Loss of lipid asymmetry in oxidized membranes

Typical cell membranes in our body are asymmetric regarding lipid composition. The inner leaflet is usually enhanced in negatively charges lipids (phosphatidylserines) whereas the outher one is composed mostly of neutral lipids (phosphatidylcholines). A loss of this asymmetry results in cell death. It is assumed that specialized proteins, so-called scramblases, are translocating negatively charged lipids from inner to outher leaflet and thus are causing the loss of membrane asymmetry.
In the paper recently published in Biophysical Journal we show that translocation of negatively charged lipids (lipid flip-flop) is enhanced in oxidized lipid membranes. In other words, we suggest that oxidation of lipids in a cell membrane, for instance, due to cell ageing may lead to the loss of lipid asymmetry without the involvement of scramblases.  We combined fluorescent spectroscopy experiments with molecular dynamics simulations. The latter included potential of mean-force calculations for the process of lipid flip-flop (see the picture).

Volinsky, Cwiklik, Jurkiewicz, Hof, Jungwirth, Kinnunen,
Biophys. J. 2011,  111, 1376-1384.
DOI: 10.1016/j.bpj.2011.07.051

Artifacts or not

Fan and Gao in a paper published few months ago in JPC B discuss long-range effects of the presence of hydrophobic walls on water in molecular dynamics simulations (J. Phys. Chem. B 2010, 114, 4246). Unusual correlations on the length-scales up to 80 nm were found. Interestingly, near hydrophobic walls water seems to be more ‘liquid-like’ than in the bulk. Correlations are observed in the 100 ns-time scale. These effects are similar for the three force-fields: SPC/E, TIP4P/ew, TIP5P. In my opinion, some computational artifacts are involved and I am looking forward for first discussions with the Fan&Gao’s work.

Charge storage in water

An interesting discussion took place in the Langmuir recently. Ovchinnikova & Pollack have shown in experiment that water can macroscopically store electric charge, in other words, that a charge separation in water is possible for significant time periods – minutes, at least (Langmuir 2009, 25, 542). Then Corti & Collussi commented that such a storage would violate the principle of electroneutrality (Langmuir, 2009, 25, 6587). In a reply to this comment (Langmuir, 2009, DOI:10.1021/la901533c) O&P argue that although the principle of electroneutrality is taken as axiomatic, “exactly where this principle originated is unclear” and that its “violations can be found at levels ranging from the atomic to the cosmic. At the atomic level, electrons remain physically separated from the nucleus. At laboratory-scale levels, regions of water near hydrophilic surfaces contain long-lasting zones of separated charge”, in the atmosphere the intercloud charge separations couse 80% of lightning during thunderstorms. At the end O&E cite a classical water dropper experiment proposed by lord Kelvin (Wikipedia link) where two buckets of water can be oppositely charged. Then Corti & Collussi commented on O&P’s reply, however, they focus on water impurities and do not argue with the validity of the electroneutrality principle (Langmuir 2009, DOI:10.1021/la902030p).

A worth-seeing video from the water dropper experiment can can be seen in the last 6 minutes of the “MIT Open Courseware” lecture (link or see below).

Fighting dogma

In the last paper of Seabra, Walker and Roitberg (DOI:10.1021/jp903474v) an interesting point is made: “It is a general dogma in the field of Computational Chemistry that the ability of theoretical methods to reproduce experimental properties is roughly proportional to computational cost.” Authors show that semiempirical Hamiltonians not always provide better results that their classical force-fields counterparts. In particular, in some QM/MM calculations of biological molecules they are defeated by classical force-fields in prediction of experimental thermodynamic properties. Btw, today I managed to (almost) perfectly describe the hydrogen bonding of dimethyl ether with water using empirical force-field. Two hours later it occurred that the quantum DFT+D in cp2k does it better, but still my classical force-field is muuuuch faster.

