Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II

Pandini, Alessandro; Schulman, Howard; Khan, Shahid

doi:10.1371/journal.pcbi.1006796

Cited by 8 publications

(3 citation statements)

References 80 publications

(132 reference statements)

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“…) equilibrium conformations were generated for the monomer and tetramer structures extracted from PDB:3SOA. The overlap between ensemble subsets was >99% when subset size was < ¼ of the total ensemble, as reported previously for CaMKII kinase domain structures 63 . The top network couplings mapped onto the AD crystal structure represented pairs above the 2significance threshold in the distribution obtained after correction for the finite size error.…”

Section: Data and Code Availabilitysupporting

confidence: 83%

Conformational Spread Drives the Evolution of the Calcium-calmodulin Protein Kinase II

Khan

2021

Preprint

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The calcium calmodulin (Ca2+CAM) dependent protein kinase II (CaMKII) decodes Ca2+ frequency oscillations. It has a central role in learning. I matched residue and organismal evolution to collective motions deduced from the atomic structure of the human CaMKIIa holoenzyme. Protein dynamic simulations and bioinformatic analysis showed its stacked ring architecture conformationally couples kinase domains (KDs) via its central hub. The simulations revealed underlying b-sheet collective motions in the hub ab association domain (AD) map onto a coevolved residue network and partition it into two distinct sectors. The holoenzyme evolved in metazoans by stabilization of ancient enzyme dimers and fold elongation to create a second, metastable sector for ring assembly. Continued evolution targeted the ring contacts for lateral conformational spread. The a isoform, predominantly expressed in the brain, emerged last and evolved rapidly in sync with the poikilotherm-homeotherm jump in the evolution of memory. The correlation between CaMKII dynamics and phylogenetics argues single residue evolution fine-tunes hub conformational spread. The central role of CaMKII ringed architecture In the brain could be to increase Ca2+ frequency response range for complex learning functions.

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Section: Data and Code Availabilitysupporting

confidence: 83%

Conformational Spread Drives the Evolution of the Calcium-calmodulin Protein Kinase II

Khan

2021

Preprint

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“…In Aurora kinase A, phosphorylation triggers transition between distinct IN orientations, rather than between IN and OUT states (74). In calcium calmodulin dependent kinase, IN and OUT DFG states are loosely coupled to kinase domain phosphorylation (75). In contrast, the multiple Y106 orientations in the wild-type FliMN-CheY complex are tightly linked to long-range changes in backbone dynamics and to the state of the D57 phosphorylation site as monitored by W58.…”

Section: Figure 10: Chey Activation and Motor Reactions In E Coli Amentioning

confidence: 99%

Allosteric priming ofE. coliCheY by the flagellar motor protein FliM

Wheatley

Pandini

Gupta

et al. 2019

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Phosphorylation of Escherichia coli CheY couple's chemoreceptor output to flagellar motor response. The N-termini of FliM subunits (FliMN) in the flagellar rotor prime CheY to bind FliN thereby inducing cooperative switching, an essential feature of bacterial chemotaxis. We analyzed molecular dynamics {MD} trajectories to identify networks of residues involved in the long-range allosteric activation of CheY by FliMN. The CheY backbone was partitioned into four dynamically coordinated sectors, with activation tracked by changes in sector size and interactions. Bound FliMN closed the central α4-β4 loop hinge to strengthen correlations between sectors around its binding interface and D57 phosphorylation site. Inward W58 sidechain movements adjacent to the CheY D57 phosphorylation site were coupled to corresponding K91 and Y106 sidechain movements at the FliMN interface. Studies of the constitutively active CheY D13K-Y106W double mutant have related its structural changes with invivo signaling properties. The MD revealed that D13K-Y106W fused the phosphorylation site and FliMN binding sectors into a new surface-exposed sector and locked the 106W sidechain in the innermost rotamer configuration in CheY-FliMN complexes. X-ray foot-printing with mass spectroscopy exploited FliMN-CheY fusion proteins to validate the concerted sidechain internalization of W58, K91 and Y106 triggered by bound FliMN and increased by D13K-Y106W. Oxidation rate was correlated with the solvent accessible surface area, with K109, another central element of the allosteric relay, an outlier likely due to hydrogen bonding. The measurements indicated the fusion proteins were an effective mimic of the crystallized complexes used for the MD simulations. In absence of the D13K-Y106W mutations, CheY Y106 sampled multiple inward rotamer states, but their coupling to backbone dynamics required bound FliMN to prolongation inward state lifetimes by bound FliMN. Thus, as simulations have found for kinases, control of CheY activation by aromatic residue reorientation is more subtle than a binary ON-OFF switch. Statement of SignificanceThe chemotaxis phospho-protein CheY is activated at the flagellar motor by the Nterminus (FliMN) of FliM subunits. Crystal structures of FliMN.CheY complexes with and without the phosphomimic D13K-Y106W double-mutation both have the residue 106 sidechain in the same IN orientation at the FliMN interface. Additional factors that explain activation were identified by atomistic simulations based on the crystal structures. Free CheY samples both IN and OUT Y106 rotamer states, but bound FliMN increases multiple IN-state lifetimes to alter backbone dynamics. D13K-Y106W triggers further alterations to select the W106 state seen in the crystals and create novel binding surfaces. Observed changes in sidechain position along the allosteric relay reported by the crystals were predicted and validated by X-ray foot-printing with mass-spectroscopy.

