The structure and function of antiamoebin I, a proline-rich membrane-active polypeptide

Snook, C.F.; Woolley, G. Andrew; Oliva, Glaucius; Pattabhi, Vasantha; Wood, Stephen P.; Blundell, T.L.; Wallace, B.A.

doi:10.1016/s0969-2126(98)00079-3

Cited by 68 publications

(66 citation statements)

References 41 publications

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“…The data used (Oliva, 1988;Snook et al, 1998) were collected at room temperature on a diffractometer using Ni-®ltered Cu K radiation. Data-collection statistics are listed in It was necessary to consider in detail the parameters used in both the rotation-and translation-function solutions.…”

Section: The Data and Parameters To Be Testedmentioning

confidence: 99%

“…The ®nal R factor for the re®ned structure (using all data to 1.4 A Ê and a full-matrix least-squares re®nement (SHELXL93; Sheldrick, 1993) was 15.4% (Snook et al, 1998).…”

Section: Translation Functionmentioning

confidence: 99%

“…peptide structures have been solved using molecular replacement, including endothelin using a partial NMR model (Janes et al, 1994), a gramicidin/potassium thiocyanate complex using a gramicidin/caesium chloride complex (Doyle & Wallace, 1997), a 24-mer peptitergent using a 24-mer polyalanine -helix (Schafmeister et al, 1993) and, most recently, two different structures of antiamoebin I (AAM) from Emercelliopsis poonensis, both using Leu1±zervamicin as the starting model (Karle et al, 1998;Snook et al, 1998). This paper will concentrate on the reciprocal-space techniques used for the AAM structure determined by Snook et al (1998) and will examine some of the MR parameters important for its solution.…”

Section: Introductionmentioning

confidence: 99%

“…This paper will concentrate on the reciprocal-space techniques used for the AAM structure determined by Snook et al (1998) and will examine some of the MR parameters important for its solution.…”

Section: Introductionmentioning

confidence: 99%

“…This paper presents the parameters which had to be considered in order to achieve a successful MR solution for the structure of the peptide antiamoebin I. Details of the re®nement, the structure and its functional characterizations have recently been published (Snook et al, 1998; Duclohier et al, 1998) and will not be repeated here.…”

Section: Introductionmentioning

confidence: 99%

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The molecular-replacement solution of an intermediate-sized helical polypeptide, antiamoebin I

Snook

Wallace

1999

Acta Crystallogr D Biol Cryst

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The successful use of molecular-replacement methods for the solution of the intermediate-sized helical polypeptide antiamoebin I required the careful consideration of a number of parameters and exhibited some unusual characteristics when compared with molecular-replacement solutions of globular proteins. High-resolution data were required owing to several features, including the comma-like shape of the molecule (which results in a pseudo-symmetric structure at low resolution), the relative uniformity of the structure in the direction along the helix axis and the small differences between the two independent molecules in the P1 asymmetric unit. Other parameters which were important for the solution of this relatively low solvent content closely packed cell included the radius of integration, the use of normalized structure factors and especially the choice of starting model.

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Section: The Data and Parameters To Be Testedmentioning

confidence: 99%

“…The ®nal R factor for the re®ned structure (using all data to 1.4 A Ê and a full-matrix least-squares re®nement (SHELXL93; Sheldrick, 1993) was 15.4% (Snook et al, 1998).…”

Section: Translation Functionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The molecular-replacement solution of an intermediate-sized helical polypeptide, antiamoebin I

Snook

Wallace

1999

Acta Crystallogr D Biol Cryst

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Characterization of a type of ?-bend ribbon spiral generated by the repeating (Xaa-Yaa-Aib-Pro) motif: The solution structure of harzianin HC IX, a 14-residue peptaibol forming voltage-dependent ion channels

