Allosteric Cooperativity Research Articles

Allosteric Conformational Transition in Adenylate Kinase: Dynamic Correlations and Implication for Allostery

An essential aspect of protein science is to determine the deductive relationship between structure, dynamics, and various sets of functions. The role of dynamics is currently challenging our understanding of protein functions, both experimentally and theoretically. To verify the internal fluctuations and dynamics correlations in an enzyme protein undergoing conformational transitions, we have applied a coarse-grained dynamics algorithm using the elastic network model for adenylate kinase. Normal mode analysis reveals possible dynamical and allosteric pathways for the transition between the open and the closed states of adenylate kinase. As the ligands binding induces significant flexibility changes of the nucleotides monophosphate (NMP) domain and adenosine triphosphate (ATP) domain, the diagonalized correlation between different structural transition states shows that most correlated motions occur between the NMP domain and the helices surrounding the ATP domain. The simultaneous existence of positive and negative correlations indicates that the conformational changes of adenylate kinase take place in an allosteric manner. Analyses of the cumulated normal mode overlap coefficients and long-range correlated motion provide new insights of operating mechanisms and dynamics of adenylate kinase. They also suggest a quantitative dynamics criterion for determining the allosteric cooperativity, which may be applicable to other proteins.

Chemical Double Mutant Cycles for the Quantification of Cooperativity in H-Bonded Complexes

Chemical double mutant cycles have been used in conjunction with new H-bonding motifs for the quantification of chelate cooperativity in multiply H-bonded complexes. The double mutant cycle approach specifically deals with the effects of substituents, secondary interactions, and allosteric cooperativity on the free energy contributions from individual H-bond sites and allows dissection of the free energy contribution due to chelate cooperativity associated with the formation of intramolecular noncovalent interactions. Two different doubly H-bonded motifs were investigated in carbon tetrachloride, chloroform, 1,1,2,2-tetrachloroethane, and cyclohexane, and the results were similar in all cases, with effective molarities of 3-33 M for formation of intramolecular H-bonds. This corresponds to a free energy penalty of 3-9 kJ mol(-1) for formation of a bimolecular complex in solution, which is consistent with previous estimates of 6 kJ mol(-1). This result can be used in conjunction with the H-bond parameters, alpha and beta, to make a reasonable estimate of the stability constant for formation of a multiply H-bonded complex between two perfectly complementary partners, or to place an upper limit on the stability constant expected for a less complementary system.

Functional Reconstitution of Human ABCC3 into Proteoliposomes Reveals a Transport Mechanism with Positive Cooperativity

ABCC3 (MRP3) is a member of the family of multidrug resistance-associated proteins (MRP), which belong to the largest family of membrane transport proteins, namely, the ATP binding cassette (ABC) transporters. Members of this family contribute to the excretion of several organic anions from cells and play a critical role in conferring resistance against drugs used in the treatment of cancer. The overexpression of ABCC3 in the yeast Pichia pastoris and its subsequent purification made possible the study of substrate-dependent ATPase activity [Chloupkova, M., et al. (2007) Biochemistry 46, 7992-8003]. Here we describe the successful reconstitution of purified ABCC3 in proteoliposomes and ABCC3-dependent uptake of the anticancer drug methotrexate (MTX), as well as the physiological substrate leukotriene C(4) (LTC(4)). Our results show specific transport in a cell-free environment and in the absence of other proteins, revealing positive allosteric cooperativity for ABCC3-mediated substrate translocation. The ABCC3-mediated transport of MTX indicates a Hill coefficient of 2.3 +/- 1.7, a maximum transport rate (V(max)) of >2 micromol min(-1) mg(-1), and a K(M) in the millimolar range, whereas the translocation of LTC(4) into proteoliposomes displayed a Hill coefficient of 2.3 +/- 0.5 with a maximum transport rate of 4.7 +/- 0.8 nmol min(-1) mg(-1), and a K(M) in the micromolar range (1.7 +/- 0.3 microM). The transport of both substrates, MTX and LTC(4), was inhibited by etoposide, confirming a higher affinity of ABCC3 for LTC(4) than for MTX. The technical advances described in this report represent the basis for the extended and detailed kinetic characterization of ABCC3 with a wide range of implications for the investigation of other human ABC transporters.

