Recent developments in free energy calculations for drug discovery

E King, E Aitchison, H Li, R Luo - Frontiers in Molecular Biosciences, 2021 - frontiersin.org
The grand challenge in structure-based drug design is achieving accurate prediction of
binding free energies. Molecular dynamics (MD) simulations enable modeling of …

Parkinson's: a disease of aberrant vesicle trafficking

PK Singh, MMK Muqit - Annual review of cell and …, 2020 - annualreviews.org
Parkinson's disease (PD) is a leading cause of neurodegeneration that is defined by the
selective loss of dopaminergic neurons and the accumulation of protein aggregates called …

PINK1-dependent phosphorylation of Serine111 within the SF3 motif of Rab GTPases impairs effector interactions and LRRK2-mediated phosphorylation at …

S Vieweg, K Mulholland, B Bräuning… - Biochemical …, 2020 - portlandpress.com
Loss of function mutations in the PTEN-induced kinase 1 (PINK1) kinase are causal for
autosomal recessive Parkinson's disease (PD) whilst gain of function mutations in the …

Dysfunction of RAB39B‐mediated vesicular trafficking in Lewy Body diseases

DJ Koss, S Campesan, F Giorgini… - Movement …, 2021 - Wiley Online Library
Intracellular vesicular trafficking is essential for neuronal development, function, and
homeostasis and serves to process, direct, and sort proteins, lipids, and other cargo …

A phosphosite mutant approach on LRRK2 links phosphorylation and dephosphorylation to protective and deleterious markers, respectively

A Marchand, A Sarchione, PS Athanasopoulos… - Cells, 2022 - mdpi.com
The Leucine Rich Repeat Kinase 2 (LRRK2) gene is a major genetic determinant of
Parkinson's disease (PD), encoding a homonymous multi-domain protein with two catalytic …

Dual arginine recognition of LRRK2 phosphorylated Rab GTPases

D Waschbüsch, E Purlyte, AR Khan - Biophysical journal, 2021 - cell.com
Parkinson's-disease-associated LRRK2 is a multidomain Ser/Thr kinase that phosphorylates
a subset of Rab GTPases to control their effector functions. Rab GTPases are the prime …

Endogenous LRRK2 and PINK1 function in a convergent neuroprotective ciliogenesis pathway in the brain

E Bagnoli, YE Lin, S Burel, E Jaimon, O Antico… - bioRxiv, 2024 - biorxiv.org
Mutations in LRRK2 and PINK1 are associated with familial Parkinson's disease (PD).
LRRK2 phosphorylates Rab GTPases within the Switch II domain whilst PINK1 directly …

Modeling of Protein Assemblies Through Global Docking and Accelerated Molecular Dynamics Simulation

D Pourjafar-Dehkordi - 2022 - mediatum.ub.tum.de
Understanding the structure of protein assemblies plays a pivotal role in discovering their
function. The focus of this work is on the application of MD simulations in the structural …

Exploring phenotypes of LRRK2 phosphorylation using a phosphosite mutation approach

A Marchand - 2021 - theses.hal.science
Parkinson's disease (PD) is the most common neurodegenerative motor disease. Mutations
in the leucine rich repeat kinase 2 (LRRK2) gene are linked to autosomal dominant …

Influence of a Ser111‐phosphorylation on Rab1b GTPase conformational dynamics studied by advanced sampling simulations

D Pourjafar‐Dehkordi… - … : Structure, Function, and …, 2021 - Wiley Online Library
Rab GTPases constitute the largest branch of the Ras protein superfamily that regulate intra‐
cellular membrane trafficking. Their signaling activity is mediated by the transition between …