Another stop this year — Prague! 🇨🇿

I’ve been awarded a Visegrad Fellowship for a research stay at Charles University! I’ll be joining Prof. Jaroslav V. Burda’s group to work on gold(I) metallodrugs and thioredoxin reductase using QM/MM simulations. 🧬

— Is it going to be a great two weeks of science and collaboration in the V4 region? — Ano. 🤓

#VisegradFund #CharlesUniversity #QMMM #DrugDiscovery #Prague #Science #V4

Looking forward to comparisons, experiences, and pointers to similar tools. #ComputationalChemistry #Enzymology #QMMM #MachineLearning #MolecularSimulation #MLforScience #ReactionMechanisms #DrugDiscovery #HPC #ChemRxiv 🧵 12/12

How Do OH– and H3O+ Recombine in Water Nanodroplets?
Effects of spatial confinement on the recombination of autodissociated water ions investigated
https://www.chemistryviews.org/how-do-oh-and-h3o-recombine-in-water-nanodroplets/

#nanochemistry #nanodroplets #QMMM #chemistry #chemistryviews #chemviews

How Do OH– and H3O+ Recombine in Water Nanodroplets? - ChemistryViews

Effects of spatial confinement on the recombination of autodissociated water ions investigated

ChemistryViews

Deadline extended to May 10th!
#Postdoc position - looking for experience with Biomolecular Simulation (molecular dynamics, ideally #QMMM) and #Python, and interest in #enzymes and #ML potentials

New link:
https://www.bristol.ac.uk/jobs/find/details/?jobId=312015&jobTitle=Research%20Associate%20in%20Computational%20Enzymology

#BlackInSTEMM particularly encouraged.

Please share!
(Email me with questions)

Details | Working at Bristol | University of Bristol

Quantum mechanics of hydrated calcium in GluA2! Fun Collaboration as part of the #dynion @dfg_public research group.

Mechanism of Calcium Permeation in a #Glutamate Receptor #IonChannel #MolecularDynamics #QMMM

https://pubs.acs.org/doi/10.1021/acs.jcim.2c01494

Vol63 Issue4 #JCIM #compchem
#biophysics

Just online twitter@J_A_C_S, excelent job by Madison Berger twitter@Lilberger14:
Mutations on the beta-clamp of DNA pol III core affect DNA structure within complex, resulting in changes in dynamics and electric fields at proofreader active site 50-70 Å away!
#compchem #compbiophys #QMMM #MD
https://pubs.acs.org/doi/10.1021/jacs.2c11713

Finally online
Yazdan twitter@YazdanMaghsoud, Erik twitter@ev_montelongo, Ally twitter@Ally_Kristina and Miguel twitter@miguelesp did a great job on this exciting collaboration with Pengyu Ren and Kevin N. Dalby

#compchem #compbiophys #biophysics #hpc #QMMM #polarizable

https://pubs.acs.org/doi/10.1021/acs.jcim.2c01448

Our latest preprint is out; great collaboration with Kevin N Dalby and Pengyu Ren @ UT Austin on selective LH2 antagonists.
Nice job by Yazdan Maghsoud, Ally Smith and Erik Vázquez using #polarizable #QMMM to aid with ligand prediction
#compchem @chemistry
https://chemrxiv.org/engage/chemrxiv/article-details/6386ee9a1234cb1d69285c81
1,3-diketone analogs as selective lysyl hydroxylase 2 (LH2) antagonists

Lysyl hydroxylase 2 (LH2), an Fe(II) and α-ketoglutarate (αKG, also called 2-oxoglutarate, or 2OG)-dependent oxygenase, is an endoplasmic reticulum-resident enzyme that hydroxylates telopeptidyl lysine residues on fibrillar collagen molecules. It leads to the formation of hydroxylysine aldehyde-derived collagen cross-links (HLCCs), which are more stable than lysine aldehyde-derived collagen cross-links (LCCs) generated devoid of LH2. It has been reported that LH2 enhances lung cancer metastatic and invasive proclivity and modulates the types of collagen cross-links (HLCC-to-LCC) in the tumor stroma. Herein, we prepared a series of 1,3-diketone analogs 1–18 and identified 12 and 13 that inhibit the LH2-driven hydroxylation of a collagen peptide substrate with IC50 approximately 300 nM and 500 nM, respectively. 12 and 13 demonstrate a 9-fold selectivity for LH2 over LH1 and LH3. Quantum Mechanics/Molecular Mechanics (QM/MM) modeling indicates that in addition to the relatively stronger interactions between compounds 12 and 13 with the active site, the selectivity stems from non-covalent interactions like hydrogen bonding between the morpholine/piperazine rings with LH2-specific Arg661, where the corresponding residue in LH1 and LH3 is Pro. Migration assays in the 344SQ lung adenocarcinoma cell line reveal that 13 shows anti-migration activity.

ChemRxiv
... and other techniques. My main drive is to push #cryoET in tissues to enable #structbio in #devbio systems and get the throughput with modern #cryoFIB systems needed to do #visualproteomics. Also, from a “former lifetime” still very much into #MD #QMMM #proteindesign #CompChem
Just had the fantastic news that my @[email protected] student @[email protected] won a poster prize at #YMF2022 in Oxford! 🎉
#enzymes #QMMM @[email protected]