Functional Genome Mining Reveals a Class V Lanthipeptide Containing a d‐Amino Acid Introduced by an F420H2‐Dependent Reductase

Lantibiotics are a type of ribosomally synthesized and post‐translationally modified peptides (termed lanthipeptides) with often potent antimicrobial activity. Herein, we report the discovery of a new lantibiotic, lexapeptide, using the library expression analysis system (LEXAS) approach. Lexapeptide has rare structural modifications, including N‐terminal (N,N)‐dimethyl phenylalanine, C‐terminal (2‐aminovinyl)‐3‐methyl‐cysteine, and d ‐Ala. The characteristic lanthionine moiety in lexapeptide is formed by three proteins (LxmK, LxmX, and LxmY), which are distinct from enzymes known to be involved in lanthipeptide biosynthesis. Furthermore, a novel F₄₂₀H₂‐dependent reductase (LxmJ) from the lexapeptide biosynthetic gene cluster (BGC) is identified to catalyze the reduction of dehydroalanine to install d ‐Ala. Our findings suggest that lexapeptide is the founding member of a new class of lanthipeptides that we designate as class V. We also identified further class V lanthipeptide BGCs in actinomycetes and cyanobacteria genomes, implying that other class V lantibiotics await discovery.     

Discovery of the Lanthipeptide Curvocidin and Structural Insights into its Trifunctional Synthetase CuvL

Lanthipeptides are ribosomally-synthesized natural products from bacteria featuring stable thioether-crosslinks and various bioactivities. Herein, we report on a new clade of tricyclic class-IV lanthipeptides with curvocidin from Thermomonospora curvata as its first representative. We obtained crystal structures of the corresponding lanthipeptide synthetase CuvL that showed a circular arrangement of its kinase, lyase and cyclase domains, forming a central reaction chamber for the iterative substrate processing involving nine catalytic steps. The combination of experimental data and artificial intelligence-based structural models identified the N-terminal subdomain of the kinase domain as the primary site of substrate recruitment. The ribosomal precursor peptide of curvocidin employs an amphipathic α-helix in its leader region as an anchor to CuvL, while its substrate core shuttles within the central reaction chamber. Our study thus reveals general principles of domain organization and substrate recruitment of class-IV and class-III lanthipeptide synthetases.     

An Amphipathic Alpha‐Helix Guides Maturation of the Ribosomally‐Synthesized Lipolanthines

The recently discovered strongly anti‐Gram‐positive lipolanthines represent a new group of lipidated, ribosomally synthesized and post‐translationally modified peptides (RiPPs). They are bicyclic octapeptides with a central quaternary carbon atom (avionin), which is installed through the cooperative action of the class‐III lanthipeptide synthetase MicKC and the cysteine decarboxylase MicD. Genome mining efforts indicate a widespread distribution and unprecedented biosynthetic diversity of lipolanthine gene clusters, combining elements of RiPPs, polyketide and non‐ribosomal peptide biosynthesis. Utilizing NMR spectroscopy, we show that a (θxx)θxxθxxθ (θ=L, I, V, M or T) motif, which is conserved in the leader peptides of all class‐III and ‐IV lanthipeptides, forms an amphipathic α‐helix in MicA that destines the peptide substrate for enzymatic processing. Our results provide general rules of substrate recruitment and enzymatic regulation during lipolanthine maturation. These insights will facilitate future efforts to rationally design new lanthipeptide scaffolds with antibacterial potency.     

A Lanthipeptide‐like N‐Terminal Leader Region Guides Peptide Epimerization by Radical SAM Epimerases: Implications for RiPP Evolution

Ribosomally synthesized and posttranslationally modified peptide natural products (RiPPs) exhibit diverse structures and bioactivities and are classified into distinct biosynthetic families. A recently reported family is the proteusins, with the prototype members polytheonamides being generated by almost 50 maturation steps, including introduction of d ‐residues at multiple positions by an unusual radical SAM epimerase. A region in the protein‐like N‐terminal leader of proteusin precursors is identified that is crucial for epimerization. It resembles a precursor motif previously shown to mediate interaction in thioether bridge‐formation in class I lanthipeptide biosynthesis. Beyond this region, similarities were identified between proteusin and further RiPP families, including class I lanthipeptides. The data suggest that common leader features guide distinct maturation types and that nitrile hydratase‐like enzymes are ancestors of several RiPP classes.     