et al. 1999

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The three‐dimensional solution structure of harzianin HC IX, a peptaibol antibiotic isolated from the fungus Trichoderma harzianum, was determined using CD, homonuclear, and heteronuclear two‐dimensional nmr spectroscopy combined with molecular modeling. This 14‐residue peptide, Ac Aib1 Asn2 Leu3 Aib4 Pro5 Ala6 Ile7 Aib8 Pro9 Iva10 Leu11 Aib12 Pro13 Leuol14 (Aib, α‐aminoisobutyric acid; Iva, isovaline; Leuol, leucinol), is a main representative of a short‐sequence peptaibol class characterized by an acetylated N‐terminus, a C‐terminal amino alcohol, and the presence of three Aib‐L‐Pro motifs at positions 4–5, 8–9, and 12–13, separated by two dipeptide units. In spite of a lower number of residues, compared to the 18/20‐residue peptaibols such as alamethicin, harzianin HC IX exhibits remarkable membrane‐perturbing properties. It interacts with phospholipid bilayers, increasing their permeability and forming voltage‐gated ion channels through a mechanism slightly differing from that proposed for alamethicin. Sequence‐specific 1H‐ and 13C‐nmr assignments and conformational nmr parameters (3JNHCαH coupling constants, quantitative nuclear Overhauser enhancement data, temperature coefficients of amide and carbonyl groups, NH–ND exchange rates) were obtained in methanol solution. Sixty structures were calculated based on 98 interproton distance restraints and 6 Φ dihedral angle restraints, using high temperature restrained molecular dynamics and energy minimization. Thirty‐seven out of the sixty generated structures were consistent with the nmr data and were convergent. The peptide backbone consists in a ribbon of overlapping β‐turns twisted into a continuous spiral from Asn2 to Leuol14 and forming a 26 Å long helix‐like structure. This structure is slightly amphipathic, with the three Aib–Pro motifs aligned on the less hydrophobic face of the spiral where the Asn2 side chain is also present, while the more hydrophobic bulky side chains of leucines, isoleucine, isovaline, and leucinol are located on the concave side. The repetitive (Xaa–Yaa–Aib–Pro) tetrapeptide subunit, making up the peptide sequence, is characterized by four sets of (Φ,Ψ) torsional angles, with the following mean values: Φi = −90°, Ψi = −27°; Φi+1 = −98°, Ψi+1 = −17°; Φi+2 = −49°, Ψi+2 = −50°; Φi+3 = −78°, Ψi+3 = +3°. We term this particular structure, specifically occurring in the case of (Xaa–Yaa–Aib–Pro)n sequences, the (Xaa–Yaa–Aib–Pro)‐β‐bend ribbon spiral. It is stabilized by 4 → 1 intramolecular hydrogen bonds and differs from both the canonical 310‐helix made of a succession of type III β‐turns and from the β‐bend ribbon spiral that has been described in the case of (Aib–Pro)n peptide segments. © 1999 John Wiley & Sons, Inc. Biopoly 50: 71–85, 1999

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New sequences and new fungal producers of peptaibol antibiotics antiamoebins

Jaworski

Brückner

2000

J. Peptide Sci.

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Mixtures of the microheterogeneous 16-mer peptaibol antibiotics called antiamoebins (AAM) have been isolated from the culture broths of strains of the filamentous fungi Stilbella erythrocephala ATCC 28144, Stilbella fimetaria CBS 548.84 and Gliocladium catenulatum CBS 511.66. Sequences were determined using on-line HPLC together with positive- and negative-ion electrospray ionization mass spectrometry. Some characteristic features are recognized in the mass spectrometric fragmentation pattern of AAM. From a sample originally used for sequencing AAM (from Hindustan Antibiotics, Ltd., Pimpri, Poona-411018, India), and a sample of AAM commercially available (from Sigma Chemicals, St. Louis, MO, USA) HPLC elution profiles and sequences were assigned. Further, sequences of AAM previously isolated from Emericellopsis synnematicola CBS 176.60 and Emericellopsis salmosynnemata CBS 382.62 were determined. The peptide designated AAM I was the most abundant in all isolates and its structure could be confirmed. AAM II was detectable as a minor component (1.9%) only in the original sample of AAM, but not in the other isolates. The structures of AAM III, IV and V, which had previously been partly assigned, were definitely established, and the new sequences AAM VI-XVI were elucidated. AAM showing Phe1/Leu1 or Phe1/Val1 exchange, respectively, are produced in amounts only by S. erythrocephala. Sequences, HPLC elution profiles ('fingerprints') and relative amounts of peptides of all isolates were correlated.

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The structure and function of antiamoebin I, a proline-rich membrane-active polypeptide

Cited by 68 publications

References 41 publications

The molecular-replacement solution of an intermediate-sized helical polypeptide, antiamoebin I

The molecular-replacement solution of an intermediate-sized helical polypeptide, antiamoebin I

Characterization of a type of ?-bend ribbon spiral generated by the repeating (Xaa-Yaa-Aib-Pro) motif: The solution structure of harzianin HC IX, a 14-residue peptaibol forming voltage-dependent ion channels

New sequences and new fungal producers of peptaibol antibiotics antiamoebins

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