Peptides in membranes

So far, we have discussed only simulations that employed simplified models of water-membrane systems. Other simulations have dealt with both interfacial and transmembrane peptides in real phospholipid bilayers. Due to limited computational resources, protein folding was not addressed in these simulations but, instead, the focus was on the short-term structural stability, orientation and dynamics of these peptides. Nevertheless, in many respects, these simulations offer a richer picture of protein-membrane systems by explicitly considering specific interactions between amino acids and lipid head groups and the effects associated with the inhomogeneous, ordered nature of the membrane environment. 

The rapid disintegration of the helical portion exposed to water is somewhat surprising, considering that short poly-alanine peptides in water were found to contain a large fraction of 3io-helix [95]. Furthermore, simulations of an a-helix formed by a similar, but presumably less stable, peptide, the undecamer of polyleucine, in water revealed that the helix does not unravel on a few nanoseconds timescale [81]. It is possible that the interfacial water-membrane environment accelerates the denaturation of marginally stable, ordered protein structures but this issue requires further, systematic studies. 

Greater insight into the specific interactions that anchor and stabilize membrane-bound proteins can be gleaned from the simulation study of the protein melittin in a DMPC membrane [109]. Melittin is the major protein component of bee venom that is responsible for the lysis (opening) of the cell membrane. It is twenty-six residues long with the sequence GIGAVLKVLTTGLPALIS WIKRKRQQ. 

Experimental studies [110] have demonstrated that its structure is a-helical. The first thirteen residues (gigavlkvlttgl) are hydrophobic while its last twelve residues (aliswikrkrqq) form an amphipathic a-helix. The two segments are separated by a bend introduced by the presence of the proline. Bemeche, et al. started their simulation with the protein in the upper leaflet of the membrane, the axis of its amphipathic portion parallel to the plane of the membrane, oriented with the apolar residues facing the membrane s hydrophobic core — a configuration consistent with experiment [111]. Due to the proline-induced bend, this orientation caused the the hydrophobic portion of the helix to protrude into the hydrophobic-tail portion of the upper leaflet of the membrane. The protein did not span the membrane, however. Over the 600 ps of their simulation, this orientation was preserved, although rocking motions on the order of 5-8° were observed. 

One substantial difference between polyalanine and melittin is their effect on the membrane. Shen et al. found that the presence of the transmembrane polyalanine helix barely altered the structure and dynamics of the DMPC bilayer. Only the NMR order parameters were slightly lower, indicating that the protein did not Induce the formation of a more ordered layer of lipids. Moreover, a detailed analysis of the solvation of the helix showed that no well-defined annulus of lipids remained tethered to the protein. A similar conclusion was reached in 

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Strandberg E, Esteban-Martin S, Salgado J, Ulrich AS (2009) Orientation and dynamics of peptides in membranes calculated from 2H-NMR data. Biophys J 96 3223-3232... 

Esteban-Martin S, Strandberg E, Salgado J, Ulrich AS (2010) Solid state NMR analysis of peptides in membranes influence of dynamics and labeling scheme. BBA-biomembranes 1798 252-257... 

Grasnick D, Sternberg U, Strandberg E, Wadhwani P, Ulrich AS (2011) Irregular structure of the HIV fusion peptide in membranes demonstrated by solid-state NMR and MD simulations Eur Biophys J 40 529-543... 

Early investigations of peptides in membrane model systems included studies of mel-letin 124,125 220 221 spectra and polarization properties. This water-soluble peptide is found to be structureless in solution at neutral pH but was sensitive to environmental change. The undecapeptide hormone, substance P, a member of the tackykinin family, was also found by Choo et a].1222 to be unstructured in solution at physiological pH and to aggregate at high pH or on interaction with charged lipids. These data were used as counter-evidence to a hypothesis that the membrane surface structured the peptide to facilitate interaction with the receptor. 

Bechinger, B. (1999). The structure, dynamics and orientation of antimicrobial peptides in membranes by multidimensional solid-state NMR spectroscopy. Biochim. Biophys. Acta, 1462(1-2), 157-183. 

Chaloin, L., Vidal, P., Heitz, A., et al. (1997) Conformations of primary amphi-pathic carrier peptides in membrane mimicking environments. Biochemistry 36, 11,179-11,187. 

Reichert, J., Grasnick, D., Afonin, S., et al. (2007) A critical evaluation of the conformational requirements of fusogenic peptides in membranes. European Biophysics Journal with Biophysics Letters, 36, 405 413. 

The following examples show the use of wide-line NMR to probe structure and dynamics of lipids and peptides in membranes. Although not complete, the examples chosen represent the potential of the technique. 

Orientation of molecules (sterols, helical peptides) in membranes... 

In this chapter we show usefulness of the molecular dynamics simulations on the study of model helical peptides composed of acetyl-K2-A24-K2-amide (A24), ace-tyl-K2-L24-K2-amide (L24), acetyl-K2-(LA),2-K2-amide ((LA),2), acetyl-K2-l24-K2 amide (I24), acetyl-K2-G-L24-K2-A-amide 24) acetyl-K2-V24-K2-amide (V24) incorporated into the phospholipid bilayers (DMPC, DPPC). The behavior of some of these and other peptides in membranes of various lipid compositions has been analyzed by Host and Killian [67]. We have shown that the effect of peptides on the lipid bilayer strongly depends on membrane physieal state— gel or liquid crystalline. 

An amphipathic helix is defined as a helix in which the distribution of amino acid residues forms opposing polar and nonpolar faces. It is an important structural unit included in proteins and peptides and is responsible for interaction with biological membranes to elicit their biological functions such as membrane fusion. Influenza virus hemagglutinin [1], fertilin [1], and meltrin-a [2] contain amphipathic fusion peptides, which are likely to adopt a helical conformation during the fusion reaction. To clarify the role of amphipathic peptides in membrane fusion reactions, we synthesized five types of amphipathic model peptides and examined their helix formation, membrane binding and membrane fusion activities. 

Brasseur R, Pfllot T, Uns L, Vandekerckhove J, Rosseneu M. Peptides in membranes tipping the balance of membrane stability. Trends Biochem Sci. 1997 22(5) 167-171. 

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