Stabilities and Coordination Modes of α-Alaninephosphonic Acid in Copper(II) Heteroligand Complexes with Ethylenediamine, Diethylenetriamine or N,N,N′,N′,N″-Pentamethyldiethylene Triamine in Aqueous Solution

Solution equilibrium studies on Cu²⁺–L₁–L₂ ternary systems have been performed by pH-potentiometry, UV–Vis spectrophotometry and EPR methods (L₁ corresponds to polyamines such as ethylenediamine (en), diethylenetriamine (dien), or N,N,N′,N′,N″-pentamethyldiethylenetriamine (Me₅dien) and L₂ represents 1-aminoethylphosphonic acid (α-alaninephosphonic acid)). The obtained results suggest the formation of heteroligand complexes with [Cu(L₁)(α-Ala(P))] stoichiometry in all studied systems. Additionally, in the system with en the [Cu(en)(α-Ala(P))H₋₁]⁻ species is formed in basic solution. Our spectroscopic results indicate tetragonal geometry for the [Cu(en)(α-Ala(P))] species, geometry slightly deviated from square pyramidal for the [Cu(dien)(α-Ala(P))] complex and strongly deviated from square pyramidal towards trigonal bipyramidal for the [Cu(Me₅dien)(α-Ala(P))] species. The coordination modes in these heteroligand complexes are discussed.     

Estimation of binding constants between ristocetin and teicoplanin and peptides using on-column ligand derivatization coupled to affinity capillary electrophoresis

This work utilizes on-column ligand synthesis and affinity capillary electrophoresis (ACE) to determine binding constants (K_b) of 9-flourenylmethyloxy carbonyl (Fmoc)-amino acid derivatives to the glycopeptide antibiotics ristocetin (Rist) and teicoplanin (Teic). In this technique, two separate plugs of sample are injected on to the capillary column and electrophoresed. The initial sample plug contains a d-Ala-d-Ala terminus peptide and either one or two non-interacting standard(s). The second plug contains a Fmoc-amino acid-N-hydroxysuccinimide (NHS) ester. The electrophoresis is then carried out with an increasing concentration of Rist or Teic in the running buffer. Upon electrophoresis the initial d-Ala-d-Ala peptide reacts with the Fmoc-amino acid yielding a new Fmoc-amino acid-d-Ala-d-Ala peptide derivative. Continued electrophoresis results in the binding of Rist or Teic to the Fmoc-amino acid-d-Ala-d-Ala peptide derivatives. Analysis of the change in the relative migration time ratio (RMTR) or electrophoretic mobility () of the Fmoc-amino acid-d-Ala-d-Ala peptide derivatives relative to the non-interacting standards, as a function of the concentration of Rist and Teic, yields a value for K_b. These findings demonstrate the advantage of coupling on-column ligand synthesis to ACE for estimating binding parameters between antibiotics and ligands.Abbreviations Rist Ristocetin - Teic Teicoplanin - ACE Affinity capillary electrophoresis - RMTR Relative migration time ratio     

Electrogenerated Chemiluminescence of Lucigenin in Ethanol Solution at a Polycrystalline Gold Electrode

The electrogenerated chemiluminescence (ECL) behavior of lucigenin in ethanol solution at a polycrystalline gold electrode was studied under conventional cyclic voltammetric conditions. Compared with the ECL of lucigenin in aqueous solution, one cathodic ECL peak (ECL‐1 at ?0.98 V versus SCE) with a shoulder (S₁ at ?0.42 V) and three new anodic ECL peaks (ECL‐2 at ?0.53 V, ECL‐3 at 0.20 V, and ECL‐4 at 0.51 V) were observed, respectively, on the curve of ECL intensity versus potential. The effects of initial potential scan direction, the presence of O₂ or N₂, potential scan ranges, supporting electrolyte and the concentration of lucigenin on these ECL peaks were examined. The electrochemistry of lucigenin in ethanol solution was also studied. The emitter of all ECL peaks was identified as N‐methylacridone (NMA) by analyzing the ECL spectra. The mechanism for these ECL peaks is proposed to be due to the reactions of lucigenin and its redox products such as Luc and DBA with dissolved oxygen or O₂ electrogenerated by the dissolved oxygen at different potentials. The formation of new anodic ECL peaks in ethanol solution is due to longer lifetime of superoxide ions and easier electro‐oxidation of DBA in nonaqueous solution, revealing that the solvent plays an important role in the lucigenin ECL reactions.     

