Improved Generalized Born Solvent Model Parameters for Protein Simulations

Nguyen, Thi Hong Hai; Roe, Daniel R.; Simmerling, Carlos

doi:10.1021/ct3010485

Cited by 426 publications

(632 citation statements)

References 78 publications

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“…Finally, the linker moiety joining the peptide to the oligonucleotide was modelled in and the components of the complex assembled via xLEaP. For molecular dynamics (MD) simulations, parameters were assigned to the complex from the ff14SBonlysc [62] and GAFF force fields [63]. The complex was solvated using the generalised Born implicit solvation model (igb=5) [64] …”

Section: Molecular Modellingmentioning

confidence: 99%

miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells

et al. 2017

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Please cite this article as: Patutina OA, Bichenkova EV, Miroshnichenko SK, Mironova NL, Trivoluzzi LT, Burusco KK, Bryce RA, Vlassov VV, Zenkova MA, miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells, Biomaterials (2017Biomaterials ( ), doi: 10.1016Biomaterials ( / j.biomaterials.2017 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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Section: Molecular Modellingmentioning

confidence: 99%

miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells

et al. 2017

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“…To calculate the free energy of binding, the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) method was used. The GBn formulation [35] was implemented along with newly-developed parameters [36] and mbondi3 radii. The entropic component of binding was evaluated with the normal mode approximation.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Inactivation of Protein Tyrosine Phosphatases by Peracids Correlates with the Hydrocarbon Chain Length

Kuban–Jankowska

Górska

Tuszyński

et al. 2015

Cell Physiol Biochem

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Background/Aims: Protein tyrosine phosphatases are crucial enzymes controlling numerous physiological and pathophysiological events and can be regulated by oxidation of the catalytic domain cysteine residue. Peracids are highly oxidizing compounds, and thus may induce inactivation of PTPs. The aim of the present study was to evaluate the inhibitory effect of peracids with different length of hydrocarbon chain on the activity of selected PTPs. Methods: The enzymatic activity of human CD45, PTP1B, LAR, bacterial YopH was assayed under the cell-free conditions, and activity of cellular CD45 in human Jurkat cell lysates. The molecular docking and molecular dynamics were performed to evaluate the peracids binding to the CD45 active site. Results: Here we demonstrate that peracids reduce enzymatic activity of recombinant CD45, PTP1B, LAR, YopH and cellular CD45. Our studies indicate that peracids are more potent inhibitors of CD45 than hydrogen peroxide (with an IC50 value equal to 25 nM for peroctanoic acid and 8 µM for hydrogen peroxide). The experimental data show that the inactivation caused by peracids is dependent on hydrocarbon chain length of peracids with maximum inhibitory effect of medium-chain peracids (C8-C12 acyl chain), which correlates with calculated binding affinities to the CD45 active site. Conclusion: Peracids are potent inhibitors of PTPs with the strongest inhibitory effect observed for medium-chain peracids.

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“…In case of simulations in implicit solvent, the optimized GBn implicit solvent model (ibg =8) was used together with recommended Born radii set mbondi3. 26 Infinite cutoff (cut =9,999.0) for nonbond interactions was used and temperature was controlled with Langevin thermostat. The pmemd.cuda module from Amber 14 package was used for all the above-described simulation steps.…”

Section: Simulation Detailsmentioning

confidence: 99%

Prevention of vaginal and rectal herpes simplex virus type 2 transmission in mice: mechanism of antiviral action

Ceña-Díez¹,

Vacas-Córdoba²,

García-Broncano³

et al. 2016

IJN

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Topical microbicides to stop sexually transmitted diseases, such as herpes simplex virus type 2 (HSV-2), are urgently needed. The emerging field of nanotechnology offers novel suitable tools for addressing this challenge. Our objective was to study, in vitro and in vivo, antiherpetic effect and antiviral mechanisms of several polyanionic carbosilane dendrimers with anti-HIV-1 activity to establish new potential microbicide candidates against sexually transmitted diseases. Plaque reduction assay on Vero cells proved that G2-S16, G1-S4, and G3-S16 are the dendrimers with the highest inhibitory response against HSV-2 infection. We also demonstrated that our dendrimers inhibit viral infection at the first steps of HSV-2 lifecycle: binding/entry-mediated events. G1-S4 and G3-S16 bind directly on the HSV-2, inactivating it, whereas G2-S16 adheres to host cell-surface proteins. Molecular modeling showed that G1-S4 binds better at binding sites on gB surface than G2-S16. Significantly better binding properties of G1-S4 than G2-S16 were found in an important position for affecting transition of gB trimer from G1-S4 prefusion to final postfusion state and in several positions where G1-S4 could interfere with gB/gH–gL interaction. We demonstrated that these polyanionic carbosilan dendrimers have a synergistic activity with acyclovir and tenofovir against HSV-2, in vitro. Topical vaginal or rectal administration of G1-S4 or G2-S16 prevents HSV-2 transmission in BALB/c mice in values close to 100%. This research represents the first demonstration that transmission of HSV-2 can be blocked by vaginal/rectal application of G1-S4 or G2-S16, providing a step forward to prevent HSV-2 transmission in humans.

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Improved Generalized Born Solvent Model Parameters for Protein Simulations

Cited by 426 publications

References 78 publications

miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells

miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells

Inactivation of Protein Tyrosine Phosphatases by Peracids Correlates with the Hydrocarbon Chain Length

Prevention of vaginal and rectal herpes simplex virus type 2 transmission in mice: mechanism of antiviral action

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