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Anisotropy of fluctuation dynamics of proteins with an elastic network model.
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.
Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells
Red redistribution of cardiolipin serves as an ‘eat-me’ signal for the elimination of damaged mitochondria from neuronal cells as well as the engulfment of mitochondria by the autophagic system.
Gaussian Dynamics of Folded Proteins
Vibrational dynamics of folded proteins is studied using a Gaussian model in which the protein is viewed as a network, residues representing the junctions, and the connectivity being established by a…
Coarse-grained normal mode analysis in structural biology.
ProDy: Protein Dynamics Inferred from Theory and Experiments
Summary: We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of…
Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.
The main structural difference between proteins and other chain molecules is that, under physiological conditions, proteins sample a significantly narrower distribution of conformations compared to disordered polymers, which may facilitate the diffusion of oxygen into the heme cavity of myoglobin or the permeation of ions across selectivity filters in ion channels.
Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis.
It is discovered that ferroptosis involves a highly organized oxygenation center, wherein oxidation in endoplasmic-reticulum-associated compartments occurs on only one class of phospholipids (phosphatidylethanolamines (PEs) and is specific toward two fatty acyls-arachidonoyl (AA) and AdA (AdA).
Global dynamics of proteins: bridging between structure and function.
Observed correlations between functional changes in structures observed in experiments and the global motions predicted by coarse-grained analyses suggest that computational methods may be advantageously employed for assessingfunctional changes in structure and allosteric mechanisms intrinsically favored by the native fold.
Bistability in apoptosis: roles of bax, bcl-2, and mitochondrial permeability transition pores.
This study supports contention, based on mathematical modeling, that cooperativity in apoptosome formation is critically important for determining the healthy responses to apoptotic stimuli, and helps define the roles of Bax, Bcl-2, and MPTP vis-à-vis apoptosomes formation.