[ L] υ = (3) [ L] n. Q: What are the units of K in Eq. (3)? (Why is units placed in quotations.) What is the relationship to K in Eq. (1)?
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1 Chem 78 Spr. M. Wes Bdg Polyomals Bdg Polyomals We ve looked at three cases of lgad bdg so far: The sgle set of depedet stes (ss[]s [ ] [ ] Multple sets of depedet stes (ms[]s, or m[]ss All or oe, or two-state cooperatvty ( [ ] [ ] ( m [ ] [ ] ( ( & ( are the lmtg cases of o cooperatve teractos, ad very strog cooperatve teractos, respectvely, for a system wth oe type of bdg ste. Q: What are the uts of Eq. (? (Why s uts placed quotatos. What s the relatoshp to Eq. (? Equatos to spell out the statstcal dstrbutos of prote mcrostates, wth specfc referece to the extet of lgad bdg (ad assumptos about the ature of the bdg. I geeral, the umerator of υ accouts for the umber of moles of boud lgad, ad the deomator accouts for the umber moles of prote. The geeral case wth bdg stes s wrtte as [ P] [ P ] [ P ] [ P ] [ P] [ P] [ P ] [ P ] [ P ] ( Have there bee assumptos made about whether the stes teract, or whether there s oe or more class of stes? (The aswer to both s o, hece ts geeralty. Also, wthout loss of geeralty, substtutos ca be made for the P (where rages from 0 to. [ P][ ] [ P][ ] [ P][ ] [ P][ ] [ P] [ P][ ] [ P][ ] [ P][ ] [ P][ ] (5 page
2 Chem 78 Spr. M. Wes Bdg Polyomals From here, relatoshps amog bdg costats ca be assumed ad the exploted Equato 5 to reach Equatos to. Some of the subtletes Equato 5 are, part, a matter of defto. through are macroscopc assocato costats; the relatoshp to the uderlyg trsc costat(s wll chage accordg to the umber of sets (or classes of stes, ad the ature of the teracto amog stes,.e. are there teractos, or ot. I all cases [P] ca be factored out to gve: [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ( Factorg out [P] mplctly ackowledges t ([P] as a referece state wth respect to statstcal ad eergetc cosderatos, more o ths below. Q: What are the expressos for terms of the trsc assocato costats, f ( there s a sgle set of depedet stes, ( there are sets of depedet stes, ( there s oe set of strogly (all or oe teractg stes? SSS. The relatoshp betwee the macroscopc assocato costats ad a sgle trsc assocato costat (, smply reflects the statstcs of lgad bdg through a sgle class of stes. The dvdual steps of the bdg process, catalogued accordg to the umber of lgads boud, are gve by P P [P]/[P][] P P [P ]/[P][] P P [P ]/[P ][] (7 P - P [P ]/[P - ][] The (macroscopc costats are related to (the trsc costat by Ω, (8 Ω, where Ω, ad Ω,- represet the umber of ways of assortg ad - lgad molecules, respectvely, o depedet, equvalet bdg stes.! Ω (9, (!! Equato 9 s recogzable as the equato for coeffcets of the bomal expaso. For small values of, e.g., the valdty of the Equatos 8 ad 9 geeratg the page
3 Chem 78 Spr Bdg Polyomals. M. Wes page relatoshps betwee the ad ca be valdated by eumeratg the dfferet mcroscopc forms of P ad P - dagrammatcally. Cosder the stuato wth stes. I Equato 0, the formulae for the, expressed terms of (va Equato 8 have bee substtuted to Equato 5 ( [ ] ( ( [ ] ( ( ( [ ] ( ( ( ( [ ] ( [ ] ( ( [ ] ( ( ( [ ] ( ( ( ( [ ] υ (0 The terms the umerator are collected such as fasho to accetuate the umber of stes (. ( [ ] ( [ ] ( [ ] ( [ ] [ ] [ ] [ ] [ ] υ ( Factorg out [] the umerator produces a rd order polyomal. The deomator s a th order polyomal. [ ] [ ] [ ] [ ] { } [ ] [ ] [ ] [ ] υ ( Both of these are of the form ( [], [ ] [ ] ( [ ] ( [ ] [ ] ( υ ( Geeralzg to stes gves Equato. The Partto Fucto, Q. The deomator of Equato s equal to the total prote cocetrato dvded by the cocetrato of free prote s [P] tot /[P]. Ths quatty has meag statstcal mechacs; t s a example of a partto fucto, Q. [ ] [ ] [ ] [ ] Q ( Q s the sum of the umber of ways a gve eergy state may be formed. [P], represeted by the leadg term o the rght had sde of Equato, s the referece state ad has a relatve eergy equal to, ad a statstcal factor equal to. The partto fucto for the equvalet stes (sss model wth stes s [ ] [ ] [ ] [ ] Q (5 Whe wrtte a slghtly dfferet way, as Equato,
