R. A. Stein

Alternating Access of a Neurotransmitter:Sodium Symporter Bacterial Homolog Determined from AlphaFold2 Ensembles and DEER Spectroscopy

This paper uses AlphaFold2 and DEER spectroscopy to study the conformational dynamics of MhsT, revealing energy landscapes and environmental effects on transporter function.

Rosetta Energy Analysis of AlphaFold2 models: Point Mutations and Conformational Ensembles

This study evaluates AlphaFold2's ability to predict the effects of point mutations and conformational ensembles using Rosetta, showing robust results when mutations are applied across the MSA.

Cucurbituril Enhances Distance Measurements of Spin-Labeled Proteins

This paper demonstrates that cucurbituril enhances spin-label immobilization and improves DEER measurement sensitivity for studying protein distances.

Approximating conformational Boltzmann distributions with AlphaFold2 predictions

This study shows AlphaFold2 contact distance distributions can approximate conformational Boltzmann distributions and predict mutation effects in some protein systems.

Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter

This study uses cryo-EM, DEER, and MD simulations to analyze the conformational dynamics of BmrCD, revealing asymmetric ATP and substrate interactions that drive its transport cycle.

Molecular mechanisms of functional impairment for active site mutations in glucose-6-phosphatase catalytic subunit 1 linked to glycogen storage disease.

This study identifies atomic interactions and energetic perturbations in G6PC1 active site mutations linked to glycogen storage disease type 1a using computational models and experimental validation.

Structural characterization of an intermediate reveals a unified mechanism for the CLC Cl-/H+ transport cycle

The paper presents a 2.6 Å structure of a CLC mutant, revealing a global conformational change that supports a unified transport mechanism for CLC proteins.

Sequence and Structural Determinants of Ligand-dependent Alternating Access of a MATE Transporter

This study identifies sequence and structural determinants of ligand-dependent alternating access in PfMATE using DEER, mutagenesis, and functional assays.

Protein fold prediction using simulated DEER distance distributions and decay traces

This paper introduces RosettaDEER, a method that simulates DEER distance distributions and decay traces to improve protein fold prediction using sparse experimental data.

Confidence Analysis of DEER Data and its Structural Interpretation with Ensemble-Biased Metadynamics

The paper develops methods to assess confidence in DEER data and improves structural interpretation using uncertainty-aware molecular simulations.