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Biosynthetic Protein Folding and Molecular Chaperons

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Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification

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Evaluation of the roles of hydrophobic residues in the N-terminal region of archaeal trehalase in its folding

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Client recognition differences between PDI and ERp46 to guide oxidative foldingPreprint

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Thermodynamic profiles for cotranslational trigger factor substrate recognition

Herling, T. W., Cassaignau, A. M. E., Wentink, A. S., Peter, Q. A. E., Kumar, P. C., Kartanas, T., Schneider, M. M., Cabrita, L. D., Christodoulou, J. C., & Knowles, T. P. J. (2024) · Science Advances · doi:10.1126/sciadv.adn4824 · Cited by 4

Statistical Survey of Chemical and Geometric Patterns on Protein Surfaces as a Blueprint for Protein‐Mimicking Nanoparticles

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Trigger Factor-Induced Nascent Chain Dynamics Changes Suggest Two Different Chaperone-Nascent Chain Interactions during Translation

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Zinc-Dependent Oligomerization of Thermus thermophilus Trigger Factor Chaperone

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Advanced NMR spectroscopy methods to study protein structure and dynamics

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Protein Dynamics at the Heart of Chaperone Function: Insights from Solution NMR

Ge, P., Dai, L., Kalodimos, C. G., & Huang, C. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169377 · Cited by 4

A Semiautomated Assignment Protocol for Methyl Group Side Chains in Large Proteins

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PRAT Proteins Operate in Organellar Protein Import and Export in Arabidopsis thaliana

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A Balance Between Capture and Release: How Nanochaperones Regulate Refolding of Thermally Denatured Proteins

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Nascent chains derived from a foldable protein sequence interact with specific ribosomal surface sites near the exit tunnel

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NMR Structural Biology Using Paramagnetic Lanthanide Probe

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Backbone and methyl resonance assignments of the 42 kDa human Hsc70 nucleotide binding domain in the ADP state

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Molecular chaperones impacts in growth, metabolism, pathogenicity and production of virulence factors in bacterial pathogen

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Structural polymorphism and substrate promiscuity of a ribosome-associated molecular chaperone

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Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies

Sučec, I., & Schanda, P. (2023) · Royal Society of Chemistry eBooks · doi:10.1039/bk9781839165986-00136 · Cited by 2

Molecular dynamics simulations shows real-time lid opening in Hsp70 chaperone

Mahto, F. K., Bhattacharya, A., & Bhattacharya, S. (2024) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2024.108726 · Cited by 2

Dosage constraint of the ribosome-associated molecular chaperone drives the evolution and fates of its duplicates in bacteria

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Mechanisms of Chaperones as Active Assistant/Protector for Proteins: Insights from NMR Studies

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Methyl-TROSY NMR Spectroscopy in the Investigation of Allosteric Cooperativity in Large Biomolecular Complexes

Huang, R. (2022) · Royal Society of Chemistry eBooks · doi:10.1039/9781839165702-00303 · Cited by 2

Exploring the roles of substrate‐binding surface of the chaperone site in the chaperone activity of trigger factor

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Generalizable Compositional Features Influencing the Proteostatic Fates of Polar Low-Complexity Domains

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Structural Biology Applications of Synchrotron Radiation and X-Ray Free-Electron Lasers

Soichi Wakatsuki, A. (2020) · Springer eBooks · doi:10.1007/978-3-030-23201-6_44 · Cited by 2

Protein folding

Pal, S. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814855-6.00007-9 · Cited by 2

Structural features of chloroplast trigger factor determined at 2.6 Å resolution

Carius, Y., Ries, F., Gries, K., Trentmann, O., Lancaster, C. R. D., & Willmund, F. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322009068 · Cited by 2

Probing Single Chaperone Substrates

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Aggregation and degradation scales for prion-like domains: sequence features and context weigh in

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Structure-function relationships in wax producing enzymes

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Toxic PR poly-dipeptides encoded by the C9orf72 repeat expansion target Kapβ2 and dysregulate phase separation of low-complexity domainsPreprint

Nanaura, H., Kawamukai, H., Fujiwara, A., Uehara, T., Nakanishi, M., Shiota, T., Hibino, M., Aiba, Y., Wiriyasermkul, P., Kikuchi, S., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/812099 · Cited by 2

Preparing chaperone—client protein complexes for biophysical and structural studiesPreprint

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Mechanism of chaperone coordination during cotranslational protein folding in bacteriaPreprint

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Ca 2+ -driven PDIA6 phase separation to ensure proinsulin quality controlPreprint

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Regulation of Liquid-Liquid Phase Separation by Molecular Chaperones

