Allostery in chaperonins

Horovitz, Amnon; Fridmann, Yael; Kafri, Galit; Yifrach, Ofer

doi:10.1007/bf02904504

Cited by 9 publications

(14 citation statements)

References 71 publications

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“…A different perspective on the origin of negative cooperativity. The currently accepted model for nested cooperativity advanced by Horovitz et al (7) makes an arbitrary assumption to explain the decline of ATPase activity observed at higher [ATP], the hallmark of negative cooperativity. This is that the activity of a GroEL ring in the R conformation is greater when the distal ring is in the T conformation (i.e., T 7 R 7 ) than when the distal ring is in the R conformation (i.e., R 7 R 7 ).…”

Section: Resultsmentioning

confidence: 99%

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Setting the chaperonin timer: The effects of K ⁺ and substrate protein on ATP hydrolysis

Grason¹,

Gresham²,

Widjaja³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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allostery ͉ chaperonin GroEL ͉ potassium ion ͉ timing mechanism M uch mechanistic and structural information related to the operation of the chaperonin nanomachine has accumulated (1-11). As with many other cellular machines, the chaperonin nanomachine has evolved to operate at variable speed in response to biological demand. This implies the presence of one or more timing devices or switches that govern the cycling of the machinery through the various functional and conformational states. In the presence of GroES, the two rings of GroEL operate 180°out of phase with one another in the manner of a two-stroke, reciprocating motor (1, 2). A complete chaperonin cycle consequently consists of two hemicycles and two reciprocal resting states (12).In the accompanying article (12), we used stopped-flow FRET experiments to monitor the association and dissociation of GroES to and from the asymmetric, resting-state complex comprising (GroEL cis -[ADP]-[GroES]/GroEL trans -ADP), where the square brackets indicate ligands that are not free to exchange with unbound ligand. We showed that the dominant timing mechanism is located on the trans ring. This timer is regulated by allosteric transitions in the trans ring that are both responsive to the nucleotides ADP and ATP, the potassium ion, and substrate protein (SP) and which are communicated to the cis ring. Here, our focus is on the hydrolysis of ATP. We show that the steady-state hydrolysis of ATP is largely governed by the trans ring timer and its response to the nucleotides ADP and ATP, K ϩ , and SP. We also show, paradoxically, that the hydrolysis of ATP in the newly formed cis ring is largely indifferent to the presence of encapsulated SP and to variations in [K ϩ ] that have profound effects on the rate of ATP hydrolysis in the steady state.

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Section: Resultsmentioning

confidence: 99%

“…allostery ͉ chaperonin GroEL ͉ potassium ion ͉ timing mechanism M uch mechanistic and structural information related to the operation of the chaperonin nanomachine has accumulated (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). As with many other cellular machines, the chaperonin nanomachine has evolved to operate at variable speed in response to biological demand.…”

mentioning

confidence: 99%

Setting the chaperonin timer: The effects of K ⁺ and substrate protein on ATP hydrolysis

Grason¹,

Gresham²,

Widjaja³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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“…A large body of literature dealing with many mechanistic and structural aspects has accumulated (for reviews, see refs. [5][6][7][8][9][10][11]. However, despite this progress, surprisingly little is known about the timing mechanism of the chaperonin machine (however, see ref.…”

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confidence: 99%

“…This is well described by the nested model of allostery, extensively applied to the chaperonin system by Horovitz and colleagues (8). Briefly, ATP is bound and hydrolyzed preferentially, but not exclusively, to the relaxed (R) conformation.…”

mentioning

confidence: 99%

Setting the chaperonin timer: A two-stroke, two-speed, protein machine

Grason¹,

Gresham²,

Lorimer

2008

Proc. Natl. Acad. Sci. U.S.A.

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In a study of the timing mechanism of the chaperonin nanomachine we show that the hemicycle time (HCT) is determined by the mean residence time (MRT) of GroES on the cis ring of GroEL. In turn, this is governed by allosteric interactions within the trans ring of GroEL. Ligands that enhance the R (relaxed) state (residual ADP, the product of the previous hemicycle, and K ؉ ) extend the MRT and the HCT, whereas ligands that enhance the T (taut) state (unfolded substrate protein, SP) decrease the MRT and the HCT. In the absence of SP, the chaperonin machine idles in the resting state, but in the presence of SP it operates close to the speed limit, set by the rate of ATP hydrolysis by the cis ring. Thus, the conformational states of the trans ring largely control the speed of the complete chaperonin cycle.allostery ͉ GroEL ͉ timing mechanism ͉ GroES ͉ FRET P rotein machines and their man-made, macroscopic counterparts share several common attributes, e.g., concerted, coordinated movements, cyclical operation, and energy transduction. These machines are seldom reversible because each cycle generally involves at least one irreversible step, e.g., the consumption of fuel. Often these machines operate at variable speed, a plethora of timing devices adjusting the cycle speed in response to demand.An exemplary bipartite protein machine is the chaperonin system, typified by GroEL and GroES from Escherichia coli. GroEL is composed of 2 heptameric rings, stacked back to back, which, in the presence of GroES, operate out of phase with one another in the manner of a 2-stroke, reciprocating motor (1, 2). Driven by the hydrolysis of ATP, the chaperonin proteins function as a biological simulated annealing machine (3, 4), optimizing the folding of their substrate proteins (SPs) whose passage to biologically functional conformations is thus assured. A large body of literature dealing with many mechanistic and structural aspects has accumulated (for reviews, see refs. 5-11). However, despite this progress, surprisingly little is known about the timing mechanism of the chaperonin machine (however, see ref. 12). Here, we explore the location and operation of this timing device. We show that the timer is located on the trans ring and that it is regulated by allosteric transitions responsive to the nucleotides ADP and ATP, the potassium ion, and SPs.The subunits of the chaperonin machine display 2 forms of cooperativity: positive cooperativity between the subunits of 1 ring and negativity cooperativity between the subunits of different rings. This is well described by the nested model of allostery, extensively applied to the chaperonin system by Horovitz and colleagues (8). Briefly, ATP is bound and hydrolyzed preferentially, but not exclusively, to the relaxed (R) conformation. The influence of K ϩ is paradoxical. On one hand, it is needed for ATP hydrolysis in the steady state (13). However, at saturating concentrations of ATP, the rate of ATP hydrolysis is inversely proportional to the K ϩ concentration: the higher the K ϩ concentra...

