Reconciling the “old” and “new” views of protein allostery: A molecular simulation study of chemotaxis Y protein (CheY)

Formaneck, Mark S.; Ma, Liang; Cui, Qiang

doi:10.1002/prot.20893

Cited by 104 publications

(139 citation statements)

References 96 publications

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“…Our previous biased MD simulations 11 and the x-ray study that revealed the "meta-active" CheY 21 suggested that the β4-α4 loop may gate the Tyr 106 rotation. In this work, the free energy and TPS results show that the β4-α4 loop transition has a much higher energy cost and only minimal adjustments (mainly associated with the sidechain orientation of Ala90) are needed to leave Tyr106 rotation sufficiently low in barrier.…”

Section: B the Role Of The β4-α4 Loopmentioning

confidence: 98%

“…11 These variables include the position of Ala 90 (Fig.3a), which may sterically gate the rotation of Tyr106, two variables that characterize the configuration of the β4-α4 loop (Fig.3b,c), and the width of the "doorway" towards the buried site under the β4-α4 loop (Fig.3d), which is formed by Ile 95 and Val 108. All these variables show bi-modal distribution along the χ angle, which again supports the use of χ as the order parameter.…”

Section: A Transition Path Samplingmentioning

confidence: 99%

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Activation Mechanism of a Signaling Protein at Atomic Resolution from Advanced Computations

Cui

2007

J. Am. Chem. Soc.

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Advanced computational techniques including transition path sampling and free energy calculations are combined synergistically to reveal the activation mechanism at unprecedented resolution for a small signaling protein, chemotaxis protein Y. In the conventional "Y-T coupling" model for response regulators, phosphorylation induces the displacement of the conserved Thr87 residue through hydrogen-bond formation, which in turn makes it sterically possible for Tyr106 to isomerize from a solvent exposed configuration to a buried rotameric state. More than 160 unbiased activation trajectories show, however, that the rotation of Tyr106 does not rely on the displacement of Thr87 per se. Free energy calculations reveal that the Tyr106 rotation is a low-barrier process in the absence of the Thr87-phosphate hydrogen bond although the rotation is stabilized by the formation of this interaction. The simulations also find that structural change in the β4 − α4 loop does not gate the Tyr106 rotation as suggested previously; rather, the rotation of Tyr106 stabilizes the activated configuration of this loop. The computational strategy used and mechanistic insights obtained have impact on the study of signaling proteins and allosteric systems in general.

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Section: B the Role Of The β4-α4 Loopmentioning

confidence: 98%

Section: A Transition Path Samplingmentioning

confidence: 99%

Activation Mechanism of a Signaling Protein at Atomic Resolution from Advanced Computations

Cui

2007

J. Am. Chem. Soc.

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“…On the other hand, the rearrangement of the flexible loop may occur in a sequential way depending on the binding of each molecule of ATP, following the induced fit model of allostery where ligand binding and conformation switching are concomitant (38). This concerted collective motion associated to sequential local structural changes is certainly a more coherent mechanistic picture of the transition process, reconciling the induced fit and the population shift models for protein allostery by emphasizing the kinetic and thermodynamic aspects of allosteric transition (26).…”

Section: Discussionmentioning

confidence: 99%

Structural Analysis of the Bacterial HPr Kinase/Phosphorylase V267F Mutant Gives Insights into the Allosteric Regulation Mechanism of This Bifunctional Enzyme

