Tag Archives: Protein dynamics

A new way to study protein dynamics

“Fields of 1,000,000 Volts/centiMeter are dangerously large from a laboratory point of view” — true enough, but that’s merely one TENTH of the potential difference/distance ratio found across the plasma membrane of all our cells. Here’s why after a bit of background

We wouldn’t exist without the membranes enclosing our cells which are largely hydrocarbon. Chemists know that fatty acids have one end (the carboxyl group) which dissolves in water while the rest is pure hydrocarbon. The classic is stearic acid — 18 carbons in a straight chain with a carboxyl group at one end. 3 molecules of stearic acid are esterified to glycerol in beef tallow (forming a triglyceride). The pioneers hydrolyzed it to make soap. Saturated fatty acids of 18 carbons or more are solid at body temperature (soap certainly is), but cellular membranes are fairly fluid, and proteins embedded in them move around pretty quickly. Why? Because most fatty acids found in biologic membranes over 16 carbons have double bonds in them. Guess whether they are cis or trans. Hint: the isomer used packs less well into crystals — you’ve got it, all the double bonds found in oleic (18 carbons 1 double bond), arachidonic (20 carbons, 4 double bonds) are cis this keeps membranes fluids as well. The cis double bond essentially puts a 60 degree kink in the hydrocarbon chain, making it much more difficult to pack in a liquid crystal type structure with all the hydrocarbon chains stretched out. Then there’s cholesterol which makes up 1/5 or so of membranes by weight — it also breaks up the tendency of fatty acid hydrocarbon chains to align with each other because it doesn’t pack with them very well. So cholesterol is another fluidizer of membranes.

How thick is the cellular membrane? If you figure the hydrocarbon chains of a saturated fatty acid stretched out as far as they can go, you get 1.54 Angstroms * cosine (30 degrees) = 1.33 Angstroms/carbon — times 16 = 21 Angstroms. Now double that because cellular membranes are lipid bilayers meaning that they are made of two layers of hydrocarbons facing each other, with the hydrophilic ends (carboxyls, phosphate groups) pointing outward. So we’re up to 42 Angstroms of thickness for the hydrocarbon part of the membrane. Add another 10 Angstroms or so for the hydrophilic ends (which include things like serine, choline etc. etc.) and you’re up to about 60 Angstroms thickness for the membrane (which is usually cited as 70 Angstroms — I don’t know why).

Because the electric field across our membranes is huge. The potential difference across our cell membranes is 70 milliVolts — 70 x 10^-3 volts. 70 Angstroms is 7 nanoMeters (7 x 10^-9) meters. Divide 70 x 10^-3 volts by 7 x 10^-9 and you get a field of 10,000,000 Volts/centiMeter.

So our membrane proteins live and function quite nicely in this intense electric field. Which brings us to [ Nature vol. 540 pp. 400 – 405 ’16 ] which zaps protein crystals with electric fields of this intensity, and then does Xray crystallography at various intervals to watch how the protein backbone and side chains move. The technique is called Electric Field stimulated Xray crystallography (EF-X). Unlike solution where proteins are all in slightly different conformations, the starting line is the same as is the finish line.

The electric pulse durations range from 50 – 500 nanoSeconds (50 – 500 * 10^-9 seconds). The xray pulse for doing Xray crystallography lasts all of 100 picoSeconds (100 * 10^’12). By timing the delay between the electric pulse and the Xray pulse you watch the protein move in time in response to the electric pulse. Hardly physiologic, but it seems likely that protein motions will follow the path of least resistance, which should tell us which conformations are closest in energy to the energy minimum found in proteins. The pulses are collected 50, 100, 200 nanoSeconds after pulse onset. The crystals tolerated ‘huncreds’ of 100 – 500 nanoSecond megaVolt electric field pulses. But even 50 nanoSeconds is pretty long when protein dynamics is concerned, as bond vibrations are as fast as a few femtoSeconds (10^-15 seconds). An electric field of this strength exerts a force of 10^

The technology enabling this is fantastic, but it is quite similar in concept what the late Nobelist Ahmed Zewail was doing. Of course his work was even faster looking at chemical reactions at the femtoSecond level of time (10^-15 seconds). So as the year draws to a close, it’s nice to see his ideas live on, even if he didn’t.