Author

D. L. Stokes

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 6 Biochemistry· 1

Signature Assays, Organisms & Methods

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Research Focus:cell signaling & trafficking· 5 Approach:experimental assay· 5 Assay:cryo-EM· 3 Research Focus:protein folding & dynamics· 3 Organism:bacteria (other)· 2 Organism:E. coli· 2 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1

Frequent Co-Authors

B. P. Pedersen· 4 shared X. Zhang· 3 shared H. Khandelia· 2 shared M. E. Sweet· 2 shared O. Beckstein· 2 shared S. Fan· 2 shared A. Bohush· 1 shared A. Hussein· 1 shared

Activity by Year

2020-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

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4 shared papersBiophysics

B. P. Pedersen

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Author profile →

7 papers

Recent·Most cited

Conformational changes in the Niemann-Pick Type C1 protein NCR1 drive sterol translocation

K. M. Frain, E. Dedic, L. Nel, A. Bohush, E. Olesen, D. L. Stokes, B. P. Pedersen

This study identifies a glycocalyx in yeast vacuoles and presents cryo-EM structures of NCR1 showing conformational changes that drive sterol translocation across the glycocalyx.

bioRxiv · Sep 8, 2023Biochemistry

Energy Coupling and Stoichiometry of Zn2+/H+ Antiport by the Cation Diffusion Facilitator YiiP

A. Hussein, S. Fan, M. L. Lopez-Redondo, I. Kenney, X. Zhang, O. Beckstein, D. L. Stokes

This study investigates the structural and functional roles of Zn2+/H+ antiport in YiiP using cryo-EM, thermophoresis, and simulations, revealing a transport stoichiometry of 1 Zn2+ to 2-3 H+.

bioRxiv · Feb 23, 2023 · PreprintBiophysics

Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter

C. D. Kinz-Thompson, M. Lopez Redondo, C. Mulligan, D. B. Sauer, J. J. Marden, J. Song, E. Tajkhorshid, J. F. Hunt, D. L. Stokes, J. A. Mindell, D.-N. Wang, R. L. Gonzalez

This study uses single-molecule experiments to show that VcINDY, a sodium-coupled dicarboxylate transporter, uses stochastic elevator-like motions for substrate translocation, with non-cooperative protomer movements and cooperative binding.

bioRxiv · May 1, 2022Biophysics

An intracellular pathway controlled by the N-terminus of the pump subunit inhibits the bacterial KdpFABC ion pump in high K+ conditions

H. Khandelia, D. L. Stokes, B. P. Pedersen, V. Dubey

This study uses molecular dynamics simulations to show phosphorylation of KdpB traps it in an inactive conformation by hydrating the ion-binding site via an intracellular pathway.

bioRxiv · Jan 13, 2021Biophysics

Structural basis for Potassium transport by KdpFABC

M. E. Sweet, C. Larsen, X. Zhang, M. Schlame, B. P. Pedersen, D. L. Stokes

This study determines the structural basis of K+ transport by KdpFABC using cryo-EM, revealing a pathway and mechanism involving conformational changes in KdpB and a static KdpA.

bioRxiv · Jan 9, 2021 · PreprintBiophysics

Zinc Dependent Conformational Changes in the Cation Diffusion Facilitator YiiP from S. oneidensis

M. Lopez-Redondo, S. Fan, A. Koide, S. Koide, O. Beckstein, D. L. Stokes

This study examines how Zn2+ binding affects the conformational changes in YiiP from S. oneidensis using cryo-EM and molecular dynamics simulations, revealing an intermediate state and a hydrophobic gate closure mechanism.

bioRxiv · Dec 29, 2020Biophysics

Serine Phosphorylation Regulates the P-type Potassium pump KdpFABC

M. E. Sweet, V. L. Dubey, X. Zhang, H. Erdjument-Bromage, T. A. Neubert, B. P. Pedersen, H. Khandelia, D. L. Stokes

The paper shows that serine phosphorylation of KdpB inhibits the KdpFABC potassium pump when K+ levels are restored, with mutations affecting pump activity.

bioRxiv · Jan 28, 2020Biophysics