A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides

Gao, Ya; Zhang, Chaomin; Wang, Xianwei; Zhu, Tong

doi:10.1016/j.cplett.2017.04.074

Cited by 23 publications

(15 citation statements)

References 52 publications

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“…Its folding kinetics and ther-modynamics have been studied extensively by timeresolved spectroscopy, [30][31][32][33][34] and its folding mechanism has been probed extensively using molecular simulation studies. [35][36][37] Moreover, an impressively large number of site-directed mutants of WW domain have been constructed to investigate folding mechanism and discover fast-folding variants, including the Fip mutant (Fip35) of human pin1 WW domain, for which mutations in first hairpin loop region resulting in a fast folding time of ∼13.3 µs at 77.5 • C. 31,38 Further mutation of the the second hairpin loop of Fip35 produced an even faster-folding variant, called GTT, in which the native sequence Asn-Ala-Ser (NAS) was replaced with Gly-Thr-Thr (GTT), resulting in a a fast relaxation time ∼4.3 µs at 80 • C. NTL9(1-39) domain is a 39-residue truncation variant of the N-terminal domain of ribosomal protein L9, whose folded state consists of an α-helix and three-strand βsheet. NTL9(1-39), which has a folding relaxation time of ∼1.5 ms at 25 • C, 39 has been extensively probed by both experimental and computational studies.…”

Section: Seeding Of a 1-d Potential Energy Surfacementioning

confidence: 99%

Adaptive Markov state model estimation using short reseeding trajectories

Wan

Voelz

2020

The Journal of Chemical Physics

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In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on slow timescales. A promising approach to enhanced sampling of MSMs is to use so-called adaptive methods, in which new MD trajectories are seeded preferentially from previously identified states. Here, we investigate the performance of various MSM estimators applied to reseeding trajectory data, for both a simple 1D free energy landscape, and for mini-protein folding MSMs of WW domain and NTL9(1-39). Our results reveal the practical challenges of reseeding simulations, and suggest a simple way to reweight seeding trajectory data to better estimate both thermodynamic and kinetic quantities.

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Section: Seeding Of a 1-d Potential Energy Surfacementioning

confidence: 99%

Adaptive Markov state model estimation using short reseeding trajectories

Wan

Voelz

2020

The Journal of Chemical Physics

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“…The six polypyrrole-pyrethrin con gurations were energy minimized and subjected to 100 ps NVT (N for the number of atoms, V for volume, and T for temperature) equilibration at 300 K. Then, the six systems were respectively run for 50 ns of NPT (N for the number of atoms, P for pressure, and T for temperature) production. In this study, we carried out a series of all-atom MD simulations using the standard AMBER99SB force eld (Hornak et al 2006;Gao et al 2017) at pH 3.0 and 6.5. Under the two pH values of mimic environment, the side chains of the Asp55, Glu75 and Glu194 were modeled to take different charge states: neutral at pH 3 and negatively charged at pH 6.5 (Rostkowski et al 2011).…”

Section: Molecular Dynamics (Md) Simulationsmentioning

confidence: 99%

Heterologous expression, characterization and evolution prediction of a diaphorase from Geobacillus sp. Y4.1MC1

et al. 2022

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β-hydroxybutyric acid is the most sensitive indicator in ketoacidosis detection, and accounts for nearly 78% of the ketone bodies. Diaphorase is commonly used to detect the β-hydroxybutyric acid in clinical diagnosis. However, the extraction of diaphorase from animal myocardium is complex and low-yield, which is not convenient for large-scale production. In this study, a diaphorase from Geobacillus sp. Y4.1MC1 was e ciently heterologous expressed and puri ed in E. coli a yield of 110 mg/L culture. The optimal temperature and pH of this recombinant diaphorase (rDIA) were 55 °C and 6.5, respectively. It was proved that rDIA was a dual acid-and thermo-stable enzyme, and which showed much more accurate detection of β-hydroxybutyric acid than the commercial enzyme. Additionally, we also investigated the molecular interaction of rDIA with the substrate, and the conformation transition in different pH values by using homology modeling and molecular dynamics (MD) simulation. The results showed that 141-161 domain of rDIA played important role in the structure changes and conformations transmission at different pH values. Moreover, it was predicted that F105W, F105R and M186R mutants were able to improve the binding a nity of rDIA, and A2Y, P35F, Q36D, N210L, F211Y mutants were bene t for the stability of rDIA.

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“…(Li and Merz, 2016;Li and Merz, 2017). The substrate and protein were described by the AMBER14SB (Gao et al, 2017) and AMBER GAFF force fields (Wang et al, 2004), respectively. The partial atomic charges of CO 2 were determined by the restrained electrostatic potential (RESP) (Bayly et al, 1993) charge at the HF/6-31G* level with Gaussian 09.…”

Section: Setup Of Enzyme-substrate Complex Modelmentioning

confidence: 99%

Conformational Change of H64 and Substrate Transportation: Insight Into a Full Picture of Enzymatic Hydration of CO2 by Carbonic Anhydrase

Fan

Zhang

et al. 2021

Front. Chem.

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The enzymatic hydration of CO2 into HCO3− by carbonic anhydrase (CA) is highly efficient and environment-friendly measure for CO2 sequestration. Here extensive MM MD and QM/MM MD simulations were used to explore the whole enzymatic process, and a full picture of the enzymatic hydration of CO2 by CA was achieved. Prior to CO2 hydration, the proton transfer from the water molecule (WT1) to H64 is the rate-limiting step with the free energy barrier of 10.4 kcal/mol, which leads to the ready state with the Zn-bound OH−. The nucleophilic attack of OH− on CO2 produces HCO3− with the free energy barrier of 4.4 kcal/mol and the free energy release of about 8.0 kcal/mol. Q92 as the key residue manipulates both CO2 transportation to the active site and release of HCO3−. The unprotonated H64 in CA prefers in an inward orientation, while the outward conformation is favorable energetically for its protonated counterpart. The conformational transition of H64 between inward and outward correlates with its protonation state, which is mediated by the proton transfer and the product release. The whole enzymatic cycle has the free energy span of 10.4 kcal/mol for the initial proton transfer step and the free energy change of −6.5 kcal/mol. The mechanistic details provide a comprehensive understanding of the entire reversible conversion of CO2 into bicarbonate and roles of key residues in chemical and nonchemical steps for the enzymatic hydration of CO2.

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A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides

Cited by 23 publications

References 52 publications

Adaptive Markov state model estimation using short reseeding trajectories

Adaptive Markov state model estimation using short reseeding trajectories

Heterologous expression, characterization and evolution prediction of a diaphorase from Geobacillus sp. Y4.1MC1

Conformational Change of H64 and Substrate Transportation: Insight Into a Full Picture of Enzymatic Hydration of CO2 by Carbonic Anhydrase

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