A Dynamics Criterion to Determine Allostery

Dynamics coupling, correlated motion and allosteric cooperativity appear to be conserved in the long range communication and conformational transitions of many globular proteins. For example, a simple mutation can produce marked effects at distal sites via undefined pathways for a conventionally non-allosteric protein. There are reconciling evidences on allostery mechanisms for the ‘induced-fit’ scheme and the ‘population-shift’ theory, where dynamics plays an essential role in allosteric regulations. We develop a dynamics criterion to determine possible allostery in general proteins: Given two distinctive conformational states, dynamical fluctuations and correlations, either amongst the distant functional motifs or different subunits, can be accounted for by the conformational transitions between them. If the dynamics correlations result in both correlated and anti-correlated modes of motions (Figure 1), allosteric cooperativity will occur simultaneously.Figure 1Difference matrix of dynamic correlations in protein - the Aquifex AdK case: red, a correlated motion; blue, an anti-correlated motion; and red (blue) regions correspond to same (opposite) direction distortions. The presence of both positive and negative correlations indicates the existence of an allosteric cooperativity during conformational changes, as was proved by NMR experiments.View Large Image | View Hi-Res Image | Download PowerPoint Slide

A Biophysical Model Of Interactions Between Transcription Factors And Chromatin

Binding of transcription factors (TFs) to DNA is critical for triggering a cascade of events that lead to gene expression. The role of chromatin in this process is not considered by traditional biochemical models of protein-DNA interaction, or is limited to the passive DNA sequestration by the nucleosomes. Taking into account dynamic structure of chromatin is important for understanding transcription regulation in eukaryotes.Here we present a biophysical model of interactions between TFs and chromatinized DNA. The model takes into account dynamics of nucleosomes as well as other important features of eukaryotic regulatory regions such as the clustering TF binding sites, nucleosome-positioning DNA signals etc. Our model demonstrates that a wide range of biological phenomena can be explained by interactions between TFs and chromatin, and provides a quantitative description of the following processes:•cooperative binding and synergistic action of non-interacting TFs;•access of TFs to chromatinized DNA;•displacement of nucleosomes from regulatory regions;•rapid evolutionary changes in arrangement and membership of TF-binding sites in eukaryotic regulatory regions.Strikingly, we found that cooperative binding of TFs to chromatinized DNA is identical to the Monod-Wyman-Changeux model of allosteric cooperativity in hemoglobin, pointing at a general mechanism of cooperativity employed in a range of biological systems. This parallel allowed us to use classical results in biochemistry to gain deep insights into the mechanisms of gene regulation.

Protein oligomerization in the bacterial outer membrane (Review)

The formation of homo-oligomeric assemblies is a well-established characteristic of many soluble proteins and enzymes. Oligomerization has been shown to increase protein stability, allow allosteric cooperativity, shape reaction compartments and provide multivalent interaction sites in soluble proteins. In comparison, our understanding of the prevalence and reasons behind protein oligomerization in membrane proteins is relatively sparse. Recent progress in structural biology of bacterial outer membrane proteins has suggested that oligomerization may be as common and versatile as in soluble proteins. Here we review the current understanding of oligomerization in the bacterial outer membrane from a structural and functional point of view.

Catalytic Mechanism and Substrate Specificity of the β-Subunit of the Voltage-Gated Potassium Channel

The beta-subunits of voltage-gated potassium (Kv) channels are members of the aldo-keto reductase (AKR) superfamily. These proteins regulate inactivation and membrane localization of Kv1 and Kv4 channels. The Kvbeta proteins bind to pyridine nucleotides with high affinity; however, their catalytic properties remain unclear. Here we report that recombinant rat Kvbeta2 catalyzes the reduction of a wide range of aldehydes and ketones. The rate of catalysis was slower (0.06-0.2 min(-1)) than those of most other AKRs but displayed the expected hyperbolic dependence on substrate concentration, with no evidence of allosteric cooperativity. Catalysis was prevented by site-directed substitution of Tyr-90 with phenylalanine, indicating that the acid-base catalytic residue, identified in other AKRs, has a conserved function in Kvbeta2. The protein catalyzed the reduction of a broad range of carbonyls, including aromatic carbonyls, electrophilic aldehydes and prostaglandins, phospholipids, and sugar aldehydes. Little or no activity was detected with carbonyl steroids. Initial velocity profiles were consistent with an ordered bi-bi rapid equilibrium mechanism in which NADPH binding precedes carbonyl binding. Significant primary kinetic isotope effects (2.0-3.1) were observed under single- and multiple-turnover conditions, indicating that the bond-breaking chemical step is rate-limiting. Structure-activity relationships with a series of para-substituted benzaldehydes indicated that the electronic interactions predominate during substrate binding and that no significant charge develops during the transition state. These data strengthen the view that Kvbeta proteins are catalytically active AKRs that impart redox sensitivity to Kv channels.