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Reconstitution of Septacidin Biosynthesis in Escherichia coli by Redirecting an ADP-Heptose Precursor from Primary Metabolism

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Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations

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Pathways of Protein Secretion in Prokaryotes and Eukaryotes: Molecular Mechanisms, Biological Functions, and Therapeutic Opportunities

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One-pot synthesis of high-concentration mixed-shell polymeric micelles as nanochaperones for the renaturation of bulk proteins

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Describing Dynamic Chaperone–Client Complexes by Solution NMR Spectroscopy

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Structural Biology Applications of Synchrotron Radiation and X-Ray Free-Electron Lasers

Soichi Wakatsuki, A. (2015) · Springer eBooks · doi:10.1007/978-3-319-04507-8_44-1 · Cited by 1

Structural Biology Applications of Synchrotron Radiation and X-Ray Free-Electron Lasers

Soichi Wakatsuki, A. (2016) · Springer eBooks · doi:10.1007/978-3-319-14394-1_44 · Cited by 1

Visualization of Chaperone Mediated Protein Folding Using X-ray Crystallography

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Accessing Structure, Dynamics and Function of Biological Macromolecules by NMR Through Advances in Isotope Labeling

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Quarterly intrinsic disorder digest (April–May–June, 2014)

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Evolutionary adaptation of the folding pathway for secretabilityPreprint

Smets, D., Tsirigotaki, A., Smit, J. H., Krishnamurthy, S., Portaliou, A. G., Vorobieva, A. A., Vranken, W., Spyridoula Karamanou, A., & Economou, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.03.486881 · Cited by 1

Dynamic statistical models of biological cognition: insights from communications theory

Wallace, R. (2014) · Connection Science · doi:10.1080/09540091.2014.955838

Roles of periplasmic chaperones and BamA in outer membrane protein folding

Schiffrin, R. (2016) · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)

How the E. Coli Hsp70 Molecular Chaperone, DnaK, Binds a Client Protein

Tilitsky, J. M. (2021) · Scholarworks (University of Massachusetts Amherst) · doi:10.7275/10586279

Βιοχημικές μελέτες ενζύμων του μεταβολισμού του γλυκογόνου

Stravodimos, G. (2018) · doi:10.12681/eadd/43863

Structural Basis for Protein Folding and Holding Mediated by Molecular Chaperones

Saio, T., & Ishimori, K. (2019) · Seibutsu Butsuri · doi:10.2142/biophys.59.197

Chaperones/Chaperonins, Tertiary, and Quaternary Structure

Dods, R. F. (2019) · Springer eBooks · doi:10.1007/978-3-030-28303-2_4

Native Ion Mobility-Mass Spectrometry Techniques for Characterizing the Structure and Lipid Binding of Bacterial Pore-Forming Toxins

Wilson, J. (2020) · Scholars' Bank (University of Oregon)

Reply on RC3

Hsu, S. D. (2021) · Magnetic Resonance · doi:10.5194/mr-2021-9-ac3

Reply on RC2

Hsu, S. D. (2021) · Magnetic Resonance · doi:10.5194/mr-2021-9-ac2

Reply on RC1

Hsu, S. D. (2021) · Magnetic Resonance · doi:10.5194/mr-2021-9-ac4

Reply on RC1

Hsu, S. D. (2021) · Magnetic Resonance · doi:10.5194/mr-2021-9-ac1

Faculty Opinions recommendation of Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex.

Turgay, K. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.739359243.793584698

Literature Search and Review

Davis, M. I., Simeonov, A. M., Lea, W., & Auld, D. (2014) · Assay and Drug Development Technologies · doi:10.1089/adt.2014.1206.lr

Faculty Opinions recommendation of Nature and regulation of protein folding on the ribosome.

Chazin, W. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736169786.793574065

Comment on mr-2021-9

(2021) · Magnetic Resonance · doi:10.5194/mr-2021-9-rc2

Comment on mr-2021-9

(2021) · Magnetic Resonance · doi:10.5194/mr-2021-9-rc3

Faculty Opinions recommendation of Regulation of α-synuclein by chaperones in mammalian cells.

