Kinetics of allosteric conformational transition of a macromolecule prior to ligand binding: analysis of stopped-flow kinetic experiments

A simple method to resolve rate constants when the binding mechanism obeys induced fit or conformational selection

Many interactions involving a ligand and its molecular target are studied by rapid kinetics using a stopped-flow apparatus. Information obtained from these studies is often limited to a single, saturable relaxation that is insufficient to resolve all independent rate constants even for a two-step mechanism of binding obeying induced fit (IF) or conformational selection (CS). We introduce a simple method of general applicability where this limitation is overcome. The method accurately reproduces the rate constants for ligand binding to the serine protease thrombin determined independently from the analysis of multiple relaxations. Application to the inactive zymogen precursor of thrombin, prethrombin-2, resolves all rate constants for a binding mechanism of IF or CS from a single, saturable relaxation. Comparison with thrombin shows that the prethrombin-2 to thrombin conversion enhances ligand binding to the active site not by improving accessibility through the value of kon but by reducing the rate of dissociation koff. The conclusion holds regardless of whether binding is interpreted in terms of IF or CS and has general relevance for the mechanism of zymogen activation of serine proteases. The method also provides a simple test of the validity of IF and CS and indicates when more complex mechanisms of binding should be considered.

Mechanisms of ligand binding

Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.

Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin

A pre-existing, allosteric equilibrium between closed (E*) and open (E) conformations of the active site influences the level of activity in the trypsin fold and defines ligand binding according to the mechanism of conformational selection. Using the clotting protease thrombin as a model system, we investigate the molecular determinants of the E*-E equilibrium through rapid kinetics and X-ray structural biology. The equilibrium is controlled by three residues positioned around the active site. W215 on the 215-217 segment defining the west wall of the active site controls the rate of transition from E to E* through hydrophobic interaction with F227. E192 on the opposite 190-193 segment defining the east wall of the active site controls the rate of transition from E* to E through electrostatic repulsion of E217. The side chain of E217 acts as a lever that moves the entire 215-217 segment in the E*-E equilibrium. Removal of this side chain converts binding to the active site to a simple lock-and-key mechanism and freezes the conformation in a state intermediate between E* and E. These findings reveal a simple framework to understand the molecular basis of a key allosteric property of the trypsin fold.

UvrD helicase activation by MutL involves rotation of its 2B subdomain

Escherichia coli UvrD is a superfamily 1 helicase/translocase that functions in DNA repair, replication, and recombination. Although a UvrD monomer can translocate along single-stranded DNA, self-assembly or interaction with an accessory protein is needed to activate its helicase activity in vitro. Our previous studies have shown that an Escherichia coli MutL dimer can activate the UvrD monomer helicase in vitro, but the mechanism is not known. The UvrD 2B subdomain is regulatory and can exist in extreme rotational conformational states. By using single-molecule FRET approaches, we show that the 2B subdomain of a UvrD monomer bound to DNA exists in equilibrium between open and closed states, but predominantly in an open conformation. However, upon MutL binding to a UvrD monomer-DNA complex, a rotational conformational state is favored that is intermediate between the open and closed states. Parallel kinetic studies of MutL activation of the UvrD helicase and of MutL-dependent changes in the UvrD 2B subdomain show that the transition from an open to an intermediate 2B subdomain state is on the pathway to helicase activation. We further show that MutL is unable to activate the helicase activity of a chimeric UvrD containing the 2B subdomain of the structurally similar Rep helicase. Hence, MutL activation of the monomeric UvrD helicase is regulated specifically by its 2B subdomain.