Allosteric Cooperativity in Inhibition of Protein Kinase a Catalytic Subunit

Allosteric cooperativity in inhibition of protein kinase A was studied for the first time kinetically, by using the second-order rate constants of kemptide phosphorylation, measured in the absence and presence of inhibitors, and the ef- fect of cooperativity was characterized in terms of the interaction factor  . This kinetic method was evaluated for differ- ently targeted inhibitors H89 and LRRAALG-NH2, and interaction of these compounds with the free enzyme and the en- zyme-substrate complexes was quantified. The inhibitory effect of these compounds was asymmetric relatively ATP and kemptide, and allosteric enhancement of LRRAALG-NH2 binding in the presence of ATP was revealed. This cooperative effect was compared with results of ligand binding studies and the principle better binding - stronger allostery was formulated and formalized in terms of a linear-free-energy relationship p( ) = C + S pKi, where p( ) stands for the negative logarithm of the interaction factor and pKi characterizes affinity of the free enzyme for the inhibitory peptide, C=-2.7 and S=0.9, r=0.92.

Sensitivity amplification in the phosphorylation-dephosphorylation cycle: Nonequilibrium steady states, chemical master equation, and temporal cooperativity

A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105, 585 (2003); Annu. Rev. Phys. Chem. 58, 113 (2007)] emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It utilizes multiple kinetic cycles in time, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein. In the present paper, we thoroughly investigate both the deterministic (microscopic) and stochastic (mesoscopic) models and focus on the identification of the source of temporal cooperativity via comparing with allosteric cooperativity. A thermodynamic analysis confirms again the claim that the chemical equilibrium state exists if and only if the phosphorylation potential DeltaG=0, in which case the amplification of sensitivity is completely abolished. Then we provide comprehensive theoretical and numerical analysis with the first-order and zero-order assumptions in PdPC, respectively. Furthermore, it is interestingly found that the underlying mathematics of temporal cooperativity and allosteric cooperativity are equivalent, and both of them can be expressed by "dissociation constants," which also characterizes the essential differences between the simple and ultrasensitive PdPC switches. Nevertheless, the degree of allosteric cooperativity is restricted by the total number of sites in a single enzyme molecule that cannot be freely regulated, while temporal cooperativity is only restricted by the total number of molecules of the target protein that can be regulated in a wide range and gives rise to the ultrasensitivity phenomenon.

Coarse-grained dynamics of the receiver domain of NtrC: Fluctuations, correlations and implications for allosteric cooperativity

Receiver domains are key molecular switches in bacterial signaling. Structural studies have shown that the receiver domain of the nitrogen regulatory protein C (NtrC) exists in a conformational equilibrium encompassing both inactive and active states, with phosphorylation of Asp54 allosterically shifting the equilibrium towards the active state. To analyze dynamical fluctuations and correlations in NtrC as it undergoes activation, we have applied a coarse-grained dynamics algorithm using elastic network models. Normal mode analysis reveals possible dynamical pathways for the transition of NtrC from the inactive state to the active state. The diagonalized correlation between the inactive and the active (phosphorylated) state shows that most correlated motions occur around the active site of Asp54 and in the region Thr82 to Tyr101. This indicates a coupled correlation of dynamics in the "Thr82-Tyr101" motion. With phosphorylation inducing significant flexibility changes around the active site and alpha3 and alpha4 helices, we find that this activation makes the active-site region and the loops of alpha3/beta4 and alpha4/beta5 more stable. This means that phosphorylation entropically favors the receiver domain in its active state, and the induced conformational changes occur in an allosteric manner. Analyses of the local flexibility and long-range correlated motion also suggest a dynamics criterion for determining the allosteric cooperativity of NtrC, and may be applicable to other proteins.

