May 15, 2012 Meeting

Our stated goal ...

Topic: Energy transduction & use via molecular machines - pumping/transport, coupled reactions.  Cells use a set of closely related non-equilibrium mechanisms to get things done.  We want to understand the (simple) underlying kinetic mechanisms and discuss a few examples.

Reading (see References): Read about active transport in your favorite book.  Some choices:

• Alberts, Ch. 11
• Baby Alberts, Ch 12
• Berg, Ch 13, Section 14.1

Meeting summary - Tues, May 15 meeting

We attempted to address the question, “How does driven (coupled) transport work?”  Thus, for example, how can a difference in ion concentrations across a membrane be used to drive the flow of some small molecule across that membrane? 

Our discussion focused around Fig. 13.11 of Berg which shows a putative cycle of states for coupled transport.  The key element in the cycle is the coupling of binding and conformational change.  From a physics point of view, a cycle appears to be reversible, so it is necessary to understand how a cycle can be driven.  In our discussion, we used equilibrium as a reference point.  In equilibrium there is equal flow in both directions around a cycle and so no active pumping can occur.  But if a (non-equilbirium) uni-directional  flow can be added at any point in the cycle, the cycle will be driven in the direction of  that flow.  (Here flow refers to flow through the space of states, which typically also will imply flow of matter.)

Our abstract discussion of cycles suggested that there is no reason why the same basic description could not be used to explain both “symporters”  and “antiporters” – that is, where the physical flow of the driven species is in the same direction or opposite that of the driving species.

We also discussed how a uni-directional chemical reaction (e.g., hydrolysis of ATP) could be used for active transport if it can be coupled to a suitable conformational change in a transporter.  A cycle related to that of Berg Fig. 13.11 can be drawn.  In principle, any “activated” (out-of-equilibrium) molecule/carrier can be used to drive transport.

Our discussion did not probe the structural mechanisms by which binding events can be couple to conformational changes suitable for transport.  Hopefully we will cover this next time.