Protein folding in vitro and in the cell: From a solitary journey to a team effort

Breakdown of supersaturation barrier links protein folding to amyloid formation

(2021) Masahiro Noji et al.   Communications Biology

Analysis of Tandem Repeat Protein Folding Using Nearest-Neighbor Models

(2021) Mark Petersen et al.   Annual Review of Biophysics

On the evolution of chaperones and cochaperones and the expansion of proteomes across the Tree of Life

(2021) Mathieu E. Rebeaud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Macromolecular crowding modulates α-synuclein amyloid fiber growth

(2021) Istvan Horvath et al.   BIOPHYSICAL JOURNAL

Fluorescence Anisotropy Decays and Microscale-Volume Viscometry Reveal the Compaction of Ribosome-Bound Nascent Proteins

(2021) Rachel B. Hutchinson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nonrefoldability is Pervasive Across the E. coli Proteome

(2021) Philip To et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

The Hsp70-Chaperone Machines in Bacteria

(2021) Matthias P. Mayer   Frontiers in Molecular Biosciences

Mechanisms of Cotranslational Protein Maturation in Bacteria

(2021) Jiří Koubek et al.   Frontiers in Molecular Biosciences

Interactions between nascent proteins and the ribosome surface inhibit co-translational folding

(2021) Anaïs M. E. Cassaignau et al.   Nature Chemistry

Deep learning opens up protein science’s next frontiers

(2021) Johanna L. Miller   PHYSICS TODAY

An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel

(2021) Valeria Guzman-Luna et al.   Communications Biology

Engineered Protein Scaffolds as Next-Generation Therapeutics

(2020) Michaela Gebauer et al.   Annual Review of Pharmacology and Toxicology

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

(2020) Amir Bitran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Hsp70 resolves misfolded states and accelerates productive folding of a multi-domain protein

(2020) Rahmi Imamoglu et al.   Nature Communications

Recent advances in understanding catalysis of protein folding by molecular chaperones

(2020) David Balchin et al.   FEBS LETTERS

Chaperone client proteins evolve slower than non-client proteins

(2020) Manish Prakash Victor et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Complementary Role of Co- and Post-Translational Events in De Novo Protein Biogenesis

(2020) Rayna M. Addabbo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of protein structure on evolution of cotranslational folding

(2020) Victor Zhao et al.   BIOPHYSICAL JOURNAL

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Differences in the path to exit the ribosome across the three domains of life

(2019) Khanh Dao Duc et al.   NUCLEIC ACIDS RESEARCH

The Ribosome Cooperates with a Chaperone to Guide Multi-domain Protein Folding

(2019) Kaixian Liu et al.   MOLECULAR CELL

Hsp70 molecular chaperones: multifunctional allosteric holding and unfolding machines

(2019) Eugenia M. Clerico et al.   BIOCHEMICAL JOURNAL

The Hsp70 chaperone network

(2019) Rina Rosenzweig et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nature and Regulation of Protein Folding on the Ribosome

(2019) Christopher A. Waudby et al.   TRENDS IN BIOCHEMICAL SCIENCES

Proteins are Solitary! Pathways of Protein Folding and Aggregation in Protein Mixtures

(2019) Valentino Bianco et al.   Journal of Physical Chemistry Letters

The molecular mechanism of cotranslational membrane protein recognition and targeting by SecA

(2019) Shuai Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Kinetic trapping in protein folding

(2019) Angela E Varela et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Successes and challenges in simulating the folding of large proteins

(2019) Anne Gershenson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural and functional analysis of the Hsp70/Hsp40 chaperone system

(2019) Qinglian Liu et al.   PROTEIN SCIENCE

A metastable subproteome underlies inclusion formation in muscle proteinopathies

(2019) Prajwal Ciryam et al.   Acta Neuropathologica Communications

Co-Translational Folding Trajectory of the HemK Helical Domain

(2018) Evan Mercier et al.   BIOCHEMISTRY

SRP, FtsY, DnaK and YidC Are Required for the Biogenesis of the E. coli Tail-Anchored Membrane Proteins DjlC and Flk

(2018) Markus Peschke et al.   JOURNAL OF MOLECULAR BIOLOGY

Kinetic Trapping of Folded Proteins Relative to Aggregates under Physiologically Relevant Conditions

