A variable target intensity-restrained global optimization (VARTIGO) procedure for determining three-dimensional structures of polypeptides from NOESY data: Application to gramicidin-S

Xu, Yifeng; Sugár, István P.; Krishna, N. Rama

doi:10.1007/bf00227468

Cited by 52 publications

(86 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…GS is a cationic cyclic decapeptide with the primary structure [cyclo-(Val-Orn-Leu-D-Phe-Pro) 2 ] and has an antiparallel b-sheet structure supported by two type II 0 b-turns [5][6][7]. GS molecule is amphiphilic, with two charged Orn side chains and two D-Phe rings projecting from one side of the molecule and four hydrophobic Val and Leu side chains projecting from the other.…”

Section: Introductionmentioning

confidence: 99%

Gramicidin S identified as a potent inhibitor for cytochrome bd‐type quinol oxidase

Mogi

Shiomi

et al. 2008

FEBS Letters

View full text Add to dashboard Cite

Gramicidin S, a cationic cyclic decapeptide, exhibits the potent antibiotic activity through perturbation of lipid bilayers of the bacterial membrane. From the screening of natural antibiotics, we identified gramicidin S as a potent inhibitor for cytochrome bd-type quinol oxidase from Escherichia coli. We found that gramicidin S inhibited the oxidase with IC 50 of 3.5 lM by decreasing V max and the affinity for substrates but showed the stimulatory effect at low concentrations. Our findings would provide a new insight into the development of gramicidin S analogs, which do not share the target and mechanism with conventional antibiotics.

show abstract

Section: Introductionmentioning

confidence: 99%

Gramicidin S identified as a potent inhibitor for cytochrome bd‐type quinol oxidase

Mogi

Shiomi

et al. 2008

FEBS Letters

View full text Add to dashboard Cite

show abstract

“…Surprisingly, GS does not readily produce X-ray quality single crystals; hence, highly artificial crystallization conditions were applied in both cases, in part explaining these discrepancies. The picture is somewhat more consistent for the NMR-derived structures that have been obtained in membrane-mimicking solutions, such as dimethyl sulfoxide (DMSO) (13) or a CHCl 3 -methanol mixture (14), but in most NMR studies GS derivatives have been used rather than real GS. Most significantly, GS is a membrane-active peptide; hence, functionally relevant structural information should be acquired when it is bound to a genuine lipid bilayer.…”

Section: T He Cyclic Decapeptide Gramicidin S (Gs) Contains a Repeat mentioning

confidence: 79%

“…High-yield microbiological production of GS by fermentation of the natural producer Aneurinibacillus migulanus requires a growth medium that contains a large amount of amino nitrogen. This condition makes uniformly 13 C/ 15 N-labeled media very costly. Furthermore, the overall yields from nonribosomal peptide biosynthesis depend strongly on the individual amino acids supplemented, as they deviate in this respect from the "normal" biosynthesis involving ribosomes.…”

Section: T He Cyclic Decapeptide Gramicidin S (Gs) Contains a Repeat mentioning

confidence: 99%

See 1 more Smart Citation

Fermentation and Cost-Effective ¹³ C/ ¹⁵ N Labeling of the Nonribosomal Peptide Gramicidin S for Nuclear Magnetic Resonance Structure Analysis

Berditsch

Afonin

Steineker

et al. 2015

Appl Environ Microbiol

View full text Add to dashboard Cite

Gramicidin S (GS) is a nonribosomally synthesized decapeptide from Aneurinibacillus migulanus. Its pronounced antibiotic activity is attributed to amphiphilic structure and enables GS interaction with bacterial membranes. Despite its medical use for over 70 years, the peptide-lipid interactions of GS and its molecular mechanism of action are still not fully understood. Therefore, a comprehensive structural analysis of isotope-labeled GS needs to be performed in its biologically relevant membranebound state, using advanced solid-state nuclear magnetic resonance (NMR) spectroscopy. Here, we describe an efficient method for producing the uniformly 13 C/ 15 N-labeled peptide in a minimal medium supplemented by selected amino acids. As GS is an intracellular product of A. migulanus, we characterized the producer strain DSM 5759 (rough-convex phenotype) and examined its biosynthetic activity in terms of absolute and biomass-dependent peptide accumulation. We found that the addition of either arginine or ornithine increases the yield only at very high supplementing concentrations (1% and 0.4%, respectively) of these expensive 13 C/ 15 N-labeled amino acids. The most cost-effective production of 13 (Fig. 1A). Since its discovery about 70 years ago, GS has been used as a topical antibiotic in Russia and neighboring countries, exploiting its pronounced antimicrobial activity against Gram-positive bacteria (1, 2). For example, GS is the bioactive agent in GrammidinNeo, the lozenge against sore throat and mouth ulcer produced by the Russian JSC Valenta Pharmaceuticals. Notably, despite a long medication history, no clinical cases of bacterial resistance against GS have been reported, which suggest that this peptide may be an exceptionally promising resistance-free antibiotic (3).The biological activity of GS was first described as membranolytic, which is believed to determine its profound antimicrobial as well as hemolytic activities in vitro. Less acknowledged are GS activities not directly related to interaction with membrane bilayers: the peptide has been shown to inhibit membrane enzymes, such as bacterial NADH dehydrogenase and cytochrome bd terminal oxidase (4), and to delocalize the peripheral cell division regulator MinD, the lipid II biosynthesis protein MurG, and cytochrome c (5).The main molecular target of GS is supposed to be the plasma membrane of susceptible bacterial species, where an accumulation of the amphiphilic peptide leads to a loss of the barrier function and an irreversible increase in permeability for ions and metabolites (6). This concentration-dependent effect leads to membrane depolarization (7) and an overall dysfunction of the cellular osmoregulation, which starts already at GS levels well below the respective MICs (8). However, the structure-function relationship of the peptide and its detailed molecular mechanism of action at the plasma membrane, i.e., its interaction with the lipid bilayer, are still lacking a consensus view.Over the last decades, the molecular structure of GS has been stud...

