Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic Molecules

Vassetti, Dario; Pagliai, Marco; Procacci, Piero

doi:10.1021/acs.jctc.8b01039

Cited by 197 publications

(137 citation statements)

References 65 publications

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“…4 To explore the effect of a force eld on the thermal, structural and dynamic properties of n-eicosane, we considered 10 different force elds. All-atom models included GAFF, [48][49][50] GAFF2, 51,52 OPLS-AA, 39,40,55 L-OPLS-AA, 56 and CHARMM36 (ref. 53 and 54) force elds, while OPLS-UA, 12,13 NERD, [19][20][21] TraPPE, [16][17][18] PYS, [22][23][24][25] and GROMOS96 45A3 (ref.…”

Section: Force Eldsmentioning

confidence: 99%

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Toward realistic computer modeling of paraffin-based composite materials: critical assessment of atomic-scale models of paraffins

et al. 2019

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Section: Force Eldsmentioning

confidence: 99%

“…GAFF2 is an improved version of the GAFF force eld, whose development is still ongoing. 51,52 CHARMM is another family of all-atom general-purpose force elds that covers a full range of biomolecules. As far as n-alkanes are concerned, the most relevant CHARMM force eld is CHARMM36.…”

Section: Introductionmentioning

confidence: 99%

Toward realistic computer modeling of paraffin-based composite materials: critical assessment of atomic-scale models of paraffins

et al. 2019

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“…The RESP atomic charges for the second adenosine nucleoside in m 7 GpppA analog were obtained from the RNA library of AMBER16 . All other force field parameters for the cap‐analogs were derived from GAFF2 database available through the Antechamber module in AMBER16 . The phosphate group in phosphorylated serine was also considered to be in the dianionic state with a net charge of “‐2e”.…”

Section: Methodsmentioning

confidence: 99%

Deciphering the mechanistic effects of eIF4E phosphorylation on mRNA‐cap recognition

Verma

2019

Protein Science

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The mRNA cap-binding oncoprotein "eIF4E" is phosphorylated at residue S209 by Mnk kinases, and is closely associated with tumor development and progression. Despite being well-established, mechanistic details at the molecular level of mRNA recognition by eIF4E due to phosphorylation have not been clearly elucidated. We investigated this through molecular modeling and simulations of the S209 phosphorylated derivative of eIF4E and explored the associated implication on the binding of the different variants of mRNA-cap analogs.A key feature that emerges as a result of eIF4E phosphorylation is a salt-bridge network between the phosphorylated S209 (pS209) and a specific pair of lysine residues (K159 and K162) within the cap-binding interface on eIF4E. This interaction linkage stabilizes the otherwise dynamic C-terminal region of the protein, resulting in the attenuation of the overall plasticity and accessibility of the binding pocket. The pS209-K159 salt-bridge also results in an energetically

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“…The amber library files for the phosphoserine residue was obtained from http://research.bmh.manchester.ac.uk/bryce/amber. The force field parameters with BCC atomic charges for PIP3-dic4 were derived from the GAFF2 database [45] through the Antechamber module in AMBER18 (Case, D.A., et al 2018, University of California, San Francisco).…”

Section: Modelling and Simulationmentioning

confidence: 99%

TRAF4 inhibits bladder cancer progression by promoting BMP/SMAD signalling pathway

Iyengar

Marvin

Tan

et al. 2020

Preprint

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Bladder cancer is one of the most prevalent cancer types in the world, frequently exhibiting invasion and metastasis and therefore associated with poor prognosis. It is a progressive disease with high recurrence rates even after surgery, which calls for the urgent need for early intervention and diagnosis. The E3 ubiquitin ligase TNF Receptor Associated Factor 4 (TRAF4) has been largely implicated as a tumour-promoting element in a wide range of cancers. Over-expression and amplification of this gene product has been a common observation in breast and other metastatic tumours. In contrast, we observed that expression of TRAF4 negatively correlated with overall patient survival. Moreover, its expression was repressed at epigenetic levels in aggressive bladder cancer cells. We also describe an ERK kinase phosphorylation site on TRAF4 that inhibits its stability and localization to plasma membrane in such cells. Furthermore, knockdown of TRAF4 in epithelial bladder cancer cell lines leads to gain of mesenchymal genes and a loss of epithelial integrity. Reciprocally, stable over-expression of TRAF4 in mesenchymal cells leads to decreased migratory and invasive properties. Transcriptomic analysis upon TRAF4 mis-expression in bladder cancer cell lines revealed that higher TRAF4 expression enhanced BMP/SMAD and dampened NF-κB signalling pathways. Importantly, this notion was confirmed in bladder cancer patient material. Mechanistically, we showed that TRAF4 targets the E3 ubiquitin ligase SMURF1, a negative regulator of BMP/SMAD signalling, for proteasomal degradation in bladder cancer cells. We show that genetic and pharmacological inhibition of SMURF1 or its function inhibited migration of aggressive (mesenchymal) bladder cancer cells.

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Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic Molecules

Cited by 197 publications

References 65 publications

Toward realistic computer modeling of paraffin-based composite materials: critical assessment of atomic-scale models of paraffins

Toward realistic computer modeling of paraffin-based composite materials: critical assessment of atomic-scale models of paraffins

Deciphering the mechanistic effects of eIF4E phosphorylation on mRNA‐cap recognition

TRAF4 inhibits bladder cancer progression by promoting BMP/SMAD signalling pathway

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