor subtypes but also shows activities not shared by SS. CST and SS are often co-expressed in the same neurons but are regulated by different stimuli. Moreover, CST, but not SS, also binds the GH secretagogue (GHS) receptor. We compared the effects of CST-14 and SS-14 (2.0 microg/kg/h i.v. from -30 to +90 min) on the endocrine response to hexarelin (HEX, 1.0 microg/kg i.v. at 0 min), a synthetic GHS, in 6 normal volunteers [age (mean+/-SEM): 28.7+/-2.9 yr; body mass index: 23.4+/-0.8 kg/m2]. GH, PRL, ACTH, cortisol, insulin and glucose levels were measured at each time point. CST-14 inhibited spontaneous GH secretion [delta-areas under curves (-AUC): -83.57+/-44.8 vs 2.3+/-2.7 microg/l/h, p<0.01] to the same extent of SS-14 (-186.1+/-162.9 microg/l/h, p<0.01). CST-14 as well as SS-14 also inhibited insulin secretion (p<0.05). The GH response to HEX was similarly inhibited by either CST-14 (AUC: 3814.1+/-924.2 vs 1212.9+/-379.8 microg/l/h, p<0.05) or SS-14 (720.9+/-158.6 microg/l/h, p<0.05). HEX significantly increased PRL, ACTH and cortisol levels but these responses were not modified by either CST-14 or SS-14. The effects of CST-14 and SS-14 on insulin and glucose levels were not modified by HEX. In conclusion, this study shows that CST-14 inhibits the GH response to HEX to the same extent of SS-14. Like SS-14, CST-14 also inhibits insulin secretion but both do not modify the stimulatory effects of HEX on lactotroph and corticotroph secretion. Thus, CST-14 exerts full SS-14 activity in humans.
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| 14594810 |
The role of lysine 532 in the catalytic mechanism of human topoisomerase I |
10.1074/jbc.M309959200. |
J Biol Chem |
The role of lysine 532 in the catalytic mechanism of human topoisomerase I
Abstract
- Based on co-crystal structures of human topoisomerase I with bound DNA, Lys(532) makes a minor groove contact with the strongly preferred thymidine residue at the site of covalent attachment (-1 position). Replacement of Lys(532) with either arginine or alanine has essentially no effect on the sequence preference of the enzyme, indicating that this interaction is not required for the preference for a T at the -1 position. Although both the cleavage and religation activities of the K532R mutant enzyme are reduced, cleavage is reduced to a greater extent than religation. The reverse is true for the K532A mutant enzyme with religation so impaired that the nicked intermediate accumulates during plasmid relaxation assays. Consistent with the shift in the cleavage religation equilibrium toward cleavage for the K532A mutant enzyme, expression of the mutant enzyme in Saccharomyces cerevisiae is cytotoxic, and thus this mutant enzyme mimics the effects of the anticancer drug camptothecin. Cleavage assays with the mutant enzymes using an oligonucleotide containing a 5'-bridging phosphorothiolate indicate that Lys(532) functions as a general acid during cleavage to protonate the leaving 5'-oxygen. It is possible that the contact with the -1 base is important during catalysis to provide positional rigidity to the active site. The corresponding residues in the vaccinia virus topoisomerase and the tyrosine recombinases may have similar critical roles in catalysis.
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| 14597613 |
Interactions of a family 18 chitinase with the designed inhibitor HM508 and its degradation product, chitobiono-delta-lactone |
10.1074/jbc.M310057200. |
J Biol Chem |
Interactions of a family 18 chitinase with the designed inhibitor HM508 and its degradation product, chitobiono-delta-lactone
Abstract
- We describe enzymological and structural analyses of the interaction between the family 18 chitinase ChiB from Serratia marcescens and the designed inhibitor N,N'-diacetylchitobionoxime-N-phenylcarbamate (HM508). HM508 acts as a competitive inhibitor of this enzyme with a K(i) in the 50 microM range. Active site mutants of ChiB show K(i) values ranging from 1 to 200 microM, providing insight into some of the interactions that determine inhibitor affinity. Interestingly, the wild type enzyme slowly degrades HM508, but the inhibitor is essentially stable in the presence of the moderately active D142N mutant of ChiB. The crystal structure of the D142N-HM508 complex revealed that the two sugar moieties bind to the -2 and -1 subsites, whereas the phenyl group interacts with aromatic side chains that line the +1 and +2 subsites. Enzymatic degradation of HM508, as well as a Trp --> Ala mutation in the +2 subsite of ChiB, led to reduced affinity for the inhibitor, showing that interactions between the phenyl group and the enzyme contribute to binding. Interestingly, a complex of enzymatically degraded HM508 with the wild type enzyme showed a chitobiono-delta-lactone bound in the -2 and -1 subsites, despite the fact that the equilibrium between the lactone and the hydroxy acid forms in solution lies far toward the latter. This shows that the active site preferentially binds the (4)E conformation of the -1 sugar, which resembles the proposed transition state of the reaction.
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| 14604342 |
Scytalidamides A and B, new cytotoxic cyclic heptapeptides from a marine fungus of the genus Scytalidium |
10.1021/jo030191z. |
J Org Chem |
Scytalidamides A and B, new cytotoxic cyclic heptapeptides from a marine fungus of the genus Scytalidium
Abstract
- Two new cyclic heptapeptides have been isolated from the culture broth of a marine fungus, Scytalidium sp., collected from the Bahamas. The planar structures of scytalidamides A (1) and B (2) were assigned on the basis of 1D and 2D NMR spectroscopic techniques, while the absolute configuration of the amino acid residues in both molecules was determined by application of the advanced Marfey's method. The absolute stereochemistry of the uncommon 3-methylproline moiety in scytalidamide B (2) was confirmed by isolation and CD measurements, as well as application of the advanced Marfey's method. Scytalidamides A (1) and B (2) showed moderate in vitro cytotoxicity toward HCT-116 human colon adenocarcinoma with IC(50) values of 2.7 and 11.0 microM, respectively.
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