Author

R. A. Stein

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

Biology Disciplines

Click to filter author papers

Biophysics· 8 Biochemistry· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:protein folding & dynamics· 7 Approach:statistical model· 5 Approach:deep learning· 4 Assay:structural biology· 3 Research Focus:benchmarking· 2 Research Focus:chromatin & epigenetic regulation· 2 Approach:experimental assay· 2 Assay:protein structure· 2

Frequent Co-Authors

H. S. Mchaourab· 5 shared E. Tajkhorshid· 3 shared H. Mchaourab· 3 shared D. P. Claxton· 2 shared J. Meiler· 2 shared M. Sinclair· 2 shared A. Koehl· 1 shared A. Rajca· 1 shared

Activity by Year

2018-2023 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

5 shared papersBiophysics

H. S. Mchaourab

Mutual co-authors in cluster

Author profile →

9 papers

Recent·Most cited

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

R. A. Stein, H. S. Mchaourab

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.

bioRxiv · Sep 5, 2023 · PreprintBiochemistry

Cucurbituril Enhances Distance Measurements of Spin-Labeled Proteins

Z. Yang, R. A. Stein, M. Pink, P. Madzelan, T. Ngendahimana, S. Rajca, M. A. Wilson, S. S. Eaton, G. R. Eaton, H. S. Mchaourab, A. Rajca

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

bioRxiv · Aug 22, 2023Biophysics

Approximating conformational Boltzmann distributions with AlphaFold2 predictions

B. P. Brown, R. A. Stein, J. Meiler, H. Mchaourab

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

bioRxiv · Aug 6, 2023Biophysics

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

Q. Tang, M. Sinclair, H. S. Hasdemir, R. A. Stein, E. Karakas, E. Tajkhorshid, H. Mchaourab

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.

bioRxiv · May 29, 2023Biophysics

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

M. Sinclair, R. A. Stein, J. Sheehan, E. M. Hawes, R. M. O'Brien, E. Tajkhorshid, D. P. Claxton

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.

bioRxiv · Mar 13, 2023Biophysics

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

T. S. Chavan, R. C. Cheng, T. Jiang, I. I. Mathews, R. A. Stein, A. Koehl, H. S. Mchaourab, E. Tajkhorshid, M. Maduke

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.

bioRxiv · Nov 27, 2019Biophysics

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

K. L. Jagessar, D. P. Claxton, R. A. Stein, H. S. Mchaourab

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

bioRxiv · Sep 18, 2019Biophysics

Protein fold prediction using simulated DEER distance distributions and decay traces

D. del Alamo, M. Tessmer, R. A. Stein, J. B. Feix, H. S. Mchaourab, J. Meiler

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

bioRxiv · Mar 18, 2019 · PreprintBiophysics

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

E. J. Hustedt, F. Martinelli, R. A. Stein, J. Faraldo-Gomez, H. Mchaourab

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

bioRxiv · Jul 10, 2018Biophysics