Coming soon to a worm near you....

Three possible stop codons are common in mRNA: UGA, UAA and UAG. These codons usually bind release factors, that prompt the release of of the nascent amino acid chain from the ribosome. Some organisms, however, contain tRNA complementary to one of these codons. In these organisms, that codon no longer triggers the ending of the translation process, but codes an amino acid instead. Several researchers have used this special tRNA to develop mutant cells with expanded genetic codes.Greiss and Chin have now taken this a step further: they have engineered a mutant strain of the worm C. elegans that translates every UAG codon as an artificial aminoacid. It was a complex endeavour (details are in their paper...) that surely would have deserved a well-publicized press conference :-)

Puns and wordplay in Science

In 1975, E. M. Southern developed an elegant method to detect specific DNA after gel electrophoresis (J. Mol. Biol. 98, 503-517) . His technique soon became known as "the Southern blot", and the paper has so far gathered >35 thousand citations. This number is a dramatic under-estimate of the impact of Southern blot in the field of molecular biology, as the technique has became routine and "common knowledge", which means that most practitioners no longer cite the original paper. In 1977, a variation of the technique was developed by Alwine et al. to detect RNA. The name "Northern blotting" was soon proposed for their technique, as a wordplay on the original method. The application of a similar technique on proteins is called "Western blotting".

Naming methods (or variations) using wordplay is not limited to biochemical techniques. In computational chemistry, novel basis sets obtained from the well-known aug-cc-pVXZ basis set family by decreasing the number of polarization basis functions have recently been proposed by Don Truhlar. In a humorous touch, the aug- prefix (originally an abreviation of augmented) was considered an abbreviation of August. The new, smaller, basis sets aretherefore called apr-cc-pVXZ, may-cc-pVXZ, jun-cc-pVXZ and jul-cc-pVXZ. Not outright comedy material, but it does bring a quirky smile to your lips, right?

QM molecular dynamics

In classical molecular dynamics simulations, we follow the evolution of a system of particles that interact with each other according to newtonian mechanics. The correct description of chemical bonds, angles and torsions in classical mechanics can only be achieved by introducing carefully parameterized expressions that represent the change in electronic energy upon stretching/compressing a bond, or bending an angle. These parameterized force fields (AMBER, CHARMM, GROMOS, YASARA, OPLS) allow the simulation of very large systems (>10000 atoms) for long simulation times (>20 ns) with an obvious drawback: the quality of the simulations is only as good as the quality of the parameterized expressions, and therefore one is limited to the simulation of specific classes of previously characterized molecules/functional groups. Simulating chemical reactions is generally not possible without special protocols (like thermodynamic integration).

Ab initio molecular simulations (e.g. Car-Parrinello MD) are much more expensive, and are generally limited to (at most) a few dozen atoms and <100 ps. Two papers from Prof. Shogo Sakai's group show that QM molecular simulations can be performed with considerable time-savings if the system is partitioned into several smaller systems. They have not yet developed the theory to the point where one can attempt bond-breaking, but theirs seems a fruitful approach to the problem.

Fe-S clusters

Biological Fe-S clusters come in many sizes and flavours:

2Fe-2S clusters ligated by four cysteines

2Fe-2S clusters ligated by three cysteines and one aspartate

2Fe-2S clusters ligated by cysteines and histidines (the so-called Rieske clusters)

3Fe-4S clusters ligated by three cysteines

4Fe-4S clusters ligated by four cysteines

4Fe-4S clusters ligated by three cysteines and one aspartate

the hideously complex cluster present in hybrid cluster protein (also known as fuscoredoxin or "prismane protein")

the P-cluster in nitrogenase

etc., etc., etc.
The large number of electrons in Fe and the complexity of the possible couplings between spin states make the theoretical analysis of the electronic structures in Fe-S clusters quite difficult.
Takano et al. have recently published a paper on the differences between a Cys₃Asp ligated 4Fe-4S cluster and the "regular" (all Cys) 4Fe-4S cluster. The authors nicely analyze the influence of the Asp (and other) ligands on the electronic structure of the 4Fe-4S cluster, observe a -0.10 V difference in redox potential (vs. normal 4Fe-4S) in high dielectric constants, and offer this observation as the reason for the low potential of this cluster.
I do not accept this last conclusion for two reasons:

redox potentials of Cys-ligated 4Fe-4S clusters may differ by >0.4 V from each other, which shows that the influence of the charge distribution of the protein is much more important than the small difference observed by the authors

the 0.1 V difference found amounts to ca. 2.3 kcal/mol, which is well within the error range of the computational methods used.