Discovery of daspyromycins A and B, 2-aminovinyl-cysteine containing lanthipeptides,through a genomics-based approach

Lanthipeptides are one of the largest groups of ribosomally synthesized and post-translationally modified peptides(RiPPs) and are characterized by the presence of lanthionine(Lan) or methyllanthionine residues(MeLan). Only very few lanthipeptides contain a C-terminal 2-aminovinyl-cysteine(AviCys) motif, but all of them show potent antibacterial activities. Recent advances of genome sequencing led to the rapid accumulation of new biosynthetic gene clusters(BGCs) for lanthipeptides. In this study,...     

Determination of Binding Constants of Polyethylene Glycol Vancomycin Derivatives to Peptide Ligands Using Affinity Capillary Electrophoresis

Vancomycin (Van) from Streptomyces orientalis has been derivatized with polyethylene glycol [PEG; PEG-550 (1), 750 (2), 1,100 (3), 2,000 (4), 5,000 (5), and 8,000 (6) g mol⁻¹] at the N-terminus of the glycopeptide backbone and their binding to d-Ala-d-Ala terminus peptides assessed using affinity capillary electrophoresis (ACE). Utilizing ACE, a plug of Van-PEG and non-interacting standards are injected and electrophoresed. Analysis of the change in the relative migration time ratio of the Van-PEG species, relative to the non-interacting standards, as a function of the concentration of peptide, yields a value for the binding constant (K _b). Values of K _b for N-acetyl-d-Ala-d-Ala, 7 to the Van-PEG derivatives are weaker than those for N _α,N _ε-diacetyl-Lys-d-Ala-d-Ala, 8 (for example, values of K _b for 7-1 and 8-1 are 1.8 and 47.7 × 10³ M⁻¹, respectively). These results demonstrate that derivatization of Van with PEG has little effect on the affinity of d-Ala-d-Ala peptide ligands to it. The findings further prove the versatility of ACE and its ability to estimate binding parameters of ligands to antibiotics.     

Preparation and Structure of Melemium Melem Perchlorate HC6N7(NH2)3ClO4·C6N7(NH2)3

A new perchlorate salt of melem (2,6,10‐triamino‐s‐heptazine, C₆N₇(NH₂)₃) was obtained from an aqueous solution of HClO₄ at lower concentration than the ones reported for the synthesis of melemium perchlorate monohydrate (HC₆N₇(NH₂)₃)ClO₄·H₂O. The new salt was identified as melemium melem perchlorate (HC₆N₇(NH₂)₃)ClO₄·C₆N₇(NH₂)₃ representing a melem adduct of water free melemium perchlorate. The crystal structure was solved by single‐crystal X‐ray methods ( , no. 2, Z = 2, a = 892.1(2), b = 992.7(2), c = 1201.5(2) pm, α = 112.30(3), β = 96.96(3), γ = 95.38(3)°, V = 965.8(4)·10⁶ pm³, 4340 data, 387 parameters, R1 = 0.039). Melemium melem perchlorate crystallizes in a layer‐like structure containing both protonated HC₆N₇(NH₂)₃ and non protonated C₆N₇(NH₂)₃ moieties in the coplanar layers as well as perchlorate ions between them, all of which being interconnected by hydrogen bonds. Vibrational spectroscopic investigations (FTIR and Raman) of the salt were conducted.     

