Membrane association and selectivity of the antimicrobial peptide NK‐2: a molecular dynamics simulation study

In an effort to better understand the initial mechanism of selectivity and membrane association of the synthetic antimicrobial peptide NK‐2, we have applied molecular dynamics simulation techniques to elucidate the interaction of the peptide with the membrane interfaces. A homogeneous dipalmitoylphosphatidylglycerol (DPPG) and a homogeneous dipalmitoylphosphatidylethanolamine (DPPE) bilayers were taken as model systems for the cytoplasmic bacterial and human erythrocyte membranes, respectively. The results of our simulations on DPPG and DPPE model membranes in the gel phase show that the binding of the peptide, which is considerably stronger for the negatively charged DPPG lipid bilayer than for the zwitterionic DPPE, is mostly governed by electrostatic interactions between negatively charged residues in the membrane and positively charged residues in the peptide. In addition, a characteristic distribution of positively charged residues along the helix facilitates a peptide orientation parallel to the membrane interface. Once the peptides reside close to the membrane surface of DPPG with the more hydrophobic side chains embedded into the membrane interface, the peptide initially disturbs the respective bilayer integrity by a decrease of the order parameter of lipid acyl chain close to the head group region, and by a slightly decrease in bilayer thickness. We found that the peptide retains a high content of helical structure on the zwitterionic membrane‐water interface, while the loss of α‐helicity is observed within a peptide adsorbed onto negatively charged lipid membranes. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

Lateral gradients significantly enhance static magnetic field‐induced inhibition of pain responses in mice—a double blind experimental study

Recent research demonstrated that exposure of mice to both inhomogeneous (3–477 mT) and homogeneous (145 mT) static magnetic fields (SMF) generated an analgesic effect toward visceral pain elicited by the intraperitoneal injection of 0.6% acetic acid. In the present work, we investigated behavioral responses such as writhing, entry avoidance, and site preference with the help of a specially designed cage that partially protruded into either the homogeneous (ho) or inhomogeneous (inh) SMF. Aversive effects, cognitive recognition of analgesia, and social behavior governed mice in their free locomotion between SMF and sham sides. The inhibition of pain response (I) for the 0–5, 6–20, and 21–30 min periods following the challenge was calculated by the formula I = 100 (1 ? x/y) in %, where x and y represent the number of writhings in the SMF and sham sides, respectively. In accordance with previous measurements, an analgesic effect was induced in exposed mice (I_ho = 64%, P < 0.0002 and I_inh = 62%, P < 0.002). No significant difference was found in the site preference (SMF_{ho, inh} vs. sham) indicating that SMF is neither aversive nor favorable. Comparison of writhings observed in the sham versus SMF side of the cage revealed that SMF exposure resulted in significantly fewer writhings than sham (I_ho = 64%, P < 0.004 and I_inh = 81%, P < 0.03). Deeper statistical analysis clarified that the lateral SMF gradient between SMF and sham sides could be responsible for most of the analgesic effect (I_ho = 91%, P < 0.02 and I_inh = 54%, P < 0.02). Bioelectromagnetics 34:385–396, 2013. © 2012 Wiley Periodicals, Inc.     

Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: a molecular dynamics simulation study

Major histocompatibility (MHC) Class II cell surface proteins present antigenic peptides to the immune system. Class II structures in complex with peptides but not in the absence of peptide are known. Comparative molecular dynamics (MD) simulations of a Class II protein (HLA-DR3) with and without CLIP (invariant chain-associated protein) peptide were performed starting from the CLIP-bound crystal structure. Depending on the protonation of acidic residues in the P6 peptide-binding pocket the simulations stayed overall close to the start structure. The simulations without CLIP showed larger conformational fluctuations especially of alpha-helices flanking the binding cleft. Largest fluctuations without CLIP were observed in a helical segment near the peptide C-terminus binding region matching a segment recognized by antibodies specific for empty Class II proteins. Simulations on a Val86Tyr mutation that fills the peptide N-terminus binding P1 pocket or of a complex with a CLIP fragment (dipeptide) bound to P1 showed an unexpected long range effect. In both simulations the mobility not only of P1 but also of the entire binding cleft was reduced compared to simulations without CLIP. It correlates with the experimental finding that the CLIP fragment binding to P1 is sufficient to prevent antibody recognition specific for the empty form at a site distant from P1. The results suggest a mechanism how a local binding event of small peptides or of an exchange factor near P1 may promote peptide binding and exchange through a long range stabilization of the whole binding cleft in a receptive (near bound) conformation.     

A thorough study of a Paratylenchus sp. in glasshouse‐grown lettuce: Characterisation,population dynamics,host plants and damage threshold as keys to its integrated management

In glasshouses practising monoculture of butterhead lettuce in Belgium, high densities of pin nematodes (Paratylenchus spp.) are frequently associated with reduced plant growth. Growers currently apply chemical soil disinfestation measures to manage this problem, although stricter phytosanitary regulations are forcing a shift towards integrated management. Efficient implementation of such management requires knowledge about the factors influencing nematode population dynamics, and the damage threshold for lettuce. The nematode populations in five Belgian glasshouses were monitored for at least 1 year by frequently soil sampling at 0–30 cm and 30–60 cm depth. An undescribed species of Paratylenchus was identified in all glasshouses based on morphological and molecular features. High nematode densities (>20,000 (100 ml soil)^?1) occurred in winter and spring. Chemical soil disinfestation lowered these populations greatly, although up to 14% survived in the deeper soil layer. After soil steaming under negative pressure, no pin nematodes were found. After 2 months of black fallow pin nematode densities were reduced by 50%–76%. Lamb's lettuce, parsley and wild rocket were found to be poor hosts in a pot experiment, while reproduction factors (P_f/P_i) on lettuce cultivars varied between 1 and 3. In three experiments with butterhead lettuce ‘Cosmopolia’ in pots with a series of 9 or 10 densities of Paratylenchus sp. [up to 35,000 (100 ml soil)^?1], no damage to lettuce heads was observed. However, root weight and root quality were reduced, and the corresponding damage thresholds were rather low [1,754 and 362 Paratylenchus sp. (100 ml soil)^?1, respectively]. Management strategies such as crop rotation, soil disinfestation or fallow are recommended to avoid pin nematode population build‐up.