Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
[HTML][HTML] Recent advances in computational protocols addressing intrinsically disordered proteins
S Bhattacharya, X Lin - Biomolecules, 2019 - mdpi.com
Intrinsically disordered proteins (IDP) are abundant in the human genome and have recently
emerged as major therapeutic targets for various diseases. Unlike traditional proteins that …
emerged as major therapeutic targets for various diseases. Unlike traditional proteins that …
Exploring the aggregation free energy landscape of the amyloid-β protein (1–40)
A predictive coarse-grained protein force field [associative memory, water-mediated,
structure, and energy model for molecular dynamics (AWSEM)-MD] is used to study the …
structure, and energy model for molecular dynamics (AWSEM)-MD] is used to study the …
AWSEM-IDP: a coarse-grained force field for intrinsically disordered proteins
The associative memory, water-mediated, structure and energy model (AWSEM) has been
successfully used to study protein folding, binding, and aggregation problems. In this work …
successfully used to study protein folding, binding, and aggregation problems. In this work …
[HTML][HTML] Transient misfolding dominates multidomain protein folding
Neighbouring domains of multidomain proteins with homologous tandem repeats have
divergent sequences, probably as a result of evolutionary pressure to avoid misfolding and …
divergent sequences, probably as a result of evolutionary pressure to avoid misfolding and …
Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape
The timescale for the microscopic dynamics of proteins during conformational transitions is
set by the intrachain diffusion coefficient, D. Despite the central role of protein misfolding and …
set by the intrachain diffusion coefficient, D. Despite the central role of protein misfolding and …
Aggregation landscapes of Huntingtin exon 1 protein fragments and the critical repeat length for the onset of Huntington's disease
M Chen, PG Wolynes - … of the National Academy of Sciences, 2017 - National Acad Sciences
Huntington's disease (HD) is a neurodegenerative disease caused by an abnormal
expansion in the polyglutamine (polyQ) track of the Huntingtin (HTT) protein. The severity of …
expansion in the polyglutamine (polyQ) track of the Huntingtin (HTT) protein. The severity of …
[HTML][HTML] Dimeric interactions and complex formation using direct coevolutionary couplings
We develop a procedure to characterize the association of protein structures into
homodimers using coevolutionary couplings extracted from Direct Coupling Analysis (DCA) …
homodimers using coevolutionary couplings extracted from Direct Coupling Analysis (DCA) …
Sequence-and temperature-dependent properties of unfolded and disordered proteins from atomistic simulations
We use all-atom molecular simulation with explicit solvent to study the properties of selected
intrinsically disordered proteins and unfolded states of foldable proteins, which include …
intrinsically disordered proteins and unfolded states of foldable proteins, which include …
Fighting against amyotrophic lateral sclerosis (ALS) with flavonoids: a computational approach to inhibit superoxide dismutase (SOD1) mutant aggregation
SM Noorbakhsh Varnosfaderani… - Journal of …, 2023 - Taylor & Francis
Protein aggregation is a biological process that occurs when proteins misfold. Misfolding
and aggregation of human superoxide dismutase (hSOD1) cause a neurodegenerative …
and aggregation of human superoxide dismutase (hSOD1) cause a neurodegenerative …