Solution conformation of the Pseudomonas syringae MSU 16H phytotoxic lipodepsipeptide Pseudomycin A determined by computer simulations using distance geometry and molecular dynamics from NMR data

Abstract

Pseudomycin A is a cyclic lipodepsinonapeptide phytotoxin produced by a strain of the plant pathogenic bacterium Pseudomonas syringae. Like other members of this family of bacterial metabolites, it is characterised by a fatty acylated cyclic peptide with mixed chirality and lactonic closure. Several biological activities of Pseudomycin A are lower than those found for some of its congeners, a difference which might depend on the diverse number and distribution of charged residues in the peptide moiety. Hence, it was of interest to investigate its conformation in solution. After the complete interpretation of the two-dimensional NMR spectra, NOE data were obtained and the structure was determined by computer simulations, applying distance geometry and molecular dynamics procedures. The conformation of the large ring of Pseudomycin A in solution includes three rigid structural regions interrupted by three short flexible regions that act as hinges. The overall three-dimensional structure of the cyclic moiety is similar to that of previously studied bioactive lipodepsinonapeptides produced by other pseudomonads.Keywords : lipodepsinonapeptide ; molecular dynamics; NMR; Pseudomonas syringae; Pseudomycin A; solution structure. Pseudomycin A is the major component of a family of antimycotic lipodepsipeptides isolated from cultures of Pseudomonas syringae MSU 16H (Harrison et al., 1991), a bacterium proposed for the biocontrol of Ophiostoma (Ceratocystis) ulmi, the causal agent of the highly destructive Dutch elm disease (Lam et al., 1987). Recently, the covalent structure of this bacterial metabolite, including the chirality of amino acid residues (Ballio et al., 1994a), and some of its biological activities (Di Giorgio et al., 1997) have been reported. Pseudomycin A, as well as its congeners Pseudomycin B, Pseudomycin C and Pseudomycin C′, belongs to the group of pseudomonads lipodepsinonapeptides which includes Syringomycins (Segre et al., 1989;Fukuchi et al., 1990a), Syringotoxins (Ballio et al., 1990;Fukuchi et al., 1990b) and Syringostatins (Isogai et al., 1990). At variance with the latter metabolites, the pseudomycins contain an aspartate residue and a lysine residue in the peptide moiety, features which might influence their conformation and biological properties. A comparison between the activities of Pseudomycin A and SyrinCorrespondence to V. M. Coiro, Dipartimento di Chimica, Università di Roma 'La Sapienza', p.le Aldo Moro 5, I-00185 Rome, Italy Fax: ϩ39 6 490324. E-mail: coiro@monet.chem.uniroma1.it Abbreviations. A 2 bu, 2,4-diaminobutyric acid; Asp(OH), 3-hydroxyaspartic acid; 2D, two-dimensional; DG, distance geometry; allo-Thr, allo-threonine; Dhb, (Z)-2,3-dehydro-2-aminobutanoic acid; NOE, nuclear Overhauser effect; MD, molecular dynamics ; Thr(Cl), 4-chlorothreonine; TPPI, time proportional phase increment; SA, simulated annealing ; WLIP, white line inducing principle. gomycin E, the prototype of pseudomonad lipodepsinonapeptides, in a number of in vivo and in vitro biological tests has shown that, ...

Conformations in solution of the fuscopeptins

“…The conformation of the lactone ring is similar to that found in the two`small' lipodepsipeptides syringotoxin [20] and pseudomycin A [19] as well as in syringopeptin 25A. This conformation, resembling the seam of a tennis ball, was found for the first time in the bioactive lipodepsinonapeptide WLIP: white line inducing principle, produced by Pseudomonas reactans [25].…”

“…A motif of two consecutive hydrogen‐bonded turns (see Fig. 8) was previously observed in the lactone macrocycle of pseudomycin A [19].…”

“…Interproton distance restraints were estimated from two‐dimensional NOESY spectra. All NOEs were classified into three groups as strong, medium or weak and given upper limits r ij = 0.32, 0.40 and 0.50 nm, respectively [18], according to previous calculations on other lipodepsipeptides [6,19,20]. When possible, stereospecific assignments of prochiral methylene protons or methyl groups were made.…”

“…According to the procedure proposed by Nilges et al . [15] and to previous calculations performed on related lipodepsipeptides [6,19,20], we used 100 cycles of Powell minimization [21] of van der Waals’, bond and NOE terms and 100 subsequent cycles of the bond angle terms to improve the covalent geometry of the embedded structures. They were followed by a molecular dynamics simulation stage, starting at a temperature of 2000 K, to introduce the chirality and planarity.…”

Structure, conformation and biological activity of a novel lipodepsipeptide from Pseudomonas corrugata: cormycin A

“…The first one is formed by nonapeptide lactones acylated by a long chain of 3-hydroxy fatty acids. This group includes the SRs (syringomycins) [7,8], the STs (syringotoxins) [9], the SSs (syringostatins) [10] and the PSs (pseudomycins) [11]. The second group consists of lipopeptides formed by a long and highly hydrophobic peptide chain, containing a polar lactonized penta-or octa-peptide moiety at the C-terminus.…”