Biology subjects

Marciniak, A.

Publications and source records attributed to Marciniak, A..

4 recordsLinked to original sources

bioRxiv2023

Low-barrier hydrogen bond determines target-binding affinity and specificity of the antitubercular drug bedaquiline

The role of short strong hydrogen bonds (SSHB) in ligand-target binding remains largely unexplored, thereby hindering a potentially important avenue in the rational drug design. Here, we investigate the interaction between bedaquiline (Bq), a potent anti-tuberculosis drug, and the mycobacterial ATP synthase, to unravel the role of a specific hydrogen bond to a conserved acidic residue in the target affinity and specificity. Our ab initio molecular dynamics simulations reveal that this bond belongs to the SSHB category and accounts for a substantial fraction of the target binding energy. We also demonstrate that the presence of an extra acidic residue (D32), found exclusively in mycobacteria, cooperatively enhances the HB strength ensuring the specificity for the mycobacterial target. Consistently, we show that the removal of D32 markedly weakens the affinity, leading to Bq resistance associated with mutations of D32 to non-acidic residues. By designing simple Bq analogs, we then explore the possibility to overcome the resistance and potentially broaden the Bq antimicrobial spectrum by making the SSHB independent on the presence of the extra acidic residue.

biophysics↗

bioRxiv2023

Coevolution-driven method for efficiently simulating conformational changes in proteins reveals molecular details of ligand effects in the beta2AR receptor

With the advent of AI-powered structure prediction, the scientific community is inching ever closer to solving protein folding. An unresolved enigma, however, is to accurately, reliably and deterministically predict alternative conformational states that are crucial for the function of e.g. transporters, receptors or ion channels where conformational cycling is innately coupled to protein function. Accurately discovering and exploring all conformational states of membrane proteins has been challenging due to the need to retain atomistic detail while enhancing the sampling along interesting degrees of freedom. The challenges include but are not limited to finding which degrees of freedom are relevant, how to accelerate the sampling along them, and then quantifying the populations of each micro- and macrostate. In this work, we present a methodology that finds the relevant degrees of freedom by combining evolution and physics through machine learning and apply it to the {beta}2 adrenergic receptor conformational sampling. In addition to predicting new conformations that are beyond the training set, we have computed free energy surfaces associated with the proteins conformational landscape. We then show that the methodology is able to quantitatively predict the effect of an array of ligands on the {beta}2 adrenergic receptor activation, and that the full conformational landscape, including states related to biased signaling, is discovered using this procedure. Lastly, we also stake out the structural determinants of activation and inactivation pathway signaling through different ligands.

biophysics↗

bioRxiv2023

Mutant analysis of Kcng4b reveals how the different functional states of the voltage-gated potassium channel regulate ear development

The voltage gated (Kv) slow-inactivating delayed rectifier channel regulates the development of hollow organs of the zebrafish. The functional tetramer consists of an electrically active subunit (Kcnb1, Kv2.1) and a modulatory silent subunit (Kcng4b, Kv6.4). The two mutations in zebrafish kcng4b - kcng4b-C1 and kcng4b-C2 (Gasanov et al., 2021) - have been studied during ear development using electrophysiology, developmental biology and in silico structural modelling. kcng4b-C1 mutation causes a C-terminal truncation characterized by mild Kcng4b loss-of-function (LOF) manifested by failure of kinocilia to extend and formation of ectopic otoliths. In contrast, the kcng4b-C2-/- mutation causes the C-terminal domain to elongate and the ectopic seventh transmembrane (TM) domain to form, converting the intracellular C-terminus to an extracellular one. Kcng4b-C2 acts as a Kcng4b gain-of-function (GOF) allele. Otoliths fail to develop and kinocilia are reduced in kcng4b-C2-/-. These results show that different mutations of the silent subunit Kcng4 can affect the activity of the Kv channel and cause a wide range of developmental defects.

developmental biology↗

bioRxiv2021

Determinants of directionality and efficiency of the ATP synthase Fo motor at atomic resolution

Fo subcomplex of ATP synthase is an membraneembedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motors directionality naturally arises from the interplay between intra-protein interactions and energetics of protonation of the c-ring. Notably, our calculations reveal that the strictly conserved arginine in the a-subunit (R176) serves as a jack-of-all-trades: it dictates the direction of rotation, controls the protonation state of the proton-release site and separates the two proton-access half-channels. Therefore, arginine is necessary to avoid slippage between the proton flux and the mechanical output and guarantees highly efficient energy conversion. We also provide mechanistic explanations for the reported defective mutations of R176, reconciling the structural information on the Fo motor with previous functional and single-molecule data.

biophysics↗