A Comparative Study of Stabilities and Coordination Modes of β-Alaninephosphonic Acid in Copper(II) Heteroligand Complexes with Ethylenediamine, Diethylenetriamine or N,N,N′,N′,N″-Pentamethyldiethylene Triamine in Aqueous Solution

Solution equilibrium studies on Cu²⁺?CL₁?CL₂ ternary systems have been performed by pH-potentiometry, UV?CVis spectrophotometry and EPR methods {where L₁ corresponds to a polyamine such as ethylenediamine (en), diethylenetriamine (dien), N,N,N??,N??,N??-pentamethyldiethylenetriamine (Me₅dien)} and L₂ denotes 2-aminoethylphosphonic acid (??-alaninephosphonic acid)}. The results suggest the formation of heteroligand complexes with [Cu(L₁)(??-Ala(P))] stoichiometry in all of the studied systems. Additionally, in the system with en, [Cu(en)(??-Ala(P))H_?1]^? is formed in basic solutions. Our spectroscopic results indicate tetragonal geometry for the [Cu(en)(??-Ala(P))] species, a geometry slightly deviated from square pyramidal for the [Cu(dien)(??-Ala(P))] complex, and somewhat stronger geometry distortion was present for the [Cu(Me₅dien)(??-Ala(P))] complex. The coordination modes in these heteroligand complexes are discussed.     

Asymmetric synthesis ofS-alkyl-substituted (R)-cysteinesvia a chiral NiII complex of the Schiff's base of dehydroalanine with (S)-2-N-(N-benzylprolyl)aminobenzophenone

An efficient procedure was developed for the asymmetric synthesis ofS-alkyl derivatives of (R)-cysteine by nucleophilic addition of alkanethiols (BuⁿSH, Bu^tSH, ortert-C₅H₁₁SH) to the C=C bond of the dehydroalanine fragment in the Ni^II complex of the Schiff's base of Δ-Ala with (S)-2-N-(N-benzylprolyl)aminobenzophenone [(S)-BPB-Δ-Ala]Ni^II. Under conditions of thermodynamic control of the reaction, the diastereomeric excess of the complexes with the (S.R)-configuration was 88–96%. After decomposition of the complexes,(R)-S-butylcysteine,(R)-S-tert-butylcysteine, and(R)-S-tert-pentylcysteine were isolated with an enantiomeric purity of >97%. Published inIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1467–1470, August, 2000.     

Development of Entanglements in a Fully Disentangled Polymer Melt

A long‐lived metastable “new melt” state of polymers has been recently reported, where monomers exhibit different mobilities due to an unusual distribution of entanglements. We study the relaxation of (fully disentangled) globules to the entangled state by means of computer simulations, and compare our data to the scenario of de Gennes' explosion upon melting. The entanglement length N_e is measured using the primitive path analysis method. The results show that in the case of relatively short chains (N ≈ 20N_e), the relaxation of the entanglement length is very fast compared to that of the chains' size which slows down as the chain length N exceeds the equilibrium value of N_e.

     

Synthesis and characterization of oxovanadium(IV), vanadium(IV) and oxovanadium(V) complexes of tetradentate Schiff bases. Attempted preparation of vanadium-carbon bonded compounds through desilylation

Condensation of 1,3-diaminopropane-2-ol with diacetylmonoxime, acetylacetone, salicylaldehyde and orthohydroxyacetophenone yielded the tetradentate Schiff bases N,N′-(2-hydroxy)propylenebis{(2-imino-3-oximino)butane} (H₂dampnol), N,N′-(2-hydroxy)propylenebis(acetylacetoneimine) (H₂acacpnol), N,N′-(2-hydroxy)propylenebis-(salicyalaldimine) (H₂salpnol) and N,N′-(2-hydroxy)propylenebis(7-methylsalicylaldimine) (H₂ohacpnol), respectively. The ligands form complexes with oxovanadium(IV), vanadium(IV) and oxovanadium(V) salts. Some mixed ligand complexes involving σ-bonded phenyl and benzyl radical along with tetradentate ligand, H₂L (where, H₂L stands for H₂dampnol, H₂acacpnol, H₂salpnol or H₂ohacpnol) of the types [(L)V(C₆H₅)₂]CH₃OH and [(L)V(CH₂Ph)₂]CH₃OH have been synthesized, characterized and also provide the syntheses of some new organovanadium(IV) complexes. Silylation coupled with desilylation have been employed as a route to new organovanadium(IV) complexes. All the complexes have been characterized with the help of elemental analyses, molar conductance values, molecular weights, magnetic moments and spectroscopic (IR, UV-Vis, ESR) data.     