Membrane interactions of intrinsically disordered proteins: The example of alpha-synuclein

Peripheral membrane proteins associate reversibly with biological membranes that, compared to protein binding partners, are structurally labile and devoid of specific binding pockets. Membranes in different subcellular compartments vary primarily in their chemical composition and physical properties, and recognition of these features is therefore critical for allowing such proteins to engage their proper membrane targets. Intrinsically disordered proteins (IDPs) are well-suited to accomplish this task using highly specific and low- to moderate-affinity interactions governed by recognition principles that are both similar to and different from those that mediate the membrane interactions of rigid proteins. IDPs have also evolved multiple mechanisms to regulate membrane (and other) interactions and achieve their impressive functional diversity. Moreover, IDP-membrane interactions may have a kinetic advantage in fast processes requiring rapid control of such interactions, such as synaptic transmission or signaling. Herein we review the biophysics, regulation and functional implications of IDP-membrane interactions and include a brief overview of some of the methods that can be used to study such interactions. At each step, we use the example of alpha-synuclein, a protein involved in the pathogenesis of Parkinson's disease and one of the best characterized membrane-binding IDP, to illustrate some of the principles discussed.

Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure

Folding of an RNA from secondary to tertiary structure often depends on divalent ions for efficient electrostatic charge screening (nonspecific association) or binding (specific association). To measure how different divalent cations modify folding kinetics of the 60 nucleotide Ecoli rRNA GTPase center, we combined stopped-flow fluorescence in the presence of Mg²⁺, Ca²⁺, or Sr²⁺ together with time-resolved small angle X-ray scattering (SAXS) in the presence of Mg²⁺ to observe the folding process. Immediately upon addition of each divalent ion, the RNA undergoes a transition from an extended state with secondary structure to a more compact structure. Subsequently, specific divalent ions modulate populations of intermediates in conformational ensembles along the folding pathway with transition times longer than 10 msec. Rate constants for the five folding transitions act on timescales from submillisecond to tens of seconds. The sensitivity of RNA tertiary structure to divalent cation identity affects all but the fastest events in RNA folding, and allowed us to identify those states that prefer Mg²⁺ The GTPase center RNA appears to have optimized its folding trajectory to specifically utilize this most abundant intracellular divalent ion.

Induced Fit Is a Special Case of Conformational Selection

Conformational selection (CS) and induced fit (IF) are two widely used interpretations of binding of a ligand to biological macromolecules. Both mechanisms envision a two-step reaction in which a conformational transition either precedes (CS) or follows (IF) the binding step. Under pseudo-first-order conditions where the ligand is in excess compared to the macromolecule, both mechanisms produce two relaxations. A fast one eventually increases linearly with ligand concentration and reflects the binding interaction. A slow one saturates to a constant value after decreasing or increasing hyperbolically with ligand concentration. This relaxation is the one most often accessible to experimental measurements and is potentially diagnostic of the mechanism involved. A relaxation that decreases unequivocally identifies CS, but a hyperbolic increase is compatible with both CS and IF. The potential ambiguity between the two mechanisms is more than qualitative. Here we show that the entire kinetic repertoire of IF is nothing but a mathematical special case of CS as revealed by a simple transformation of the rate constants, which emphasizes the need for independent support of either mechanism from additional experimental evidence. We discuss a simple strategy for distinguishing between IF and CS under the most common conditions encountered in practice, i.e., when the ligand is in excess compared to the macromolecule and a single relaxation is accessible to experimental measurements.

Conformational selection and induced fit as a useful framework for molecular motor mechanisms

The linkage between macromolecular binding and conformational change that is ubiquitous in biological molecules can be understood in the context of the mechanisms of conformational selection and induced fit. Here, we explore mappings between these mechanisms of ligand binding and those underlying the translocation of molecular motors and the nucleic acid unwinding of helicases. The mechanism of biased motion exhibited by molecular motors is typically described as either a thermal ratchet or a power-stroke and nucleic acid helicases are characterized by either active or passive unwinding mechanisms. We posit that both Brownian ratchet translocation and passive unwinding are examples of conformational selection and that both power-stroke translocation and active unwinding are examples of induced fit. Furthermore, in ligand-binding reactions, both conformational selection and induced fit may exist in parallel leading to a ligand-dependent flux through the different mechanistic pathways. Given the mappings we describe, we propose that motors may be able to function via parallel ratchet and stroke mechanisms and that helicases may be able to function via parallel active and passive mechanisms.