Open access at MIT

The Wired just informed that MIT decided to promote open access to the papers published by its faculty members (link). It is not a new move, NIH did it before, however, with some limitations (only for papers more than 12 month old). As I understand, MIT scientists should publish their new papers on the web – not only for internal but also for a world-wide use. It is still unclear for me if this decision regards preprint versions or already peer-revieved and corrected papers. Some journals (Nature, for instance) are quite sensitive in this matter therefore MIT will allow to keep some special (whatever it means) papers to remain ‘closed’. I am personally thinking what I should put on my ‘Publication’ page – I have there DOI links  to the journals but I am planning to add at least manuscript versions of my papers. Most people do it this way, I mean just no-pear-reviewed manuscripts, but recently I found some personal pages with full pdf-s taken from journals. Other question, should I use some preprint server (Nature has offered one, I was writing about it – link) or do it myself. Unfortunately, arXiv has some limitations for me (preprints need to be formally accepted there and also this is a physical site). Anyway, I will have to enhance my ‘Publications’ page soon.

Hydroxide in ice – a new structure

In recent months I was working on the problem of proton mobility in water ice. Proton mobility involves hydroxide and hydronium ions. The first part of this study was focused on OH- ion (hydroxide) and its behavior in the bulk of ice. We found a new structure which OH- prefers in ice and which is a trap for OH-. This “off-the-lattice” configuration, as we called it, immobilizes hydroxide and hinders the overall proton mobility. The article describing our results was accepted as a communication in PhysChemChemPhys and was selected as a “Hot Paper”. Moreover, it made a cover picture in the last issue of PCCP which makes me especially glad (the second cover picture of mine).
(DOI: 10.1039/b820031a)

Benzene, pyridine and dispersion interactions

Some time ago a paper dealing with adsorption and reactivity of aromatic hydrocarbons on the surface of water was published. My part of work was to perform ab initio molecular dynamics simulations of benzene and pyridine adsorbed on water. I was using a moderately small slab (72 water molecules + hydrocarbon) and, as usual, cp2k/Quickstep code with DFT method for electronic structure. Pretty soon it occured tha pure DFT is giving wrong results, namely, benzene ring was not adsorbed on water surface at all. The dispersion interactions which are ommited by DFT are crucial for ‘gluing’ benzene and water molecules. With assistance of Jan Rezac from prof. Hobza’s group, we employed DFT+D scheme in Quickstep and that really helped. Pyridine behaved the same way – only DFT+D scheme was able to describe its adsorption on water. These ab initio MD simulations were only a support for classical MD were the time scale was large enough to get a proper statistics for localization of both benzene and pyridine rings on water. In addition to these classical and ab initio MD simulations the calculations using SAPT method were used. On the top of that a lot of experimantal work of our colleagues was done so the final paper looks very interesting.
(DOI: 10.1021/jp711813p)

Slashdot: Are Academic Journals Obsolete?

A new discussion driven by the question about a role of academic journals in the world of easy access to the excess of information accessible online is going on at Slashdot today (link). Young academics are writing along with non-academic people discussing the impact of the journals on science itself, scientific carrier and the issues regarding the free access to scientific data. To cite one opinion about the peer-review (by Ichoran): ” But even with these flaws, the process does a pretty good job at rejecting junk”.

Imidazole paper

Scientific papers are just like, as somebody said, buses in Jerusalem, you wait for one hour and nothing, and then at one moment five of them appear in a row. Two days after my “sodium paper” was published a new one, this time “imidazole” is published as well. My involvement in the latter one was minor, I was preparing hydrated imidazole structures using ab initio MD for further, higher level calculations. This imidazole project is developing nicely, and my colleagues from Jerusalem, Prague, and Berlin are continuing it with very interesting results.
PS. Some decent people also say: one paper a day is not bad
(DOI: 10.1021/jp711476g)

Sodium in water clusters – a new paper

A first paper regarding our studies of sodium atom in water clusters was published yesterday. We investigated the formation of solvated electron in clusters of 34 water molecules after a collision with sodium atom. We were also able to reproduce experimental vibrational spectra in O-H stretch region. By coincidence, today Waldek and Piotrek, our co-authors from Poland, were presenting these results during a seminar in the Department of Theoretical Chemistry of Jagiellonian University.
(DOI: 10.1063/1.2902970)