Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process?

Co‐translational folding of nascent polypeptides: Multi‐layered mechanisms for the efficient biogenesis of functional proteins

(2021) Kevin Maciuba et al.   BIOESSAYS

The ribosome modulates folding inside the ribosomal exit tunnel

(2021) Florian Wruck et al.   Communications Biology

Hydrophobic and electrostatic interactions modulate protein escape at the ribosomal exit tunnel

(2021) Phuong Thuy Bui et al.   BIOPHYSICAL JOURNAL

Single-Molecule Force Spectroscopy of Protein Folding

(2021) Rafayel Petrosyan et al.   JOURNAL OF MOLECULAR BIOLOGY

The protein folding problem: The role of theory

(2021) Roy Nassar et al.   JOURNAL OF MOLECULAR BIOLOGY

Nonrefoldability is Pervasive Across the E. coli Proteome

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

Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling

(2021) Anne-Xander van der Stel et al.   Nature Communications

Fundamentals to function: Quantitative and scalable approaches for measuring protein stability

(2021) Beatriz Atsavapranee et al.   Cell Systems

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

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

Nascent chains can form co-translational folding intermediates that promote post-translational folding outcomes in a disease-causing protein

(2021) Elena Plessa et al.   Nature Communications

Kinetic control of nascent protein biogenesis by peptide deformylase

(2021) Lena A. K. Bögeholz et al.   Scientific Reports

Ornithine capture by a translating ribosome controls bacterial polyamine synthesis

(2020) Alba Herrero del Valle et al.   Nature Microbiology

Evolutionary Processes and Biophysical Mechanisms: Revisiting Why Evolved Proteins Are Marginally Stable

(2020) Amanda E. Wilson et al.   JOURNAL OF MOLECULAR EVOLUTION

How Does the Ribosome Fold the Proteome?

(2020) Anaïs M.E. Cassaignau et al.   Annual Review of Biochemistry

Single-Molecule Studies of Protein Folding with Optical Tweezers

(2020) Carlos Bustamante et al.   Annual Review of Biochemistry

Protein escape at the ribosomal exit tunnel: Effect of the tunnel shape

(2020) Phuong Thuy Bui et al.   JOURNAL OF CHEMICAL PHYSICS

Computational Modeling of Protein Stability: Quantitative Analysis Reveals Solutions to Pervasive Problems

(2020) Aron Broom et al.   STRUCTURE

ATP-Driven Nonequilibrium Activation of Kinase Clients by the Molecular Chaperone Hsp90

(2020) Huafeng Xu   BIOPHYSICAL JOURNAL

ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years

(2020) Rahul Nikam et al.   NUCLEIC ACIDS RESEARCH

Visualizing Protein Folding and Unfolding

(2019) Jennifer Ferina et al.   JOURNAL OF MOLECULAR BIOLOGY

Hsp70 molecular chaperones: multifunctional allosteric holding and unfolding machines

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

Nature and Regulation of Protein Folding on the Ribosome

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

Non-equilibrium dynamics of a nascent polypeptide during translation suppress its misfolding

(2019) Lisa M. Alexander et al.   Nature Communications

The human secretome

(2019) Mathias Uhlén et al.   Science Signaling

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

(2019) Salvatore Assenza et al.   eLife

Modeling protein folding in vivo

(2018) Irina Sorokina et al.   Biology Direct

Non-equilibrium coupling of protein structure and function to translation–elongation kinetics

(2018) Ajeet K Sharma et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein Folding Mediated by Trigger Factor and Hsp70: New Insights from Single-Molecule Approaches

(2018) Florian Wruck et al.   JOURNAL OF MOLECULAR BIOLOGY

Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins

(2018) Pierre Goloubinoff et al.   Nature Chemical Biology

Pathway of Actin Folding Directed by the Eukaryotic Chaperonin TRiC

(2018) David Balchin et al.   CELL

Protein escape at the ribosomal exit tunnel: Effects of native interactions, tunnel length, and macromolecular crowding

(2018) Phuong Thuy Bui et al.   JOURNAL OF CHEMICAL PHYSICS

Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale

(2018) Upneet Kaur et al.   JOURNAL OF PROTEOME RESEARCH

Transmembrane but not soluble helices fold inside the ribosome tunnel

(2018) Manuel Bañó-Polo et al.   Nature Communications

Computational tools help improve protein stability but with a solubility tradeoff

(2017) Aron Broom et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

There and back again: Two views on the protein folding puzzle

(2017) Alexei V. Finkelstein et al.   Physics of Life Reviews

Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium

(2017) Shaon Chakrabarti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning

(2017) Justin R. Klesmith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chaperones rescue the energetic landscape of mutant CFTR at single molecule and in cell

(2017) Miklos Bagdany et al.   Nature Communications

The ribosome and its role in protein folding: looking through a magnifying glass

(2017) Abid Javed et al.   Acta Crystallographica Section D-Structural Biology

Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase

(2017) Célia Deville et al.   Science Advances

Principles and equations for measuring and interpreting protein stability: From monomer to tetramer

(2016) Hugues Bedouelle   BIOCHIMIE

The role of the backbone torsion in protein folding

(2016) Irina Sorokina et al.   Biology Direct

Defying the activity–stability trade-off in enzymes: taking advantage of entropy to enhance activity and thermostability

(2016) Khawar Sohail Siddiqui   CRITICAL REVIEWS IN BIOTECHNOLOGY

Hsp70 biases the folding pathways of client proteins

(2016) Ashok Sekhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Holdase activity of secreted Hsp70 masks amyloid-β42 neurotoxicity inDrosophila

(2016) Pedro Fernandez-Funez 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

Is Catalytic Activity of Chaperones a Selectable Trait for the Emergence of Heat Shock Response?

