The Proteome Folding Problem and Cellular Proteostasis

The breakthrough in protein structure prediction

(2021) Andrei N. Lupas et al.   BIOCHEMICAL JOURNAL

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions

(2020) Jeong-Mo Choi et al.   Annual Review of Biophysics

Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness

(2020) Ian M. Walsh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liquid–Liquid Phase Separation and Its Mechanistic Role in Pathological Protein Aggregation

(2020) W. Michael Babinchak et al.   JOURNAL OF MOLECULAR BIOLOGY

Small molecule strategies to harness the unfolded protein response: where do we go from here?

(2020) Julia M.D. Grandjean et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

(2020) Micayla A. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein storytelling through physics

(2020) Emiliano Brini et al.   SCIENCE

Proteostasis is adaptive: Balancing chaperone holdases against foldases

(2020) Adam MR de Graff et al.   PLoS Computational Biology

The Protein Disulfide Isomerase Family: from proteostasis to pathogenesis

(2019) Motonori Matsusaki et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Kinetic versus thermodynamic control of mutational effects on protein homeostasis: A perspective from computational modeling and experiment

(2019) Kristine Faye R. Pobre et al.   PROTEIN SCIENCE

On the nature of the optimal form of the holdase‐type chaperone stress response

(2019) Damien Hall   FEBS LETTERS

Proteostasis collapse is a driver of cell aging and death

(2019) Mantu Santra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cryo-EM structure of a transthyretin-derived amyloid fibril from a patient with hereditary ATTR amyloidosis

(2019) Matthias Schmidt et al.   Nature Communications

Unveiling invisible protein states with NMR spectroscopy

(2019) T Reid Alderson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Regulated Proteolysis in Bacteria

(2018) Samar A. Mahmoud et al.   Annual Review of Biochemistry

Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation

(2018) Thomas C.T. Michaels et al.   Annual Review of Physical Chemistry

Thermal proteome profiling in bacteria: probing protein state in vivo

(2018) André Mateus et al.   Molecular Systems Biology

Physical Chemistry of Cellular Liquid Phase Separation

(2018) Emily P. Bentley et al.   CHEMISTRY-A EUROPEAN JOURNAL

The stop and go traffic regulating protein biogenesis: how translation kinetics control proteostasis

(2018) Kevin C. Stein et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Recent advances in the structural and mechanistic aspects of Hsp70 molecular chaperones

(2018) Matthias P Mayer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cryo-EM structures of tau filaments from Alzheimer’s disease

(2017) Anthony W. P. Fitzpatrick et al.   NATURE

Ligand-promoted protein folding by biased kinetic partitioning

(2017) Karan S Hingorani et al.   Nature Chemical Biology

The HSP90 chaperone machinery

(2017) Florian H. Schopf et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cotranslational folding of spectrin domains via partially structured states

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

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

(2017) Ke Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial proteostasis balances energy and chaperone utilization efficiently

(2017) Mantu Santra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prion protein dynamics before aggregation

(2017) Kinshuk Raj Srivastava et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water

(2017) Joshua A. Riback et al.   SCIENCE

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability

(2017) Pascal Leuenberger et al.   SCIENCE

Regulating Secretory Proteostasis through the Unfolded Protein Response: From Function to Therapy

(2017) Lars Plate et al.   TRENDS IN CELL BIOLOGY

Cotranslational folding of spectrin domains via partially structured states

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

Mammalian Autophagy: How Does It Work?

(2016) Carla F. Bento et al.   Annual Review of Biochemistry

The integrated stress response

(2016) Karolina Pakos‐Zebrucka et al.   EMBO REPORTS

Atomic-resolution structure of a disease-relevant Aβ(1–42) amyloid fibril

(2016) Marielle Aulikki Wälti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Pharmacological Chaperone Therapy: Preclinical Development, Clinical Translation, and Prospects for the Treatment of Lysosomal Storage Disorders

(2015) Giancarlo Parenti et al.   MOLECULAR THERAPY

Structure of the toxic core of α-synuclein from invisible crystals

(2015) Jose A. Rodriguez et al.   NATURE

Targeting protein aggregation for the treatment of degenerative diseases

(2015) Yvonne S. Eisele et al.   NATURE REVIEWS DRUG DISCOVERY

Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape

(2015) Hao Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Individual and Collective Contributions of Chaperoning and Degradation to Protein Homeostasis in E. coli

(2015) Younhee Cho et al.   Cell Reports

The small molecule ISRIB reverses the effects of eIF2α phosphorylation on translation and stress granule assembly

(2015) Carmela Sidrauski et al.   eLife

Glucocorticoid Receptor Function Regulated by Coordinated Action of the Hsp90 and Hsp70 Chaperone Cycles

