GAD65 conformational dynamics paper published in PNAS

Cofactor-dependent conformational heterogeneity of GAD65 and its role in autoimmunity and neurotransmitter homeostasis

Kass et al, PNAS, Early online edition June 9th, 2014

See also Monash Media releases:

‘Jekyll and Hyde’ protein linked to type 1 diabetes

The autoimmune cost of shape-shifting brain protein 

Open and closed dimers of GAD65 and the mechanism of dimer opening in holo → apo conversion

The human neuroendocrine enzyme glutamate decarboxylase (GAD) catalyses the synthesis of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) using pyridoxal 5′-phosphate as a cofactor. GAD exists as two isoforms named according to their respective molecular weights: GAD65 and GAD67. Although cytosolic GAD67 is typically saturated with the cofactor (holoGAD67) and constitutively active to produce basal levels of GABA, the membrane-associated GAD65 exists mainly as the inactive apo form. GAD65, but not GAD67, is a prevalent autoantigen, with autoantibodies to GAD65 being detected at high frequency in patients with autoimmune (type 1) diabetes and certain other autoimmune disorders. The significance of GAD65 autoinactivation into the apo form for regulation of neurotransmitter levels and autoantibody reactivity is not understood. We have used computational and experimental approaches to decipher the nature of the holo → apo conversion in GAD65 and thus, its mechanism of autoinactivation. Molecular dynamics simulations of GAD65 reveal coupling between the C-terminal domain, catalytic loop, and pyridoxal 5′-phosphate–binding domain that drives structural rearrangement, dimer opening, and autoinactivation, consistent with limited proteolysis fragmentation patterns. Together with small-angle X-ray scattering and fluorescence spectroscopy data, our findings are consistent with apoGAD65 existing as an ensemble of conformations. Antibody-binding kinetics suggest a mechanism of mutually induced conformational changes, implicating the flexibility of apoGAD65 in its autoantigenicity. Although conformational diversity may provide a mechanism for cofactor-controlled regulation of neurotransmitter biosynthesis, it may also come at a cost of insufficient development of immune self-tolerance that favors the production of GAD65 autoantibodies.


6 New MD papers published

Peptide dynamics in the MHC groove


Bosco K Ho, David Perahia, Ashley M Buckle (2012)  Hybrid approaches to molecular simulation.  Current Opinion in Structural Biology, Volume 22, Issue 3, Pages 386-393.  


Reboul CF, Meyer GR, Porebski BT, Borg NA, Buckle AM (2012) Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex. PLoS Comput Biol 8(3): e1002404. doi:10.1371/journal.pcbi.1002404


Reboul CF, Porebski BT, Griffin MDW, Dobson RCJ, Perugini MA, et al. (2012) Structural and Dynamic Requirements for Optimal Activity of the Essential Bacterial Enzyme Dihydrodipicolinate Synthase. PLoS Comput Biol 8(6): e1002537. doi:10.1371/journal.pcbi.1002537


Kass, Knaupp, Bottomley, Buckle. (2012). Conformational properties of the disease-causing Z variant of alpha1 antitrypsin revealed by molecular dynamics simulations.    Biophys. J.102(12):2856-65.


Atkinson SC, Dogovski C, Downton MT, Pearce FG, Reboul CF, Buckle AM, Gerrard JA, Dobson RC, Wagner J, Perugini al. (2012) Crystal, Solution andIn silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine. PLoS ONE 7(6): e38318. doi:10.1371/journal.pone.0038318


Kass I, Reboul CF, Buckle AM. (2012) Computational methods for studying serpin conformational change and structural plasticity. Methods Enzymol. 2011;501:295-323.

Orchard is planted!

The Orchard is planted!

While most of the world was still recovering from the Easter break, we were in bright & early on the Wednesday after Easter to begin setting up the Orchard cluster.

The Orchard cluster is now racked, stacked & cabled… next stage power & networking! Be sure to check out the Orchard page for the full details.

Monash University Press release can be found here