Allosteric cooperativity in protein kinase A

Allosteric signaling in proteins requires long-range communication mediated by highly conserved residues, often triggered by ligand binding. In this article, we map the allosteric network in the catalytic subunit of protein kinase A using NMR spectroscopy. We show that positive allosteric cooperativity is generated by nucleotide and substrate binding during the transitions through the major conformational states: apo, intermediate, and closed. The allosteric network is disrupted by a single site mutation (Y204A), which also decouples the cooperativity of ligand binding. Because protein kinase A is the prototype for the entire kinome, these findings may serve as a paradigm for describing long-range coupling in other protein kinases.

Single-subunit allostery in the kinetics of peptide phosphorylation by protein kinase A

Allosteric cooperativity between peptide and ATP binding sites on cAMP-dependent protein kinase catalytic subunit was studied kinetically for the reaction of phosphorylation of seven peptide substrates. The allosteric effect was quantified i n terms of the interaction factor α by comparing binding effectiveness of a substrate molecule with the free enzyme and with the enzyme complex with another substrate. It was discovered that the magnitude of the allosteric feedback between these binding sites was governed by the effectiveness of substrate binding, which was varied by using different peptides, and the principle 'better binding: stronger allostery' was formulated. This inte rrelationship was further formalized in terms of a linear-free-en ergy relationship b pC p , S K α =+ holding between the free energy of the allosteric interaction, quantified by the negative logarithm of the interaction factor α (p ) α and the effectiveness of substrate binding quantified by b p. K For the peptide phosphorylation reaction C1 .4 =− and 0.4 S = were obtained. The negative intercept C indicated that the positive cooperativity between the binding sites, characterized by 1 α at millimolar b K values. This means that inversion of the cooperative effect was induced by substrate structure, and allostery was used by this enzyme as an additional mechanism to discriminate between substrates, facilitating phosphorylation of good substrates and providing additional protection against phosphorylation of bad substrates. Some implications of this allosteric mechanism on substrate specificity of protein kinases were discussed.

Influence of major structural features of tocopherols and tocotrienols on their ω-oxidation by tocopherol-ω-hydroxylase

Human cytochrome P450 4F2 (CYP4F2) catalyzes the initial omega-hydroxylation reaction in the metabolism of tocopherols and tocotrienols to carboxychromanols and is, to date, the only enzyme shown to metabolize vitamin E. The objective of this study was to characterize this activity, particularly the influence of key features of tocochromanol substrate structure. The influence of the number and positions of methyl groups on the chromanol ring, and of stereochemistry and saturation of the side chain, were explored using HepG2 cultures and microsomal reaction systems. Human liver microsomes and microsomes selectively expressing recombinant human CYP4F2 exhibited substrate activity patterns similar to those of HepG2 cells. Although activity was strongly associated with substrate accumulation by cells or microsomes, substantial differences in specific activities between substrates remained under conditions of similar microsomal membrane substrate concentration. Methylation at C5 of the chromanol ring was associated with markedly low activity. Tocotrienols exhibited much higher Vmax values than their tocopherol counterparts. Side chain stereochemistry had no effect on omega-hydroxylation of alpha-tocopherol (alpha-TOH) by any system. Kinetic analysis of microsomal CYP4F2 activity revealed Michaelis-Menten kinetics for alpha-TOH but allosteric cooperativity for other vitamers, especially tocotrienols. Additionally, alpha-TOH was a positive effector of omega-hydroxylation of other vitamers. These results indicate that CYP4F2-mediated tocopherol-omega-hydroxylation is a central feature underlying the different biological half-lives, and therefore biopotencies, of the tocopherols and tocotrienols.