(2018) Angela Elizabeth Varela et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cellular Handling of Protein Aggregates by Disaggregation Machines

(2018) Axel Mogk et al.   MOLECULAR CELL

Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome

(2018) José Arcadio Farías-Rico et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks

(2018) Eric C. Greenwald et al.   CHEMICAL REVIEWS

Folding pathway of an Ig domain is conserved on and off the ribosome

(2018) Pengfei Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Key features of an Hsp70 chaperone allosteric landscape revealed by ion-mobility native mass spectrometry and double electron-electron resonance

(2017) Alex L. Lai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cotranslational folding of spectrin domains via partially structured states

(2017) Ola B Nilsson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The case for defined protein folding pathways

(2017) S. Walter Englander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein homeostasis of a metastable subproteome associated with Alzheimer’s disease

(2017) Rishika Kundra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational heterogeneity in the Hsp70 chaperone-substrate ensemble identified from analysis of NMR-detected titration data

(2017) Ashok Sekhar et al.   PROTEIN SCIENCE

Cotranslational folding of spectrin domains via partially structured states

(2017) Ola B Nilsson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Widespread position-specific conservation of synonymous rare codons within coding sequences

(2017) Julie L. Chaney et al.   PLoS Computational Biology

Promiscuous binding by Hsp70 results in conformational heterogeneity and fuzzy chaperone-substrate ensembles

(2017) Rina Rosenzweig et al.   eLife

A Novel Method to Evaluate Ribosomal Performance in Cell-Free Protein Synthesis Systems

(2017) Noémie Kempf et al.   Scientific Reports

How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway

(2016) H. Jane Dyson et al.   ACCOUNTS OF CHEMICAL RESEARCH

Globular Protein Folding In Vitro and In Vivo

(2016) Martin Gruebele et al.   Annual Review of Biophysics

Protein Folding—How and Why: By Hydrogen Exchange, Fragment Separation, and Mass Spectrometry

(2016) S. Walter Englander et al.   Annual Review of Biophysics

Small protein domains fold inside the ribosome exit tunnel

(2016) Jacopo Marino et al.   FEBS LETTERS

The Molecular Chaperone DnaK Is a Source of Mutational Robustness

(2016) José Aguilar-Rodríguez et al.   Genome Biology and Evolution

DnaK-Dependent Accelerated Evolutionary Rate in Prokaryotes

(2016) A. Samer Kadibalban et al.   Genome Biology and Evolution

Dynamic Behavior of Trigger Factor on the Ribosome

(2016) J. Deeng et al.   JOURNAL OF MOLECULAR BIOLOGY

Trigger Factor Reduces the Force Exerted on the Nascent Chain by a Cotranslationally Folding Protein

(2016) Ola B. Nilsson et al.   JOURNAL OF MOLECULAR BIOLOGY

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

(2016) Florian Buhr et al.   MOLECULAR CELL

Alternative modes of client binding enable functional plasticity of Hsp70

(2016) Alireza Mashaghi et al.   NATURE

Quantitative determination of ribosome nascent chain stability

(2016) Avi J. Samelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In vivo aspects of protein folding and quality control

(2016) D. Balchin et al.   SCIENCE

A simple two-state protein unfolds mechanically via multiple heterogeneous pathways at single-molecule resolution

(2016) Jörg Schönfelder et al.   Nature Communications

Chaperone-assisted protein aggregate reactivation: Different solutions for the same problem

(2015) Alejandra Aguado et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Gradual Folding of an Off-Pathway Molten Globule Detected at the Single-Molecule Level

(2015) Simon Lindhoud et al.   JOURNAL OF MOLECULAR BIOLOGY

How Hsp70 Molecular Machines Interact with Their Substrates to Mediate Diverse Physiological Functions

(2015) Eugenia M. Clerico et al.   JOURNAL OF MOLECULAR BIOLOGY

The PURE system for the cell-free synthesis of membrane proteins

(2015) Yutetsu Kuruma et al.   Nature Protocols

High-resolution structure of the Escherichia coli ribosome

(2015) Jonas Noeske et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Amyloid Polymorphism: Structural Basis and Neurobiological Relevance

(2015) Robert Tycko   NEURON

Heterogeneous binding of the SH3 client protein to the DnaK molecular chaperone

(2015) Jung Ho Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translational tuning optimizes nascent protein folding in cells

(2015) S. J. Kim et al.   SCIENCE

Supersaturation is a major driving force for protein aggregation in neurodegenerative diseases

(2015) Prajwal Ciryam et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

High-resolution structure of the Escherichia coli ribosome

(2015) Jonas Noeske et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cotranslational Protein Folding inside the Ribosome Exit Tunnel

(2015) Ola B. Nilsson et al.   Cell Reports

Machine Learning: How Much Does It Tell about Protein Folding Rates?

