PMID:23029461

Citation	Lee, Y, Kim, S, Lazar, P, Moon, JC, Hwang, S, Thangapandian, S, Shon, Y, Lee, KO, Lee, SY and Lee, KW (2012) Comparative molecular modeling study of Arabidopsis NADPH-dependent thioredoxin reductase and its hybrid protein. PLoS ONE 7:e46279
Abstract	2-Cys peroxiredoxins (Prxs) play important roles in the protection of chloroplast proteins from oxidative damage. Arabidopsis NADPH-dependent thioredoxin reductase isotype C (AtNTRC) was identified as efficient electron donor for chloroplastic 2-Cys Prx-A. There are three isotypes (A, B, and C) of thioredoxin reductase (TrxR) in Arabidopsis. AtNTRA contains only TrxR domain, but AtNTRC consists of N-terminal TrxR and C-terminal thioredoxin (Trx) domains. AtNTRC has various oligomer structures, and Trx domain is important for chaperone activity. Our previous experimental study has reported that the hybrid protein (AtNTRA-(Trx-D)), which was a fusion of AtNTRA and Trx domain from AtNTRC, has formed variety of structures and shown strong chaperone activity. But, electron transfer mechanism was not detected at all. To find out the reason of this problem with structural basis, we performed two different molecular dynamics (MD) simulations on AtNTRC and AtNTRA-(Trx-D) proteins with same cofactors such as NADPH and flavin adenine dinucleotide (FAD) for 50 ns. Structural difference has found from superimposition of two structures that were taken relatively close to average structure. The main reason that AtNTRA-(Trx-D) cannot transfer the electron from TrxR domain to Trx domain is due to the difference of key catalytic residues in active site. The long distance between TrxR C153 and disulfide bond of Trx C387-C390 has been observed in AtNTRA-(Trx-D) because of following reasons: i) unstable and unfavorable interaction of the linker region, ii) shifted Trx domain, and iii) different or weak interface interaction of Trx domains. This study is one of the good examples for understanding the relationship between structure formation and reaction activity in hybrid protein. In addition, this study would be helpful for further study on the mechanism of electron transfer reaction in NADPH-dependent thioredoxin reductase proteins.
Links	PubMed PMC3459921 Online version:10.1371/journal.pone.0046279
Keywords	Amino Acid Sequence; Arabidopsis/chemistry; Arabidopsis/enzymology; Arabidopsis Proteins/chemistry; Arabidopsis Proteins/genetics; Arabidopsis Proteins/metabolism; Catalytic Domain; Cysteine/chemistry; Cysteine/metabolism; Electron Transport; Electrons; Flavin-Adenine Dinucleotide/chemistry; Flavin-Adenine Dinucleotide/metabolism; Isoenzymes/chemistry; Isoenzymes/genetics; Isoenzymes/metabolism; Molecular Chaperones/chemistry; Molecular Chaperones/genetics; Molecular Chaperones/metabolism; Molecular Dynamics Simulation; Molecular Sequence Data; NADP/chemistry; NADP/metabolism; Protein Structure, Tertiary; Recombinant Fusion Proteins/chemistry; Recombinant Fusion Proteins/genetics; Recombinant Fusion Proteins/metabolism; Structure-Activity Relationship; Thioredoxin-Disulfide Reductase/chemistry; Thioredoxin-Disulfide Reductase/genetics; Thioredoxin-Disulfide Reductase/metabolism
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
ARATH:TRXB2		GO:0004791: thioredoxin-disulfide reductase activity	ECO:0000247:	UniProtKB:P0A9P4	F		Fig. 1D	complete CACAO 7396
ARATH:TRXB2	enables	GO:0004791: thioredoxin-disulfide reductase activity	ECO:0000247: sequence alignment evidence used in manual assertion	UniProtKB:P0A9P4	F		Seeded From UniProt	complete

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