The SARS-CoV-2 Spike variant D614G favors an open conformational state

RA Mansbach, S Chakraborty, K Nguyen… - Biophysical …, 2021 - cell.com
The COVID-19 global pandemic is an international health emergency. It is caused by the
SARS-CoV-2 virus, which binds with its trimeric Spike protein to the ACE2 receptor in the …

Comparative perturbation-based modeling of the SARS-CoV-2 spike protein binding with host receptor and neutralizing antibodies: Structurally adaptable allosteric …

GM Verkhivker, S Agajanian, DY Oztas, G Gupta - Biochemistry, 2021 - ACS Publications
In this study, we used an integrative computational approach to examine molecular
mechanisms and determine functional signatures underlying the role of functional residues …

Molecular insights into the misfolding and dimerization dynamics of the full-length α-synuclein from atomistic discrete molecular dynamics simulations

Y Zhang, Y Wang, Y Liu, G Wei, F Ding… - ACS chemical …, 2022 - ACS Publications
The misfolding and pathological aggregation of α-synuclein forming insoluble amyloid
deposits is associated with Parkinson's disease, the second most common …

Integrated biophysical modeling of the SARS-CoV-2 spike protein binding and allosteric interactions with antibodies

GM Verkhivker, L Di Paola - The Journal of Physical Chemistry B, 2021 - ACS Publications
Structural and biochemical studies of the severe acute respiratory syndrome (SARS)-CoV-2
spike glycoproteins and complexes with highly potent antibodies have revealed multiple …

Dynamic network modeling of allosteric interactions and communication pathways in the SARS-CoV-2 spike trimer mutants: Differential modulation of conformational …

GM Verkhivker, L Di Paola - The Journal of Physical Chemistry B, 2021 - ACS Publications
The rapidly growing body of structural and biochemical studies of the SARS-CoV-2 spike
glycoprotein has revealed a variety of distinct functional states with radically different …

[HTML][HTML] Efficient preparation and analysis of membrane and membrane protein systems

M Javanainen, H Martinez-Seara - Biochimica et Biophysica Acta (BBA) …, 2016 - Elsevier
Molecular dynamics (MD) simulations have become a highly important technique to
consider lipid membrane systems, and quite often they provide considerable added value to …

Dynamic profiling of binding and allosteric propensities of the SARS-CoV-2 spike protein with different classes of antibodies: mutational and perturbation-based …

G Verkhivker, S Agajanian, D Oztas… - Journal of chemical …, 2021 - ACS Publications
The functional adaptability and conformational plasticity of SARS-CoV-2 spike proteins allow
for the efficient modulation of complex phenotypic responses to the host receptor and …

Substitution of PINK1 Gly411 modulates substrate receptivity and turnover

FC Fiesel, D Fričová, CS Hayes, MA Coban, R Hudec… - Autophagy, 2023 - Taylor & Francis
The ubiquitin (Ub) kinase-ligase pair PINK1-PRKN mediates the degradation of damaged
mitochondria by macroautophagy/autophagy (mitophagy). PINK1 surveils mitochondria and …

Integrin activation by the lipid molecule 25-hydroxycholesterol induces a proinflammatory response

SM Pokharel, NK Shil, JB Gc, ZT Colburn… - Nature …, 2019 - nature.com
Integrins are components of cell-matrix adhesions, and function as scaffolds for various
signal transduction pathways. So far no lipid ligand for integrin has been reported. Here we …

Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations

TD Romo, N Leioatts… - Journal of computational …, 2014 - Wiley Online Library
LOOS (Lightweight Object Oriented Structure‐analysis) is a C++ library designed to facilitate
making novel tools for analyzing molecular dynamics simulations by abstracting out the …