Abstract:
:Bacterial populations present in Hg-rich environments have evolved biological mechanisms to detoxify methylmercury and other organometallic mercury compounds. The most common resistance mechanism relies on the H(+)-assisted cleavage of the Hg-C bond of methylmercury by the organomercurial lyase MerB. Although the initial reaction steps which lead to the loss of methane from methylmercury have already been studied experimentally and computationally, the reaction steps leading to the removal of Hg(2+) from MerB and regeneration of the active site for a new round of catalysis have not yet been elucidated. In this paper, we have studied the final steps of the reaction catalyzed by MerB through quantum chemical computations at the combined MP2/CBS//B3PW91/6-31G(d) level of theory. While conceptually simple, these reaction steps occur in a complex potential energy surface where several distinct pathways are accessible and may operate concurrently. The only pathway which clearly emerges as forbidden in our analysis is the one arising from the sequential addition of two thiolates to the metal atom, due to the accumulation of negative charges in the active site. The addition of two thiols, in contrast, leads to two feasible mechanistic possibilities. The most straightforward pathway proceeds through proton transfer from the attacking thiol to Cys159 , leading to its removal from the mercury coordination sphere, followed by a slower attack of a second thiol, which removes Cys96. The other pathway involves Asp99 in an accessory role similar to the one observed earlier for the initial stages of the reaction and affords a lower activation enthalpy, around 14 kcal mol(-1), determined solely by the cysteine removal step rather than by the thiol ligation step. Addition of one thiolate to the intermediates arising from either thiol attack occurs without a barrier and produces an intermediate bound to one active site cysteine and from which Hg(SCH3)2 may be removed only after protonation by solvent-provided H3O(+). Thiolate addition to the active site (prior to any attack by thiols) leads to pathways where the removal of the first cysteine becomes the rate-determining step, irrespective of whether Cys159 or Cys96 leaves first. Comparisons with the recently computed mechanism of the related enzyme MerA further underline the important role of Asp99 in the energetics of the MerB reaction. Kinetic simulation of the mechanism derived from our computations strongly suggests that in vivo the thiolate-only pathway is operative, and the Asp-assisted pathway (as well as the conversion of intermediates of the thiolate pathway into intermediates of the Cys-assisted pathway) is prevented by steric factors absent from our model and related to the precise geometry of the organomercurial binding-pocket.
journal_name
PeerJjournal_title
PeerJauthors
Silva PJ,Rodrigues Vdoi
10.7717/peerj.1127subject
Has Abstractpub_date
2015-07-28 00:00:00pages
e1127issn
2167-8359pii
1127journal_volume
3pub_type
杂志文章相关文献
PeerJ文献大全abstract::Twist1, a basic helix-loop-helix transcription factor that regulates a number of genes involved in epithelial-to-mesenchymal transition (EMT), is upregulated in prostate cancer. Androgen regulation of Twist1 has been reported in a previous study. However, the mechanism of androgen regulation of the Twist1 gene is not ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.8921
更新日期:2020-04-09 00:00:00
abstract::Language WorkBenches (LWBs) are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advant...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.241
更新日期:2014-01-02 00:00:00
abstract:Background:Quality of life is an important health outcome for older persons. It predicts the adverse outcomes of institutionalization and premature death. The aim of this cross-sectional study was to determine the influence of both disability in activities of daily living (ADL) and instrumental activities of daily livi...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5425
更新日期:2018-08-09 00:00:00
abstract::Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC-600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirac...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1066
更新日期:2015-08-06 00:00:00
abstract::The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.275
更新日期:2014-03-18 00:00:00
abstract::Secondary cavity nesting (SCN) birds breed in holes that they do not excavate themselves. This is possible where there are large trees whose size and age permit the digging of holes by primary excavators and only rarely happens in forest plantations, where we expected a deficit of both breeding holes and SCN species. ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1806
更新日期:2016-03-15 00:00:00
abstract::Potential natural vegetation (PNV) is the vegetation cover in equilibrium with climate, that would exist at a given location if not impacted by human activities. PNV is useful for raising public awareness about land degradation and for estimating land potential. This paper presents results of assessing machine learnin...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5457
更新日期:2018-08-22 00:00:00
abstract::In the Western honey bee, Apis mellifera, queens and workers have different longevity although they share the same genome. Queens consume royal jelly (RJ) as the main food throughout their life, including as adults, but workers only eat worker jelly when they are larvae less than 3 days old. In order to explore the ef...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.3118
更新日期:2017-03-28 00:00:00
abstract::Prion diseases are a group of fatal neurodegenerative disorders that affect humans and animals. They are characterized by the accumulation in the central nervous system of a pathological form of the host-encoded prion protein (PrP(C)). The prion protein is a membrane glycoprotein that consists of two domains: a globul...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.811
更新日期:2015-03-19 00:00:00
abstract::A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov.Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were brie...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6866
更新日期:2019-05-02 00:00:00
abstract::There is currently great interest in applying neural networks to prediction tasks in medicine. It is important for predictive models to be able to use survival data, where each patient has a known follow-up time and event/censoring indicator. This avoids information loss when training the model and enables generation ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6257
更新日期:2019-01-25 00:00:00
abstract::Climatic fluctuations during the Quaternary significantly affect many species in their intraspecific divergence and population structure across northwest China. In order to investigate the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Sequences of...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6264