Allosteric modulation of [ 3H]EBOB binding to GABA A receptors by diflunisal analogues

Allosteric modulatory effects of 12 biphenyl derivatives of diflunisal and two fenamates were studied on A-type receptors of GABA (GABA AR) via [ 3H]4′-ethynylbicycloorthobenzoate (EBOB) binding to synaptic membrane preparations of rat forebrain. A simplified ternary allosteric model was used to determine binding affinities of the compounds and the extents of cooperativity with GABA. Structure activity analysis revealed that 4-hydroxy substituents of the biphenyls contribute to their micromolar binding affinities more than 3-carboxyl groups. Electron-withdrawing fluorinated substituents, especially in ortho position, were also advantageous. These factors also strongly enhanced the cooperativity with GABA binding. The correlation between displacing potency of the allosteric agents and cooperativity with GABA suggests that these processes are associated with common mechanisms. The pharmacological relevance of these interactions is discussed. These data help to differentiate the structural requirements of these agents to act on GABAergic neurotransmission versus nonsteroidal anti-inflammatory effects.

Morpheeins – a new structural paradigm for allosteric regulation

Classic models for the allosteric regulation of protein function consider an equilibrium among protein structures of constant oligomeric multiplicity. The morpheein (mor-phee'-in) concept expands this model to include a dynamic equilibrium of protein structures wherein a protein monomer can exist in more than one conformation and each monomer conformation dictates a different quaternary structure of finite multiplicity and different functionality. The morpheein concept provides a new framework for understanding allosteric regulation, kinetic cooperativity and hysteresis. Porphobilinogen synthase constitutes a prototype morpheein ensemble comprising several interconverting quaternary structure isoforms; one monomer conformation dictates assembly of a high-activity octamer, whereas an alternative monomer conformation dictates assembly of a low-activity hexamer. It is proposed here that the behavior of some other allosteric enzymes reflect dynamic morpheein equilibrium systems and six candidate proteins are enumerated.

The 13 Å Structure of a Chaperonin GroEL–Protein Substrate Complex by Cryo-electron Microscopy

The 13 angstroms resolution structures of GroEL bound to a single monomer of the protein substrate glutamine synthetase (GS(m)), as well as that of unliganded GroEL have been determined from a heterogeneous image population using cryo-electron microscopy (cryo-EM) coupled with single-particle image classification and reconstruction techniques. We combined structural data from cryo-EM maps and dynamic modeling, taking advantage of the known X-ray crystallographic structure and normal mode flexible fitting (NMFF) analysis, to describe the changes that occur in GroEL structure induced by GS(m) binding. The NMFF analysis reveals that the molecular movements induced by GS(m) binding propagate throughout the GroEL structure. The modeled molecular motions show that some domains undergo en bloc movements, while others show more complex independent internal movements. Interestingly, the substrate-bound apical domains of both the cis (GS(m)-bound ring) and trans (the opposite substrate-free ring) show counterclockwise rotations, in the same direction (though not as dramatic) as those documented for the ATP-GroEL-induced structure changes. The structural changes from the allosteric substrate protein-induced negative cooperativity between the GroEL rings involves upward concerted movements of both cis and trans equatorial domains toward the GS(m)-bound ring, while the inter-ring distances between the heptamer contact residues are maintained. Furthermore, the NMFF analysis identifies the secondary structural elements that are involved in the observed approximately 5 angstroms reduction in the diameter of the cavity opening in the unbound trans ring. Understanding the molecular basis of these substrate protein-induced structural changes across the heptamer rings provides insight into the origins of the allosteric negative cooperative effects that are transmitted over long distances (approximately 140 angstroms).

Role of cooperative H+/e− Linkage (redox Bohr effect) at heme a/CuA and heme a 3/CuB in the proton pump of cytochrome c oxidase

It is a pleasure to contribute to the special issue published in honor of Vladimir Skulachev, a distinguished scientist who greatly contributes to maintain a high standard of biochemical research in Russia. A more particular reason can be found in his work, where observations anticipating some ideas presented in my article were reported. Cytochrome c oxidase exhibits protonmotive, redox linked allosteric cooperativity. Experimental observations on soluble bovine cytochrome c oxidase are presented showing that oxido-reduction of heme a/Cu(A) and heme a(3)/Cu(B) is linked to deprotonation/protonation of two clusters of protolytic groups, A(1) and A(2), respectively. This cooperative linkage (redox Bohr effect) results in the translocation of 1 H(+)/oxidase molecule upon oxido-reduction of heme a/Cu(A) and heme a(3)/Cu(B), respectively. Results on liposome-reconstituted oxidase show that upon oxidation of heme a/Cu(A) and heme a(3)/Cu(B) protons from A(1) and A(2) are released in the outer aqueous phase. A(1) but not A(2) appears to take up protons from the inner aqueous space upon reduction of the respective redox center. A cooperative model is presented in which the A(1) and A(2) clusters, operating in close sequence, constitute together the gate of the proton pump in cytochrome c oxidase.

Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction

Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation–dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the free energy from hydrolysis inside cells, ΔG (phosphorylation potential), controls the amplification and sensitivity of the switch-like cellular module; the response coefficient of the sensitivity amplification approaches the optimal 1 and the Hill coefficient increases with increasing ΔG. We discover that zero-order ultrasensitivity is mathematically equivalent to allosteric cooperativity. Furthermore, we show that the high amplification in ultrasensitivity is mechanistically related to the proofreading kinetics for protein biosynthesis. Both utilize multiple kinetic cycles in time to gain temporal cooperativity, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein.

Di-substituted cyclohexyl derivatives bind to two identical sites with positive cooperativity on the voltage-gated potassium channel, K(v)1.3.

Di-substituted cyclohexyl (DSC) derivatives inhibit the voltage-gated potassium channel, K(v)1.3, and have immunosuppressant activity (Schmalhofer et al. (2002) Biochemistry 41, 7781-7794). This class of inhibitors displays Hill coefficients of near 2 in functional assays, and trans DSC analogues appear to selectively interact with K(v)1.3 channel conformations related to C-type inactivation. To further understand the details of the DSC inhibitor interaction with potassium channels, trans-1-(N-n-propylcarbamoyloxy)-4-phenyl-4-(3-(2-methoxyphenyl)-3-oxo-2-azaprop-1-yl)cyclo-hexane (trans-NPCO-DSC) was radiolabeled with tritium, and its binding characteristics to K(v)1.3 channels were determined. Specific binding of [(3)H]-trans-NPCO-DSC to K(v)1.3 channels is a saturable, time-dependent, and fully reversible process. Saturation binding isotherms and competition binding experiments are consistent with the presence of two receptor sites for DSC derivatives on the K(v)1.3 channel that display positive allosteric cooperativity. The high affinity interaction of [(3)H]-trans-NPCO-DSC with K(v)1.3 channels appears to correlate with the rates of C-type inactivation of the channel. These data, taken together, mark the first demonstration of the existence of multiple binding sites for an inhibitor of an ion channel and suggest that the high affinity interaction of trans-NPCO-DSC and similar inhibitors with K(v)1.3 channels could be exploited for the development of selective molecules that target this protein.

Nucleoside transporter and nucleotide vesicular transporter: Two examples of mnemonic regulation

AbstractAccording to their relevant roles in the regulation and availability of extracellular levels of purinergic signals, the nucleoside transporter and the nucleotide vesicular transporter are subject to acute regulation. The plasma membrane nucleoside transporter has been shown to exhibit several regulatory mechanisms, such as regulation by long‐term signals, phosphorylation/dephosphorylation processes, and allosteric modulation. The present work reviews studies concerning allosteric modulation of nucleoside and nucleotide vesicular transporters, as the first reported examples of mnemonic behavior in transporter proteins, presenting kinetic and allosteric cooperativity. This fact implies that the protein can exhibit different conformations, each one with specific kinetic parameters. Transport substrates are able to induce slow conformational changes between the different forms of the transporter. This kinetic mechanism can provide several physiological advantages, since it allows strict control of transport capacity by changes in substrate concentrations. This allosteric modulation has been confirmed in several experimental models, the nucleoside transporter in chromaffin and endothelial cells from adrenal medulla and the nucleotide vesicular transporter in the chromaffin cell granules and rat brain synaptic vesicles. Taking into account these considerations, the mnemonic regulation described here could be a widespread mechanism among transporter proteins. Drug Dev. Res. 52:11–21, 2001. © 2001 Wiley‐Liss, Inc.