A Kinetic Signature for Parallel Pathways: Conformational Selection and Induced Fit. Links and Disconnects between Observed Relaxation Rates and Fractional Equilibrium Flux under Pseudo-First-Order Conditions

Molecular association plays a ubiquitous role in biochemistry and is often accompanied by conformational exchange in one or both binding partners. Traditionally, two limiting mechanisms are considered for the association of two molecules. In a conformational selection (CS) mechanism, a ligand preferentially binds to a subset of conformations in its binding partner. In contrast, an induced fit (IF) mechanism describes the ligand-dependent isomerization of the binding partner in which binding occurs prior to conformational exchange. Measurements of the ligand concentration dependence of observed rates of relaxation are commonly used to probe whether CS or IF is taking place. Here we consider a four-state thermodynamic cycle subject to detailed balance and demonstrate the existence of a relatively unexplored class of kinetic signatures where an initial decrease in the observed rate is followed by a subsequent increase under pseudo-first-order conditions. We elucidate regions of rate space necessary to generate a nonmonotonic observed rate and show that, under certain conditions, the position of the minimum of the observed rate correlates with a transition in equilibrium flux between CS and IF pathways. Furthermore, we demonstrate that monotonic trends in the observed rate can occur when both CS and IF mechanisms are taking place, suggesting that caution must be taken not to overinterpret monotonic trends as evidence of the absence of either CS or IF. Lastly, we conclude that a nonmonotonic kinetic signature is uniquely unambiguous in the sense that when this trend is observed, one may conclude that both CS and IF mechanistic paths are utilized.

High performance enzyme kinetics of turnover, activation and inhibition for translational drug discovery

INTRODUCTION

Enzymes are the macromolecular catalysts of many living processes and represent a sizable proportion of all druggable biological targets. Enzymology has been practiced just over a century during which much progress has been made in both the identification of new enzymes and the development of novel methodologies for enzyme kinetics. Areas covered: This review aims to address several key practical aspects in enzyme kinetics in reference to translational drug discovery research. The authors first define what constitutes a high performance enzyme kinetic assay. The authors then review the best practices for turnover, activation and inhibition kinetics to derive critical parameters guiding drug discovery. Notably, the authors recommend global progress curve analysis of dose/time dependence employing an integrated Michaelis-Menten equation and global curve fitting of dose/dose dependence. Expert opinion: The authors believe that in vivo enzyme and substrate abundance and their dynamics, binding modality, drug binding kinetics and enzyme's position in metabolic networks should be assessed to gauge the translational impact on drug efficacy and safety. Integrating these factors in a systems biology and systems pharmacology model should facilitate translational drug discovery.

Discrimination between conformational selection and induced fit protein-ligand binding using Integrated Global Fit analysis

Molecular recognition between proteins and small molecule ligands is at the heart of biological function in cellular systems and the basis of modern rational drug development. Therefore, the mechanisms governing protein-ligand interaction have been objects of research for many decades. The last 15 years has seen a revival of a discussion whether conformational selection (CS) or induced fit (IF) is the most relevant binding mechanism. A decreasing observed rate constant, k obs, with increasing ligand concentration was considered to be a hallmark of CS, but according to contemporary knowledge, a positive saturating behavior of k obs can be explained by both CS and IF mechanisms. The only currently recognized kinetic method to differentiate between both binding mechanisms includes the measurement of two separate series of binding kinetics with variation of either protein or ligand under pseudo-first-order conditions. This study avoids the disadvantage of high protein concentrations and provides evidence that a comprehensive Integrated Global Fit analysis of sets of binding kinetics with just varied ligand concentration in combination with equilibrium data and optional displacement kinetics can effectively differentiate between CS and IF binding mechanisms. The limiting situation, when physical binding dominates over the previous (CS) or subsequent (IF) conformational changes, is carefully analyzed. Finally, the relevance of kinetic methods and the elucidation of more complex binding mechanisms are discussed for advanced rational selection and optimization of drug candidates.

