Posts Tagged ‘active site’

Pidapalooza!

Thursday, November 10th, 2016

This is sent from the Pidapalooza event in Reykjavik, Iceland, and is a short collection of notable things I learnt or which attracted my attention.

Firstly, what IS PIDapalooza[1]? Well, it’s all about persistent identifiers, but don’t let that put you off! Another way of putting it is that it’s a way of finding things scientific on the Web. Not just publications, but conferences, social media, teaching, research datasets, infrastructure, grants, organizations, instruments, scientific objects and samples and no doubt much more. These (will) live in an inter-connected eco-system, and so the idea goes, will become an integral part of how a scientist accumulates and disseminates information nowadays. Yes, the conference itself has its own PID: 10.5438/11.0001  and the individual talks will also appear as both a collection and with their own  PID in the near future.

  1. The first example comes from WikiData, a collection of carefully curated data, from which can be dynamically assembled say a periodic table of the elements. All the data here is included from other objects, and everything is referenced by its PID. Since it’s all assembled from data, if say the name of element 118 is assigned, then it will automatically be absorbed into this presentation.
  2. This next example proved highly contentious, but is included here anyway. It is templated PIDs, as in http://doi.org/10.5446/12780#t=00:20.00:27 which allows navigation to a particular part of an object referenced by the PID. In this case a time code for a movie, but it might be say an active site in a protein, or a key atom or group in a molecular complex for example.  This might never happen (for reasons only the computer scientists currently understand!) but it does show one way in which the humble DOI might evolve.
  3. http://typeregistry.org exists for registering data types. It has almost no chemistry at the moment, but perhaps it should have! 
  4. There was a great deal about  ORCIDs, and the ways in which uses of this particular  PID are evolving.  For example, the next big effort is to use the ORCID system for organisations.  You will find my ORCID at the top of this post.
  5. PIDs are also being mooted for instruments. The idea is that instrumental capabilities, settings, calibration etc are often an integral part of the data acquisition for a project. So if data is generated using such a device, why not quote its  PID in any derived article so that others can more easily replicate a particular experiment in their own laboratory.
  6. A quote by one of the speakers was attributed to Bill Gates around 1997 “We need  banking. We don’t need banks anymore” (think how this might apply to 2016. Was he correct?).  This was followed by straw men such as: “We need publications. We don’t need publishers anymore”. Or “We need archiving. We don’t need libraries anymore”. Just like Gates’ own quote, the reality is of course far more complex.
  7. And PID fatigue;  I hope you are not getting too much of that at the moment.

There are lots more I have learnt which I need to fix/enhance/address in our own experiments in the use of PIDs in chemistry, so I have better get on with it now!

References

  1. ORCID., DataCite., Crossref., and California Digital Library., "PIDapalooza 2016", 2016. https://doi.org/10.5438/11.0001

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The Fine-tuned principle in chemistry

Sunday, November 29th, 2009

The  so-called  Fine tuned model of the universe asserts that any small change in several of the dimensionless fundamental physical constants would make the universe radically different (and hence one in which life as we know it could not exist). I suggest here that there may be molecules which epitomize the same principle in chemistry. Consider for example dimethyl formamide. The NMR spectra of this molecule reveal that at room temperature, the two methyl groups are inequivalent, indicating that the rate constant for rotation about the C-N bond has a very particular range of values at the temperatures at which most living organisms exist on our planet.

Dimethyl formamide

Dimethyl formamide

The half-restricted room-temperature rotation about the C-N bond arises from exactly the right amount of resonance contribution from the ionic form shown on the right, and this in turn depends on the relative energies of the nitrogen pair and the π system of the carbonyl group having the correct relationship. It is probably also true that the environment that this grouping finds itself in will alter the contribution (i.e. stabilize the ionic form over the neutral one).   A little less contribution and the C-N bond would rotate much more easily, a little more and it would be much more rigid. Since this peptide bond is an essential and repeated feature of the structure of most biological proteins and enzymes, one might speculate that if that bond could rotate more easily, most enzymes would be much floppier than they are, and may not be easily induced to fold in a repeatable manner into the conformations that enable all the metabolic processes and make them the efficient catalysts they are. If the bond rotated less easily, it might be that the same enzymes would end up being too rigid, and this may prevent them from flexing sufficiently to allow key metabolites to enter or leave the active site.

Nowadays, the flexing of proteins is commonly studied using techniques of molecular dynamics,  the driving forces for which are specified using molecule mechanics force fields. Here, the rotation about the C-N bond is defined by simple mechanical force constants or torsional barriers. I ask here how sensitive the dynamics of protein folding and catalysis are to the C-N rotational barrier? Is this truly a fine-tuned molecule, or might it be that the existence of life as we know it has a wide tolerance to the strength of the C-N bond?

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