Wednesday, January 10, 2007

What this blog is about

Water in the living cell is a bit like quantum mechanics: anyone who says they understand it probably doesn’t. At least, for everyone who would make such a claim, there will be someone who disagrees with them. The simplistic descriptions of liquid water and macromolecular hydration given in biochemical textbooks (these things might not be considered at all in cell biology textbooks) are often caricatures that bear little relation to the current state of knowledge (or rather, of ignorance).

And yet the question of what cell water is like matters hugely. It determines how macromolecules acquire their biochemically active conformations, how they interact with one another, how they move about, how substances are partitioned in the cell, how signals are transmitted, and much more. To neglect water in a description of biomolecular function is rather like neglecting it in a description of swimming.

Here are just a few of the outstanding questions:
- what is the structure of bulk liquid water (yes, truly, this is still controversial)?
- is water in the cytoplasm bulk-like or not?
- what is the effect of nanoscale confinement of water?
- how does water behave close to hydrophobic and hydrophilic surfaces
- what is the structure of water around proteins, and around nucleic acids?
- …and what is the dynamics?
- how does the hydrophobic force work?
- is there a long-ranged hydrophobic force, and if so, why?
- what accounts for the Hofmeister series, the power of ions to precipitate proteins?
- is water necessarily unqiue as a solvent for life?

I have written a long review article that attempts to bring together what we know about these things – it is currently under review for Chemical Reviews, but a preprint can be downloaded from my web site (or can be very soon). But I’m trying to hit a moving target. Almost every week there is some relevant new disclosure about water and its roles in molecular biology. This blog will serve as a repository for such contributions. My hope is that it will be used by anyone who wishes, to keep a record of new results, what they might mean, and why they are important. And I would like this to be a forum for debate – because there is plenty to debate. Anyone who wishes to be among the posting group for this site should contact me for the login details. I’ll attempt to keep some kind of order, but not to be responsible for the site’s content.

2 comments:

RSB said...

A very good contribution, this blog. I look forward to some very fruitful dialogue. Regarding the structure of water next to proteins and how it differs from bulk water, those interested might want to look at this paper: F. Despa, A. Fernández and R. S. Berry, Phys. Rev. Lett. 93, 228194 (2005). It's about water next to hydrophobic regions, not polar or charged regions. Challenging question: What structure does water take in the boundaries between hydrophobic and polar or charged regions? And what happens to response times and dielectric functions in such regions?

Ashutosh said...

Is the review on your site yet? I am really looking forward to it.