Backbone dynamics of the channel‐forming antibiotic zervamicin IIB studied by ¹⁵N NMR relaxation

Abstract

The backbone dynamics of the channel-forming peptide antibiotic zervamicin IIB (Zrv-IIB) in methanol were studied by 15 N nuclear magnetic resonance relaxation measurements at 11.7, 14.1 and 18.8 T magnetic fields. The anisotropic overall rotation of the peptide was characterized based on 15 N relaxation data and by hydrodynamic calculations.`Model-free' analysis of the relaxation data showed that the peptide is fairly rigid on a sub-nanosecond time-scale. The residues from the polar side of Zrv-IIB helix are involved in micro^millisecond time-scale conformational exchange. The conformational exchange observed might indicate intramolecular processes or specific intermolecular interactions of potential relevance to Zrv-IIB ion channel formation. ß 2001 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.

Antiamoebin I in Methanol Solution: Rapid Exchange between Right‐Handed and Left‐Handed 310‐Helical Conformations

“…These large errors are possibly originated from the dependence of Dd( N-nuclei relaxation is a standard NMR method, which can give a detailed information about motions in the peptide backbone. A previous application of this approach to zervamicin revealed a conformational exchange process on the polar face of the peptide helix [52]. In case of antiamoebin, the presently observed exchange process that involves seven residues (Phe 1 -Gly 6 and Aib 8 ) should also seriously influence the relaxation of the 15 N-nuclei.…”

“…It should be noted that Zrv-IIB also exhibits a conformational exchange process in MeOH solution [52], but this process is localized on a few residues and is caused by fluctuation (a/3 10 ) of helical H-bonds [39]. The high motional propensity might significantly influence the dynamic behavior of antiamoebin in H 2 O and in the membrane-bound states.…”

“…The parameters for Karplus equation for 3 J H a N (dependence from torsion angle y) were taken from [37]. The T1 and T2 relaxation times for the 15 N nuclei ( 15 N-labeled Aam-I sample) were measured on a Varian Unity 600 spectrometer (Varian, Palo Alto, CA) by methods reported in [52].…”

Self‐aggregation properties of spin‐labeled zervamicin IIA as studied by PELDOR spectroscopy

“…(5) and (6) The value of the fraction of nonaggregated spin labels, L 1 , can be obtained from the Eqs. (5) and (6) assuming that p a N max Ӷ 1. In the first case N max ϭ 2 and therefore the fraction of nonaggregated spin labels is L 1 Ϸ 2 ϪN*; in the second L 1 Ϸ 1 Ϫ (N* Ϫ 1)/(Q Ϫ 1).…”

“…4 More recently, the solution and micelle bound structures have been determined by high-resolution NMR spectroscopy. [5][6][7] The transmembrane orientation of zervamicin in phospholipid double layers has been investigated by solid-state NMR spectroscopy. 8 However, despite intensive research, detailed information about the structure of its self-assembled aggregate is still lacking.…”