(2015) Murat Çetinbaş et al.   BIOPHYSICAL JOURNAL

Protein stability: computation, sequence statistics, and new experimental methods

(2015) Thomas J Magliery   CURRENT OPINION IN STRUCTURAL BIOLOGY

Non-equilibrium conformational dynamics in the function of molecular chaperones

(2015) Alessandro Barducci et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Getting to the core of protein pharmaceuticals – Comprehensive structure analysis by mass spectrometry

(2015) Ulrike Leurs et al.   EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS

Advanced protein formulations

(2015) Wei Wang   PROTEIN SCIENCE

Cotranslational Protein Folding inside the Ribosome Exit Tunnel

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

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

(2015) Kushagra Singhal et al.   PLoS Computational Biology

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Protein Folding In Vivo Revisited

(2014) Seong Choi et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Learning To Fold Proteins Using Energy Landscape Theory

(2014) Nicholas P. Schafer et al.   ISRAEL JOURNAL OF CHEMISTRY

Active Cage Mechanism of Chaperonin-Assisted Protein Folding Demonstrated at Single-Molecule Level

(2014) Amit J. Gupta et al.   JOURNAL OF MOLECULAR BIOLOGY

Chaperonins Resculpt Folding Free Energy Landscapes to Avoid Kinetic Traps and Accelerate Protein Folding

(2014) Xin Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

General Mechanism of Two-State Protein Folding Kinetics

(2014) Geoffrey C. Rollins et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural Asymmetry in the Closed State of Mitochondrial Hsp90 (TRAP1) Supports a Two-Step ATP Hydrolysis Mechanism

(2014) Laura A. Lavery et al.   MOLECULAR CELL

Occurrence of protein disulfide bonds in different domains of life: a comparison of proteins from the Protein Data Bank

(2014) I. Bosnjak et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption

(2014) Paolo De Los Rios et al.   eLife

Inclusion bodies: not that bad…

(2014) Ana Ramón et al.   Frontiers in Microbiology

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

(2013) Lavanya Kannan et al.   Biology Direct

Proteomic data from human cell cultures refine mechanisms of chaperone-mediated protein homeostasis

(2013) Andrija Finka et al.   CELL STRESS & CHAPERONES

Co-translational mechanisms of protein maturation

(2013) Felix Gloge et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural and energetic determinants of co-translational folding

(2013) Heinrich Krobath et al.   JOURNAL OF CHEMICAL PHYSICS

Chaperone machines for protein folding, unfolding and disaggregation

(2013) Helen Saibil   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Folding the proteome

(2013) Esther Braselmann et al.   TRENDS IN BIOCHEMICAL SCIENCES

You Got to Know When to Hold (or Unfold) ‘Em…

(2012) Daniel N. Hebert et al.   MOLECULAR CELL

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems

(2011) Thomas J Magliery et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling

(2011) Daniel N Wilson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

What distinguishes GroEL substrates from other Escherichia coli proteins?

(2011) Ariel Azia et al.   FEBS Journal

Structural stability of E. coli transketolase to temperature and pH denaturation

(2011) Raha R.F. Jahromi et al.   JOURNAL OF BIOTECHNOLOGY

Molecular chaperones in protein folding and proteostasis

(2011) F. Ulrich Hartl et al.   NATURE

Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis

(2011) Athi N. Naganathan et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Solubilization of inclusion body proteins using n -propanol and its refolding into bioactive form

(2011) Surinder M. Singh et al.   PROTEIN EXPRESSION AND PURIFICATION

The Ribosome Modulates Nascent Protein Folding

(2011) C. M. Kaiser et al.   SCIENCE

The Cryo-EM Structure of a Complete 30S Translation Initiation Complex from Escherichia coli

(2011) Patricia Julián et al.   PLOS BIOLOGY

A systematic survey of in vivo obligate chaperonin-dependent substrates

(2010) Kei Fujiwara et al.   EMBO JOURNAL

Stability of Protein Pharmaceuticals: An Update

(2010) Mark Cornell Manning et al.   PHARMACEUTICAL RESEARCH

A novel protein refolding system using lauroyl-l-glutamate as a solubilizing detergent and arginine as a folding assisting agent

(2010) Motonori Kudou et al.   PROTEIN EXPRESSION AND PURIFICATION

An atlas of chaperone–protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell

(2009) Yunchen Gong et al.   Molecular Systems Biology

The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins

(2009) Günter Kramer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Recovery of Free Energy Branches in Single Molecule Experiments

(2009) Ivan Junier et al.   PHYSICAL REVIEW LETTERS

Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group

(2009) Woon Ki Lim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amyloids in bacterial inclusion bodies

(2009) Natalia S. de Groot et al.   TRENDS IN BIOCHEMICAL SCIENCES

Single-Molecule Studies of Protein Folding

(2008) Alessandro Borgia et al.   Annual Review of Biochemistry

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Fourier transform infrared spectroscopy analysis of the conformational quality of recombinant proteins within inclusion bodies

(2008) Silvia Maria Doglia et al.   Biotechnology Journal

Gene content of LUCA, the last universal common ancestor

(2008) Arcady Mushegian   Frontiers in Bioscience-Landmark

Indicators from archaeal secretomes

(2008) Mazen Saleh et al.   MICROBIOLOGICAL RESEARCH

Convergence of Molecular, Modeling, and Systems Approaches for an Understanding of the Escherichia coli Heat Shock Response

(2008) E. Guisbert et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A structural understanding of the dynamic ribosome machine

(2008) Thomas A. Steitz   NATURE REVIEWS MOLECULAR CELL BIOLOGY