Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
Visualization of reaction route map and dynamical trajectory in reduced dimension
In the quantum chemical approach, chemical reaction mechanisms are investigated based
on a potential energy surface (PES). Automated reaction path search methods enable us to …
on a potential energy surface (PES). Automated reaction path search methods enable us to …
Salt-induced transitions in the conformational ensembles of intrinsically disordered proteins
Salts modulate the behavior of intrinsically disordered proteins (IDPs) and influence the
formation of membraneless organelles through liquid–liquid phase separation (LLPS). In …
formation of membraneless organelles through liquid–liquid phase separation (LLPS). In …
Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop
Molecular dynamics (MD) simulations have become increasingly powerful and can now
describe the folding/unfolding of small biomolecules in atomic detail. However, a major …
describe the folding/unfolding of small biomolecules in atomic detail. However, a major …
Lighting up Nobel Prize-winning studies with protein intrinsic disorder
L Piersimoni, M Abd el Malek, T Bhatia… - Cellular and Molecular …, 2022 - Springer
Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology
are becoming increasingly recognized in biology, biochemistry, molecular biology and …
are becoming increasingly recognized in biology, biochemistry, molecular biology and …
Intrinsically disordered proteins: ensembles at the limits of Anfinsen's dogma
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they
are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as …
are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as …
Examining the ensembles of amyloid-β monomer variants and their propensities to form fibers using an energy landscape visualization method
MN Sanches, K Knapp, AB Oliveira Jr… - The Journal of …, 2021 - ACS Publications
The amyloid-β (Aβ) monomer, an intrinsically disordered peptide, is produced by the
cleavage of the amyloid precursor protein, leading to Aβ-40 and Aβ-42 as major products …
cleavage of the amyloid precursor protein, leading to Aβ-40 and Aβ-42 as major products …
Probing Mastoparan-like Antimicrobial Peptides Interaction with Model Membrane Through Energy Landscape Analysis
Antimicrobial Peptides (AMPs) have emerged as promising alternatives to conventional
antibiotics due to their capacity to disrupt the lipid packing of bacterial cell membranes. This …
antibiotics due to their capacity to disrupt the lipid packing of bacterial cell membranes. This …
Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective
Novel coronavirus (SARS-CoV-2) enters its host cell through a surface spike protein. The
viral spike protein has undergone several modifications/mutations at the genomic level …
viral spike protein has undergone several modifications/mutations at the genomic level …
Exploring the folding landscape of leptin: Insights into threading pathways
The discovery of new protein topologies with entanglements and loop-crossings have
shown the impact of local amino acid arrangement and global three-dimensional structures …
shown the impact of local amino acid arrangement and global three-dimensional structures …