Functional role of metalloproteins in genome stability

Zhang, Chunqiang; Zhang, Fan; Zhou, Ping; Zhang, Caiguo

doi:10.1007/s11515-016-1392-4

Cited by 9 publications

(5 citation statements)

References 132 publications

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“…Transition metals play important roles for processes including electron transport, oxidation reactions, or oxygen transport. [26][27][28][29] Also, metal complexes find broad applications for both homogeneous and heterogeneous catalysis in organic synthesis. 30 However, atomistic simulations using empirical force fields for metals in particular and hypervalent compounds in general pose particular challenges.…”

Section: Introductionmentioning

confidence: 99%

“…Hence, if the energetics and dynamics of reactive processes involving metals need to be characterized, alternative methods to describe the energetics of the systems are required. Transition metals play important roles for processes including electron transport, oxidation reactions, or oxygen transport. − Also, metal complexes find broad applications for both homogeneous and heterogeneous catalysis in organic synthesis . However, atomistic simulations using empirical force fields for metals in particular and hypervalent compounds in general pose particular challenges.…”

Section: Introductionmentioning

confidence: 99%

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Multi-State VALBOND for Atomistic Simulations of Hypervalent Molecules, Metal Complexes, and Reactions

Schmid

Das

Landis

et al. 2018

J. Chem. Theory Comput.

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The implementation, validation, and application of the multi-state VALBOND method for transition-metal-containing and hypervalent molecules are presented. This approach is particularly suited for molecules with unusual shapes and systems that need to be described by a superposition of resonance structures, each of which satisfies the octet rule. The implementation is based on the original VALBOND force field and allows us to smoothly switch between resonance structures, each of which can be characterized by its own force field, including varying charge distributions and coupling terms between the states. The implementation conserves total energy for simulations in the gas phase and in solution and is applied to a number of topical systems. For the small hypervalent molecule ClF, the barrier for pseudorotation is found to be 4.3 kcal/mol, which compares favorably with the experimentally measured value of 4.8 kcal/mol. A transition-metal-containing complex, cisplatin, is characterized by six resonance states, for which the vibrational spectrum is found to be in good agreement with experiment. Finally, umbrella sampling simulations of the S2 reaction BrMe + Cl → Br + MeCl in solution yield a barrier height of 24.6 kcal/mol, in good agreement with experiment (24.7 kcal/mol).

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Multi-State VALBOND for Atomistic Simulations of Hypervalent Molecules, Metal Complexes, and Reactions

Schmid

Das

Landis

et al. 2018

J. Chem. Theory Comput.

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“…We speculate that disruption of these genes affects bioleaching indirectly by modifying the expression of metabolic pathways that produce metal solubilizing compounds. For example, metal ion binding proteins are often associated with signaling, sensing, and regulation [46][47][48][49] , suggesting that their disruption could alter G. oxydans' bioleaching capabilities. Similarly, disruption of the nucleotide-repair system could impair the ability of G. oxydans to respond to damage generated by oxidative stress resulting from initial biolixiviant production 50,51 and thus alter further biolixiviant production.…”

Section: Metal Binding and Dna Repair Gene Ontologies Are Highly Enri...mentioning

confidence: 99%

Direct Genome-Scale Screening ofGluconobacter oxydansB58 for Rare Earth Element Bioleaching

Marecos,

Pian,

Medin

et al. 2024

Preprint

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The transition to a sustainable energy economy will require an enormous increase in the supply of rare earth elements (REE). Bioleaching offers a promising alternative to conventional hydrometallurgical methods for REE extraction from low-grade ores. However, exploiting this potential remains challenging due to large gaps in our understanding of the genetics involved, and inadequate biological tools to address them. We generated a highly non-redundant whole genome knockout collection for the bioleaching microbeGluconobacter oxydansB58, reducing redundancy by 85% compared to the previous best collection. This new collection was directly screened for bioleaching neodymium from a synthetic monazite powder, identifying 89 genes important for bioleaching, 68 of which have not previously been associated with this mechanism. We conducted bench-scale experiments to validate the extraction efficiency of promising strains: 8 demonstrated significant increases in bioleaching by up to 111% (G. oxydansδGO_1598, a disruption of the gene encoding the orotate phosphoribosyltransferase enzyme PyrE), and one strain significantly reduced it by 97% (δGO_1096, a disruption of the gene encoding the GTP-binding protein TypA). Notable changes in biolixiviant pH were only observed for 3 strains, suggesting an important role for non-acid mechanisms in bioleaching. These findings provide valuable insights into further enhancing REE-bioleaching byG. oxydans’ through targeted genetic engineering.

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“…Approximately one-third of all the studied proteins require at least one metal ion to carry out its function ( Shi and Chance, 2011 ). The interactions between protein and bound prosthetic metal atom in metalloproteins help them to complete the diverse functions of catalysis, regulation and structure stabilization ( Andreini et al, 2013 ; Zhang et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

In silico Study of Iron, Zinc and Copper Binding Proteins of Pseudomonas syringae pv. lapsa: Emphasis on Secreted Metalloproteins

Sharma

Verma

2018

Front. Microbiol.

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The phytopathogenic bacteria, Pseudomonas syringae pv. lapsa (P. syringae pv. lapsa) infects the staple food crop wheat. Metalloproteins play important roles in plant-pathogen interactions. Hence, the present work is aimed to predict and analyze the iron (Fe), zinc (Zn), and copper (Cu) binding proteins of P. syringae pv. lapsa which help in its growth, adaptation, survival and pathogenicity. A total of 232 Fe, 307 Zn, and 38 Cu-binding proteins have been identified. The functional annotation, subcellular localization and gene ontology enriched network analysis revealed their role in wide range of biological activities of the phytopathogen. Among the identified metalloproteins, a total of 29 Fe-binding, 31 Zn-binding, and 5 Cu-binding proteins were found to be secreted in nature. These putative secreted metalloproteins may perform diverse cellular and biological functions ranging from transport, response to oxidative stress, proteolysis, antimicrobial resistance, metabolic processes, protein folding and DNA repair. The observations obtained here may provide initial information required to draft new schemes to control microbial infections of staple food crops and will further help in developing sustainable agriculture.

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Functional role of metalloproteins in genome stability

Cited by 9 publications

References 132 publications

Multi-State VALBOND for Atomistic Simulations of Hypervalent Molecules, Metal Complexes, and Reactions

Multi-State VALBOND for Atomistic Simulations of Hypervalent Molecules, Metal Complexes, and Reactions

Direct Genome-Scale Screening ofGluconobacter oxydansB58 for Rare Earth Element Bioleaching

In silico Study of Iron, Zinc and Copper Binding Proteins of Pseudomonas syringae pv. lapsa: Emphasis on Secreted Metalloproteins

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