Biology subjects

Lemkul, J. A.

Publications and source records attributed to Lemkul, J. A..

9 recordsLinked to original sources

bioRxiv2026

Pick your poison: Tetrodotoxin variants give Pacific newts a potential leg up in the coevolutionary arms race with resistant garter snake predators

Coevolution proceeds through the evolution of traits that mediate ecological interactions and evolutionary outcomes. In the arms race between toxic Pacific newts (Taricha) and their garter snake predators (Thamnophis), this interface involves tetrodotoxin (TTX), an antipredator defense that inhibits nerve and muscle function by blocking voltage-gated sodium channels. In response, snakes have evolved TTX-resistant channels, in some cases leading to snake populations that are nearly invulnerable to TTX. For decades, newt TTX has been treated as a single defensive trait, yet TTX occurs as a family of structurally related analogs that may represent alternative defenses against snakes. Here, we characterize TTX analog diversity in all four species of Taricha and evaluate how these compounds interact with sodium channels in coevolved garter snakes. Using LC-MS analysis of newt skin secretions, we detected a diverse suite of TTX analogs previously unrecognized in Pacific newts. We then used molecular docking models to evaluate interactions between various TTX analogs and variants of the skeletal muscle channel (NaV1.4) that span the range of TTX resistance in garter snakes. We found that some TTX analogs docked better than canonical TTX in resistant snake channels. Notably, we show that 11-deoxy-4-epi-TTX and 11-deoxy-TTX have favorable interactions with hydrophobic amino-acid substitutions in extremely resistant garter snake sodium channels, potentially circumventing predator resistance to canonical TTX. Our results suggest a complex arms race involving multiple newt TTX analogs and multiple snake sodium channel variants. As such, newts may keep pace with snakes by diversifying their arsenal of chemical weapons. SignificanceIn western North America, some newts have enough toxin in their skin to kill most predators, but coevolution has led to toxin resistance in their garter snake predators that in some cases is so extreme that snakes should be able to withstand more toxin than newts could possibly possess. Here, we explore the possibility that newts may be able to fight back against these resistant predators through the by evolving a diverse repertoire of toxins. We use chemical analyses and computational modeling to show that newts have a wide variety of toxins, some of which are likely to be more effective against resistant snakes, suggesting that coevolution may continue to occur even when snakes become very resistant.

evolutionary biology↗

bioRxiv2025

Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design

The growing interest in nucleic acids as therapeutic targets has prompted the devel-opment of novel computational methods to facilitate drug discovery. In this study, we extend the Site Identification by Ligand Competitive Saturation (SILCS) methodology to characterize ligand-nucleic acid interactions using the Drude polarizable force field. We demonstrate the ability of the Drude force field to better model solute-nucleic acid interactions, resulting in improved identification of known binding sites and ligand binding favorability predictions across a diverse set of nucleic acid structures. This new workflow addresses limitations in previous SILCS studies by exploiting the en-hanced sampling of solutes in the original SILCS-RNA workflow, accurately modeling the interactions of charged species, and improving solute sampling in minor groove binding sites. These results establish this Drude-based SILCS workflow as a valuable tool for structure-based drug design targeting nucleic acids and offer insights into solute preferences that can guide rational ligand design.

biophysics↗

bioRxiv2025

Interface integrity in septin protofilaments is maintained by an arginine residue conserved from yeast to man.

The septins are conserved, filament-forming, guanine nucleotide binding cytoskeletal proteins. They assemble into palindromic protofilaments which polymerize further into higher-ordered structures that participate in essential intracellular processes such as cytokinesis or polarity establishment. Septins belong structurally to the P-Loop NTPases but, unlike their relatives Ras or Rho, do not mediate signals to effectors through GTP binding and hydrolysis. Biochemical approaches addressing how and why septins utilize nucleotides are hampered by the lack of nucleotide free complexes. Using molecular dynamics simulations, we determined structural alterations and inter-subunit binding free energies in human and yeast septin dimer structures and in their in silico generated apo forms. An interchain saltbridge network in the septin unique {beta}-meander, conserved across all kingdoms of septin containing species, is destabilized upon nucleotide removal, concomitant with disruption of the entire G-interface. Within this network, we identified a conserved arginine residue, Arg({beta}b), as the central interaction hub. The essential role of Arg({beta}b) for interface integrity was confirmed species-overlapping in human and yeast septins by in vitro and in vivo experimentation.

