Crystal structure of the C107S/C112S mutant of yeast nuclear 2‐Cys peroxiredoxin

Choi, Joon‐Hwan; Choi, Suji; Chon, Jae Kyung; Choi, Jungwon; Cha, Mee‐Kyung; Kim, Il-Han; Shin, Wonjae

doi:10.1002/prot.20704

Cited by 16 publications

(10 citation statements)

References 24 publications

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“…All peroxidate C P residues in Prxs are strictly conserved, but resolving C R residues are not, and are situated at a number of positions according to the types of the atypical 2-Cys subfamilies. 26 The known resolving C R residues are boxed in red. The top two-thirds of helix α3 of XcBCP is locally unfolded after oxidation and their sequences are annotated as a blue rectangle, with the four totally invisible K78-D81 residues boxed in blue.…”

Section: Resultsmentioning

confidence: 99%

“…[1][2][3]10 The tertiary structures of several 1-Cys 11,12 and typical 2-Cys Prxs [13][14][15][16][17][18][19][20] have been determined, and the oligomerization states of typical 2-Cys Prxs were found to be correlated with their activity. 21,22 However, atypical 2-Cys Prxs, [23][24][25][26][27] including the bacterioferritin comigratory protein (BCP), are less well characterized, although some of their biological activities have been illustrated. [28][29][30][31] Here, we report the crystal structure of XcBCP, which is a novel member of the atypical 2-Cys Prxs from the plant pathogen Xanthomonas campestris, in three different states.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Insights into the Alkyl Peroxide Reduction Pathway of Xanthomonas campestris Bacterioferritin Comigratory Protein from the Trapped Intermediate–Ligand Complex Structures

Liao

Yang

Chin

et al. 2009

Journal of Molecular Biology

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Insights into the Alkyl Peroxide Reduction Pathway of Xanthomonas campestris Bacterioferritin Comigratory Protein from the Trapped Intermediate–Ligand Complex Structures

Liao

Yang

Chin

et al. 2009

Journal of Molecular Biology

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“…Peroxiredoxins exhibit a wide variety of oligomeric states, ranging from monomeric (YPrx, [19]), to large decameric or dodecameric assemblies like TryP [20], AhpC [21] and other typical 2-Cys peroxiredoxins, including PrxIII from bovine mitochondria, which forms two concatenated dodecamers [22]. These assemblies are often dependent on redox state, dissociating into homodimers upon oxidation [23].…”

Section: Resultsmentioning

confidence: 99%

Structural Characterisation of Tpx from Yersinia pseudotuberculosis Reveals Insights into the Binding of Salicylidene Acylhydrazide Compounds

et al. 2012

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Thiol peroxidase, Tpx, has been shown to be a target protein of the salicylidene acylhydrazide class of antivirulence compounds. In this study we present the crystal structures of Tpx from Y. pseudotuberculosis ( yp Tpx) in the oxidised and reduced states, together with the structure of the C61S mutant. The structures solved are consistent with previously solved atypical 2-Cys thiol peroxidases, including that for “forced” reduced states using the C61S mutant. In addition, by investigating the solution structure of yp Tpx using small angle X-ray scattering (SAXS), we have confirmed that reduced state yp Tpx in solution is a homodimer. The solution structure also reveals flexibility around the dimer interface. Notably, the conformational changes observed between the redox states at the catalytic triad and at the dimer interface have implications for substrate and inhibitor binding. The structural data were used to model the binding of two salicylidene acylhydrazide compounds to the oxidised structure of yp Tpx. Overall, the study provides insights into the binding of the salicylidene acylhydrazides to yp Tpx, aiding our long-term strategy to understand the mode of action of this class of compounds.

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“…Timings for the OMx methods are also representative for MNDO-type methods, because the most time-consuming parts of the calculations are the same in both cases. Consequently, similar wall clock times are obtained: for example, one SCF (self-consistent field) iteration in MNDO, AM1, PM3, OM1, OM2, and OM3 calculations on a cluster of 1000 water molecules takes 80,84,89,73,87, and 83 seconds, respectively, on a single Intel Xeon X5670 CPU core [39]. Hence, it is sufficient to consider only OM3 in the following.…”

Section: Computational Bottlenecksmentioning

confidence: 98%

“…We have selected a set of eight proteins that are denoted as P x (x being the number of residues) and listed in Table 11.1, for the purpose of profiling OM3 calculations in a systematic manner [68][69][70][71][72][73][74][75]. Timings for the OMx methods are also representative for MNDO-type methods, because the most time-consuming parts of the calculations are the same in both cases.…”

Section: Computational Bottlenecksmentioning

confidence: 99%

Semiempirical Quantum Chemistry

Koslowski

Thiel

2016

Electronic Structure Calculations on Graphics Processing Units

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In this chapter, we demonstrate how graphics processing units (GPUs) can be used to accelerate large-scale semiempirical quantum-chemical calculations on hybrid CPU-GPU platforms. We examine the computational bottlenecks using a series of calculations on eight proteins with up to 3558 atoms and outline how relevant operations are parallelized and ported to GPUs, making use of multiple devices where possible. Significant speedups are achieved that enable simulations on large systems with thousands of atoms. As an example we present results for geometry optimizations of three representative proteins with α-helix, β-sheet, and random coil structures using several common semiempirical Hamiltonians. IntroductionSemiempirical quantum chemical methods are cost-effective tools for chemists to study the structure, stability, and spectroscopy of molecules as well as chemical reactions [1] (see also Chapter 3). They are based on the Hartree-Fock method commonly used in ab initio molecular orbital (MO) theory [2]. The different semiempirical models simplify the Hartree-Fock procedure by introducing distinct approximations to the Hamiltonian, neglecting many integrals to speed up computations by several orders of magnitude [3]. The remaining integrals are modeled using empirical functions with adjustable parameters that are calibrated against a large number of accurate experimental or high-level theoretical reference data to make semiempirical methods as reliable and general as possible. These features make semiempirical models well suited to many research areas in chemistry, and enabled a large number of semiempirical applications already in the 1970s and 1980s. Since the 1990s, density functional theory (DFT) has become the major workhorse in computational chemistry [4]. However, considering that semiempirical methods are ∼1000× faster than standard DFT approaches [5], they are still valuable computational tools nowadays, for example, for screening large numbers of drug

show abstract

Crystal structure of the C107S/C112S mutant of yeast nuclear 2‐Cys peroxiredoxin

Cited by 16 publications

References 24 publications

Insights into the Alkyl Peroxide Reduction Pathway of Xanthomonas campestris Bacterioferritin Comigratory Protein from the Trapped Intermediate–Ligand Complex Structures

Insights into the Alkyl Peroxide Reduction Pathway of Xanthomonas campestris Bacterioferritin Comigratory Protein from the Trapped Intermediate–Ligand Complex Structures

Structural Characterisation of Tpx from Yersinia pseudotuberculosis Reveals Insights into the Binding of Salicylidene Acylhydrazide Compounds

Semiempirical Quantum Chemistry

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