Biology subjects

Bekker, G.-J.

Publications and source records attributed to Bekker, G.-J..

4 recordsLinked to original sources

bioRxiv2024

Molecular dynamics unveils multiple-site binding of inhibitors with reduced activity on the surface of dihydrofolate reductase

The sensitivity to protein inhibitors is altered by modifications or protein mutations, as represented by drug resistance. The mode of stable drug binding to the protein pocket has been experimentally clarified. However, the nature of the binding of inhibitors with reduced sensitivity remains unclear at the atomic level. In this study, we analyzed the thermodynamics and kinetics of inhibitor binding to the surface of wild-type and mutant dihydrofolate reductase (DHFR) using molecular dynamics simulations combined with Markov state modeling. A strong inhibitor of methotrexate (MTX) showed a preference for the active site of wild-type DHFR with minimal binding to unrelated (secondary) sites. Deletion of a side-chain fragment in MTX largely destabilized the active site-bound state, with clear evidence of binding to secondary sites. Similarly, the F31V mutation in DHFR diminished the specificity of MTX binding to the active site. These results reveal the presence of multiple-bound states whose stabilities are comparable to or higher than those of the unbound state, suggesting that a reduction in the binding affinity for the active site significantly elevates the fractions of these states. This study sheds light on the specific drug recognition by proteins and the selectivity of drug binding sites on protein surfaces. (199 words)

biophysics↗

bioRxiv2023

Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics

Binding of a small and flexible molecule, ribocil A (non-binder) or B (binder), to the deep pocket of the aptamer domain of the FMN riboswitch was studied by mD-VcMD, which is a generalized-ensemble method based on molecular dynamics (MD) simulation. Ribocil A and B are structurally similar because they are optical isomers mutually. In the initial conformation of simulation, both ligands and the aptamer were completely dissociated in explicit solvent. The resultant free-energy landscape of ribocil B binding to the aptamer was funnel-like, whereas that of ribocil A was rugged, which agrees qualitatively with an experiment. When entering the gate (named "front gate") of the pocket, the ligand interacted with the aptamer by native and non-native {pi}-{pi} stackings, and the stackings restrained the molecular orientation of the ligands to be advantageous to reach the binding site smoothly. The simulation showed another pathway, which also led the ligands to the binding site. Its gate (maned "rear gate") located completely opposite to the front gate on the aptamers surface. However, approach from the rear gate required overcoming a free-energy barrier before reaching the binding site, and the ligands should rotate largely and sharply at the free-energy barrier. This ligands orientation property is discussed referring to a ligand orientation selection mechanism exserted by a membrane protein capturing its ligand.

biophysics↗

bioRxiv2022

Fly-casting with ligand-sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible molecule

To elucidate computationally a binding mechanism of a middle-sized flexible molecule, bosentan, to a GPCR protein, human endothelin receptor type B (hETB), a GA-guided multidimensional virtual-system coupled molecular dynamics (GA-mD-VcMD) simulation was performed. This method is one of generalized ensemble methods and produces a free-energy landscape of the ligand-receptor binding by searching large-scale motions accompanied with stably keeping the fragile cell-membrane structure. All molecular components (bosentan, hETB, membrane, and solvent) were represented with an all-atom model, and sampling was carried out from conformations where bosentan was distant from the binding site in the hETBs binding pocket. The deepest basin in the resultant free-energy landscape was assigned to the native-like complex conformation. The obtained binding mechanism is as follows. First, bosentan fluctuating randomly in solution is captured by a tip region of the flexible N-terminal tail of hETB via nonspecific attractive interactions (fly-casting). Bosentan then occasionally slides from the tip to root of the N-terminal tail (ligand-sliding). In this sliding, bosentan passes the gate of the binding pocket from outside to inside of the pocket with accompanying a quick reduction of the molecular orientational variety of bosentan (orientational selection). Last, in the pocket, ligand-receptor attractive native contacts are formed, and eventually the native-like complex is completed. The bosentan-captured conformations by the tip- and root-regions of the N-terminal tail correspond to two basins in the free-energy landscape, and the ligand-sliding corresponds to overcoming a free-energy barrier between the basins.

biophysics↗

bioRxiv2020

Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

Capturing the dynamic processes of biomolecular systems in atomistic detail remains difficult despite recent experimental advances. Although molecular dynamics (MD) techniques enable atomic-level observations, simulations of "slow" biomolecular processes (with timescales longer than submilliseconds) are challenging, due to current computer speed limitations. Therefore, we developed a new method to accelerate MD simulations by high-frequency ultrasound perturbation. The binding events between the protein CDK2 and its small-molecule inhibitors were nearly undetectable in 100-ns conventional MD, but the new method successfully accelerated their slow binding rates by up to 10-20 times. The accelerated MD simulations revealed a variety of microscopic kinetic features of the inhibitors on the protein surface, such as the existence of different binding pathways to the active site. Moreover, the simulations allowed estimating the corresponding kinetic parameters and exploring other druggable pockets. This method can thus provide deeper insight into the microscopic interactions controlling biomolecular processes.

biophysics↗