Na/K-ATPase Glutathionylation: in silico Modeling of Reaction Mechanisms

Na,K-ATPase is a redox-sensitive transmembrane protein. Understanding the mechanisms of Na,K-ATPase redox regulation can help to prevent impairment of Na,K-ATPase functioning under pathological conditions and reduce damage and death of cells. One of the basic mechanisms to protect Na,K-ATPase against stress oxidation is the glutathionylation reaction that is aimed to reduce several principal oxidized cysteines (244, 458, and 459) that are involved in Na,K-ATPase action regulation. In this study, we carried out in silico modeling to evaluate glutathione affinity on various stages of Na,K-ATPase action cycle, as well as to discover a reaction mechanism of disulfide bond formation between reduced glutathione and oxidized cysteine. To achieve this goal both glutathione and Na,K-ATPase conformer sampling was applied, the reliability of the protein-ligand complexes was examined by MD assay, the reaction mechanism was studied using semi-empirical PM6-D3H4 approach that could have a deal with large organic systems optimization.

[1]  Varan Govind,et al.  Glutathione Conformations and Its Implications for in vivo Magnetic Resonance Spectroscopy , 2017, Journal of Alzheimer's disease : JAD.

[2]  Eugene Stepanov,et al.  Structural Transition States Explored With Minimalist Coarse Grained Models: Applications to Calmodulin , 2019, Front. Mol. Biosci..

[3]  Federico D. Sacerdoti,et al.  Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters , 2006, ACM/IEEE SC 2006 Conference (SC'06).

[4]  A. Malmivaara,et al.  Total hip replacement in patients eighty years of age and older. , 2008, The Journal of bone and joint surgery. American volume.

[5]  Jindřich Fanfrlík,et al.  Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes. , 2009, Journal of chemical theory and computation.

[6]  Eugene Stepanov,et al.  Modeling conformational redox‐switch modulation of human succinic semialdehyde dehydrogenase , 2015, Proteins.

[7]  Robert Abel,et al.  OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. , 2019, Journal of chemical theory and computation.

[8]  Frank Neese,et al.  Software update: the ORCA program system, version 4.0 , 2018 .

[9]  Vladimir A Mitkevich,et al.  Na,K-ATPase α-subunit conformation determines glutathionylation efficiency. , 2019, Biochemical and biophysical research communications.

[10]  Asya Makhro,et al.  S-Glutathionylation of the Na,K-ATPase Catalytic α Subunit Is a Determinant of the Enzyme Redox Sensitivity* , 2012, The Journal of Biological Chemistry.

[11]  Z. Deng,et al.  Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. , 2004, Journal of medicinal chemistry.

[12]  C. Bannwarth,et al.  B97-3c: A revised low-cost variant of the B97-D density functional method. , 2018, The Journal of chemical physics.

[13]  Anna Bogdanova,et al.  Cysteine residues 244 and 458–459 within the catalytic subunit of Na,K-ATPase control the enzyme's hydrolytic and signaling function under hypoxic conditions , 2017, Redox biology.

[14]  Matthew P. Repasky,et al.  Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. , 2006, Journal of medicinal chemistry.