Energy metabolism in brain

It is a well-known "fact" that under normal conditions glucose is responsible for providing almost all the energy needed by the healthy brain. However, it is not at all clear why that should be so: after all, fatty acids are well known to cross the brain-blood barrier. Why souldn't they be substrates for beta-oxidation in neurons? After browsing the literature, I still do not have an answer for that question. The Gene Expression Database reports that the enzymes involved in beta-oxidation are indded expressed in brain, but it is not clear if the data are from tissue homogeneates ot form purified neurons/astrocytes, etc. Back in 1993, Ebert et al.  showed that ca. 20% of the brain's energy needs may be met by medium-chain fatty acids. Drawing on earlier research by other authors, Ebert et al. concluded that astrocytes probably account for the fatty acids oxidation, while the neurons survive on glucose alone (or a mixture of glucose and lactate provided by the astrocytes themselves).

I would still like to find out any explanation for the neurons' dependence on glucose (or glucose/lactate).. Any ideas?

Should we suspect any shameless self-promotion in some Impact Factors?

Selecting the journal for your next submission is a decision with lots of variables:

how likely is the journal to find your work "sexy" enough?

what is its impact factor?

how long does the journal take from acceptance to online/paper publication?

how desperate are you to get your paper published?




Ideally, impact factor would be an objective measurement... We all know, however, that the actual relationship between "real journal impact" and the impact factor is not always perfect: a single paper with many citations in a small journal may increase its IF dramatically, even if all other papers in that journal are less cited than the papers form preceding years; citations may be inflated artificially by the authors self-citing themselves to exhaustion, bad papers may be highly cited (e.g. in refutations), etc.
I have now found (entirely by accident) a journal that increased its impact factor five-fold from 2009 to 2010. That would be surprising in itself. But the real surprise is that in August 2010, this journal published a paper that has thus far received 37 citations, ALL IN THIS SAME JOURNAL.

You may check for yourselves in Web of Science.. The paper is

Aman MJ , Karauzum H , Bowden MG , Nguyen TL (2010) "Structural Model of the Pre-pore Ring-like Structure of Panton-Valentine Leukocidin: Providing Dimensionality to Biophysical and Mutational Data" J. Biomol. Struct. Dyn., 28, 1-12



This is not the only surprise. Other papers with high citations are:

Tao Y , Rao ZH , Liu SQ (2010) "Insight Derived from Molecular Dynamics Simulation into Substrate-Induced Changes in Protein Motions of Proteinase K" J. Biomol. Struct. Dyn., 28, 143-157 (36 citations, of which 35 in J. Biomol. Struct. Dyn.)


Sklenovsky P, Otyepka M (2010) "In Silico Structural and Functional Analysis of Fragments of the Ankyrin Repeat Protein P18(INK4c)" J. Biomol. Struct. Dyn., 27, 521-539 (36 citations, of which 35 in J. Biomol. Struct. Dyn.)


Zhang JP (2009) "Studies on the Structural Stability of Rabbit Prion Probed by Molecular Dynamics Simulations" J. Biomol. Struct. Dyn., 27, 159-162 (36 citations, of which 31 in J. Biomol. Struct. Dyn. and 4 others are self-citations by the author)

Chen CYC, Chen YF, Wu CH, Tsai (2008) "What is the effective component in suanzaoren decoction for curing insomnia? Discovery by virtual screening and molecular dynamic simulation " J. Biomol. Struct. Dyn., 26, 57-64 (35 citations, of which 21 in J. Biomol. Struct. Dyn. and 11 others are self-citations by the author)

Mittal A, Jayaram B, Shenoy S, Bawa TS (2010) "A Stoichiometry Driven Universal Spatial Organization of Backbones of Folded Proteins: Are there Chargaff's Rules for Protein Folding?" J. Biomol. Struct. Dyn., 28, 133-142 (34 citations, of which 33 in J. Biomol. Struct. Dyn.)

"We are pleased to invite you....."

The recent trend toward open access science publishing has yielded a very uneven crop of journals. We do have a few respected Open Access-only publications with high quality research (PLoS ONE and many titles on BioMedCentral) but there is also a very large number of publishing firms that email researchers to solicit submissions to brand new Open Access journals. I have received several of these emails, which always claim to have selected me because of my expertise on the topic even though I have often not published anything on it, or even on related subjects. So far, I have received requests to submit reviews to:

a special issue on protein biogenesis in "Archaea". (I have studied enzymes of P. furiosus, but never did any on protein biogenesis or post-translational modifications)

International Journal of Medicinal Chemistry

Recent Patents on DNA and Gene Sequences (I have never done any sequencing, but that did not prevent the editors from considering me an expert on the area ;-)

This morning I received the most ludicrous example of "scientific" spam: I was invited to present my work on "A tale of two acids: when arginine is a more appropriate acid than H₃O⁺" to the "EPS Montreal International Renewable Energy Forum 2011". Definitely off-topic!