Kinetic dissection of the pre-existing conformational equilibrium in the trypsin fold

Structural biology has recently documented the conformational plasticity of the trypsin fold for both the protease and zymogen in terms of a pre-existing equilibrium between closed (E*) and open (E) forms of the active site region. How such plasticity is manifested in solution and affects ligand recognition by the protease and zymogen is poorly understood in quantitative terms. Here we dissect the E*-E equilibrium with stopped-flow kinetics in the presence of excess ligand or macromolecule. Using the clotting protease thrombin and its zymogen precursor prethrombin-2 as relevant models we resolve the relative distribution of the E* and E forms and the underlying kinetic rates for their interconversion. In the case of thrombin, the E* and E forms are distributed in a 1:4 ratio and interconvert on a time scale of 45 ms. In the case of prethrombin-2, the equilibrium is shifted strongly (10:1 ratio) in favor of the closed E* form and unfolds over a faster time scale of 4.5 ms. The distribution of E* and E forms observed for thrombin and prethrombin-2 indicates that zymogen activation is linked to a significant shift in the pre-existing equilibrium between closed and open conformations that facilitates ligand binding to the active site. These findings broaden our mechanistic understanding of how conformational transitions control ligand recognition by thrombin and its zymogen precursor prethrombin-2 and have direct relevance to other members of the trypsin fold.

Identification of two-step chemical mechanisms using small temperature oscillations and a single tagged species

In order to identify two-step chemical mechanisms, we propose a method based on a small temperature modulation and on the analysis of the concentration oscillations of a single tagged species involved in the first step. The thermokinetic parameters of the first reaction step are first determined. Then, we build test functions that are constant only if the chemical system actually possesses some assumed two-step mechanism. Next, if the test functions plotted using experimental data are actually even, the mechanism is attributed and the obtained constant values provide the rate constants and enthalpy of reaction of the second step. The advantage of the protocol is to use the first step as a probe reaction to reveal the dynamics of the second step, which can hence be relieved of any tagging. The protocol is anticipated to apply to many mechanisms of biological relevance. As far as ligand binding is considered, our approach can address receptor conformational changes or dimerization as well as competition with or modulation by a second partner. The method can also be used to screen libraries of untagged compounds, relying on a tracer whose concentration can be spectroscopically monitored.

Essential role of conformational selection in ligand binding

Two competing and mutually exclusive mechanisms of ligand recognition - conformational selection and induced fit - have dominated our interpretation of ligand binding in biological macromolecules for almost six decades. Conformational selection posits the pre-existence of multiple conformations of the macromolecule from which the ligand selects the optimal one. Induced fit, on the other hand, postulates the existence of conformational rearrangements of the original conformation into an optimal one that are induced by binding of the ligand. In the former case, conformational transitions precede the binding event; in the latter, conformational changes follow the binding step. Kineticists have used a facile criterion to distinguish between the two mechanisms based on the dependence of the rate of relaxation to equilibrium, kobs, on the ligand concentration, [L]. A value of kobs decreasing hyperbolically with [L] has been seen as diagnostic of conformational selection, while a value of kobs increasing hyperbolically with [L] has been considered diagnostic of induced fit. However, this simple conclusion is only valid under the rather unrealistic assumption of conformational transitions being much slower than binding and dissociation events. In general, induced fit only produces values of kobs that increase with [L] but conformational selection is more versatile and is associated with values of kobs that increase with, decrease with or are independent of [L]. The richer repertoire of kinetic properties of conformational selection applies to kinetic mechanisms with single or multiple saturable relaxations and explains the behavior of nearly all experimental systems reported in the literature thus far. Conformational selection is always sufficient and often necessary to account for the relaxation kinetics of ligand binding to a biological macromolecule and is therefore an essential component of any binding mechanism. On the other hand, induced fit is never necessary and only sufficient in a few cases. Therefore, the long assumed importance and preponderance of induced fit as a mechanism of ligand binding should be reconsidered.