4 Chem 78 Spr. M. Wes Bdg Polyomals [ ] 0 [ ] [ ] [ ] [ ] Q 0 ( shows explctly the cotrbutos from statstcs (the lead umercal coeffcets ad terms that represet the eerges of the dfferet prote forms wth oe or more lgad molecules boud ( []. These are relatve eergy terms, relatve to the eergy of the referece state [P], ad are also kow as statstcal weghts (they weght the statstcal cotrbuto. Q, for the geeral case for equvalet bdg stes s Q 0 Ω [ ], (7 Each term the summato of Equato 7 s the product betwee the umber of dstgushable mcroscopc arragemets (Ω, ad the statstcal weght, []. ([] s sometmes referred to as the reduced lgad cocetrato. The [] represet ratos of prote forms, e.g. [P ]/[P], a Boltzma-lke maer, [P ]/[P] exp[δg/k B T], where Δg Δg 0 k B Tl[]. The progressve bdg of lgad cremetally adds to the statstcal weght. Note that for the depedet stes model, the eergy cremet s the same for each lgad molecule that bds to the prote: statstcal weght ato Δg 0 0 [] 0 [P]/[P] 0 [] [P]/[P] Δg [] [P ]/[P] Δg [] [P ]/[P] Δg [] [P ]/[P] Δg Fally, t s terestg to ote that ( [ ] dq dlq (8 Q d ( [ ] dl( [ ] Dscussos of the relatoshp betwee expermetal observables ad the partto fucto, of whch Equato 8 s a example, are foud statstcal thermodyamcs ad bophyscs textbooks. Two Models of Fte Cooperatvty Cooperatvty s rarely adequately descrbed by a all or oe scearo, so other models have bee developed. Two wdely used models are the cocerted ad sequetal models. page
5 Chem 78 Spr. M. Wes Bdg Polyomals. The Mood-Wyma-Chageux (MWC, or cocerted, model was publshed 95. A cetral assumpto s that cooperatve protes cosst of a olgomerc cluster of protomers (subuts, whch all the protomers are the same coformato, although the prote ca udergo a trasto betwee (at least two coformatoal states a cocerted fasho. The dfferet coformatos have dfferet lgad bdg afftes. The detals of the assumptos are foud the paper that descrbed the model: Mood, Wyma & Chageux. 95. J. Mol. Bol., (Posted o the course webste. Also, see Cator & Schmmel, Vol. III, Chapter 7 the full referece for ths book s o the course webste. The two assumptos of the MWC model ( that two coformatos of the macromolecule are assumed, ad ( that a dfferece bdg affty exsts betwee these two forms, are combed a way that geerates postve cooperatvty. The relaxed ( ad tese (T forms of the macromolecule, each egage lgad bdg equlbra. (Here the lgad s represeted by the letter F. F F T F TF F F F TF F TF F F F TF F TF (9 F - F F TF - F TF A equlbrum, whch exsts betwee the ad T forms the absece of lgad, s gve by T 0 [T]/[] (0 where 0 s geerally greater tha oe, whch s mples that the T form (the low affty form s more stable tha the form the absece of lgad. The relatoshp betwee lgad bdg costats to the T ad forms, whch are characterzed by the trsc assocato costats T ad, respectvely, s gve by c T / ( By defto the T form bds lgad less tghtly tha the form, c <. The average degree of saturato takes o a specfc form, whch s llustrated by a prote wth four lgad-bdg stes [ F] [ F ] [ F ] [ F ] [ TF] [ TF ] [ TF ] [ TF ] [ ] [ F] [ F ] [ F ] [ F ] [ T] [ TF] [ TF ] [ TF ] [ TF ] ( Factorg the polyomals the same maer, as had bee doe for the sgle stes model, gves page 5
6 Chem 78 Spr. M. Wes Bdg Polyomals [ ][ F] ( [ F] T[ T][ F] ( T[ F] [ ] ( [ F] [ T] ( [ F] ( Applcato of the deftos for c ( T c ad 0 ([T] 0 [] allows [T] ad T to be factored out [ F] ( [ F] c0[ F] ( c[ F] ( [ F] ( c [ F] ( Geeralzato to the prote that has bdg stes, gves [ F] ( [ F] c0[ F] ( c[ F] ( [ F] ( c [ F] 0 (5 0 T What values of c ad 0 must take o to reduce to ether ( the sgle-set-of-stes model, or ( the all-or-oe model?. The oshlad-nemethy-flmer (NF Sequetal Model geerates cooperatvty by allowg the trsc costats chage a way that reflects the chagg probablty of a prote subut to udergo the lgad-depedet trasto from a low to a hgh affty state, whch s flueced by lgad bdg to oe (or more eghborg subuts. A two-ste model suffces to llustrate the pot [ F] [ F] [ F] [ F] ( where ad are trsc bdg costats. I the sequetal model, < dcates postve cooperatvty, > dcates egatve cooperatvty, ad dcates depedet stes. The exact ature of the bdg polyomal ad the teracto terms depeds o the symmetry of the macromolecule. See the orgal referece for detals. (oshlad, Nemethy ad Flmer. 9. Bochemstry. 5:5-85; posted at the course webste page
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