This study presents purification, activity characterization, and 1 H NMR study of the novel antifungal peptide EcAMP1 from kernels of barnyard grass Echinochloa crus-galli. The peptide adopts a disulfide-stabilized ␣-helical hairpin structure in aqueous solution and thus represents a novel fold among naturally occurring antimicrobial peptides. Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens. Confocal microscopy revealed intensive EcAMP1 binding to the surface of fungal conidia followed by internalization and accumulation in the cytoplasm without disturbance of membrane integrity. Close spatial structure similarity between EcAMP1, the trypsin inhibitor VhTI from seeds of Veronica hederifolia, and some scorpion and cone snail toxins suggests natural elaboration of different functions on a common fold.Antimicrobial peptides (AMPs) 4 are a structurally diverse group of generally small, positively charged peptides produced by various living organisms and demonstrating a wide spectrum of antimicrobial activity (1, 2). Natural sources of AMPs range from prokaryotes to higher animals, and their targets include bacteria, fungi, protozoa, and viruses. The mechanism of action of most known AMPs involves their direct or receptor-mediated interaction with microbial membranes (3-5). It has been generally accepted that membrane-disruptive AMPs kill microorganisms by provoking in different ways an increase in plasma membrane permeability. Non-membrane-disruptive peptides have been shown to target cell wall formation or traverse membranes and affect various internal cellular processes, for example, RNA, DNA, and/or protein biosynthesis. Some AMPs can combine disruptive and non-disruptive mechanisms of action (6). Moreover, mechanisms of action of the same peptide may differ depending on the target. Recent studies have also indicated that AMPs are multifunctional molecules; they can interact with host membrane receptors and influence diverse intracellular processes modulating the immune response of the host organism (7,8).Essential variety in detailed mechanisms of action and multifunctionality imply structural diversity among AMPs. The following structural groups are usually recognized: (i) linear peptides that form ␣-helices in contact with membranes; (ii) disulfide-containing with predominance of ␤-structural elements; and (iii) linear non-␣-helix-forming, usually with a high content of certain amino acid residues (1, 2, 9). Most of the approximately 200 AMP spatial structures known at present (see the Antimicrobial Peptide Database v2.26 (10)) fall into one of the first two groups. Further classification is based on unique features in the sequences and/or structures of AMPs. For example, thionins, defensins, nonspecific lipid transfer proteins, and hevein-and knottin-like peptides have been identified in plants (11-13).To characterize the array of AMPs produced by a plant under certain physiological conditions, we have carried out a systematic analysis of these peptides from...

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The wealth of data accumulated on the bacterial ribonuclease barnase is complemented by molecular dynamics trajectories starting from four different experimental structures and covering a total of >10 ns. Using principal component analysis, the simulations are interpreted in view of dynamic domains and hinges promoting relative motions of these domains. Two domains with residues 7-22 and 52-108 for the first domain and residues 25-51 for the second domain were consistently observed. Hinge regions consist primarily of Tyr24, Ser50, Ile51, and Gly52. Earlier mutation studies have demonstrated that the residues of the hinge regions play essential roles for the stability and activity of barnase. The domain motions are correlated to inter-domain interactions involving functionally important active site residues, such as Lys27 and Glu73. A model is presented that combines the observation of dynamic domains and their motions with the extensive mutation data from the literature. Enthalpic energy contributions originating from specific inter-domain interactions as well as entropic energy contributions due to the domain motions are discussed in the frame of this model and compared with destabilization energies measured for corresponding mutants.

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