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

Abstract
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.

 

New papers published

Yersinia enterocolitica Provides the Link between Thyroid-Stimulating Antibodies and Their Germline Counterparts in Graves’ Disease.

Hargreaves CE, Grasso M, Hampe CS, Stenkova A, Atkinson S, Joshua GW, Wren BW, Buckle AM, Dunn-Walters D, Banga JP.

Molecular determinants of the substrate specificity of the complement initiating protease, C1r.

Wijeyewickrema LC, Yongqing T, Tran TP, Thompson PE, Viljoen JE, Coetzer TH, Duncan RC, Kass I, Buckle AM, Pike RN.

J Biol Chem. 2013 Apr 15. [Epub ahead of print]

Mechanism-based selection of a potent kallikrein-related peptidase 7 inhibitor from a versatile library based on the sunflower trypsin inhibitor SFTI-1.

de Veer SJ, Ukolova SS, Munro CA, Swedberg JE, Buckle AM, Harris JM.

Biopolymers. 2013 Mar 11. doi: 10.1002/peps.22231. [Epub ahead of print]

Structural characterization of the mechanism through which human glutamic acid decarboxylase auto-activates.

Langendorf CG, Tuck KL, Key TL, Fenalti G, Pike RN, Rosado CJ, Wong AS, Buckle AM, Law RH, Whisstock JC.

Biosci Rep. 2013 Jan 11;33(1):137-44. doi: 10.1042/BSR20120111.

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 MA.et 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.

2 New Papers

The Rate of PolyQ-Mediated Aggregation Is Dramatically Affected by the Number and Location of Surrounding Domains

Amy L. Robertson, Mark A. Bate, Ashley M. Buckle, Stephen P. Bottomley

J Mol Biol. 2011 Nov 4;413(4):879-87. Epub 2011 Sep 16.

Computational methods for studying serpin conformational change and structural plasticity.

Kass I, Reboul CF, Buckle AM.

Methods Enzymol. 2011;501:295-323.

Two new papers published

MrGrid:

Schmidberger JS,  Bate MA, Reboul CF, Androulakis SG, Phan JMN, Whisstock JC, Goscinski WJ, Abramson A, and Buckle AM (2010) MrGrid: A Portable Grid Based Molecular Replacement Pipeline. PLoS One. Apr 6;5(4):e10049. PubMed link

Apple University Consortium (AUC) in Australia wrote an article on our grid computing in their newsletter Wheels of the Mind (PDF)

MUSTANG-MR Server:

Konagurthu AS, Reboul CF, Schmidberger JS,  Irving, JA, Lesk AM, Stuckey PJ, Whisstock JC, and Buckle AM (2010) MUSTANG-MR Structural Sieving Server: Applications in Protein Structural Analysis and Crystallography. PLoS One. Apr 6;5(4):e10048.  PubMed link

Four new papers published:

Swedberg JE, Nigon LV, Reid JC, de Veer SJ, Walpole CM, Stephens CR, Walsh TP, Takayama TK, Hooper JD, Clements JA, Buckle AM & Harris, JM.  (2009) Substrate-guided design of a potent and selective kallikrein-related peptidase inhibitor for kallikrein 4.  Chemistry & Biology, 16, 633-43. PubMed Link

Fischer K,Langendorf  CG, Irving  JA, Reynolds S, Willis C, Beckham S, Law RHP, Yang S, Bashtannyk-Puhalovich TA, McGowan S, Whisstock JC, PikeRN, KempDJ, and Buckle AM  (2009) Structural Mechanisms of Inactivation in Scabies Mite Serine Protease Paralogues. J. Mol. Biol. 390(4):635-45. PubMed Link

Fenalti G and Buckle AM (2010) Structural Biology of the GAD Autoantigen. Autoimmunity Reviews 9(3):148-52. Epub 2009 May 22. PubMed Link

Arafat Y, Fenalti G, Whisstock JC, Mackay IR, Garcia de la Banda M, Rowley MJ and Buckle AM (2009) Structural Determinants of GAD Antigenicity. Molecular Immunology, 47(2-3):493-505. PubMed Link