Modeling membrane proteins: The importance of cysteine amino-acids.

Computational modeling of membrane proteins is critical to understand biochemical systems and to support chemical biology. In this work, we use a dataset of 448 non-redundant membrane protein chains to expose a "rule" that governs membrane protein structure: free cysteine thiols are not found accessible to oxidative compartments such as the extracellular space, but are rather involved in disulphide bridges. Taking as examples the 1018 three-dimensional models produced during the GPCR Dock 2008, 2010 and 2013 competitions and 390 models for a GPCR target in CASP13, we show that this rule was not accounted for by the modeling community. We thus highlight a new direction for model development that should lead to more accurate membrane protein models, especially in the loop domains.

Study of interaction between PEG carrier and three relevant drug molecules: piroxicam, paclitaxel, and hematoporphyrin.

Molecular dynamics simulation has been used to study the specific interactions between poly(ethylene glycol) (PEG) and three drug molecules for which PEG is used to aid delivery: paclitaxel and piroxicam, where PEG is a carrier agent, and hematoporphyrin, where PEG is covalently attached to form a "stealth shield". Simulating at physiological salt concentration, we found no evidence of any specific interaction between paclitaxel or piroxicam with PEG, but found a strong interaction for the case of hematoporphyrin. This interaction is lipophilic in nature, between the nonpolar (CH(2))(2) groups of the PEG and the porphin ring of the hematoporphyrin. This interaction was found to be strong enough that the PEG aggregated to the hematoporphyrin, independent of whether or not it was covalently bound. Interestingly, when the simulation was repeated in absence of salt we found evidence of this interaction being weakened. This led us to hypothesize a previously unforeseen mechanism: interaction with salt cations cause the PEG to coil around the salt ions, each ion binding to many PEG oxygens, increasing the exposure of the nonpolar ethylene groups, thus increasing the effective hydrophobicity of PEG. The Hydrophobic ethylene groups of the PEG chains adhere strongly to the hydrophobic porphin ring. Experiments involving absorption spectra measurements were conducted, and these results also indicated that presence of salt at physiological level increases the effective attractive interaction between PEG and hematoporphyrin. Taken together, our results demonstrate that while PEG, due to its solubility in both polar and nonpolar solvents, may act as a dissolution aid for paclitaxel and piroxicam, of the three drug molecules studied it will only have a protective role for the case of the hematoporphyrin.

Interaction of hematoporphyrin with lipid membranes.

Natural or synthetic porphyrins are being used as photosensitizers in photodiagnosis (PD) and photodynamic therapy (PDT) of malignancies and some other diseases. Understanding the interactions between porphyrins and cell membranes is therefore important to rationalize the uptake of photosensitizers and their passive transport through cell membranes. In this study, we consider the properties of hematoporphyrin (Hp), a well-known photosensitizer for PD and PDT, in the presence of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer that we use as a model system for protein-free cell membranes. For this purpose, we employed 200 ns atomic-scale molecular dynamics (MD) simulations for five systems containing the neutral (Hp(0)) or the dianionic form (Hp(2-)) of Hp and the POPC bilayer. MD simulations allowed one to estimate the position, orientation, and dynamics of Hp molecules inside the membrane. The dye molecules were found to reside in the phospholipid headgroup area close to the carbonyl groups of the POPC acyl chains. Their orientations were dependent on the protonation state of two propionic groups. Hp(2-) was found to have a lower affinity to enter the membrane than the neutral form. The dianions, being in the aqueous phase, formed stable dimers with a strictly determined geometry. Our results fully supported the experimental data and provide a more detailed molecular-level description of the interactions of photosensitizers with lipid membranes.

Molecular dynamics simulation of PEGylated bilayer interacting with salt ions: a model of the liposome surface in the bloodstream.

PEGylation is an effective mechanism to prolong the bloodstream lifetime, and thus efficacy, of drug delivery liposomes. The mechanism through which poly(ethylene glycol) (PEG) increases bloodstream lifetime is, however, not completely understood. The interaction with salt ions found in the bloodstream is known to play a role in this. We have used all-atom molecular dynamics simulation to study the effect of PEGylated lipid density, salt concentration, and the interaction with KCl and CaCl(2) salts in addition to NaCl. Increasing the PEGylated lipid concentration in the formulation from 1:18 to 1:9 molar density decreased the extent to which the Cl(-) ions penetrated the PEG layer, thus causing the PEG layer to become effectively positively charged. The interaction of the PEG with the K(+) ions was weaker than for the Na(+) ions, and nonexistent for the Ca(2+) ions. This work expands on our previous work where we studied the gel and liquid crystalline membranes in physiological salt concentration. Our results provide both an explanation for the experimental observation that PEGylation inhibits calcium-induced liposome fusion and further insight into the mechanisms through which PEG may inhibit uptake of the liposome by the reticuloendothilial system (RES).

Analysis of cause of failure of new targeting peptide in PEGylated liposome: molecular modeling as rational design tool for nanomedicine.