Chaptal

Vincent

Gueguen-Chaignon

et al. 2007

Journal of Biological Chemistry

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The HPr kinase/phosphorylase (HPrK/P) is a bifunctional enzyme that controls the phosphorylation state of the phosphocarrier protein HPr, which regulates the utilization of carbon sources in Gram-positive bacteria. It uses ATP or pyrophosphate for the phosphorylation of serine 46 of HPr and inorganic phosphate for the dephosphorylation of Ser(P)-46-HPr via a phosphorolysis reaction. HPrK/P is a hexameric protein kinase of a new type with a catalytic core belonging to the family of nucleotide-binding protein with Walker A motif. It exhibits no structural similarity to eukaryotic protein kinases. So far, HPrK/P structures have shown the enzyme in its phosphorylase conformation. They permitted a detailed characterization of the phosphorolysis mechanism. In the absence of a structure with bound nucleotide, we used the V267F mutant enzyme to assess the kinase conformation. Indeed, the V267F replacement was found to cause an almost entire loss of the phosphorylase activity of Lactobacillus casei HPrK/P. In contrast, the kinase activity remained conserved. To elucidate the structural alterations leading to this drastic change of activity, the x-ray structure of the catalytic domain of L. casei HPrK/P-V267F was determined at 2.6 Å resolution. A comparison with the structure of the wild type enzyme showed that the mutation induces conformation changes compatible with the switch from phosphorylase to kinase function. Together with nucleotide binding fluorescence measurements, these results allowed us to decipher the cooperative behavior of the protein and to gain new insights into the allosteric regulation mechanism of HPrK/P.In Gram-positive bacteria, HPr kinase/phosphorylase (HPrK/P) 6 is the central regulator of carbon catabolite repression, the paradigm of signal transduction (1). In response to certain metabolites that change their concentration in the presence of rapidly metabolizable carbon sources, HPrK/P either phosphorylates or dephosphorylates Ser-46 of the histidine-containing protein HPr. In Gram-positive bacteria, Ser(P)-46-HPr functions as co-repressor for carbon catabolite repression by interacting with the transcriptional regulator CcpA (catabolite control protein A) that regulates the expression of many genes (2, 3) (for a review, see Ref. 4). In the Gram-negative Neisseria meningitidis devoid of CcpA-mediated carbon catabolite repression, Ser(P)-46-HPr is involved in the cell adhesion process (5), suggesting that HPrK/P might constitute a potential target for new antimicrobial agents in pathogenic bacteria. Finally, the formation of Ser(P)-46-HPr inhibits PrfA, a transcription activator of several virulence genes in Listeria monocytogenes (6).HPrK/P was first identified as a serine protein kinase, and this activity is enhanced in the presence of glycolytic intermediates such as fructose-1, 6-bisphosphate (FBP) and inhibited in the presence of inorganic phosphate (P i ) (7). Dephosphorylation of Ser(P)-46-HPr by HPrK/P was assumed to be hydrolytic. However, P i was also reported to stimulate the HPrK/P-c...

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“…In fact, many recent studies of allosteric systems tend to support the mechanism in which large-scale motions occur (at least to a significant degree) prior to activation, and the role of the activation event is to stabilize, rather than induce, the activate conformation [5,52]. Evidently, the interplay between motions along soft, collective modes, and local, sequential structural rearrangements in allosteric systems such as molecular motors remains to be thoroughly explored [53,54]. Experimentally, powerful tests would include X-ray structures for mutants or inhibitor complexes that might trap the system in a transitional structural state, as has been done for ras-p21 [55] and CheY [56,57]; in these two examples, the X-ray structures in fact provided strong support for TMDtype simulations of these systems.…”

Section: Relation Between the Tmd Simulations To The Previous Mep Anamentioning

confidence: 99%

“…Therefore, the three approaches are likely to be complementary to each other. Other methods for addressing the collective [15,16] and local [59] motions in allostery are available and may be used; the vital point here is to advocate addressing both types of contributions [54]; most previous studies focused on only one of them.…”

Section: Residues Important To Mechanochemical Couplingmentioning

confidence: 99%

Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues

Yu¹,

Li²,

Yang³

et al. 2005

PLoS Comput Biol

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An important challenge in the analysis of mechanochemical coupling in molecular motors is to identify residues that dictate the tight coupling between the chemical site and distant structural rearrangements. In this work, a systematic attempt is made to tackle this issue for the conventional myosin. By judiciously combining a range of computational techniques with different approximations and strength, which include targeted molecular dynamics, normal mode analysis, and statistical coupling analysis, we are able to identify a set of important residues and propose their relevant function during the recovery stroke of myosin. These analyses also allowed us to make connections with previous experimental and computational studies in a critical manner. The behavior of the widely used reporter residue, Trp501, in the simulations confirms the concern that its fluorescence does not simply reflect the relay loop conformation or active-site open/close but depends subtly on its microenvironment. The findings in the targeted molecular dynamics and a previous minimum energy path analysis of the recovery stroke have been compared and analyzed, which emphasized the difference and complementarity of the two approaches. In conjunction with our previous studies, the current set of investigations suggest that the modulation of structural flexibility at both the local (e.g., active-site) and domain scales with strategically placed ''hotspot'' residues and phosphate chemistry is likely the general feature for mechanochemical coupling in many molecular motors. The fundamental strategies of examining both collective and local changes and combining physically motivated methods and informatics-driven techniques are expected to be valuable to the study of other molecular motors and allosteric systems in general.

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Reconciling the “old” and “new” views of protein allostery: A molecular simulation study of chemotaxis Y protein (CheY)

Cited by 104 publications

References 96 publications

Activation Mechanism of a Signaling Protein at Atomic Resolution from Advanced Computations

Activation Mechanism of a Signaling Protein at Atomic Resolution from Advanced Computations

Structural Analysis of the Bacterial HPr Kinase/Phosphorylase V267F Mutant Gives Insights into the Allosteric Regulation Mechanism of This Bifunctional Enzyme

Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues

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