biochemistry↗

bioRxiv2024

Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer

The cell membrane functions as a semi-permeable barrier that governs the transport of materials into and out of cells. The bilayer features a distinct dielectric gradient due to the amphiphilic nature of its lipid components. This gradient influences various aspects of small molecule permeation and the folding and functioning of membrane proteins. Here, we employ polarizable molecular dynamics simulations to elucidate the impact of the electronic environment on the permeation process. We simulated eight distinct amino acid sidechain analogs within a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer using the Drude polarizable force field (FF). Our approach including both unbiased and umbrella sampling simulations. By using a polarizable FF, we sought to investigate explicit dipole responses in relation to local electric fields along the membrane normal. We evaluate molecular dipole moments, which exhibit variation based on their localization within the membrane, and compare the outcomes with analogous simulations using the nonpolarizable CHARMM36 FF. This comparative analysis aims to discern characteristic differences in the free energy surfaces of permeation for the various amino acid analogs. Our results provide the first systematic quantification of the impact of employing an explicitly polarizable FF in this context compared to the fixed-charge convention inherent to nonpolarizable FFs, which may not fully capture the influence of the membrane dielectric gradient.

biophysics↗

bioRxiv2024

Dynamics, Electrostatics, and Thermodynamics ofBase Pairing at the LTR-III Quadruplex:Duplex Junction

G-quadruplexes (GQs) play key regulatory roles within the human genome and have also been identified to play similar roles in other eukaryotes, bacteria, archaea, and viruses. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immunodeficiency syndrome (AIDS), can form two GQs in its long terminal repeat (LTR) promoter region, each of which act to regulate viral gene expression in opposing manners. The major LTR GQ, called LTR-III, is a distinct hybrid GQ containing a 12-nucleotide duplex loop attached to the quadruplex motif. The resulting quadruplex:duplex junction (QDJ) has been hypothesized to serve as a selective drug targeting site. To better understand the dynamics of this QDJ, we performed conventional and enhanced-sampling molecular dynamics simulations using the Drude-2017 force field. We observed unbiased and reversible formation of additional base pairs in the QDJ, between Ade4:Thy14 and Gua3:Thy14. Both base pairs were electrostatically favored but geometric constraints within the junction may drive the formation of, and preference for, the Ade4:Thy14 base pair. Finally, we demonstrated that the base pairs are separated only by small energy barriers that may enable transitions between both base-paired states. Together, these simulations provide new insights into the dynamics, electrostatics, and thermodynamics of the LTR-III QDJ. SIGNIFICANCEHere, we characterize the quadruplex:duplex junction of the HIV-1 LTR-III G-quadruplex. We find that two additional base pairs can form in the junction and are driven by electrostatic, thermodynamic, and geometric factors. G-quadruplexes containing such junctions are rather recent discoveries, and it has been proposed that these junctions can act as selective targets for drugs. These results further identify distinct chemical and electrostatic characteristics that can be used to guide drug design studies.

biophysics↗

bioRxiv2024

Structural dynamics of the methyl-coenzyme M reductase active site are influenced by coenzyme F430 modifications

Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in methanogens and anaerobic methanotrophs (ANME), respectively. The prosthetic group of MCR is coenzyme F430, a nickel-containing tetrapyrrole derivative. Additionally, a few modified versions of F430 have been discovered, including the 172-methylthio-F430 (mt-F430) that functions with ANME-1 MCR. This study employs molecular dynamics (MD) simulations to unravel the intricacies of the active-site dynamics of MCR from Methanosarcina acetivorans and ANME-1 when bound to the canonical F430 compared to 172-thioether coenzyme F430 variants and substrates for methane formation. Overall, our simulations indicate that each MCR active site is optimized for a given version of F430 and support the importance of the Gln to Val substitution in accommodating the 172 methylthio modification. Notably, modifications in the 172 position disrupt the canonical coordination among cofactors in M. acetivorans MCR, implicating structural perturbations, but evidence of active site reorganization to maintain substrate positions suggest that the modified F430s could be accommodated in a methanogenic MCR. We additionally report the first quantitative estimate of MCR intrinsic electric fields pivotal in driving methane formation. Our results suggest that the electric field aligned along the CH3-S-CoM thioether bond facilitates homolytic bond cleavage, coinciding with the proposed catalytic mechanism. Structural perturbations, however, weaken and misalign these electric fields, emphasizing the significance of the active site structure in maintaining their integrity. In conclusion, our results deepen the understanding of MCR active-site dynamics, the enzymes organizational role in intrinsic electric fields for catalysis, and the interplay between active site structure and electrostatics. This work not only advances our comprehension of MCR functionality but also provides a foundation for future investigations employing sophisticated models to capture the complex electronic properties of MCR active sites quantitatively.

