Elucidation of the structural stability and dynamics of heterogeneous intermediate ensembles in unfolding pathway of the N-terminal domain of TDP-43

A single N‐terminal phosphomimic disrupts TDP‐43 polymerization, phase separation, and RNA splicing

(2018) Ailin Wang et al.   EMBO JOURNAL

Comparative analysis of thermal unfolding simulations of RNA recognition motifs (RRMs) of TAR DNA-binding protein 43 (TDP-43)

(2018) Amresh Prakash et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Phosphorylation-induced changes in the energetic frustration in human Tank binding kinase 1

(2018) Shahrukh Husain et al.   JOURNAL OF THEORETICAL BIOLOGY

Point mutations in the N-terminal domain of transactive response DNA-binding protein 43 kDa (TDP-43) compromise its stability, dimerization, and functions

(2017) Miguel Mompeán et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation

(2017) Tariq Afroz et al.   Nature Communications

The N-terminal dimerization is required for TDP-43 splicing activity

(2017) Lei-Lei Jiang et al.   Scientific Reports

Delineating the relationship between amyotrophic lateral sclerosis and frontotemporal dementia: Sequence and structure-based predictions

(2016) Vijay Kumar et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

The extreme N-terminus of TDP-43 mediates the cytoplasmic aggregation of TDP-43 and associated toxicity in vivo

(2016) Hiroki Sasaguri et al.   BRAIN RESEARCH

Therapeutic progress in amyotrophic lateral sclerosis-beginning to learning

(2016) Vijay Kumar et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

The TDP-43 N-terminal domain structure at high resolution

(2016) Miguel Mompeán et al.   FEBS Journal

Untangling the structure of the TDP-43 N-terminal domain

(2016) Chung-ke Chang et al.   FEBS Journal

Structural basis of urea-induced unfolding: Unraveling the folding pathway of hemochromatosis factor E

(2016) Parvez Khan et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Quantification of the Relative Contributions of Loss-of-function and Gain-of-function Mechanisms in TAR DNA-binding Protein 43 (TDP-43) Proteinopathies

(2016) Roberta Cascella et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Spectroscopic and MD simulation studies on unfolding processes of mitochondrial carbonic anhydrase VA induced by urea

(2016) Danish Idrees et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

GdmCl-induced unfolding studies of human carbonic anhydrase IX: a combined spectroscopic and MD simulation approach

(2016) Amresh Prakash et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

(2016) R. Gonzalo Parra et al.   NUCLEIC ACIDS RESEARCH

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Thermal- and urea-induced unfolding processes of glutathione S-transferase by molecular dynamics simulation

(2015) Jiahuang Li et al.   BIOPOLYMERS

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

The structural integrity of TDP-43 N-terminus is required for efficient aggregate entrapment and consequent loss of protein function

(2015) Valentina Romano et al.   Prion

Nuclear TDP-43 causes neuronal toxicity by escaping from the inhibitory regulation by hnRNPs

(2014) Hiroaki Suzuki et al.   HUMAN MOLECULAR GENETICS

TDP-43 loss of cellular function through aggregation requires additional structural determinants beyond its C-terminal Q/N prion-like domain

(2014) Mauricio Budini et al.   HUMAN MOLECULAR GENETICS

Multistage Unfolding of an SH3 Domain: An Initial Urea-Filled Dry Molten Globule Precedes a Wet Molten Globule with Non-Native Structure

(2014) Amrita Dasgupta et al.   JOURNAL OF PHYSICAL CHEMISTRY B

TDP-43 N terminus encodes a novel ubiquitin-like fold and its unfolded form in equilibrium that can be shifted by binding to ssDNA

(2014) Haina Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein

(2014) Stefano Gianni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frustration in biomolecules

(2014) Diego U. Ferreiro et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Conformational dynamics of xylanase a fromStreptomyces lividans: Implications for TIM-barrel enzyme thermostability

(2013) Yanrui Ding et al.   BIOPOLYMERS

The dual functions of the extreme N-terminus of TDP-43 in regulating its biological activity and inclusion formation

(2013) Yong-Jie Zhang et al.   HUMAN MOLECULAR GENETICS

Correlated Motions and Residual Frustration in Thrombin

(2013) Brian Fuglestad et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43

(2013) Peter J Lukavsky et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Converging Mechanisms in ALS and FTD: Disrupted RNA and Protein Homeostasis

(2013) Shuo-Chien Ling et al.   NEURON

Unfolding Simulations of Holomyoglobin from Four Mammals: Identification of Intermediates and β-Sheet Formation from Partially Unfolded States

(2013) Pouria Dasmeh et al.   PLoS One

Native contacts determine protein folding mechanisms in atomistic simulations

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

Using simulations to provide the framework for experimental protein folding studies

(2012) Bruno Rizzuti et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

The N-terminus of TDP-43 promotes its oligomerization and enhances DNA binding affinity

(2012) Chung-ke Chang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions

(2012) Anna Vangone et al.   BMC BIOINFORMATICS

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Protein frustratometer: a tool to localize energetic frustration in protein molecules

(2012) M. Jenik et al.   NUCLEIC ACIDS RESEARCH

Urea and Guanidinium Induced Denaturation of a Trp-Cage Miniprotein

(2011) Jan Heyda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Gains or losses: molecular mechanisms of TDP43-mediated neurodegeneration

(2011) Edward B. Lee et al.   NATURE REVIEWS NEUROSCIENCE

The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

(2011) Anshuman Dixit et al.   PLoS One

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

(2011) Wenfei Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the role of frustration in the energy landscapes of allosteric proteins

(2011) Diego U. Ferreiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rethinking ALS: The FUS about TDP-43

(2009) Clotilde Lagier-Tourenne et al.   CELL

Microscopic Reversibility of Protein Folding in Molecular Dynamics Simulations of the Engrailed Homeodomain†

(2008) Michelle E. McCully et al.   BIOCHEMISTRY

Urea and Guanidinium Chloride Denature Protein L in Different Ways in Molecular Dynamics Simulations

(2008) C. Camilloni et al.   BIOPHYSICAL JOURNAL

Characterization of the Protein Unfolding Processes Induced by Urea and Temperature

(2007) Alessandro Guerini Rocco et al.   BIOPHYSICAL JOURNAL