Self-As­sem­bly For Me

by Elio

I have the grat­ing feel­ing that the sub­ject of self-as­sem­bly of com­plex bi­o­log­i­cal struc­tures may not al­ways amass the level of re­spect it de­serves. I reckon that its im­por­tance is gen­er­ally ap­pre­ci­ated but, as top­ics go, it tends at times to be set aside. Yet, this is one of the most mag­nif­i­cent as­pects of bi­ol­ogy, one that beau­ti­fully com­bines logic with me­chan­ics and at­tests forcibly to the power of evo­lu­tion. And it goes back a ways. The pi­o­neer­ing study on the self-as­sem­bly of phages played an in­te­gral role in the de­vel­op­ment of mol­e­c­u­lar bi­ol­ogy.

To­day, the as­sem­bly of the bac­te­r­ial fla­gel­lar mo­tor rates high on the list of ex­cit­ing self-as­sem­bly phe­nom­ena, pos­si­bly vy­ing with that of vi­ral struc­ture (for an ex­am­ple of the lat­ter, see here). The mo­tor is a key con­stituent of bac­te­r­ial fla­gella. It is lo­cated at the base of the struc­ture and is re­spon­si­ble both for an­chor­ing it to the bac­te­ria and pro­vid­ing the mech­a­nism for its ro­ta­tion. It is a struc­ture with many com­po­nents, and its as­sem­bly con­sti­tutes an amaz­ing en­gi­neer­ing feat. One of the ear­li­est in­di­ca­tions of its com­plex­ity was re­cently ex­posed in these pages. Go­ing back to 1971, pu­ri­fied fla­gella were con­vinc­ingly shown to have an in­tri­cate base, con­sist­ing of sev­eral rings pre­sumed to an­chor the fla­gel­lum to the bac­te­r­ial en­velopes in a ro­tor-sta­tor arrange­ment. This struc­tural de­sign for a mol­e­c­u­lar ma­chine de­light­fully ex­plained how fla­gella could both ro­tate and be kept in place.

Fig­ure 1. The bac­te­r­ial fla­gel­lar mo­tor is a ro­tary mo­tor dri­ven by the flow of ions across the cy­to­plas­mic mem­brane. Its pur­pose is to ro­tate the long he­li­cal fil­a­ments that pro­trude from the bac­terium and pro­pel it to swim. The di­a­gram on the left de­picts a typ­i­cal Gram-neg­a­tive fla­gella basal body; the L- and P- rings are as­so­ci­ated with the outer mem­brane and pepti­doglycan layer. In Gram-pos­i­tive bac­te­ria, fla­gel­lar basal bod­ies lack the L- and P- rings. Source. The im­age on the right is a three-di­men­sional re­con­struc­tion of S. en­ter­ica fla­gel­lar mo­tor ob­tained by cryo-elec­tron mi­croscopy. Source

Time passed since this spec­tac­u­lar early im­agery, and with it came the de­vel­op­ment of tech­niques of pre­vi­ously unimag­in­able power. High among these is elec­tron cry­oto­mog­ra­phy, a way to re­veal the 3D arrange­ments in un­fixed bi­o­log­i­cal ma­te­r­ial un­der the elec­tron mi­cro­scope. This is some­what anal­o­gous to a CAT scan but in­stead of the op­ti­cal sec­tions be­ing par­al­lel, they are pro­duced by tilt­ing the spec­i­men at var­i­ous an­gles. With this tech­nique, along with the com­put­er­ized analy­sis of sin­gle im­ages (elec­tron cry­oto­mog­ra­phy and subto­mog­ra­phy av­er­ag­ing), one can ob­serve struc­tures at "macro­mol­e­c­u­lar" (sev­eral nanome­ter) res­o­lu­tion. In other words, in ex­quis­ite mol­e­c­u­lar de­tail. The el­e­ments of the fla­gel­lar mo­tor, the var­i­ous rings, the cen­ter rod, the sta­tor com­po­nent, and what is known as the ex­port ap­pa­ra­tus, are now re­vealed in glo­ri­ous de­tail. It's like look­ing at the wheel as­sem­bly of a car re­duced about 10 mil­lion-fold.

Fig­ure 2. Fla­gel­lar mo­tor struc­tures ob­tained by elec­tron cry­oto­mog­ra­phy and subto­mo­gram av­er­ag­ing. Left col­umn 20-nm thick cen­tral slices through tomo­grams of in­di­vid­ual cells ex­hibit­ing fla­gel­lar mo­tors, arranged in the same or­der as they ap­pear on a phy­lo­ge­netic tree. Scale bar, 50 nm. Right col­umn Ax­ial slices through av­er­age re­con­struc­tions of each mo­tor. Scale bar, 10 nm. Source

Now comes a sur­prise. One would ex­pect that such a com­plex struc­ture be the prod­uct of an un­com­mon event in evo­lu­tion, con­se­quently, that it be alike in dif­fer­ent bac­te­r­ial species. Not so. A most ex­cit­ing de­tailed analy­sis of eleven dif­fer­ent species shows that al­though the ba­sic plan is the same, these tiny ma­chines vary con­sid­er­ably in de­tail. Their el­e­ments dif­fer in cur­va­ture and in the po­si­tion­ing with re­gard to the axis. True, the bac­te­ria species cho­sen in­cluded an as­sort­ment of their fla­gel­lar arrange­ment, the fla­gella be­ing po­lar in some, all over the sur­face (per­itri­c­hous) in oth­ers, and in yet oth­ers en­cased in the periplasm. One can well imag­ine that such dif­fer­ent arrange­ments might re­quire spe­cially adapted ma­chin­ery. But this find­ing does re­veal a great de­gree of plas­tic­ity in the way fla­gel­lar mo­tors are made. Isn't this amaz­ing?

Self-as­sem­bly re­quires a high de­gree of "smart­ness" by the mol­e­cules in­volved — a higher de­gree than found in our "smart­phones" that are all but self-as­sem­bled. Not only must the whole bunch of mol­e­cules carry out their in­tended func­tion, they must be able to join with oth­ers into highly so­phis­ti­cated ul­tra-tiny ma­chines. Even more fas­ci­nat­ing is that this self as­sem­bling abil­ity is self-evolved! If I were start­ing over and wanted to ded­i­cate my­self to mol­e­c­u­lar mech­a­nisms, I would be likely to turn to the study of such smart mol­e­cules.