Conformational selection is a dominant mechanism of ligand binding

Molecular recognition in biological macromolecules is achieved by binding interactions coupled to conformational transitions that precede or follow the binding step, two limiting mechanisms known as conformational selection and induced fit, respectively. Sorting out the contribution of these mechanisms to any binding interaction remains a challenging task of general interest in biochemistry. Here we show that conformational selection is associated with a vast repertoire of kinetic behaviors, can never be disproved a priori as a mechanism of ligand binding, and is sufficient to explain the relaxation kinetics documented experimentally for a large number of systems. On the other hand, induced fit features a narrow spectrum of kinetic behaviors and can be disproved in many cases in which conformational selection offers the only possible explanation. This conclusion offers a paradigm shift in the analysis of relaxation kinetics, with conformational selection acquiring preeminence as a mechanism of ligand binding. The dominant role of conformational selection supports the emerging structural view of the macromolecule as a conformational ensemble from which the ligand selects the initial optimal fit to produce a biological response.

Fluorescence intensity, anisotropy, and transient dynamic quenching stopped-flow kinetics

The kinetic mechanisms of biological reactions are predominantly addressed by spectroscopic stopped-flow or temperature-jump methods. Both the stopped-flow and the temperature-jump methods are relaxation kinetic techniques, i.e., they rely on examining the effect of perturbation on the reaction system under study. The relaxation kinetic measurements of the approach to equilibrium of the ligand-macromolecule reactions provide two independent sets of data, relaxation times and amplitudes. Although the traditional matrix method is a powerful approach, the matrix projection operator technique is an exceptionally convenient approach to analyze stopped-flow kinetics. The numerical analysis of a complex multistep reaction is reduced to finding only the eigenvalues of the original coefficient matrix. The method is illustrated by examination of the kinetics of a fluorescent nucleotide analog binding to the E. coli replicative helicase, the DnaB protein. Fluorescence intensity is one of the most often used spectroscopic signals to monitor the progress of biochemical reactions. Its properties also give an opportunity to address various structural aspects of the intermediates unavailable by any other method. The relative molar fluorescence intensities of different intermediates provide information about the physical environment surrounding the fluorophore during the course of the reaction. On the other hand, time-dependence of the fluorescence anisotropy in stopped-flow experiments provides information about the mobility of the fluorescing species in each intermediate of the observed kinetic process. Moreover, transient anisotropy data may also put additional light on the mechanism of the reaction, not obvious in studies using the emission intensity alone. Finally, collisional dynamic quenching of the fluorescence emission allows the experimenter to assess the solvent accessibility of the fluorophore. The method is mostly applied to steady-state fluorescence intensity in equilibrium. However, the same approach can be applied to address the solvent accessibility of the different intermediates, during the time course of the reaction monitored in the stopped-flow experiment.

Conformational selection or induced fit? A critical appraisal of the kinetic mechanism

For almost five decades, two competing mechanisms of ligand recognition, conformational selection and induced fit, have dominated our interpretation of ligand binding in biological macromolecules. When binding-dissociation events are fast compared to conformational transitions, the rate of approach to equilibrium, k(obs), becomes diagnostic of conformational selection or induced fit based on whether it decreases or increases, respectively, with the ligand concentration, [L]. However, this simple conclusion based on the rapid equilibrium approximation is not valid in general. Here we show that conformational selection is associated with a rich repertoire of kinetic properties, with k(obs) decreasing or increasing with [L] depending on the relative magnitude of the rate of ligand dissociation, k(off), and the rate of conformational isomerization, k(r). We prove that, even for the simplest two-step mechanism of ligand binding, a decrease in k(obs) with [L] is unequivocal evidence of conformational selection, but an increase in k(obs) with [L] is not unequivocal evidence of induced fit. Ligand binding to glucokinase, thrombin, and its precursor prethrombin-2 are used as relevant examples. We conclude that conformational selection as a mechanism for a ligand binding to its target may be far more common than currently believed.

