Coenzyme, cofactor and prosthetic group — Ambiguous biochemical jargon

Hashim, Onn Haji; Adnan, Nor Azila

doi:10.1016/0307-4412(94)90088-4

Cited by 4 publications

(2 citation statements)

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“… It is notable that (1) Ppant is the substrate of PPAT in PPAT-Ppant; (2) Ppant-Ser is covalently linked to an ACP as a prosthetic group in HGMS/ACP-Ppant-Ser; (3) CoA is the cofactor of EctA in EctA-CoA. Since covalent bonds are typically stronger than noncovalent interactions and cofactors typically remain bound with proteins, it is reasonable to expect that their binding strengths increase in the order of PPAT-Ppant, EctA-CoA, and HGMS/ACP-Ppant-Ser . Each system was simulated under reported experimental temperatures and salt concentrations.…”

Section: Resultsmentioning

confidence: 99%

“…Since covalent bonds are typically stronger than noncovalent interactions and cofactors typically remain bound with proteins, it is reasonable to expect that their binding strengths increase in the order of PPAT-Ppant, EctA-CoA, and HGMS/ACP-Ppant-Ser. 61 Each system was simulated under reported experimental temperatures and salt concentrations.…”

Section: ■ Introductionmentioning

confidence: 99%

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Development of a Pantetheine Force Field Library for Molecular Modeling

Zhao

Schaub

Tsai

et al. 2021

J. Chem. Inf. Model.

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Pantetheine is ubiquitous in nature in various forms of pantetheine-containing ligands (PCLs), including coenzyme A and phosphopantetheine. Lack of scalable force field libraries for PCLs has hampered the computational studies of biological macromolecules containing PCLs. We describe here the development of the first generation Pantetheine Force Field (PFF) library that is compatible with Amber force fields; parameterized using Gasteiger, AM1-BCC, or RESP charging methods combined with gaff 2 and f f14SB parameter sets. In addition, a "plug-and-play" strategy was employed to enable the systematic charging of computationally expensive molecules sharing common substructural motifs. The validation studies performed on the PFF library showed promising performance where molecular dynamics (MD) simulations results were compared with experimental data of three representative systems. The PFF library represents the first force field library capable of modeling systems containing PCLs in silico and will aid in various applications including protein engineering and drug discovery.

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Section: Resultsmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%