Heterogeneity in protein folding and unfolding reactions
S Bhatia, JB Udgaonkar - Chemical Reviews, 2022 - ACS Publications
Proteins have dynamic structures that undergo chain motions on time scales spanning from
picoseconds to seconds. Resolving the resultant conformational heterogeneity is essential …
picoseconds to seconds. Resolving the resultant conformational heterogeneity is essential …
Scientific novelty beyond the experiment
Practical experiments drive important scientific discoveries in biology, but theory‐based
research studies also contribute novel—sometimes paradigm‐changing—findings. Here, we …
research studies also contribute novel—sometimes paradigm‐changing—findings. Here, we …
Protein folding in vitro and in the cell: From a solitary journey to a team effort
MF Mecha, RB Hutchinson, JH Lee, S Cavagnero - Biophysical chemistry, 2022 - Elsevier
Correct protein folding is essential for the health and function of living organisms. Yet, it is
not well understood how unfolded proteins reach their native state and avoid aggregation …
not well understood how unfolded proteins reach their native state and avoid aggregation …
Molecular free energies, rates, and mechanisms from data-efficient path sampling simulations
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of
complex molecular events. However, these simulations can rarely sample the required time …
complex molecular events. However, these simulations can rarely sample the required time …
Adaptive CVgen: Leveraging reinforcement learning for advanced sampling in protein folding and chemical reactions
Enhanced sampling techniques have traditionally encountered two significant challenges:
identifying suitable reaction coordinates and addressing the exploration–exploitation …
identifying suitable reaction coordinates and addressing the exploration–exploitation …
Unveiling Metastable Ensembles of GRB2 and the Relevance of Interdomain Communication during Folding
The folding process of multidomain proteins is a highly intricate phenomenon involving the
assembly of distinct domains into a functional three-dimensional structure. During this …
assembly of distinct domains into a functional three-dimensional structure. During this …
Structural, kinetic, and thermodynamic aspects of insulin aggregation
Given the significance of protein aggregation in proteinopathies and the development of
therapeutic protein pharmaceuticals, revamped interest in assessing and modelling the …
therapeutic protein pharmaceuticals, revamped interest in assessing and modelling the …
A geometrical framework for thinking about proteins
We present a model, based on symmetry and geometry, for proteins. Using elementary
ideas from mathematics and physics, we derive the geometries of discrete helices and …
ideas from mathematics and physics, we derive the geometries of discrete helices and …
A code within a code: how codons fine-tune protein folding in the cell
AA Komar - Biochemistry (Moscow), 2021 - Springer
The genetic code sets the correspondence between the sequence of a given nucleotide
triplet in an mRNA molecule, called a codon, and the amino acid that is added to the …
triplet in an mRNA molecule, called a codon, and the amino acid that is added to the …
[HTML][HTML] Deep learning-based molecular dynamics simulation for structure-based drug design against SARS-CoV-2
Y Sun, Y Jiao, C Shi, Y Zhang - Computational and structural biotechnology …, 2022 - Elsevier
Abstract Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory
syndrome coronavirus type 2 (SARS-CoV-2), has led to a global pandemic. Deep learning …
syndrome coronavirus type 2 (SARS-CoV-2), has led to a global pandemic. Deep learning …