Kinetics and mechanism of oxidation of β-Alanine by <Emphasis Type="Italic">N</Emphasis>-bromophthalimide in the presence of Ru(III) chloride as homogenous catalyst in acidic medium

The kinetics of Ru(III) chloride-catalyzed oxidation of β-Alanine (NH₃ ⁺CH₂CH₂COOH, β-Ala) by N–bromophthalimide (NBP) in aqueous perchloric acid medium was studied at 35 °C. The rate law followed a first-order and zero-order dependence with respect to [NBP] and [β-Ala], respectively. The reaction followed first-order kinetics with respect to [Ru(III)] chloride at a range of low concentrations while the order changed from first- to zero-order at high concentration of [Ru(III)] chloride; demonstrating the catalytic effect for the oxidation of β-Ala by NBP. The rate decreased with increase in acidity. Chloride ions positively influenced the rate of the reaction. Neither phthalimide (NHP) nor Hg(II) influenced the reaction rate. Ionic strength (I) and dielectric constant (D) of the medium had no significant effect on the rate. Activation parameters of the reactions were determined by studying the reaction at different temperatures (30–50 °C). The colorimetric, FTIR, and GC-MS techniques were used to identify methyl cyanide (CH₃CN) and CO₂ as products of the reaction. In the reaction, approximately 2.3 moles of NBP oxidized one mole of β-Ala. A reaction scheme of the oxidation of β-Ala by NBP in the presence of Ru(III) chloride was found to be in consistent with the rate law and the reaction stoichiometry.     

The interaction of antitumor active vanadocene dichloride with sulfur-containing amino acids

Vanadocene dichloride (1) reacts with sulfur-containing amino acids, cysteine and methionine, giving new complexes with five- or six-membered chelate ring, but the structure of isolated compounds is affected by the pH value of the reaction mixture. Methionine reacts with aqueous 1 in the pH range of 3-8 affording chelate structure [Cp₂V(N,O-met)]Cl (4). Similar reaction with cysteine gives two different products depending on pH. In the acidic solution, the complex [Cp₂V(O,S-cys)]Cl (2) is present, whereas in neutral media the compound [Cp₂V(N,S-cys)] (3) could be identified. On inspection of spectroscopic measurements, particularly EPR and vibrational spectroscopy, it is evident that sulfur atom of amino acid is bonded directly to the vanadium atom of [Cp₂V]²⁺ moiety. For the purpose of comparison the complexes [Cp₂V(O,S-mpa)] (5) and [Cp₂V(N,S-csam)]⁺ (6a) with related chelating ligands, 3-mercaptopropionic acid (mpa) and cysteamine (csam), respectively, were prepared and spectroscopically characterized. The structure of the complex [Cp₂V(N,S-csam)]BPh₄ (6b) was also determined by X-ray diffraction analysis.     

Non-Dissociative Activation of Chemisorbed Dinitrogen on One or Two Vanadium Atoms Supported by a Mo6S8 Cluster

Adsorption of N₂ on Mo₆S₈^q_V_x clusters (x=0, 1, 2; q=0, ±1) were systematically studied by density functional theory calculations with dispersion corrections. It was found that the N₂ can be chemisorbed and undergo non-dissociative activation on single or double metal atoms. The adsorption and activation are influenced by metal types (V or Mo), N₂ coordination modes and charge states of the clusters. Particularly, anionic Mo₆S₈⁻_V₂ clusters have remarkable ability to fix and activate N₂. In Mo₆S₈⁻_V₂, two V atoms prefer to adsorb on two adjacent S−Mo−S hollow sites, leading to the formation of a supported V…V unit. The N₂ is bridged side-on coordinated with these two V atoms with high adsorption energy and significant charge transfer. The bond order, bond length and vibration frequency of the adsorbed N₂ are close to those of a N−N single bond.     