更新日期:2019-01-24 00:00:00
abstract::A prolonged preservation duration of blood specimens at 4 °C may occur due to the distance from collection points to storage facilities in many biobanks, especially for multicenter studies. This could lead to RNA degradation, affecting downstream analyses. However, effects of preservation durations at 4 °C on RNA qual...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.8940
更新日期:2020-04-10 00:00:00
abstract::Coastal birds are critical ecosystem constituents on sandy shores, yet are threatened by depressed reproductive success resulting from direct and indirect anthropogenic and natural pressures. Few studies examine clutch fate across the wide range of environments experienced by birds; instead, most focus at the small si...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.2460
更新日期:2016-09-13 00:00:00
abstract::The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these differen...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.761
更新日期:2015-02-17 00:00:00
abstract::Environmental DNA (eDNA) is an emerging tool for monitoring invasive and imperiled species, particularly at low densities. However, the factors that control eDNA production, transport, and persistence in aquatic systems remain poorly understood. For example, the extent to which carcasses produce detectable eDNA is unk...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.9333
更新日期:2020-06-11 00:00:00
abstract::Background. Genome-wide association studies have succeeded in detecting novel common variants which associate with complex diseases. As a result of the fast changes in next generation sequencing technology, a large number of sequencing data are generated, which offers great opportunities to identify rare variants that...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.2139
更新日期:2016-06-16 00:00:00
abstract::Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6080
更新日期:2019-01-11 00:00:00
abstract::The objective of this study was to quantify consumption of clothianidin-treated corn seed by birds following standard planting practices. Based on post-planting seed counts on 21 fields in southwestern Ontario, Canada, between 29 and 813 seeds/ha (mean of 224 ± 167 (SD)) were estimated to remain on the soil surface im...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5880
更新日期:2018-11-07 00:00:00
abstract:Background:Cyclin A overexpression is found in a variety of human tumors and correlates with unfavorable outcome. We analyzed immunohistochemical expression of cyclin A in Wilms tumor (WT) in relation to clinicopathological characteristics, preoperative chemotherapy (PrOpChTh), and overall survival (OS). Methods:This ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6212
更新日期:2019-01-11 00:00:00
abstract::According to the synthesis of 30 years of multidisciplinary studies, parthenogenetic species of rock lizards of genus Darevskia were formed as a result of different combination patterns of interspecific hybridization of the four bisexual parental species: Darevskia raddei, D. mixta, D. valentini, and D. portschinskii....
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6360
更新日期:2019-01-30 00:00:00
abstract::We documented significantly increasing trends in atmospheric loading of ammonium (NH4) and nitrate/nitrite (NO2/3) and decreasing trends in total phosphorus (P) and sulfate (SO4) to Flathead Lake, Montana, from 1985 to 2004. Atmospheric loading of NO2/3 and NH4 increased by 48 and 198% and total P and SO4 decreased by...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.841
更新日期:2015-03-19 00:00:00
abstract:BACKGROUND:Quercus infectoria G. Olivier (Fagaceae) nutgalls have been widely employed in traditional Asian medicine for several treatments, especially wounds and skin disorders. However, the effects of this plant on wound healing have not yet been clearly elucidated. This present work was focused on utilization of Que...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.3608
更新日期:2017-07-24 00:00:00
abstract:Background:Carbon (C), nitrogen (N) and phosphorus (P) stoichiometric ratios are important indicators of ecosystem function and productivity. However, few studies have assessed the nutrient relationship between plant, litter and soil, and the nutrient stock in different secondary mixed forest types. Methods:We investi...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.9274
更新日期:2020-06-03 00:00:00
abstract::Rhizoctonia solani causes the disease peanut sheath blight, involving symptoms of maceration and necrosis of infected tissue, mainly caused by cell-wall-degrading enzymes (CWDEs). This study investigated the production of CWDEs including polygalacturonase (PG), polymethyl-galacturonase (PMG), cellulase (Cx) and β-gluc...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5580
更新日期:2018-09-05 00:00:00
abstract::[This corrects the article DOI: 10.7717/peerj.4110.]. ...
journal_title:PeerJ
pub_type: 杂志文章,已发布勘误
doi:10.7717/peerj.4110/correction-1
更新日期:2017-12-20 00:00:00
abstract::In contrast to reports of wild primates, studies of captive primates' flexibility often reveal conservatism: individuals are unable to switch to new and more efficient strategies when task demands change. We propose that such conservatism might be a result of task design and hypothesize that conservatism might be link...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6195
更新日期:2019-01-08 00:00:00
abstract:Background:Yunnanolepidoids constitute either the most basal consecutive segments or the most primitive clade of antiarchs, a highly diversified jawed vertebrate group from the Silurian and Early Devonian periods. Although the general morphology of yunnanolepidoids is well established, their endocranial features remain...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4808
更新日期:2018-05-28 00:00:00
abstract::On the purpose of enhancing the forensic efficiency of CODIS STR loci, new STR loci have been gradually discovered and developed into some commercial multiplex systems. Recently, 22 STR loci including 18 non-CODIS STR loci and four CODIS STR loci were investigated in 501 unrelated healthy individuals of Kazakh ethnic ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6802
更新日期:2019-04-25 00:00:00
abstract::In species that live in one-male groups, resident males monopolize access to a group of females and are assumed to have higher reproductive success than bachelors. We tested this assumption using genetic, demographic, and behavioral data from 8 groups of wild blue monkeys observed over 10 years to quantify reproductio...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1043
更新日期:2015-06-23 00:00:00