biophysics↗

bioRxiv2023

Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes

AbstractThe formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs play crucial roles in regulating transcription, translation, and replication; and maintaining the genome, among others, thus changes to their structures can lead to diseases such as cancer. Previous studies using polarizable molecular dynamics simulations have shown differences in ion binding properties between telomeric and TERRA GQs despite architectural similarities. Here, we used volume-based metady-namics and repulsive potential simulations in conjunction with polarizable force fields to quantify the impact of ion binding on GQ dynamics and ion binding free energies. Furthermore, we describe how GQs exert electric fields on their surroundings to link dynamics with variations in electronic structure. Our findings provide new insights into the energetic, physical, and conformational properties of GQs and expose subtle, but important, differences between DNA and RNA GQs with the same fold.

biophysics↗

bioRxiv2022

An in silico approach to determine inter-subunit affinities in human septin complexes

The septins are a conserved family of filament-forming guanine nucleotide binding proteins, often named the fourth component of the cytoskeleton. Correctly assembled septin structures are required for essential intracellular processes such as cytokinesis, vesicular transport, polarity establishment, and cellular adhesion. Structurally, septins belong to the P-Loop NTPases but they do not mediate signals to effectors through GTP binding and hydrolysis. GTP binding and hydrolysis are believed to contribute to septin complex integrity, but biochemical approaches addressing this topic are hampered by the stability of septin complexes after recombinant expression and the lack of nucleotide-depleted complexes. To overcome this limitation, we used a molecular dynamics-based approach to determine inter-subunit binding free energies in available human septin dimer structures and in their apo forms, which we generated in silico. The nucleotide in the GTPase active subunits SEPT2 and SEPT7, but not in SEPT6, was identified as a stabilizing element in the G interface as it is coordinated at its ribose ring to conserved amino acids. Removal of GDP from SEPT2 and SEPT7 results in flipping of a conserved Arg residue and disruption of an extensive hydrogen bond network in the septin unique element, concomitant with a decreased inter-subunit affinity.

biochemistry↗

bioRxiv2018

FusoPortal: An interactive repository of hybrid MinION sequenced Fusobacterium genomes improves gene identification and characterization

Here we present FusoPortal, an interactive repository of Fusobacterium genomes that were sequenced using a hybrid MinION long-read sequencing pipeline, followed by assembly and annotation using a diverse portfolio of predominantly open-source software. Significant efforts were made to provide genomic and bioinformatic data as downloadable files, including raw sequencing reads, genome maps, gene annotations, protein functional analysis and classifications, and a custom BLAST server for FusoPortal genomes. FusoPortal has been initiated with eight complete genomes, of which seven were previously only drafts that varied from 24-67 contigs. We showcase that genomes in FusoPortal provide accurate open reading frame annotations, and have corrected a number of large genes (>3 kb) that were previously misannotated due to contig boundaries. In summary, FusoPortal (http://fusoportal.org) is the first database of MinION sequenced and completely assembled Fusobacterium genomes, and this central Fusobacterium genomic and bioinformatic resource will aid the scientific community in developing a deeper understanding of how this human pathogen contributes to an array of diseases including periodontitis and colorectal cancer.\n\nImportanceIn this study, we report a hybrid MinION whole genome sequencing pipeline, and describe the genomic characteristics of the first eight strains deposited in the FusoPortal database. This collection of highly accurate and complete genomes drastically improves upon previous multi-contig assemblies by correcting and newly identifying a significant number of open reading frames. We believe this resource will result in the discovery of proteins and molecular mechanisms used by an oral pathogen, with the potential to further our understanding of how F. nucleatum contributes to a repertoire of diseases including periodontitis, pre-term birth, and colorectal cancer

microbiology↗