(2015) Marc Corrales et al.   PLoS One

Probing the Non-Native H Helix Translocation in Apomyoglobin Folding Intermediates

(2014) Phillip C. Aoto et al.   BIOCHEMISTRY

GroEL/ES Chaperonin Modulates the Mechanism and Accelerates the Rate of TIM-Barrel Domain Folding

(2014) Florian Georgescauld et al.   CELL

Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs)

(2014) Francois-Xavier Theillet et al.   CHEMICAL REVIEWS

DnaJ-Promoted Binding of DnaK to Multiple Sites on  32 in the Presence of ATP

(2014) A. Noguchi et al.   JOURNAL OF BACTERIOLOGY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein

(2014) Ruth Kellner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The nature of protein folding pathways

(2014) S. Walter Englander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis for Protein Antiaggregation Activity of the Trigger Factor Chaperone

(2014) T. Saio et al.   SCIENCE

Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

(2013) Thomas R. M. Barends et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Molecular Chaperone Functions in Protein Folding and Proteostasis

(2013) Yujin E. Kim et al.   Annual Review of Biochemistry

Transmembrane Segments Form Tertiary Hairpins in the Folding Vestibule of the Ribosome

(2013) LiWei Tu et al.   JOURNAL OF MOLECULAR BIOLOGY

Reshaping of the conformational search of a protein by the chaperone trigger factor

(2013) Alireza Mashaghi et al.   NATURE

Protein rescue from aggregates by powerful molecular chaperone machines

(2013) Shannon M. Doyle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP

(2013) Ruifeng Qi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Folding of a large protein at high structural resolution

(2013) B. T. Walters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry

(2013) W. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unraveling the Mechanism of Protein Disaggregation Through a ClpB-DnaK Interaction

(2013) R. Rosenzweig et al.   SCIENCE

Diversity in the mechanisms of cosolute action on biomolecular processes

(2012) Shahar Sukenik et al.   FARADAY DISCUSSIONS

From Macroscopic Measurements to Microscopic Mechanisms of Protein Aggregation

(2012) Samuel I.A. Cohen et al.   JOURNAL OF MOLECULAR BIOLOGY

Multidomain Protein Solves the Folding Problem by Multifunnel Combined Landscape: Theoretical Investigation of a Y-Family DNA Polymerase

(2012) Yong Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Loss of the DnaK-DnaJ-GrpE Chaperone System among the Aquificales

(2012) Tobias Warnecke   MOLECULAR BIOLOGY AND EVOLUTION

Concerted Action of the Ribosome and the Associated Chaperone Trigger Factor Confines Nascent Polypeptide Folding

(2012) Anja Hoffmann et al.   MOLECULAR CELL

Structure and Dynamics of the ATP-Bound Open Conformation of Hsp70 Chaperones

(2012) Roman Kityk et al.   MOLECULAR CELL

Global analysis of chaperone effects using a reconstituted cell-free translation system

(2012) T. Niwa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cavities determine the pressure unfolding of proteins

(2012) J. Roche et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinguishing crystal-like amyloid fibrils and glass-like amorphous aggregates from their kinetics of formation

(2012) Y. Yoshimura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

(2012) W. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transient interactions of a slow-folding protein with the Hsp70 chaperone machinery

(2012) Ashok Sekhar et al.   PROTEIN SCIENCE

Protein folding rates and thermodynamic stability are key determinants for interaction with the Hsp70 chaperone system

(2012) Ashok Sekhar et al.   PROTEIN SCIENCE

DnaK Functions as a Central Hub in the E. coli Chaperone Network

(2012) Giulia Calloni et al.   Cell Reports

Protein Folding at the Exit Tunnel

(2011) Daria V. Fedyukina et al.   Annual Review of Biophysics

Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo

(2011) Eugene Oh et al.   CELL

Metastability of Native Proteins and the Phenomenon of Amyloid Formation

(2011) Andrew J. Baldwin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Behind the folding funnel diagram

(2011) Martin Karplus   Nature Chemical Biology

Reductive evolution of proteomes and protein structures

(2011) M. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Do Prokaryotes Have More Kinetically Stable Proteins Than Eukaryotic Organisms?