Kinetic mechanism of the ssDNA recognition by the polymerase X from African Swine Fever Virus. Dynamics and energetics of intermediate formations

Kinetic mechanism of the ssDNA recognition by the polymerase X of African Swine Fever Virus (ASFV) and energetics of intermediate formations have been examined, using the fluorescence stopped-flow method. The association is a minimum three-step process PolX + ssDNA k(1) <-- --> k(-1) (P-ssDNA)(1) k(2) <-- --> k(-2) (P-ssDNA)(2) k(3) <-- --> k(-3) (P-ssDNA)(3). The nucleic acid makes the initial contact through the C-terminal domain, which generates most of the overall ΔG°. In the second step the nucleic acid engages the N-terminal domain, assuming the bent structure. In equilibrium, the complex exists in at least two different states. Apparent enthalpy and entropy changes, characterizing formations of intermediates, reflect association of the DNA with the C-terminal domain and gradual engagement of the catalytic domain by the nucleic acid. The intrinsic DNA-binding steps are entropy-driven processes accompanied by the net release of water molecules. The final conformational transition of the complex does not involve any large changes of the DNA topology, or the net release of the water molecules.

Mechanisms of interactions of the nucleotide cofactor with the RepA protein of plasmid RSF1010. Binding dynamics studied using the fluorescence stopped-flow method

The dynamics of the nucleotide binding to a single, noninteracting nucleotide-binding site of the hexameric helicase RepA protein of plasmid RSF1010 has been examined, using the fluorescence stopped-flow method. The experiments have been performed with fluorescent analogues of ATP and ADP, TNP-ATP and TNP-ADP, respectively. In the presence of Mg(2+), the association of the cofactors proceeds as a sequential three-step process [Formula: see text] The sequential nature of the mechanism indicates the lack of significant conformational equilibria of the helicase prior to nucleotide binding. The major conformational change of the RepA helicase-nucleotide complex occurs in the formation of (H-N)(2), which is characterized by a very high value of the partial equilibrium constant and large positive changes in the apparent enthalpy and entropy. Strong stabilizing interactions between subunits of the RepA hexamer contribute to the observed dynamics and energetics of the internal transitions of the formed complexes. Magnesium cations mediate the efficient and fast conformational transitions of the protein, in a manner independent of the structure of the cofactor phosphate group. The ssDNA bound to the enzyme preferentially selects a single intermediate of the RepA-ATP analogue complex, (H-N)(2), while the DNA has no effect on the intermediates of the RepA-ADP complex. Allosteric interactions between the nucleotide- and DNA-binding site are established in the initial stages of formation of the complex. Moreover, in the presence of the single-stranded DNA, all the transitions in the nucleotide binding to the helicase become sensitive to the structure of the phosphate group of the cofactor.

Interactions of the Escherichia coli DnaB-DnaC protein complex with nucleotide cofactors. 1. Allosteric conformational transitions of the complex