(2014) Elaine Kirschke et al.   CELL

Polyphosphate Is a Primordial Chaperone

(2014) Michael J. Gray et al.   MOLECULAR CELL

Energy landscapes of functional proteins are inherently risky

(2014) Anne Gershenson et al.   Nature Chemical Biology

The intrinsic and extrinsic effects of N-linked glycans on glycoproteostasis

(2014) Daniel N Hebert et al.   Nature Chemical Biology

The amyloid state and its association with protein misfolding diseases

(2014) Tuomas P. J. Knowles et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Proteome Folding Kinetics Is Limited by Protein Halflife

(2014) Taisong Zou et al.   PLoS One

Protein aggregation can inhibit clathrin-mediated endocytosis by chaperone competition

(2014) A. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteostasis impairment in protein-misfolding and -aggregation diseases

(2014) Mark S. Hipp et al.   TRENDS IN CELL BIOLOGY

Molecular Chaperone Functions in Protein Folding and Proteostasis

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

Protein quality control and elimination of protein waste: The role of the ubiquitin–proteasome system

(2013) Ingo Amm et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

A systems biology approach to optimising hosts for industrial protein production

(2013) Kate Royle et al.   BIOTECHNOLOGY LETTERS

Molecular Structure of β-Amyloid Fibrils in Alzheimer’s Disease Brain Tissue

(2013) Jun-Xia Lu et al.   CELL

PolyQ Proteins Interfere with Nuclear Degradation of Cytosolic Proteins by Sequestering the Sis1p Chaperone

(2013) Sae-Hun Park et al.   CELL

Shedding light on protein folding landscapes by single-molecule fluorescence

(2013) Priya R. Banerjee et al.   CHEMICAL SOCIETY REVIEWS

Protein Homeostasis as a Therapeutic Target for Diseases of Protein Conformation

(2013) Barbara Calamini et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Diversity in the origins of proteostasis networks — a driver for protein function in evolution

(2013) Evan T. Powers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Protein rescue from aggregates by powerful molecular chaperone machines

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

Folding the proteome

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

Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli

(2013) Alex Dickson et al.   PLoS Computational Biology

Protein Quality Control Acts on Folding Intermediates to Shape the Effects of Mutations on Organismal Fitness

(2012) Shimon Bershtein et al.   MOLECULAR CELL

Activation of Hsp70 reduces neurotoxicity by promoting polyglutamine protein degradation

(2012) Adrienne M Wang et al.   Nature Chemical Biology

Counteracting chemical chaperone effects on the single-molecule  -synuclein structural landscape

(2012) A. C. M. Ferreon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

FoldEco: A Model for Proteostasis in E. coli

(2012) Evan T. Powers et al.   Cell Reports

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

(2012) Giulia Calloni et al.   Cell Reports

Osmolyte effects on protein stability and solubility: A balancing act between backbone and side-chains

(2011) Matthew Auton et al.   BIOPHYSICAL CHEMISTRY

Amyloid-like Aggregates Sequester Numerous Metastable Proteins with Essential Cellular Functions

(2011) Heidi Olzscha et al.   CELL

Protein Crowding Tunes Protein Stability

(2011) Andrew C. Miklos et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Macromolecular Crowding Fails To Fold a Globular Protein in Cells

(2011) Alexander P. Schlesinger et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins

(2011) Madeleine B. Borgia et al.   NATURE

Small-molecule proteostasis regulators for protein conformational diseases

(2011) Barbara Calamini et al.   Nature Chemical Biology

Physicochemical Determinants of Chaperone Requirements

(2010) Gian Gaetano Tartaglia et al.   JOURNAL OF MOLECULAR BIOLOGY

Heat shock factors: integrators of cell stress, development and lifespan

(2010) Malin Åkerfelt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biological and Chemical Approaches to Diseases of Proteostasis Deficiency

(2009) Evan T. Powers et al.   Annual Review of Biochemistry

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

Chaperonin-mediated protein folding: using a central cavity to kinetically assist polypeptide chain folding

(2009) Arthur L. Horwich et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data

(2009) Joost Van Durme et al.   PLoS Computational Biology

The Protein Folding Problem

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

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou et al.   Annual Review of Biophysics

The two faces of protein misfolding: gain- and loss-of-function in neurodegenerative diseases

(2008) Konstanze F Winklhofer et al.   EMBO JOURNAL

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

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

Adapting Proteostasis for Disease Intervention

(2008) William E. Balch et al.   SCIENCE

A polymer physics perspective on driving forces and mechanisms for protein aggregation

(2007) Rohit V. Pappu et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS