M. Zacharias

APP substrate ectodomain defines A beta length by restraining gamma-secretase processivity and facilitating product release

The paper investigates how the APP ectodomain regulates gamma-secretase processivity and A beta peptide length, identifying it as a target for Alzheimer's disease therapies.

Unravelling ATP processing by the AAA+ protein p97 at the atomic level

This study uses cryo-EM, NMR, and MD simulations to reveal the atomic-level mechanism of ATP processing by p97, identifying a metastable ADP.Pi state and its role in coordinating subunit actions.

Intra-membrane client recognition potentiates the chaperone functions of Calnexin

This study shows that Calnexin uses its transmembrane domain to recognize and bind misfolded membrane proteins, enhancing its chaperone functions in the ER.

Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis

This study shows that the lipid bilayer stabilizes the active site geometry of the intramembrane protease PSH, enhancing its catalytic activity compared to micelles.

Altered fibrin clot structure contributes to thrombosis risk in severe COVID-19

The paper shows that altered fibrin clot structure in severe COVID-19 patients contributes to thrombosis risk by forming compact, fibrinolysis-resistant clots.

Dissociation of β2m from MHC Class I Triggers Formation of Noncovalent, Transient Heavy Chain Dimers

This study investigates the formation of non-covalent MHC-I heavy chain dimers after dissociation of β2m and peptide, revealing a dimerization interface mediated by the 3 domain.

Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS

The paper characterizes the conformational ensemble of CALX-CBD12 in the Apo state using MD simulations, NMR, and SAXS, showing preference for closed conformations and Ca2+-induced extension.

Molecular and spectroscopic characterization of green and red cyanine fluorophores from the Alexa Fluor and AF series

The paper characterizes the molecular structures and spectroscopic properties of Alexa Fluor and AF series dyes using spectroscopy, mass spectrometry, and molecular dynamics simulations.

Evolution of structural dynamics in bilobed proteins

The paper investigates how structural dynamics in bilobed proteins evolve, showing that modifications to the structural core enable functional diversification through altered interdomain interactions and substrate specificity.

Base pairing and stacking contributions to double stranded DNA formation

The paper re-analyzes dsDNA stability contributions, concluding that base stacking contributes to stability even in single-stranded DNA, while base pairing drives dsDNA formation, with hydrogen bond contributions estimated at -0.72 kcal/mol.

Phosphorylation of Ser111 in Rab8a modulates Rabin8 dependent activation by perturbation of side chain interaction networks

This study shows that phosphorylation of Ser111 in Rab8a reduces its activation by Rabin8 through perturbation of side chain interactions.

Uncovering the Binding Mode of γ-Secretase Inhibitors

The paper generates a structural model of γ-secretase bound to a transition state inhibitor, showing good agreement with experimental data and explaining the reduced affinity of an epimer.

Structural Modeling of Gamma-Secretase Aβn ComplexFormation and Substrate Processing

The paper generates structural models of GSEC-APP substrate binding and processing using MD simulations, identifying a likely binding mode and analyzing processing steps.