Biology subjects

Marciniak, A.

Publications and source records attributed to Marciniak, A..

7 recordsLinked to original sources

bioRxiv2026

Who's driving? Common evolutionary mechanism of activation of class A GPCRs

Cells communicate with their environment by integrating signals, often chemical in nature, triggered by specific molecules bind to specific membrane-bound receptors, resulting in a downstream signaling cascade. Arguably, Gprotein-coupled receptors (GPCRs) constitute the most pharmacologically important family of such receptors, binding small molecules, peptides, lipids, and hormones with high specificity. However, despite a highly conserved fold and sequence similarity, GPCRs are still mostly studied on a case-by-case basis. Here, we infer a general, evolutionarily conserved mechanism of class A GPCR activation. By leveraging coevolution and machine learning methods applied to all class A GPCRs structures, we derive a mathematical description (a so-called collective variable - CV) of the receptors activation state which is independent of its sequence. Then, we bias molecular dynamics simulations along this CV to obtain transitions between activation states of a diverse set of class A GPCR family members. To demonstrate that our model generalizes beyond GPCRs in our training set, we obtain conformational transitions of an orphan receptor, GPR183. Finally, we show that we can model ligand effect on the receptors by converging Free Energy Surfaces of activation of the {beta}2-adrenergic receptor within this common mechanism framework. These results, to our knowledge, prove for the first time the existence of a mechanism uniting all class A GPCRs. Our approach thus facilitates direct comparisons between receptors and opens up the possibility of structural and dynamical studies of many orphan and understudied GPCRs. It also serves as a blueprint for inferring family-wide protein mechanisms.

biophysics↗

bioRxiv2024

An age-specific burial practice reflected in ancient DNA preservation in Neolithic Catalhöyük

Selective funerary practices can inform about social relationships in prehistoric societies but are often difficult to discern. Here we present evidence for an age-specific practice at the Neolithic site of Catalhoyuk in Anatolia, dating to the 7th millennium BCE. Among ancient DNA libraries produced from 362 petrous bone samples, those of subadults contained three times higher average human DNA than those of adults. This difference in organic preservation was also confirmed by FTIR analysis. Studying similar datasets from seven prehistoric and historical sites, we found a similar age-related difference in only one cemetery. We propose that the organic preservation difference with age was caused by the special treatment of chosen corpses before interment, such as defleshing or drying, which was more frequently applied to Catalhoyuk adults and promoted organic decay.

evolutionary biology↗

bioRxiv2024

Female lineages and changing kinship patterns in Neolithic Catalhöyük

Arguments have long suggested that the advent of early farming in the Near East and Anatolia was linked to a Mother Goddess cult. However, evidence for a dominant female role in these societies has been scarce. We studied social organisation, mobility patterns and gendered practices in Neolithic Southwest Asia using 131 paleogenomes from Catalhoyuk East Mound (7100-5950 BCE), a major settlement in Central Anatolia with an uninterrupted occupation and an apparent egalitarian structure. In contrast to widespread genetic evidence for patrilocality in Neolithic Europe, the Catalhoyuk individuals revealed no indication of patrilocal mobility. Analysing genetic kin ties among individuals buried in the same house (co-burials) across 35 Catalhoyuk buildings, we identified close ties concentrated within buildings and among neighbours in Catalhoyuks Early period, akin to those in the preceding Pre-Pottery Neolithic in Southwest Asia. This pattern weakened over time: by the late 7th millennium BCE, subadults buried in the same building were rarely closely genetically related, despite sharing similar diets. Still, throughout the sites occupation, genetic connections within Catalhoyuk buildings were much more frequently connected via the maternal than the paternal line. We also identified differential funerary treatment of female subadults compared to those of males, with a higher frequency of grave goods associated with females. Our results reveal how kinship practices changed while key female roles persisted over one thousand years in a large Neolithic community in western Eurasia.

genomics↗

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↗