Molecular Dynamics Simulation of Transmembrane Polypeptide Orientational Fluctuations

100

219

Solid-state (2)H-NMR is routinely used to determine the alignment of membrane-bound peptides. Here we demonstrate that it can also provide a quantitative measure of the fluctuations around the distinct molecular axes. Using several dynamic models with increasing complexity, we reanalyzed published (2)H-NMR data on two representative alpha-helical peptides: 1), the amphiphilic antimicrobial peptide PGLa, which permeabilizes membranes by going from a monomeric surface-bound to a dimeric tilted state and finally inserting as an oligomeric pore; and 2), the hydrophobic WALP23, which is a typical transmembrane segment, although previous analysis had yielded helix tilt angles much smaller than expected from hydrophobic mismatch and molecular dynamics simulations. Their (2)H-NMR data were deconvoluted in terms of the two main helix orientation angles (representing the time-averaged peptide tilt and azimuthal rotation), as well as the amplitudes of fluctuation about the corresponding molecular axes (providing the dynamic picture). The mobility of PGLa is found to be moderate and to correlate well with the respective oligomeric states. WALP23 fluctuates more vigorously, now in better agreement with the molecular dynamics simulations and mismatch predictions. The analysis demonstrates that when (2)H-NMR data are fitted to extract peptide orientation angles, an explicit representation of the peptide rigid-body angular fluctuations should be included.

Section: Introductionmentioning

confidence: 88%

Orientation and Dynamics of Peptides in Membranes Calculated from 2H-NMR Data

Strandberg

Esteban-Martín

Salgado

et al. 2009

100

219

“…In most computational studies, WALP peptides display larger tilt angles compared to solid-state 2 H-NMR results. MD simulations provided values in the range 20-35 (20)(21)(22)(23)(24). This difference appears to be independent of the force field and other details of methods used in simulations.…”

Section: Comparison Between Simulations and Experimentsmentioning

confidence: 95%

“…Numerous atomistic simulation studies of WALP and KALP peptides in lipid bilayers have been reported (20)(21)(22)(23)(24). In all cases, the tilt angle predicted by the simulations was significantly larger (e.g.,~30 for WALP23 in DMPC (24)) than that determined from 2 H NMR (17)(18)(19).…”

Section: Introductionmentioning

confidence: 92%

Interpretation of 2H-NMR Experiments on the Orientation of the Transmembrane Helix WALP23 by Computer Simulations

Monticelli

Tieleman

Fuchs

2010

Orientation, dynamics, and packing of transmembrane helical peptides are important determinants of membrane protein structure, dynamics, and function. Because it is difficult to investigate these aspects by studying real membrane proteins, model transmembrane helical peptides are widely used. NMR experiments provide information on both orientation and dynamics of peptides, but they require that motional models be interpreted. Different motional models yield different interpretations of quadrupolar splittings (QS) in terms of helix orientation and dynamics. Here, we use coarse-grained (CG) molecular dynamics (MD) simulations to investigate the behavior of a well-known model transmembrane peptide, WALP23, under different hydrophobic matching/mismatching conditions. We compare experimental (2)H-NMR QS (directly measured in experiments), as well as helix tilt angle and azimuthal rotation (not directly measured), with CG MD simulation results. For QS, the agreement is significantly better than previously obtained with atomistic simulations, indicating that equilibrium sampling is more important than atomistic details for reproducing experimental QS. Calculations of helix orientation confirm that the interpretation of QS depends on the motional model used. Our simulations suggest that WALP23 can form dimers, which are more stable in an antiparallel arrangement. The origin of the preference for the antiparallel orientation lies not only in electrostatic interactions but also in better surface complementarity. In most cases, a mixture of monomers and antiparallel dimers provides better agreement with NMR data compared to the monomer and the parallel dimer. CG MD simulations allow predictions of helix orientation and dynamics and interpretation of QS data without requiring any assumption about the motional model.

“…Similar structure was deter-mined by solid-state NMR, and the tilting angle of the N-terminal a-helix was determined to be 21 (7). Other examples are the transmembrane domain of Neu (8), lysine-terminated alanine-leucine alternating polypeptide (9), hydrophobic peptides of Trp-and Lys-flanked leucine polypeptide (10), and the monomeric sarcolipin which regulates the sarcoplasmic reticulum Ca-ATPase activity (11), where the MD simulation were performed and the peptide structures and orientations were investigated. Recently, Kandasamy et al (12) investigated the structure of the second transmembrane domain of g-amino butyric acid receptor in lipid bilayers using solid-state NMR and MD simulation.…”

Section: Introductionmentioning

confidence: 92%

“…Although the fluctuation indicates that no specific interactions occur with the specific sites of the membrane, the strong interaction of Ser 1 and Lys 2 with the membrane headgroups works as an anchor to keep these residues in this region during the tilting behavior. Lys 9 and Lys 12 are more important among all hydrophilic residues for rotational and translational movements of BLT2 in the membrane bilayer, because these hydrophilic residues locate far from the interface region. The interaction energies among Lys 9 , Lys 12 , and lipid molecules were analyzed and the results were shown in Fig.…”

Section: Interactions Of Bombolitin-ii With a Membrane Bilayermentioning

confidence: 99%

Molecular Dynamics Simulation of Bombolitin II in the Dipalmitoylphosphatidylcholine Membrane Bilayer

Javkhlantugs

Naito

Ueda

2011

The orientation behavior of Bombolitin II (BLT2) in the dipalmitoylphosphatidylcholine membrane bilayer was investigated by using molecular-dynamics simulation. During the 20-ns simulation, the BLT2 began to tilt and finally reached the angle of 51° from the membrane-normal. The structure of the peptide formed the amphipathic α-helical structure during the entire simulation time. The peptide tilts with its hydrophobic side faced to the hydrophobic core of the bilayer. We analyzed the mechanism of the tilting behavior of the peptide associated with the membrane in detail. The analysis showed that the hydrogen-bond interaction and the electrostatic interaction were found to exist between Lys(12) and a lipid molecule. These interactions are considered to work as an important factor in tilting the peptide to the membrane-normal.