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“…In Aurora kinase A, phosphorylation triggers transition between distinct IN orientations, rather than between IN and OUT states (74). In calcium calmodulin-dependent kinase, IN and OUT DFG states are loosely coupled to kinase domain phosphorylation (75). in CheY XFMS reported D 57 WN 59 internalization was coupled to protection at the FliM N interface.…”

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confidence: 99%

Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM

Wheatley

Gupta

Pandini

et al. 2020

Biophysical Journal

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Phosphorylation of Escherichia coli CheY protein transduces chemoreceptor stimulation to a highly cooperative flagellar motor response. CheY binds to the Nterminal peptide of the FliM motor protein (FliM N ). Constitutively active D13K-Y106W CheY has been an important tool for motor physiology. The crystal structures of CheY and CheY•FliM N with and without D13K-Y106W have shown FliM N bound CheY contains features of both active and inactive states. We used molecular dynamics (MD) simulations to characterize the CheY conformational landscape accessed by FliM N and D13K-Y106W. Mutual information measures identified the central features of the long-range CheY allosteric network between D13K at the D57 phosphorylation site and Y/W106 at the FliM N interface; namely the closure of the 4-4 hinge and inward rotation of Y/W106 with W58. We used hydroxy-radical foot-printing with mass spectroscopy (XFMS) to track the solvent accessibility of these and other sidechains. The solution XFMS oxidation rate correlated with the solvent-accessible area of the crystal structures. The protection of allosteric relay sidechains reported by XFMS confirmed the intermediate conformation of the native CheY•FliM N complex, the inactive state of free D13K-Y106W CheY and the MD-based network architecture. We extended the MD analysis to determine temporal coupling and energetics during activation. Coupled aromatic residue rotation was a graded rather than a binary switch with Y/W106 sidechain burial correlated with increased FliM N affinity. Activation entrained CheY fold stabilization to FliM N affinity. The CheY network could be partitioned into four dynamically coordinated sectors. Residue substitutions mapped to sectors around D57 or the FliM N interface according to phenotype. FliM N increased sector size and interactions. These sectors fused between the substituted K13K-W106 residues to organize a tightly packed core and novel surfaces that may bind additional sites to explain the cooperative motor response. The community maps provide a more complete description of CheY priming than proposed thus far. Statement of SignificanceCheY affinity for FliM N , its binding target at the flagellar motor, is increased by phosphorylation to switch rotation sense. Atomistic simulations based on CheY and CheY•FliM N crystal structures with and without the phospho-mimetic double substitution (D13K-Y106W) showed CheY compaction is entrained to increased FliM N affinity. Burial of exposed aromatic sidechains drove compaction, as validated by tracking sidechain solvent accessibility with hydroxyl-radical foot-printing. The substitutions were localized at the phosphorylation pocket (D13K) and FliM N interface (Y106W). Mutual information measures revealed these locations were allosterically coupled by a specialized conduit when the conformational landscape of FliM N -tethered CheY was modified by the substitutions. Novel surfaces stabilized by the conduit may bind additional motor sites, essential for the high cooperativity of the flagellar switch.

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Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II

Cited by 8 publications

References 80 publications

Conformational Spread Drives the Evolution of the Calcium-calmodulin Protein Kinase II

Conformational Spread Drives the Evolution of the Calcium-calmodulin Protein Kinase II

Allosteric priming ofE. coliCheY by the flagellar motor protein FliM

Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM

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