A five‐coordinate iron(III) porphyrin complex including a neutral axial pyridine N‐oxide ligand

While six‐coordinate iron(III) porphyrin complexes with pyridine N‐oxides as axial ligands have been studied as they exhibit rare spin‐crossover behavior, studies of five‐coordinate iron(III) porphyrin complexes including neutral axial ligands are rare. A five‐coordinate pyridine N‐oxide–5,10,15,20‐tetraphenylporphyrinate–iron(III) complex, namely (pyridine N‐oxide‐κO)(5,10,15,20‐tetraphenylporphinato‐κ⁴N,N′,N′′,N′′′)iron(III) hexafluoroantimonate(V) dichloromethane disolvate, [Fe(C₄₄H₂₈N₄)(C₅H₅NO)][SbF₆]·2CH₂Cl₂, was isolated and its crystal structure determined in the space group P. The porphyrin core is moderately saddled and the Fe—O—N bond angle is 122.08 (13)°. The average Fe—N bond length is 2.03 Å and the Fe—ONC₅H₅ bond length is 1.9500 (14) Å. This complex provides a rare example of a five‐coordinate iron(III) porphyrin complex that is coordinated to a neutral organic ligand through an O‐monodentate binding mode.     

Following the streambed reaction on potential-energy surfaces: a new robust method

A simple procedure with low computational efforts is proposed to follow the reaction path of the potential-energy hypersurface (PES) starting from minima or saddle points. The method uses a modification of the so-called “following the reduced gradient” [Quapp W, Hirsch M, Imig O, Heidrich D (1998) J Comput Chem 19:1087]. The original method connects points where the gradient has a constant direction. In the present article the procedure is replaced by taking iterative varying directions of the gradient controlled by the last tangent of the searched curve. The resulting minimum energy path is that valley floor gradient extremal (GE) which belongs to the smallest (absolute) eigenvalue of the Hessian and, hence, that GE which usually leads along the streambed of a chemical reaction. The new method avoids third derivatives of the PES and obtains the GE of least ascent by second-order calculations only. Nevertheless, we are able to follow the streambed GE uphill or downhill. We can connect a minimum with its saddles if the streambed leads up to a saddle, or we find a turning point or a bifurcation point. The effectiveness and the characteristic properties of the new algorithm are demonstrated by using polynomial test surfaces, an ab initio PES of H₂O, and the analytic potentials of Lennard-Jones (LJ) clusters. By tracing the streambeds we located previously identified saddle points for LJ _N with N=3, 7, 8, and 55. Saddles for LJ _N with N=15, 20, and 30 as presented here are new results. Received: 8 March 2000 / Accepted: 17 July 2000 / Published online: 24 October 2000     

Correction: Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways

Lanthipeptides are characterized by thioether crosslinks formed by post-translational modifications. The cyclization process that favors a single ring pattern over many other possible ring patterns has been the topic of much speculation. Recent studies suggest that for some systems the cyclization pattern and stereochemistry is determined not by the enzyme, but by the sequence of the precursor peptide. However, the factors that govern the outcome of the cyclization process are not understood. This study presents the three-dimensional structures of seven lanthipeptides determined by nuclear magnetic resonance spectroscopy, including five prochlorosins and the two peptides that make up cytolysin, a virulence factor produced by Enterococcus faecalis that is directly linked to human disease. These peptides were chosen because their substrate sequence determines either the ring pattern (prochlorosins) or the stereochemistry of cyclization (cytolysins). We present the structures of prochlorosins 1.1, 2.1, 2.8, 2.10 and 2.11, the first three-dimensional structures of prochlorosins. Our findings provide insights into the molecular determinants of cyclization as well as why some prochlorosins may be better starting points for library generation than others. The structures of the large and small subunits of the enterococcal cytolysin show that these peptides have long helical stretches, a rare observation for lanthipeptides characterized to date. These helices may explain their pore forming activity and suggest that the small subunit may recognize a molecular target followed by recruitment of the large subunit to span the membrane.

To understand factors that determine ring pattern and stereochemistry of thioether cyclization of lanthipeptide natural products, the structures of five prochlorosins (blue) and two enterococcal cytolysins (red) were determined by NMR spectroscopy.