Thermodynamic Stability Versus Kinetic Lability of ZnS<sub>4</sub> Core

Picot, Delphine; Ohanessian, Gilles; Frison, Gilles

doi:10.1002/asia.200900624

Cited by 14 publications

(20 citation statements)

References 112 publications

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“…Of note, the relatively large dissociate rate constant (0.10 s À1 ) for Zn-thiolate bonds in RD is consistent with the reported kinetic lability of the ZnS 4 site (0.15 s À1 ) (8,43,44). In fact, only a few Zn tetra-alkylthiolate complexes, which serve as a model for the structural site of the ZnS 4 site in Zn metalloproteins, have been chemically synthesized and characterized.…”

Section: Mechanical Stability Of Zn-thiolate Bonds In the Zns 4 Centersupporting

confidence: 69%

Direct Measurements of the Mechanical Stability of Zinc-Thiolate Bonds in Rubredoxin by Single-Molecule Atomic Force Microscopy

Zheng

2011

Biophysical Journal

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Zinc (Zn) is one of the most abundant metals and is essential for life. Through ligand interactions, often with thiolate from cysteine residues in proteins, Zn can play important structural roles in organizing protein structure and augmenting protein folding and stability. However, it is difficult to separate the contributions of Zn-ligand interactions from those originating from intrinsic protein folding in experimental studies of Zn-containing metalloproteins, which makes the study of Zn-ligand interactions in proteins challenging. Here, we used single-molecule force spectroscopy to directly measure the mechanical rupture force of the Zn-thiolate bond in Zn-rubredoxin. Our results show that considerable force is needed to rupture Zn-thiolate bonds (~170 pN, which is significantly higher than the force necessary to rupture the coordination bond between Zn and histidines). To our knowledge, our study not only provides new information about Zn-thiolate bonds in rubredoxin, it also opens a new avenue for studying metal-ligand bonds in proteins using single-molecule force spectroscopy.

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Section: Mechanical Stability Of Zn-thiolate Bonds In the Zns 4 Centersupporting

confidence: 69%

Direct Measurements of the Mechanical Stability of Zinc-Thiolate Bonds in Rubredoxin by Single-Molecule Atomic Force Microscopy

Zheng

2011

Biophysical Journal

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“…Our active-site model results agree well with the recent calculations for an addition of phenyl thiolate to Zn(SC 6 H 5 ) 4 2-complex with a barrier of 42.8 kcal/mol and endothermicity of 12.4 kcal/mol. [57] The reaction mechanism in the water solution is similar to that in the gas phase, for example having a nearly same transition structure (Supporting Information Fig. S1 and Table S9).…”

Section: Dft Calculations With Simple Active-site Modelmentioning

confidence: 86%

Zinc–Homocysteine binding in cobalamin‐dependent methionine synthase and its role in the substrate activation: DFT, ONIOM, and QM/MM molecular dynamics studies

Abdel‐Azeim

Chung

et al. 2011

J Comput Chem

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Cobalamin-dependent methionine synthase (MetH) is an important metalloenzyme responsible for the biosynthesis of methionine. It catalyzes methyl transfer from N(5)-methyl-tetrahydrofolate to homocysteine (Hcy) by using a zinc ion to activate the Hcy substrate. Density functional theory (B3LYP) calculations on the active-site model in gas phase and in a polarized continuum model were performed to study the Zn coordination changes from the substrate-unbound state to the substrate-bound state. The protein effect on the Zn(2+) coordination exchange was further investigated by ONIOM (B3LYP:AMBER)-ME and EE calculations. The Zn(2+)-coordination exchange is found to be highly unfavorable in the gas phase with a high barrier and endothermicity. In the water solution, the reaction becomes exothermic and the reaction barrier is drastically decreased to about 10.0 kcal/mol. A considerable protein effect on the coordination exchange was also found; the reaction is even more exothermic and occurs without barrier. The enzyme was suggested to constrain the zinc coordination sphere in the reactant state (Hcy-unbound state) more than that in the product state (Hcy-bound state), which promotes ligation of the Hcy substrate. Molecular dynamics simulations using molecular mechanics (MM) and PM3/MM potentials suggest a correlation between the flexibility of the Zn(2+)-binding site and regulation of the enzyme function. Directed in silico mutations of selected residues in the active site were also performed. Our studies support a dissociative mechanism starting with the Zn-O(Asn234) bond breaking followed by the Zn-S((Hcy)) bond formation; the proposed associative mechanism for the Zn(2+)-coordination exchange is not supported.

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“…For an additional gain in speed, the resolution of identity (RI) approximation was used. This functional has been shown to give reliable relative energetical data for zinc complexes compared with other density functionals or post‐HF calculations62–65.…”

Section: Methodsmentioning

confidence: 99%

Using partition designs to enhance purification process understanding

Pieracci

Perry

Conley

2010

Biotech & Bioengineering

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Characterization of purification processes by identifying significant input parameters and establishing predictive models is vital to developing robust processes. Current experimental design approaches restrict analysis to one process step at a time, which can severely limit the ability to identify interactions between process steps. This can be overcome by the use of partition designs which can model multiple, sequential process steps simultaneously. This paper presents the application of partition designs to a monoclonal antibody purification process. Three sequential purification steps were modeled using both traditional experimental designs and partition designs and the results compared as a proof of concept study. The partition and traditional design approaches identified the same input parameters within each process step that significantly affected the product quality output examined. The partition design also identified significant interactions between input parameters across process steps that could not be uncovered by the traditional approach.

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Thermodynamic Stability Versus Kinetic Lability of ZnS₄ Core

Cited by 14 publications

References 112 publications

Direct Measurements of the Mechanical Stability of Zinc-Thiolate Bonds in Rubredoxin by Single-Molecule Atomic Force Microscopy

Direct Measurements of the Mechanical Stability of Zinc-Thiolate Bonds in Rubredoxin by Single-Molecule Atomic Force Microscopy

Zinc–Homocysteine binding in cobalamin‐dependent methionine synthase and its role in the substrate activation: DFT, ONIOM, and QM/MM molecular dynamics studies

Using partition designs to enhance purification process understanding

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Thermodynamic Stability Versus Kinetic Lability of ZnS4 Core

Cited by 14 publications

References 112 publications

Direct Measurements of the Mechanical Stability of Zinc-Thiolate Bonds in Rubredoxin by Single-Molecule Atomic Force Microscopy

Direct Measurements of the Mechanical Stability of Zinc-Thiolate Bonds in Rubredoxin by Single-Molecule Atomic Force Microscopy

Zinc–Homocysteine binding in cobalamin‐dependent methionine synthase and its role in the substrate activation: DFT, ONIOM, and QM/MM molecular dynamics studies

Using partition designs to enhance purification process understanding

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Thermodynamic Stability Versus Kinetic Lability of ZnS₄ Core