Author

S. D. Fried

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· 3

Signature Assays, Organisms & Methods

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Research Focus:protein folding & dynamics· 8 Approach:experimental assay· 7 Assay:proteomics· 6 Organism:E. coli· 5 Approach:statistical model· 3 Research Focus:cell signaling & trafficking· 2 Approach:deep learning· 2 Assay:protein structure· 2

Frequent Co-Authors

P. To· 5 shared A. M. Faustino· 3 shared E. P. O'Brien· 3 shared I. Sitarik· 3 shared Y. Jiang· 3 shared Y. Xia· 3 shared D. Yadav· 2 shared H. E. Tarbox· 2 shared

Activity by Year

2019-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 23 mutual co-author links

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5 shared papersBiophysics

P. To

Mutual co-authors in cluster

Author profile →

9 papers

Recent·Most cited

Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates

P. To, A. M. Bhagwat, H. E. Tarbox, A. Ecer, H. Wendorff, Z. Jamieson, T. Trcek, S. D. Fried

The paper shows that intrinsically disordered regions (IDRs) enhance protein refoldability from denatured states and facilitate retrieval from biomolecular condensates in yeast.

bioRxiv · Jun 25, 2023 · PreprintBiochemistry

Proteome-Wide Photo-Crosslinking Enables Residue-Level Visualization of Protein Interaction Networks in vivo

A. M. Faustino, P. Sharma, D. Yadav, S. D. Fried

This paper introduces photo-crosslinkers for proteome-wide protein interaction mapping with residue-level resolution, demonstrating their application in E. coli and showing potential for studying low-abundance proteins.

bioRxiv · Sep 20, 2022 · PreprintBiochemistry

A Newly Identified Class of Protein Misfolding in All-atom Folding Simulations Consistent with Limited Proteolysis Mass Spectrometry

Q. V. Vu, I. Sitarik, Y. Jiang, D. Yadav, P. Sharma, S. D. Fried, M. S. Li, E. P. O'Brien

The paper identifies entangled misfolded states in all-atom protein folding simulations that resemble native states and are consistent with mass spectrometry data.

bioRxiv · Jul 19, 2022 · PreprintBiophysics

Early selection of the amino acid alphabet was adaptively shaped by biophysical constraints of foldability

M. Makarov, A. C. S. Rocha, R. Krystufek, I. Cherepashuk, V. Dzmitruk, T. Charnavets, A. M. Faustino, M. Lebl, K. Fujishima, S. D. Fried, K. Hlouchova

This study investigates why the modern amino acid alphabet evolved to include 20 canonical amino acids by showing that foldability constraints shaped the selection of early amino acids.

bioRxiv · Jun 14, 2022Biophysics

A Proteome-Wide Map of Chaperone-Assisted Protein Refolding in the Cytosol

P. To, S. O. Lee, Y. Xia, T. Devlin, K. G. Fleming, S. D. Fried

This study maps chaperone-assisted protein refolding in E. coli cytosol using mass spectrometry, showing GroEL refolds most proteins and identifies intransigent proteins that fold co-translationally.

bioRxiv · Nov 20, 2021 · PreprintBiophysics

Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less-functional

D. A. Nissley, Y. Jiang, F. Trovato, I. Sitarik, K. Narayan, P. To, Y. Xia, S. D. Fried, E. P. O'Brien

The paper shows that misfolded proteins can bypass proteostasis by being structurally similar to native states and persisting for long periods.

bioRxiv · Aug 18, 2021Biochemistry

How synonymous mutations alter enzyme structure andfunction over long time scales

Y. Jiang, S. S. Neti, I. Sitarik, P. Pradhan, P. To, Y. Xia, S. D. Fried, S. J. Booker, E. P. O'Brien

This paper shows that synonymous mutations alter enzyme function over time by causing misfolded, entangled protein states that reduce catalytic activity.

bioRxiv · Aug 18, 2021 · PreprintBiophysics

Non-Refoldability is Pervasive Across the E. coli Proteome

P. To, B. Whitehead, H. E. Tarbox, S. D. Fried

This study shows that many E. coli proteins cannot refold properly after denaturation, suggesting that native stability is due to kinetic persistence rather than thermodynamic stability.

bioRxiv · Aug 28, 2020 · PreprintBiophysics

SurA is a "Groove-y" Chaperone That Expands Unfolded Outer Membrane Proteins

D. C. Marx, A. M. Plummer, A. M. Faustino, M. A. Roskopf, M. J. Leblanc, T. Devlin, H. J. Lessen, B. T. Amann, P. J. Fleming, S. Krueger, S. D. Fried, K. G. Fleming

This paper investigates how SurA, a bacterial chaperone, interacts with unfolded outer membrane proteins (uOMPs) using structural biology techniques, revealing distinct binding modes and a mechanism for uOMP expansion.

bioRxiv · Dec 17, 2019Biophysics