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“…Additional examples where inhibitor-activator duality was experimentally observed include the effects of such drugs as valinomycin, SLverapamil and colchicine on Pgp ATPase activity 51,52 , and the effect of ADP on ATP hydrolysis by GroEL 53 . As in the case of DAPT, the qualitative nature of the phenomenon and its features are similar to those predicted by our theory, but lack of single-molecule measurements prevents us from unambiguously concluding that the mechanism we describe is indeed the one at play.…”

Section: Discussionmentioning

confidence: 99%

Single-molecule theory of enzymatic inhibition predicts the emergence of inhibitor-activator duality

Robin

Reuveni

Urbakh

2016

Preprint

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The classical theory of enzymatic inhibition aims to quantitatively describe the effect of certain molecules-called inhibitors-on the progression of enzymatic reactions, but growing signs indicate that it must be revised to keep pace with the single-molecule revolution that is sweeping through the sciences. Here, we take the single enzyme perspective and rebuild the theory of enzymatic inhibition from the bottom up. We find that accounting for multiconformational enzyme structure and intrinsic randomness cannot undermine the validity of classical results in the case of competitive inhibition; but that it should strongly change our view on the uncompetitive and mixed modes of inhibition. There, stochastic fluctuations on the single-enzyme level could give rise to inhibitor-activator duality-a phenomenon in which, under some conditions, the introduction of a molecule whose binding shuts down enzymatic catalysis will counter intuitively work to facilitate product formation.We state-in terms of experimentally measurable quantities-a mathematical condition for the emergence of inhibitor-activator duality, and propose that it could explain why certain molecules that act as inhibitors when substrate concentrations are high elicit a nonmonotonic dose response when substrate concentrations are low. The fundamental and practical implications of our findings are thoroughly discussed.Enzymes spin the wheel of life by catalyzing a myriad of chemical reactions central to the growth, development, and metabolism of all living organisms 1,2 . Without enzymes, essential processes would progress so slowly that life would virtually grind to a halt; and some enzymatic reactions are so critical that inhibiting them may result in death. Enzymatic inhibitors could thus be potent poisons 3,4 but could also be used as antibiotics 5,6 and drugs to treat other forms of disease 7,8 . Inhibitors have additional commercial uses 9,10 , but the fundamental principles which govern their interaction with enzymes are not always understood in full, and have yet ceased to fascinate those interested in the basic aspects of enzyme science. The canonical description of enzymatic inhibition received much exposure 1,2,11 , but even at the level of bulk reactions its many limitations have already been pointed out 12 . Moreover, and despite rapid advancements in the study of uninhibited enzymatic reactions on the singlemolecule level, the study of inhibited reactions has barely made progress in this direction and is still based, by and large, on what is known in bulk.Single molecule approaches revolutionized our understanding of enzymatic catalysis 13,14 . Early work demonstrated that at the single molecule level enzymatic catalysis is inherently stochastic 15,16 , and that one often needs to go beyond the common Markovian description to adequately account for the observed kinetics 17,18,19,20 . Universal aspects of stochastic . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for ...

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Allostery in chaperonins

Cited by 9 publications

References 71 publications

Setting the chaperonin timer: The effects of K ⁺ and substrate protein on ATP hydrolysis

Setting the chaperonin timer: The effects of K ⁺ and substrate protein on ATP hydrolysis

Setting the chaperonin timer: A two-stroke, two-speed, protein machine

Single-molecule theory of enzymatic inhibition predicts the emergence of inhibitor-activator duality

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Allostery in chaperonins

Cited by 9 publications

References 71 publications

Setting the chaperonin timer: The effects of K + and substrate protein on ATP hydrolysis

Setting the chaperonin timer: The effects of K + and substrate protein on ATP hydrolysis

Setting the chaperonin timer: A two-stroke, two-speed, protein machine

Single-molecule theory of enzymatic inhibition predicts the emergence of inhibitor-activator duality

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Resources

About

Setting the chaperonin timer: The effects of K ⁺ and substrate protein on ATP hydrolysis

Setting the chaperonin timer: The effects of K ⁺ and substrate protein on ATP hydrolysis