Temperature dependence of binding and catalysis for the Cdc25B phosphatase

Sohn, Jungsan; Rudolph, Johannes

doi:10.1016/j.bpc.2006.11.005

Cited by 7 publications

(11 citation statements)

References 32 publications

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“…The calculated free-energy barrier is 17 kcal/mol. This value is identical to the barrier determined experimentally . In fact, H + transfer is well-advanced, but not complete, in comparison to phosphate transfer in the transition state.…”

Section: Resultssupporting

confidence: 84%

The Catalytic Acid in the Dephosphorylation of the Cdk2-pTpY/CycA Protein Complex by Cdc25B Phosphatase

Arantes

2008

J. Phys. Chem. B

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The development of anticancer therapeutics that target Cdc25 phosphatases is now an active area of research. A complete understanding of the Cdc25 catalytic mechanism would certainly allow a more rational inhibitor design. However, the identity of the catalytic acid used by Cdc25 has been debated and not established unambiguously. Results of molecular dynamics simulations with a calibrated hybrid potential for the first reaction step catalyzed by Cdc25B in complex with its natural substrate, the Cdk2-pTpY/CycA protein complex, are presented here. The calculated reaction free-energy profiles are in very good agreement with experimental measurements and are used to discern between different proposals for the general acid. In addition, the simulations give useful insight on interactions that can be explored for the design of inhibitors specific to Cdc25.

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Section: Resultssupporting

confidence: 84%

The Catalytic Acid in the Dephosphorylation of the Cdk2-pTpY/CycA Protein Complex by Cdc25B Phosphatase

Arantes

2008

J. Phys. Chem. B

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“…As shown in Figure 1A , the amounts of lysine (Lys), arginine (Arg) and Glycine (Gly) that are in acetylation samples are much higher than that of in non-acetylation samples. Indeed, a protein that has a surface that is composed mainly of negatively charged amino acids will bind to a protein with mainly positively charged molecules, such as lysine and arginine [44] , [45] , [46] , [47] , [48] . This shows that the acetylation substrates which bind to KATs are much different from non-acetylation.…”

Section: Resultsmentioning

confidence: 99%

Position-Specific Analysis and Prediction for Protein Lysine Acetylation Based on Multiple Features

et al. 2012

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Protein lysine acetylation is a type of reversible post-translational modification that plays a vital role in many cellular processes, such as transcriptional regulation, apoptosis and cytokine signaling. To fully decipher the molecular mechanisms of acetylation-related biological processes, an initial but crucial step is the recognition of acetylated substrates and the corresponding acetylation sites. In this study, we developed a position-specific method named PSKAcePred for lysine acetylation prediction based on support vector machines. The residues around the acetylation sites were selected or excluded based on their entropy values. We incorporated features of amino acid composition information, evolutionary similarity and physicochemical properties to predict lysine acetylation sites. The prediction model achieved an accuracy of 79.84% and a Matthews correlation coefficient of 59.72% using the 10-fold cross-validation on balanced positive and negative samples. A feature analysis showed that all features applied in this method contributed to the acetylation process. A position-specific analysis showed that the features derived from the critical neighboring residues contributed profoundly to the acetylation site determination. The detailed analysis in this paper can help us to understand more of the acetylation mechanism and can provide guidance for the related experimental validation.

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“…However, an experimental investigation of the temperature dependence of binding of Cdc25B with pNPP does not support this notion. Sohn and Rudolph [53] found that the binding free energy of pNPP with Cdc25B was −8 kcal mol −1 , suggesting that although binding of phosphate at the active site is somewhat weak, the formation of the Michaelis complex is thermodynamically favorable. As discussed previously, our classical MD simulations of Cdc25 and two other PTPases provide evidence to support the unique preference of Cdc25 for the monoanionic form of small molecule substrates such as pNPP.…”

Section: Resultsmentioning

confidence: 99%

Mechanism of Cdc25B Phosphatase with the Small Molecule Substrate p-Nitrophenyl Phosphate from QM/MM-MFEP Calculations

Parks

Rudolph

et al. 2009

J. Phys. Chem. B

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Cdc25B is a dual-specificity phosphatase that catalyzes the dephosphorylation of the Cdk2/CycA protein complex. This enzyme is an important regulator of the human cell cycle, and has been identified as a potential anti-cancer target. In general, protein tyrosine phosphatases are thought to bind the dianionic form of the phosphate and employ general acid catalysis via the Asp residue in the highly conserved WPD-loop. However, the Cdc25 phosphatases form a special subfamily based on their distinct differences from other protein tyrosine phosphatases. Although Cdc25B contains the (H/V)CX 5 R catalytic motif present in all other protein tyrosine phosphatases, it lacks an analogous catalytic acid residue. No crystallographic data currently exists for the complex of Cdc25B with Cdk2/CycA, so in addition to its natural protein substrate, experimental and theoretical studies are often carried out with small molecule substrates. In an effort to gain understanding of the dephosphorylation mechanism of Cdc25B with a commonly used small molecule substrate, we have performed simulations of the rate-limiting step of the reaction catalyzed by Cdc25B with the substrate p-nitrophenyl phosphate using the recently developed QM/MM Minimum Free Energy Path method (Hu, et al., J. Chem. Phys. 2008, 034105). We have simulated the first step of the reaction with both the monoanionic and dianionic forms of the substrate, and our calculations favor a mechanism involving the monoanionic form. Thus, Cdc25 may employ a unique dephosphorylation mechanism among protein tyrosine phosphatases, at least in the case of the small molecule substrate p-nitrophenyl phosphate.

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Temperature dependence of binding and catalysis for the Cdc25B phosphatase

Cited by 7 publications

References 32 publications

The Catalytic Acid in the Dephosphorylation of the Cdk2-pTpY/CycA Protein Complex by Cdc25B Phosphatase

The Catalytic Acid in the Dephosphorylation of the Cdk2-pTpY/CycA Protein Complex by Cdc25B Phosphatase

Position-Specific Analysis and Prediction for Protein Lysine Acetylation Based on Multiple Features

Mechanism of Cdc25B Phosphatase with the Small Molecule Substrate p-Nitrophenyl Phosphate from QM/MM-MFEP Calculations

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