(2010) Ke Xia et al.   BIOCHEMISTRY

The folding of single domain proteins—have we reached a consensus?

(2010) Tobin R Sosnick et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Versatility of Trigger Factor Interactions with Ribosome-Nascent Chain Complexes

(2010) Sathish Kumar Lakshmipathy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Folding Zone in the Ribosomal Exit Tunnel for Kv1.3 Helix Formation

(2010) Li Wei Tu et al.   JOURNAL OF MOLECULAR BIOLOGY

Coupled chaperone action in folding and assembly of hexadecameric Rubisco

(2010) Cuimin Liu et al.   NATURE

The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase

(2010) Sandeep K Sharma et al.   Nature Chemical Biology

α-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel

(2010) Shashi Bhushan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Kinetic evidence of an on-pathway intermediate in the folding of lysozyme

(2010) Yawen Bai   PROTEIN SCIENCE

Quench-flow experiments combined with mass spectrometry show apomyoglobin folds through an obligatory intermediate

(2010) Vickie Tsui et al.   PROTEIN SCIENCE

Principles of protein folding - A perspective from simple exact models

(2010) Ken A. Dill et al.   PROTEIN SCIENCE

Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone

(2009) Erik Martinez-Hackert et al.   CELL

Tertiary interactions within the ribosomal exit tunnel

(2009) Andrey Kosolapov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Converging concepts of protein folding in vitro and in vivo

(2009) F Ulrich Hartl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Direct evidence for a dry molten globule intermediate during the unfolding of a small protein

(2009) S. K. Jha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins

(2009) T. Niwa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate

(2009) E. B. Bertelsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Confined dynamics of a ribosome-bound nascent globin: Cone angle analysis of fluorescence depolarization decays in the presence of two local motions

(2009) Jamie P. Ellis et al.   PROTEIN SCIENCE

Chain Dynamics of Nascent Polypeptides Emerging from the Ribosome

(2008) Jamie P. Ellis et al.   ACS Chemical Biology

Nonnative Helical Motif in a Chaperone-Bound Protein Fragment

(2008) Neşe Kurt et al.   BIOPHYSICAL JOURNAL

Residue-Specific Contact Order and Contact Breadth in Single-Domain Proteins: Implications for Folding as a Function of Chain Elongation

(2008) N. Kurt et al.   BIOTECHNOLOGY PROGRESS

Protein abundance profiling of the Escherichia coli cytosol

(2008) Yasushi Ishihama et al.   BMC GENOMICS

Guidelines for the nomenclature of the human heat shock proteins

(2008) Harm H. Kampinga et al.   CELL STRESS & CHAPERONES

Molecular mechanism and structure of Trigger Factor bound to the translating ribosome

(2008) Frieder Merz et al.   EMBO JOURNAL

The Foldon Substructure of Staphylococcal Nuclease

(2008) Sabrina Bédard et al.   JOURNAL OF MOLECULAR BIOLOGY

Cotranslational Folding Promotes β-Helix Formation and Avoids Aggregation In Vivo

(2008) Michael S. Evans et al.   JOURNAL OF MOLECULAR BIOLOGY

From hatching to dispatching: the multiple cellular roles of the Hsp70 molecular chaperone machinery

(2008) Eirini Meimaridou et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Protein disaggregation by the AAA+ chaperone ClpB involves partial threading of looped polypeptide segments

(2008) Tobias Haslberger et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Protein folding: Independent unrelated pathways or predetermined pathway with optional errors

(2008) S. Bedard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hierarchical folding mechanism of apomyoglobin revealed by ultra-fast H/D exchange coupled with 2D NMR

(2008) T. Uzawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonrandom distribution of intramolecular contacts in native single-domain proteins

(2008) Bryan C. Mounce et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein therapeutics: a summary and pharmacological classification

(2007) Benjamin Leader et al.   NATURE REVIEWS DRUG DISCOVERY

Asymmetric effect of domain interactions on the kinetics of folding in yeast phosphoglycerate kinase

(2005) Szabolcs Osváth et al.   PROTEIN SCIENCE