Research Area A - Publications 2019
Finding Reactive Configurations: A Machine Learning Approach for Estimating Energy Barriers Applied to Sirtuin 5
J. Chem. Theory Comput. 2019, 15, 12, 6660–6667, https://doi.org/10.1021/acs.jctc.9b00876
J. Chem. Theory Comput., online article
Sirtuin 5 is a class III histone deacetylase that, unlike its classification, mainly catalyzes desuccinylation and demanoylation reactions. It is an interesting drug target that we use here to test new ideas for calculating reaction pathways of large molecular systems such as enzymes. A major issue with most schemes (e.g., adiabatic mapping) is that the resulting ...
DNA origami-based single-molecule force spectroscopy unravels the molecular basis of RNA Polymerase III pre-initiation complex stability
bioRxiv, doi: https://doi.org/10.1101/775528
bioRxiv, online article
The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor compound the fundamental core of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the additional intiation factor Bdp1, which is unique to the RNA polymerase (RNAP) III sytem, however, remained elusive. A poorly studied aspect in this context ...
J. Am. Chem. Soc. 2019, 141, 13643−13653, DOI: 10.1021/jacs.9b06521
J. Am. Chem. Soc., online article
Psoralens are natural compounds that serve in the light dependent treatment of certain skin diseases (PUVA therapy). They are DNA intercalators that upon photoexcitation form adducts with thymine bases. For one psoralen derivative, 4′-aminomethyl-4,5′,8-trimethylpsoralen (AMT), the photoreactions are characterized here by nanosecond UV–vis and IR absorption ...
Low-Scaling Self-Consistent Minimization of a Density Matrix Based Random Phase Approximation Method in the Atomic Orbital Space
J. Chem. Theory Comput., 2019, 15, 8, 4468–4477, https://doi.org/10.1021/acs.jctc.9b00444
J. Chem. Theory Comput., online article
An efficient minimization of the random phase approximation (RPA) energy with respect to the one-particle density matrix in the atomic orbital space is presented. The problem of imposing full self-consistency on functionals depending on the potential itself is bypassed by approximating the RPA Hamiltonian on the basis of the well-known Hartree–Fock Hamiltonian ...
Bisacylphosphane oxides as photo-latent cytotoxic agents and potential photo-latent anticancer drugs
Scientific Reports, volume 9, Article number: 6003 (2019), https://doi.org/10.1038/s41598-019-42026-y
Scientific Reports, online article
Bisacylphosphane oxides (BAPOs) are established as photoinitiators for industrial applications. Light irradiation leads to their photolysis, producing radicals. Radical species induce oxidative stress in cells and may cause cell death. Hence, BAPOs may be suitable as photolatent cytotoxic agents, but such applications have not been investigated yet. Herein, we ...
Plasmon-assisted Förster resonance energy transfer at the single-molecule level in the moderate quenching regime
Nanoscale, 2019, 11, 7674, DOI: 10.1039/c9nr01204d
Nanoscale, online article
Metallic nanoparticles were shown to affect Förster energy transfer between fluorophore pairs. However, to date, the net plasmonic effect on FRET is still under dispute, with experiments showing efficiency enhancement and reduction. This controversy is due to the challenges involved in the precise positioning of FRET pairs in the near field of a metallic ...
Calculating free energies from the vibrational density of states function: Validation and critical assessment
J. Chem. Phys., 150, 194111 (2019); doi: 10.1063/1.5079643
J. Chem. Phys., online article
We explore and show the usefulness of the density of states function for computing vibrational free energies and free energy differences between small systems. Therefore, we compare this density of states integration method (DSI) to more established schemes such as Bennett’s Acceptance Ratio method (BAR), the Normal Mode Analysis (NMA), and the Quasiharmonic ...
J. Phys. Chem., A 2019, 123, 10, 2163–2170, https://doi.org/10.1021/acs.jpca.8b12309
J. Phys. Chem., online article
The free energy is one of the central quantities in material and natural sciences. While being well-established, e.g., in drug design or catalyst optimization, computational methods lack a straightforward way to gain deeper insights into the calculated free energy, and thus the underlying chemical or physical processes. Here, we present a generally applicable, ...
Nano Lett., 2019, 19 (2), pp 1275–1281, DOI: 10.1021/acs.nanolett.8b04845
Nano Lett., online article
An ideal point light source is as small and as bright as possible. For fluorescent point light sources, homogeneity of the light sources is important as well as that the fluorescent units inside the light source maintain their photophysical properties, which is compromised by dye aggregation. Here we propose DNA origami as a rigid scaffold to arrange dye ...
PNAS, online article
A common design principle of heteromeric signaling proteins is the use of shared subunits. This allows encoding of complex messages while maintaining evolutionary flexibility. How cells regulate and control assembly of such composite signaling proteins remains an important open question. An example of particular complexity and biological relevance is the ...