Bridging the Bridging Imidazolate in the Bimetallic Center of the Cu/Zn SOD1 and ALS

Abstract

Metallation status of human Cu/Zn superoxide dismutase 1 (SOD1) plays a pivotal role in the pathogenesis of amyotrophic lateral sclerosis (ALS). All of the amino acids found in the bimetallic center have been associated with ALS except for two positions. H63 which forms the bridging imidazolate ion in the bimetallic center and K136 which is not directly involved in coordination but located in the bimetallic center were not reported to be mutated in any of the identified ALS cases. In this study, we investigated the structure and flexibility of five SOD1 variants by using classical molecular dynamics simulations. These variants include three substitutions on the non-ALS-linked positions; H63A, H63R, K136A and ALS-linked positions; G37R, H46R/H48D. We have generated four systems for each variant differing in metallation and presence of the intramolecular disulfide bond. Overall, a total of 24 different dimers including the wild-type were generated and simulated at two temperatures, 298 and 400 K. We have monitored backbone mobility, fluctuations and compactness of the dimer structures to assess whether the hypothetical mutations would behave similar to the ALS-linked variants. Results showed that particularly two mutants, H63R and K136A, drastically affected the dimer dynamics by increasing the fluctuations of the metal binding loops compared with the control mutations. Further, these variants resulted in demetallation of the dimers, highlighting probable ALS toxicity that could be elicited by the SOD1 variants of H63R and K136A. Overall, this study bridges two putative SOD1 positions in the metallic center and ALS, underlining the potential use of atomistic simulations for studying disease variants.

Protein‐based metal bio‐cleaner for detoxification of wastewater

“…Hence, the presence of specific metals in a solution or biological system can be detected by the metal‐induced changes in the fluorescence of fluorescent protein‐based biosensors. Earlier, fluorescent protein‐based biosensors were reported with static quenching, energy transfer between chromophore and colored metal ion and altered protein structure 9,10,19‐25 . In this study, the confirmation of protein with novel chemical amine moiety allowed us to evaluate the fluorescent protein‐based reagent‐less metal sensing system.…”

“…Earlier, fluorescent protein-based biosensors were reported with static quenching, energy transfer between chromophore and colored metal ion and altered protein structure. 9,10,[19][20][21][22][23][24][25] In this study, the confirmation of protein with novel chemical amine moiety allowed us to evaluate the fluorescent protein-based reagent-less metal sensing system. The metal sensing ability of the protein was determined by analyzing the change in fluorescence of amGFP upon treatment with various metal ions.…”

“…Synthetic NCAAs offer non‐natural potential with new functional chemistry for proteins with enhanced spectral properties. Frequently, two experimental approaches, namely reassignment of sense (residue‐specific incorporation) and nonsense suppression (site‐specific incorporation), are used for in vivo incorporation of NCAAs into recombinant proteins 17‐25 . In the work reported here, we aimed to introduce donor–acceptor non‐natural chemistry in the GFP chromophore, offering significant Stokes shifts to GFP 11,26 .…”

“…Frequently, two experimental approaches, namely reassignment of sense (residue-specific incorporation) and nonsense suppression (site-specific incorporation), are used for in vivo incorporation of NCAAs into recombinant proteins. [17][18][19][20][21][22][23][24][25] In the work reported here, we aimed to introduce donor-acceptor non-natural chemistry in the GFP chromophore, offering significant Stokes shifts to GFP. 11,26 We aimed to incorporate aminotyrosine as an electron-donating group (amine group) into the GFP chromophore for the development of an efficient red-shifted fluorescent protein-based biosensor that can also act as a bio-cleaner for the removal of Cu 2+ ions from environmental samples.…”

Coordination chemistry of mitochondrial copper metalloenzymes: exploring implications for copper dyshomeostasis in cell death

“…Zn(II) participates in a distorted tetrahedral coordination with His63, His71, His80, and Asp83 throughout the entire catalytic cycle for SOD1 ( 52 , 53 ). Notably, such bimetallic coordination is connected through the bridging imidazolate ring from His63, emphasizing its role in the structural flexibility of SOD1 ( 54 ). The oxidation of O 2 •− into O 2 is attributed to the reduction of Cu(II) to Cu(I), where Cu(I) can be, in turn, bound to three His residues, i.e.…”