Tuesday, October 12, 2010

Meeting summary 06.10.10 CH10 Enzymes & Molecular Machines

Sorry about the late posting of this summary!
Last week we discussed chapter 10 of Nelson which was on enzymes and molecular machines. A definition of molecular devices can be found on pages 402-403 where there is a distinction between catalysts and 1-shot machines. An example of a 1-shot machine is translocation of a protein across a membrane.

We discussed where the motive force used by Listeria fits in to there definitions of molecular devices. At the tail end of Listeria an actin nucleation site where actin polymerizes is found. This polymerization causes listeria to be pushed forward. Should the Listeria motive force be considered a one-shot machine or a cyclic motor? p402 definition of a cyclic motor suggests that by using a renewable fuel (ATP) this it should be considered cyclic.

Mitch wondered where the data in fig 10.8 comes from.

Megan mentioned that the fact that these molecular machines do work on both local and global random fluctuations was not emphasized in this chapter. They tended to be represented by a smooth switching function when they would be better represented by an energy funnel.

Gilbert & Sullivan keep interrupting the chapter.

Figure 10.26 compares rachets to kinesin. The question was raised: what role does ADP or ATP play in this mechanism? It must be coupled to free energy difference but it is not clear how this happens. p463 mentions assumptions hold for large deltaG.

ATP, ADP provides large energy that allows weak, strong binding.

Figure 10.24 load is moved on upper right, hydrolysis on lower left. motion is not coupled to fuel burning. Are the events connected irreversibly?

A nucleotide sandwich dimer was mentioned where ATP is between myosin & kinesin.

The Smoluchowski equation (10.4) was discussed. Which describes diffusion with drift with ohmic/linear response/damped/dissipitive where velocity is linear in force - this basically means low reynolds number.

We discussed section 10.4 on Michaelis-Menten kinetics and discussed non- vs un-competitive binding. See Matt & Mitch's blog posts from last for further information.

We discussed the lack of statistics/probability knowledge in science - this seems to be a common theme.

Brief discussion on potential surfaces and their usefulness.

S-rachet was presented as protein translocation through membrane. When considering molecular machines even the best once go both ways due to thermal motion KbT.

We discussed molecular models of ATP & ADP + Pi and how it is difficult to model both as a single system.

Alan posed a question: What is the cause of catalysis? Could proteins have evolved to fluctuate randomly in one degree of freedom & can this enhance the rate of reaction. Is it possible to tell the difference between the different proposals for how enzymes work? Thermodynamically they all appear the same.

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