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Molecular dynamics investigation of a redox switch in the anti‐HIV protein SAMHD1
Author(s) -
Patra Kajwal Kumar,
Bhattacharya Akash,
Bhattacharya Swati
Publication year - 2019
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25701
Subject(s) - samhd1 , tetramer , chemistry , cysteine , biophysics , molecular dynamics , redox , allosteric regulation , glutathione , monomer , stereochemistry , biochemistry , enzyme , biology , computational chemistry , reverse transcriptase , rna , organic chemistry , gene , polymer
Abstract HIV‐1 is restricted in macrophages and certain quiescent myeloid cells due to a “Scorched Earth” dNTP starvation strategy attributed to the sterile alpha motif and HD domain protein—SAMHD1. Active SAMHD1 tetramers are assembled by GTP‐Mg+2‐dNTP cross bridges and cleave the triphosphate groups of dNTPs at a K m of ~10 μM, which is consistent with dNTP concentrations in cycling cells, but far higher than the equivalent concentration in quiescent cells. Given the substantial disparity between the dNTP concentrations required to activate SAMHD1 tetramers (~10 μM) and the dNTP concentrations in noncycling cells (~10 nM), the possibility of alternate enzymatically active forms of SAMHD1, including monomers remains open. In particular, the possibility of redox regulation of such monomers is also an open question. There have been experimental studies on the regulation of SAMHD1 by Glutathione driven redox reactions recently. Therefore, in this work, we have performed all‐atom molecular dynamics simulations to study the dynamics of monomeric SAMHD1 constructs in the context of the three redox‐susceptible Cysteine residues and compared them to monomers assembled within a tetramer. Our results indicate that assembly into a tetramer causes ordering of the catalytic core and increased solvent accessibility of the Catalytic Site. We have also found that glutathionylation of surface exposed C522 causes long range allosteric disruptions extending into the protein core. Finally, we see evidence suggesting a transient interaction between C522 and C341. Such a disulfide linkage has been hypothesized by experimental models, but has never been observed in crystal structures before.