Drug nanocarriers are often derivatized with targeting moieties to achieve site specific delivery, however, the results from this approach have, as yet, not reached expectations. We have tested a new phage display based targeting moiety, the activated endothelium targeting peptide (AETP), for its vascular endothelium directed targeting efficiency, when anchored to a PEGylated liposome via maleimide chemistry. Our results have, however, not shown any evidence of improved targeting. We have hypothesized that the failure of the AETP moiety is due to its availability to target receptors being restricted, as a result of steric hindrance due to the PEG polymer, and possibly affinity for bloodstream proteins, particularly human serum albumin (HSA). In this context, molecular modeling was used to contrast the properties of the AETP moiety to those of the RGD targeting peptide, already found to be effective in previous trials. Our molecular dynamics simulation results indicate the AETP moiety is located within the PEG layer, and its hydrophobic nature causes it to be obscured by PEG to a greater extent than the more hydrophilic RGD targeting peptide. Protein-ligand docking results indicated similar affinities for HSA of both the AETP moiety and a PEG fragment, and a significantly lower affinity for the RGD peptide. We know of no means to investigate this experimentally with atomic level resolution, thus our use of computational methods to investigate this can be seen as a new tool for rational design in nanomedicine.

Study of PEGylated lipid layers as a model for PEGylated liposome surfaces: molecular dynamics simulation and Langmuir monolayer studies.

We have combined Langmuir monolayer film experiments and all-atom molecular dynamics (MD) simulation of a bilayer to study the surface structure of a PEGylated liposome and its interaction with the ionic environment present under physiological conditions. Lipids that form both gel and liquid-crystalline membranes have been used in our study. By varying the salt concentration in the Langmuir film experiment and including salt at the physiological level in the simulation, we have studied the effect of salt ions present in the blood plasma on the structure of the poly(ethylene glycol) (PEG) layer. We have also studied the interaction between the PEG layer and the lipid bilayer in both the liquid-crystalline and gel states. The MD simulation shows two clear results: (a) The Na(+) ions form close interactions with the PEG oxygens, with the PEG chains forming loops around them and (b) PEG penetrates the lipid core of the membrane for the case of a liquid-crystalline membrane but is excluded from the tighter structure of the gel membrane. The Langmuir monolayer results indicate that the salt concentration affects the PEGylated lipid system, and these results can be interpreted in a fashion that is in agreement with the results of our MD simulation. We conclude that the currently accepted picture of the PEG surface layer acting as a generic neutral hydrophilic polymer entirely outside the membrane, with its effect explained through steric interactions, is not sufficient. The phenomena we have observed may affect both the interaction between the liposome and bloodstream proteins and the liquid-crystalline-gel transition and is thus relevant to nanotechnological drug delivery device design.

Behavior of 2,6-bis(decyloxy)naphthalene inside lipid bilayer.

Interactions between small organic molecules and lipid or cell membranes are important because of their role in the distribution of biologically active substances inside the membrane and their permeation through the cell membranes. In the current paper, we have explored the effect of the attachment of long hydrocarbon tails on the behavior of small organic molecule inside the lipid membrane. Naphthalene with two decyloxy groups attached at the opposite sites of the ring (2,6-bis(decyloxy)naphthalene, 3) was synthesized and incorporated into phosphatidylcholine (PC) vesicles. Fluorescence methods as well as molecular dynamic (MD) simulations were used to estimate the position, orientation, and migration of compound 3 in PC bilayer. It was found that the naphthalene ring of compound 3 resides in the upper acyl chain region of the bilayer and the hydrocarbon tails are directed to the center of the bilayer. As was shown with cryotransmission electron microscopy (cryo-TEM), such lipidlike conformation enables compound 3 to be incorporated into liposomes at a very high content without their disintegration. Moreover, compound 3 can migrate from one leaflet to other. The mechanism of this process is, however, different from that characteristic of the flip-flop event of lipid molecules in the membrane. Finally, the possible application of compound 3 as a rotational molecular probe for monitoring fluidity of liposomal membrane in the acyl side chain region was checked by studies of the effect of cholesterol on the fluorescence anisotropy of 3.

Effects of the lipid bilayer phase state on the water membrane interface.

We performed 200 ns MD simulations of phosphatidylcholine (PC) bilayers in the liquid crystalline (L(α)) and gel (L(ß)') states to compare the properties of the water-membrane interfaces in these two thermotropic bilayer phases. Our simulations show that the membrane phase determines the behavior of water, ions, and PC head groups. When the membrane was in the gel phase, we found partial dehydration (fewer PC-water interactions), particularly in the carbonyl groups region, as well as an almost complete lack of ionic penetration into this region as compared with the bilayer in the liquid-crystalline phase. In the latter case, there is an exchange of Na(+) ions between the water layer and the interfacial region. This is mainly due to the fact that the most stable binding of Na(+) in the liquid-crystalline bilayer is to the carbonyl groups. The lack of Na(+) binding to the carbonyl groups in the gel phase bilayer can be explained by the more compact structure of the bilayer in this phase.