On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm

Marcos, Enrique Sánchez; Crehuet, Ramón; Bahar, İvet

doi:10.1371/journal.pcbi.1000738

Cited by 40 publications

(33 citation statements)

References 63 publications

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“…Note that our previous work [34] showed that ANM modes 1–3 were instrumental in accommodating the structural changes at the ATP-binding site, but had practically no effect on the NAG-binding site. This nicely illustrates how the enzyme takes advantage of different types of motions accessible to its native structure for achieving different types of functional motions.…”

Section: Resultsmentioning

confidence: 88%

Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members

2011

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Oligomerization is a functional requirement for many proteins. The interfacial interactions and the overall packing geometry of the individual monomers are viewed as important determinants of the thermodynamic stability and allosteric regulation of oligomers. The present study focuses on the role of the interfacial interactions and overall contact topology in the dynamic features acquired in the oligomeric state. To this aim, the collective dynamics of enzymes belonging to the amino acid kinase family both in dimeric and hexameric forms are examined by means of an elastic network model, and the softest collective motions (i.e., lowest frequency or global modes of motions) favored by the overall architecture are analyzed. Notably, the lowest-frequency modes accessible to the individual subunits in the absence of multimerization are conserved to a large extent in the oligomer, suggesting that the oligomer takes advantage of the intrinsic dynamics of the individual monomers. At the same time, oligomerization stiffens the interfacial regions of the monomers and confers new cooperative modes that exploit the rigid-body translational and rotational degrees of freedom of the intact monomers. The present study sheds light on the mechanism of cooperative inhibition of hexameric N-acetyl-L-glutamate kinase by arginine and on the allosteric regulation of UMP kinases. It also highlights the significance of the particular quaternary design in selectively determining the oligomer dynamics congruent with required ligand-binding and allosteric activities.

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Section: Resultsmentioning

confidence: 88%

Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members

2011

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“…These studies typically use coarse-grained models, such as normal mode analysis, to infer catalytic time scale motional similarities between protein folds (58). Generally, these studies also involve the direct comparison of simulated data with crystallographically resolved and/or NMR-resolved enzymes in apo and ligand-bound forms, inferring dynamic information through, but not limited to, residual dipolar coupling measurements and/or Debye-Waller factors (B-factors) (59). The latter provides a rough approximation of residue flexibility in protein crystals, albeit with no clear definition of dynamic time scale.…”

Section: Discussionmentioning

confidence: 99%

Conservation of Flexible Residue Clusters among Structural and Functional Enzyme Homologues

Gagné

Charest

Morin

et al. 2012

Journal of Biological Chemistry

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Background: It remains unclear whether structural homologues rely on similar concerted motions to promote enzyme function. Results: Ribonuclease homologues display similar, contiguous clustering motions that can be modulated by mutagenesis. Conclusion: Conformational flexibility can be conserved between distant structural homologues. Significance: Controlling dynamics to modulate function has broad implications in protein engineering and allosteric drug design.

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“…This behavior is characteristic of molecular systems that sample inactive conformations with a high probability, such that small perturbations are sufficient to drive the molecule or complex into the inactive state (44)(45)(46)(47). Likewise, the sensitivity of cpSRP43 to point mutations suggests that its SBD is at the threshold of a cooperative conformational change required to attain a chaperone-active conformation.…”

Section: Discussionmentioning

confidence: 99%

Two distinct sites of client protein interaction with the chaperone cpSRP43

McAvoy

Siegel

Piszkiewicz

et al. 2018

Journal of Biological Chemistry

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Integral membrane proteins are prone to aggregation and misfolding in aqueous environments and therefore require binding by molecular chaperones during their biogenesis. Chloroplast signal recognition particle 43 (cpSRP43) is an ATP-independent chaperone required for the biogenesis of the most abundant class of membrane proteins, the light-harvesting chlorophyll a/b-binding proteins (LHCPs). Previous work has shown that cpSRP43 specifically recognizes an L18 loop sequence conserved among LHCP paralogs. However, how cpSRP43 protects the transmembrane domains (TMDs) of LHCP from aggregation was unclear. In this work, alkylation-protection and sitespecific crosslinking experiments found that cpSRP43 makes extensive contacts with all the TMDs in LHCP. Site-directed mutagenesis identified a class of cpSRP43 mutants that bind tightly to the L18 sequence but are defective in chaperoning full-length LHCP. These mutations mapped to hydrophobic surfaces on or near the bridging helix and the β-hairpins lining the ankyrin repeat motifs of cpSRP43, suggesting that these regions are potential sites for interaction with the client TMDs. Our results suggest a working model for client protein interactions in this membrane protein chaperone.Proper protein folding and localization are critical for cellular protein homeostasis. The posttranslational targeting of integral membrane proteins poses an acute challenge to protein homeostasis. Before arrival at the target membrane, nascent membrane proteins are highly prone to aggregation in the cytosol and other aqueous cellular compartments. Thus, effective molecular chaperones or chaperone networks are required to minimize improper exposure of the transmembrane domains (TMDs) on newly synthesized membrane proteins and to maintain them in a soluble, translocation-competent conformation. Many examples illustrate the intimate link between chaperone function and membrane protein biogenesis, including SecB, Skp, and SurA that protect bacterial outer membrane proteins, and Hsp70 homologues implicated in the import of precursor proteins to the endoplasmic reticulum, mitochondria or chloroplast (1-7).The light-harvesting chlorophyll a/b-binding proteins (LHCP) comprise over 50% of the protein content on the thylakoid membrane of green plants and form the most abundant family of membrane proteins on earth (8). LHCPs are nuclear encoded, initially synthesized in the cytosol, and imported across the chloroplast envelope in a largely unfolded state (8). In the chloroplast stroma, LHCPs are protected in a soluble 'transit complex' by the chloroplast signal recognition particle (cpSRP), comprised of the cpSRP43 and cpSRP54 protein subunits (9-12). Via interactions between the GTPase domains of cpSRP54 and its receptor cpFtsY, LHCPs are delivered to the Alb3 translocase and inserted into the thylakoid membrane (11,(13)(14)(15)(16)(17)(18)(19)(20). Previous work showed that the cpSRP43 subunit binds tightly to and quantitatively prevents the aggregation of multiple members of the LHCP family, ...

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On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm

Cited by 40 publications

References 63 publications

Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members

Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members

Conservation of Flexible Residue Clusters among Structural and Functional Enzyme Homologues

Two distinct sites of client protein interaction with the chaperone cpSRP43

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