Interactions of nucleotide cofactors with both protein components of the Escherichia coli DnaB helicase complex with the replication factor, the DnaC protein, have been examined using MANT-nucleotide analogues. At saturation, in all examined stationary complexes, including the binary, DnaB-DnaC, and tertiary, DnaB-DnaC-ssDNA, complexes, the helicase binds six cofactor molecules. Thus, protein-protein and protein-DNA interactions do not affect the maximum stoichiometry of the helicase-nucleotide interactions. The single-stranded DNA dramatically increases the ATP analogue affinity, while it has little effect on the affinity of the NDP analogues, indicating that stationary complexes reflect allosteric interactions between the DNA- and NTP-binding site prior to the cofactor hydrolysis step and subsequent to product release. In the binary complex, the DnaC protein diminishes the intrinsic affinity and increases the negative cooperativity in the cofactor binding to the helicase; an opposite effect of the protein on the cofactor-helicase interactions occurs in the tertiary complex. The DnaC protein retains its nucleotide binding capability in the binary and tertiary complexes with the helicase. Surprisingly, the DnaC protein-nucleotide interactions, in the binary and tertiary complexes, are characterized by positive cooperativity. The DnaC assembles on the helicase as a hexamer, which exists in two conformational states and undergoes an allosteric transition, induced by the cofactor. Cooperativity of the allosteric transition depends on the structure of the phosphate group of the nucleotide. The significance of the results for the DnaB-DnaC complex activities is discussed.

Dynamics of the ssDNA recognition by the RepA hexameric helicase of plasmid RSF1010: analyses using fluorescence stopped-flow intensity and anisotropy methods

The kinetic mechanism of the single-stranded DNA (ssDNA) recognition by the RepA hexameric replicative helicase of the plasmid RSF1010 and the nature of formed intermediates, in the presence of the ATP nonhydrolyzable analog, beta,gamma-imidoadenosine-5'-triphosphate (AMP-PNP), have been examined, using the fluorescence intensity and anisotropy stopped-flow and analytical ultracentrifugation methods. Association of the RepA hexamer with the ssDNA oligomers that engage the total DNA-binding site and exclusively the strong DNA-binding subsite is a minimum four-step mechanism [formula: see text]. Extreme stability of the RepA hexamer precludes any disintegration of its structure, and the sequential character of the mechanism indicates that the enzyme exists in a predominantly single conformation prior to the association with the nucleic acid. Moreover, the hexameric helicase possesses a DNA-binding site located outside its cross channel. The reaction steps have dramatically different dynamics, with rate constants differing by 2-3 orders of magnitude. Such behavior indicates a very diverse nature of the observed transitions, which comprises binding steps and large conformational transitions of the helicase, including local opening of the hexameric structure. Steady-state fluorescence anisotropies of intermediates indicate that the entry of the DNA into the cross channel is initiated from the 5' end of the bound nucleic acid. The global structure of the tertiary complex RepA-ssDNA-AMP-PNP is very different from the structure of the binary complex RepA-AMP-PNP, indicating that, in equilibrium, the RepA hexamer-ssDNA-AMP-PNP complex exists as a mixture of partially open states.

The Kinetic Basis for Dual Recognition in Colicin Endonuclease–Immunity Protein Complexes

The antibacterial activity of E colicin endonucleases (DNases) is counteracted by the binding of immunity proteins; the affinities of cognate and non-cognate complexes differing by up to ten orders of magnitude. Here, we address the mechanism of complex formation using a combination of protein engineering, pre-steady-state kinetics and isothermal titration calorimetry, in order to understand the underlying basis for specificity. Contrary to previous work, we show that a pre-equilibrium mechanism does not explain the binding kinetics. Instead, the data are best explained by a modified induced-fit mechanism where cognate and non-cognate complexes alike form a non-specific, conformationally dynamic encounter complex, most likely centred on conserved interactions at the interface. The dynamics appear to be an intrinsic property of the encounter complex where the proteins move relative to one another, thereby sampling different conformations rather than being "induced" by binding. This allows optimal alignment of interface specificity sites, without producing energetically costly conformational changes, essential for high-affinity binding. Importantly, specificity is achieved without slowing the rate of association, an important requirement for rapid inhibition of the colicin in the producing bacterial cell. A rigid-body rotation model is also consistent with the observation that specificity contacts in colicin-immunity protein complexes can involve different regions of the interface. Such a kinetic discrimination mechanism explains the ability of DNase-specific immunity proteins to display dual recognition specificity, wherein they are broadly cross-reactive yet are highly specific, achieving femtomolar binding affinities in complexes with their cognate DNases.