Transmembrane helix 6b links proton and metal release pathways and drives conformational change in an Nramp-family transition metal transporter

Bozzi, Aaron T.; McCabe, Anne L.; Barnett, Benjamin C.; Gaudet, Rachelle

doi:10.1016/s0021-9258(17)49881-4

Cited by 6 publications

(9 citation statements)

References 59 publications

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“…This includes the coordinated waters, for example the water at the center of the Q378 network is present in more than 50% of the frames in occluded-state simulations (Extended Data Fig 4e). In line with the X-ray snapshots and simulation outcomes, mutations of any of the six residues across these networks reduces Mn 2+ transport by DraNramp 17, 19, 21, 32 , highlighting their key function in the conformational cycle of Nramps.…”

Section: Resultssupporting

confidence: 68%

“…Mutations of several residues in these polar networks reduced transport in proteoliposome-based assays (Extended Data Fig. 6f), corroborating results from cell-based assays 32 . Y54A, H237A and H232A mutations cause the largest decreases, Q89A causes a moderate decrease, and Y54F is similar to WT.…”

Section: Gating Network Differences In the CD 2+ -Bound Structure Are...supporting

confidence: 80%

“…Vestibules providing access to the orthosteric site from the extracellular or intracellular side alternately open from the motions of DraNramp’s TMs 1, 5, 6 and 10, which form the outer and inner gates during Mn 2+ transport 17, 32 . To pinpoint protein features that enable these motions, we used our Mn 2+ -bound structures to identify interaction networks with the following attributes: (i) they contain conserved polar residues from at least one of the four mobile helices; (ii) they line the gates; and (iii) they rearrange between the three resolved protein conformations (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…In the Q89 network, Q89 (TM2) hydrogen-bonds with Y54 (TM1a) and H237 (TM6b) to seal the inner gate in the outward-open 32 and occluded states (Fig. 4e).…”

Section: Resultsmentioning

confidence: 99%

“…3), and mutations to either residue affect Mn 2+ transport in a cell-based assay 32 . Cysteine accessibility measurements showed that mutations to Q89 or H237 render the outer vestibule solvent-inaccessible 32 , indicating that disrupting the Q89 network likely prevents closing of the inner gate. H232 (TM6b) is conserved across all Nramps (Supplementary Fig.…”

Section: Polar Network Latch the Gates To Achieve Alternating Accessmentioning

confidence: 99%

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High-resolution structures map the metal import pathway in an Nramp transporter

Ray

Berry

Wilson

et al. 2022

Preprint

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Transporters of the Nramp (Natural resistance-associated macrophage protein) family import divalent transition metal ions into cells of most organisms. By supporting metal homeostasis, Nramps prevent disorders related to metal insufficiency or overload. Previous studies revealed that Nramps take on a LeuT fold and identified the metal-binding site. We present high-resolution structures of Deinococcus radiodurans Nramp in three stable conformations of the transport cycle revealing that global conformational changes are supported by distinct coordination geometries of its physiological substrate, Mn2+, across conformations and conserved networks of polar residues lining the inner and outer gates. A Cd2+-bound structure highlights differences in coordination geometry for Mn2+ and Cd2+. Measurements of metal binding using isothermal titration calorimetry indicate that the thermodynamic landscape for binding and transporting physiological metals like Mn2+ is different and more robust to perturbation than for transporting the toxic Cd2+ metal.

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Section: Resultssupporting

confidence: 68%

Section: Gating Network Differences In the CD 2+ -Bound Structure Are...supporting

confidence: 80%

Section: Resultsmentioning

confidence: 99%

“…In the Q89 network, Q89 (TM2) hydrogen-bonds with Y54 (TM1a) and H237 (TM6b) to seal the inner gate in the outward-open 32 and occluded states (Fig. 4e).…”

Section: Resultsmentioning

confidence: 99%

Section: Polar Network Latch the Gates To Achieve Alternating Accessmentioning

confidence: 99%

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High-resolution structures map the metal import pathway in an Nramp transporter

Ray

Berry

Wilson

et al. 2022

Preprint

Self Cite

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Synergy and anti‐cooperativity in allostery: Molecular dynamics study of WT and oncogenic KRAS‐RGL1

Hacisuleyman,

Erman

2023

Proteins

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This study focuses on investigating the effects of an oncogenic mutation (G12V) on the stability and interactions within the KRAS‐RGL1 protein complex. The KRAS‐RGL1 complex is of particular interest due to its relevance to KRAS‐associated cancers and the potential for developing targeted drugs against the KRAS system. The stability of the complex and the allosteric effects of specific residues are examined to understand their roles as modulators of complex stability and function. Using molecular dynamics simulations, we calculate the mutual information, MI, between two neighboring residues at the interface of the KRAS‐RGL1 complex, and employ the concept of interaction information, II, to measure the contribution of a third residue to the interaction between interface residue pairs. Negative II indicates synergy, where the presence of the third residue strengthens the interaction, while positive II suggests anti‐cooperativity. Our findings reveal that MI serves as a dominant factor in determining the results, with the G12V mutation increasing the MI between interface residues, indicating enhanced correlations due to the formation of a more compact structure in the complex. Interestingly, although II plays a role in understanding three‐body interactions and the impact of distant residues, it is not significant enough to outweigh the influence of MI in determining the overall stability of the complex. Nevertheless, II may nonetheless be a relevant factor to consider in future drug design efforts. This study provides valuable insights into the mechanisms of complex stability and function, highlighting the significance of three‐body interactions and the impact of distant residues on the binding stability of the complex. Additionally, our findings demonstrate that constraining the fluctuations of a third residue consistently increases the stability of the G12V variant, making it challenging to weaken complex formation of the mutated species through allosteric manipulation. The novel perspective offered by this approach on protein dynamics, function, and allostery has potential implications for understanding and targeting other protein complexes involved in vital cellular processes. The results contribute to our understanding of the effects of oncogenic mutations on protein–protein interactions and provide a foundation for future therapeutic interventions in the context of KRAS‐associated cancers and beyond.

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Molecular Mechanism of Nramp-Family Transition Metal Transport

Bozzi

Gaudet

2021

Journal of Molecular Biology

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Transmembrane helix 6b links proton and metal release pathways and drives conformational change in an Nramp-family transition metal transporter

Cited by 6 publications

References 59 publications

High-resolution structures map the metal import pathway in an Nramp transporter

High-resolution structures map the metal import pathway in an Nramp transporter

Synergy and anti‐cooperativity in allostery: Molecular dynamics study of WT and oncogenic KRAS‐RGL1

Molecular Mechanism of Nramp-Family Transition Metal Transport

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