show abstract

“…The primary molecular target of GS is the cellular membrane, though the detailed mechanism of its cytotoxic activity is still a matter of debate (20,29,32,49). Due to its high stability and simple structure, GS is also commonly used as a reference compound in mass spectrometry and nuclear magnetic resonance spectroscopy, and it has served as a model peptide for studying functional mechanisms of membrane-active peptides (9,16,18,30,37,41,42,50). Unfortunately, however, chemically pure GS is no longer available from any open commercial sources (for example, Sigma-Aldrich stopped placing it in their catalogue as of 2000).…”

Section: Gramicidin S (Gs) Is a Cyclic Decapeptide ([Fpvolfpvol] Cyclo )mentioning

confidence: 99%

The Ability ofAneurinibacillus migulanus(Bacillus brevis) To Produce the Antibiotic Gramicidin S Is Correlated with Phenotype Variation

Berditsch

Afonin

Ulrich

2007

Appl Environ Microbiol

View full text Add to dashboard Cite

Phenotype instability of bacterial strains can cause significant problems in biotechnological applications, since industrially useful properties may be lost. Here we report such degenerative dissociation for Aneurinibacillus migulanus (formerly known as Bacillus brevis) an established producer of the antimicrobial peptide gramicidin S (GS). Phenotypic variations within and between various strains maintained in different culture collections are demonstrated. The type strain, ATCC 9999, consists of six colony morphology variants, R, RC, RP, RT, SC, and SP, which were isolated and characterized as pure cultures. Correlations between colony morphology, growth, GS production, spore formation, and resistance to their own antimicrobial peptide were established in this study. We found the original R form to be the best producer, followed by RC, RP, and RT, while SC and SP yielded no GS at all. Currently available ATCC 9999 T contains only 2% of the original R producer and is dominated by the newly described phenotypes RC and RP. No original R form is detected in the nominally equivalent strain DSM 2895 T (‫؍‬ATCC 9999 T ), which grows only as SC and SP phenotypes and has thus completely lost its value as a peptide producer. Two other strains from the same collection, DSM 5668 and DSM 5759, contain the unproductive SC variant and the GS-producing RC form, respectively. We describe the growth and maintenance conditions that stabilize certain colony phenotypes and reduce the degree of degenerative dissociation, thus providing a recommendation for how to revert the nonproducing smooth phenotypes to the valuable GS-producing rough ones.

show abstract

A variable target intensity-restrained global optimization (VARTIGO) procedure for determining three-dimensional structures of polypeptides from NOESY data: Application to gramicidin-S

Cited by 52 publications

References 43 publications

Gramicidin S identified as a potent inhibitor for cytochrome bd‐type quinol oxidase

Gramicidin S identified as a potent inhibitor for cytochrome bd‐type quinol oxidase

Fermentation and Cost-Effective ¹³ C/ ¹⁵ N Labeling of the Nonribosomal Peptide Gramicidin S for Nuclear Magnetic Resonance Structure Analysis

The Ability ofAneurinibacillus migulanus(Bacillus brevis) To Produce the Antibiotic Gramicidin S Is Correlated with Phenotype Variation

Contact Info

Product

Resources

About

A variable target intensity-restrained global optimization (VARTIGO) procedure for determining three-dimensional structures of polypeptides from NOESY data: Application to gramicidin-S

Cited by 52 publications

References 43 publications

Gramicidin S identified as a potent inhibitor for cytochrome bd‐type quinol oxidase

Gramicidin S identified as a potent inhibitor for cytochrome bd‐type quinol oxidase

Fermentation and Cost-Effective 13 C/ 15 N Labeling of the Nonribosomal Peptide Gramicidin S for Nuclear Magnetic Resonance Structure Analysis

The Ability ofAneurinibacillus migulanus(Bacillus brevis) To Produce the Antibiotic Gramicidin S Is Correlated with Phenotype Variation

Contact Info

Product

Resources

About

Fermentation and Cost-Effective ¹³ C/ ¹⁵ N Labeling of the Nonribosomal Peptide Gramicidin S for Nuclear Magnetic Resonance Structure Analysis