Jackson, S. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.737028220.793569910

Comment on mr-2021-9

(2021) · Magnetic Resonance · doi:10.5194/mr-2021-9-rc1

Protein Synthesis and Folding

(2016) · Elsevier eBooks · doi:10.1016/b978-0-323-34126-4.00017-7

How protein fold: Insights from nuclear magnetic resonance spectroscopy

Zhuravelva, A. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-90800-9.00246-8

Thermodynamic profiles for co-translational trigger factor functionPreprint

Herling, T. W., Cassaignau, A. M. E., Wentink, A. S., Peter, Q. A. E., Kumar, P. C., Kartanas, T., Schneider, M. M., Cabrita, L. D., Christodoulou, J. C., & Knowles, T. P. J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.23.554456

Solution NMR Studies of Chaperone–Client Systems

Wan, C., & Huang, C. (2023) · Royal Society of Chemistry eBooks · doi:10.1039/bk9781839165986-00086

Introduction: Molecular Chaperones and Protein Quality Control

Balchin, D., Rangel, M. A., & Samant, R. S. (2023) · Royal Society of Chemistry eBooks · doi:10.1039/bk9781839165986-00001

NMR Study of the Structure and Dynamics of Chaperone–Client Complexes

Saio, T. (2023) · Royal Society of Chemistry eBooks · doi:10.1039/bk9781839165986-00162

Structural Disorder in Chaperone Functions Probed by NMR

Hu, Y., & Liu, M. (2023) · Royal Society of Chemistry eBooks · doi:10.1039/bk9781839165986-00038

Real-time Visualization of Trigger Factor on Translating RibosomesPreprint

Núñez, E., Saha, P., Ibarluzea, M. G., Muguruza‐Montero, A., M‐Alicante, S., Ramis, R., Leonardo, A., Bergara, A., Villarroel, Á., & Rico, F. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.16.654432

Modeling chaperone-substrate interactions of alpha crystallin from the ocular lens

Ramirez, L. M. (2019) · doi:10.54014/98xj-y5zv

Docking Flexible Proteins using Polynomial Expansions.

Hoffmann, A. (2018) · doi:10.70675/55e49914z669bz4744zbc01zaa022e76e6d9

Etude des principes d’assemblage et de maturation des kinases de la famille des PIKKs chez Schizosaccharomyces pombe

Toullec, D. (2020) · theses.fr (ABES) · doi:10.70675/a7933611z0027z41dfz8436za664ba25bd4a

Etude moléculaire des étapes initiales d'importation de protéines mitochondriales

Sučec, I. (2022) · theses.fr (ABES) · doi:10.70675/b93c1147zace8z4b3ezab9azaed46edfeac5

Protein folding

Pal, S. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-33980-6.00015-x

OptoChaperone─A Biohybrid Tool for Regulating Protein Condensates in Cells and In Vitro

Tuan, D. T., Matsusaki, M., Ota, H., Kawagoe, S., Nisansala, H. D., Kumashiro, M., Isozumi, N., Kumeta, H., Kono, Y., Shimi, T., et al. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.6c04074

Fatty acid profile, physicochemical properties, and microstructure of Dangke whey evaporated milk

Malaka, R., Nahariah, Hatta, W., Yuliati, F. N., Kasmiati, Vargas, M. A. V., Arief, F. A., Arianty, Z., Kadir, R. W., Yousef, S. S. M., et al. (2026) · Applied Food Research · doi:10.1016/j.afres.2026.102407

FGFR kinase isoform and activation state modulate ATPase activity

Besch, A., Lamon, G., Zhang, Y.-K., & Traaseth, N. (2026) · iScience · doi:10.1016/j.isci.2026.117652

Multivalent weak contacts shape chaperone–nascent protein interactions

Rajasekaran, N., Toptygin, D., Liao, T., Hilser, V. J., Ha, T., & Kaiser, C. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2607201123

Molecular drivers of cotranslational protein assembly in bacteria

Schmitt, J. L., Auburger, J. J., Wruck, F., Koubek, J., Tans, S. J., Bukau, B., & Krämer, G. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2608997123

RESEARCH ARTICLE The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins

Singhal, K., Vreede, J., Mashaghi, A., & Tans, E. J. (2016)

The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins

Singhal, K., Vreede, J., Mashaghi, A., Tans, S. J., & Bolhuis, P. G. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004444 · Cited by 32

A Molecular Dynamics Study of the Flexibility and Protein-Binding of the Trigger Factor Chaperone in Solution

Singhal, K., Vreede, J., Mashaghi, A., Tans, S. J., & Bolhuis, P. G. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2012.11.3172

Oligomerization of a molecular chaperone modulates its activity

Saio, T., Kawagoe, S., Ishimori, K., & Kalodimos, C. G. (2018) · eLife · doi:10.7554/elife.35731 · Cited by 73

Exploring the roles of substrate‐binding surface of the chaperone site in the chaperone activity of trigger factor

Fan, D., Cao, S., Zhou, Q., Zhang, Y., Yue, L., Han, C. L., Yang, B., Wang, Y., Ma, Z., Zhu, L., et al. (2018) · The FASEB Journal · doi:10.1096/fj.201701576 · Cited by 2