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Poly(amidoamine) dendrimers on lipid bilayers I: Free energy and conformation of binding.

ABSTRACT: Third-generation (G3) poly(amidoamine) (PAMAM) dendrimers are simulated approaching 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) bilayers with fully atomistic molecular dynamics, which enables the calculation of a free energy profile along the approach coordinate. Three different dendrimer terminations are examined: protonated primary amine, uncharged acetamide, and deprotonated carboxylic acid. As the dendrimer and lipids become closer, their attractive force increases (up to 240 pN) and the dendrimer becomes deformed as it interacts with the lipids. The total energy release upon binding of a G3-NH3+, G3-Ac, or G3-COO- dendrimer to a DMPC bilayer is, respectively, 36, 26, or 47 kcal/mol or, equivalently, 5.2, 3.2, or 4.7x10(-3) kcal/g. These results are analyzed in terms of the dendrimers' size, shape, and atomic distributions as well as proximity of individual lipid molecules and particular lipid atoms to the dendrimer. For example, an area of 9.6, 8.2, or 7.9 nm2 is covered on the bilayer for the G3-NH3+, G3-Ac, or G3-COO- dendrimers, respectively, while interacting strongly with 18-13 individual lipid molecules.

SUBMITTER: Kelly CV

PROVIDER: S-EPMC2925445 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature

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Poly(amidoamine) dendrimers on lipid bilayers I: Free energy and conformation of binding.

Kelly Christopher V CV Leroueil Pascale R PR Nett Elizabeth K EK Wereszczynski Jeffery M JM Baker James R JR Orr Bradford G BG Banaszak Holl Mark M MM Andricioaei Ioan I

The journal of physical chemistry. B 20080712 31

Third-generation (G3) poly(amidoamine) (PAMAM) dendrimers are simulated approaching 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) bilayers with fully atomistic molecular dynamics, which enables the calculation of a free energy profile along the approach coordinate. Three different dendrimer terminations are examined: protonated primary amine, uncharged acetamide, and deprotonated carboxylic acid. As the dendrimer and lipids become closer, their attractive force increases (up to 240 pN) and ...[more]

PMID: 18620450

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Project description:Using a recently developed binary bilayer system (BBS) consisting of two patches of laterally contacting bilayers, umbrella sampling molecular dynamics (MD) simulations were performed for quantitative characterization of protein-lipid interactions. The BBS is composed of 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) with an embedded model membrane protein, a gramicidin A (gA) channel. The calculated free energy difference for the transfer of a gA channel from DLPC (hydrophobic thickness ? 21.5 Å) to DMPC (hydrophobic thickness ? 25.5 Å) bilayers, ?G(DLPC ? DMPC), is -2.2 ± 0.7 kcal/mol. This value appears at odds with the traditional view that the hydrophobic length of the gA channel is ?22 Å. To understand this discrepancy, we first note that recent MD simulations by different groups have shown that lipid bilayer thickness profiles in the vicinity of a gA channel differ qualitatively from the deformation profile predicted from continuum elastic bilayer models. Our MD simulations at low and high gA:lipid molar ratios and different membrane compositions indicate that the gA channel's effective hydrophobic length is ?26 Å. Using this effective hydrophobic length, ?G(DLPC ? DMPC) determined here is in excellent agreement with predictions based on continuum elastic models (-3.0 to -2.2 kcal/mol) where the bilayer deformation energy is approximated as a harmonic function of the mismatch between the channel's effective hydrophobic length and the hydrophobic thickness of the bilayer. The free energy profile for gA in the BBS includes a barrier at the interface between the two bilayers which can be attributed to the line tension at the interface between two bilayers with different hydrophobic thicknesses. This observation implies that translation of a peptide between two different regions of a cell membrane (such as between the liquid ordered and disordered phases) may include effects of a barrier at the interface in addition to the relative free energies of the species far from the interface. The BBS allows for direct transfer free energy calculations between bilayers without a need of a reference medium, such as bulk water, and thus provides an efficient simulation protocol for the quantitative characterization of protein-lipid interactions at all-atom resolution.

Dataset Information

Poly(amidoamine) dendrimers on lipid bilayers I: Free energy and conformation of binding.

Publications

Poly(amidoamine) dendrimers on lipid bilayers I: Free energy and conformation of binding.

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