CHARMM force field for protonated polyethyleneimine

Beu, Titus A.; Ailenei, Andrada-Elena; Farcaş, Alexandra

doi:10.1002/jcc.25637

Cited by 12 publications

(11 citation statements)

References 32 publications

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“…The molecular dynamics (MD) simulation used NAMD 2.12 [ 42 ] with the CHARMM22 [ 43 , 44 ] force field. The simulations were conducted using periodic boundary conditions, including a 12 Å cutoff for the nonbonded interactions and particle-mesh Ewald for the long-range electrostatic interactions.…”

Section: Methodsmentioning

confidence: 99%

Engineering Yarrowia lipolytica for the sustainable production of β-farnesene from waste oil feedstock

Liu

Zhang

et al. 2022

Biotechnol Biofuels

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Background β-Farnesene is a sesquiterpene with versatile industrial applications. The production of β-farnesene from waste lipid feedstock is an attractive method for sustainable production and recycling waste oil. Yarrowia lipolytica is an unconventional oleaginous yeast, which can use lipid feedstock and has great potential to synthesize acetyl-CoA-derived chemicals. Results In this study, we engineered Y. lipolytica to produce β-farnesene from lipid feedstock. To direct the flux of acetyl-CoA, which is generated from lipid β-oxidation, to β-farnesene synthesis, the mevalonate synthesis pathway was compartmentalized into peroxisomes. β-Farnesene production was then engineered by the protein engineering of β-farnesene synthase and pathway engineering. The regulation of lipid metabolism by enhancing β-oxidation and eliminating intracellular lipid synthesis was further performed to improve the β-farnesene synthesis. As a result, the final β-farnesene production with bio-engineering reached 35.2 g/L and 31.9 g/L using oleic acid and waste cooking oil, respectively, which are the highest β-farnesene titers reported in Y. lipolytica. Conclusions This study demonstrates that engineered Y. lipolytica could realize the sustainable production of value-added acetyl-CoA-derived chemicals from waste lipid feedstock.

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Section: Methodsmentioning

confidence: 99%

Engineering Yarrowia lipolytica for the sustainable production of β-farnesene from waste oil feedstock

Liu

Zhang

et al. 2022

Biotechnol Biofuels

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“…Using the above three protein structure templates, Modeller 9.12 (Eswar et al, 2006) was used for homologous modeling of PlyAB1. The MD simulation was performed using NAMD 2.12 (Nelson et al, 1996) with the CHARMM22 (Beu et al, 2018; Kim et al, 2017; Vanommeslaeghe et al, 2010) force field. The MD simulation method is similar to that in our previous work (Li et al, 2020), where the temperature of the MD simulation is changed to 303 K.…”

Section: Methodsmentioning

confidence: 99%

Enhancing thermal stability and lytic activity of phage lysin PlyAB1 from Acinetobacter baumannii

Yuan

Zhang

et al. 2022

Biotech & Bioengineering

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With the increasingly serious drug resistance of Acinetobacter baumannii, there is an increasingly urgent need for new antibacterial drugs. Phage lysin PlyAB1 has a bactericidal effect on drug‐resistant A. baumannii, which has the potential to replace antibiotics to fight infection caused by A. baumannii. However, its application is limited by its thermal stability and lytic activity. To solve these problems, molecular dynamics (MD) simulations combined with Hotspot wizard 3.0 were used to identify key residue sites affecting thermal stability, and evolutionary analysis combined with multiple sequence alignment was used to identify key residue sites affecting lytic activity. Four single‐point variants with significantly increased thermal stability and four single‐point variants with significantly lytic activity were obtained, respectively. Furthermore, by superimposing mutations, we obtained three double‐point variants, G100Q/K69R, G100R/K69R, and G100K/K69R, with significantly improved thermal stability and improved lytic activity. At 45°C, the lytic activity and half‐life of the optimal variant G100Q/K69R were 1.51‐ and 24‐fold higher than those of the wild PlyAB1, respectively. These results deepen our understanding of the structure and function of phage lysin and contribute to the application of phage lysin in antibiotic substitution.

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“…For example, the information about the end-to-end distance distribution is useful for evaluating and improving force-field parameters for molecular simulations. 20,21 We also expect to obtain new insights into the spatial dynamics of folded and IDP (intrinsically disordered polypeptide)-state proteins in aqueous solutions for biological applications. The scattered X-ray intensity is proportional to the square of the number of electrons in an atom.…”

Section: T H Imentioning

confidence: 99%

“…The present single-pair (of heavy atoms) SAXS experiments widen the applicability of SAXS interferometry from double-stranded DNA and RNA fragments to flexible small organic compounds in the physical and chemical fields. For example, the information about the end-to-end distance distribution is useful for evaluating and improving force-field parameters for molecular simulations. , …”

mentioning

confidence: 99%

Distance Distribution between Two Iodine Atoms Derived from Small-Angle X-ray Scattering Interferometry for Analyzing a Conformational Ensemble of Heavy Atom-Labeled Small Molecules

Taguchi

Saio

Kohda

2020

J. Phys. Chem. Lett.

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To obtain unbiased information about the dynamic conformational ensemble of a molecule in solution, one promising approach is small-angle X-ray scattering (SAXS). Conventionally, SAXS data are converted to a pair distribution function, which describes the distance distribution between all pairs of atoms within a molecule. If two strong X-ray scatterers are introduced and the background contributions from the other atoms are suppressed, then the distance distribution between the two scatterers provides spatial information about a flexible molecule. Gold nanocrystals can provide such information for distances of >50 Å. Here, we synthesized a chemical compound containing two iodine atoms attached to the ends of a flexible polyethylene glycol chain and used the relevant singly labeled and unlabeled compounds to suppress the background contribution. This is a feasibility demonstration to prove that the distance distribution in the range of 10−30 Å can be experimentally accessed by SAXS.

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CHARMM force field for protonated polyethyleneimine

Cited by 12 publications

References 32 publications

Engineering Yarrowia lipolytica for the sustainable production of β-farnesene from waste oil feedstock

Engineering Yarrowia lipolytica for the sustainable production of β-farnesene from waste oil feedstock

Enhancing thermal stability and lytic activity of phage lysin PlyAB1 from Acinetobacter baumannii

Distance Distribution between Two Iodine Atoms Derived from Small-Angle X-ray Scattering Interferometry for Analyzing a Conformational Ensemble of Heavy Atom-Labeled Small Molecules

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