Biology subjects

Lyu, W.

Publications and source records attributed to Lyu, W..

23 records · Page 2Linked to original sources

bioRxiv2022

Abl2 mediates microtubule nucleation and repair via tubulin co-condensation.

Abl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with microtubules to regulate axon guidance and neuronal morphogenesis. Vertebrate Abl2 binds to microtubules and promotes their plus-end elongation both in vitro and in cells, but the molecular mechanisms by which Abl2 regulates microtubule (MT) dynamics were unclear. We report here that Abl2 regulates MT assembly via condensation and direct interactions with both the MT lattice and tubulin dimers. We find that Abl2 promotes MT nucleation, which is further facilitated by the ability of the Abl2 C-terminal half to undergo phase separation and form co-condensates with tubulin. A naturally occurring tubulin binding-deficient Abl2 splice isoform fails to promote nucleation. Abl2 binds to regions adjacent to MT damage and facilitates their repair via fresh tubulin recruitment and increases MT rescue frequency and lifetime. MT recovery after nocodazole treatment is greatly slowed in Abl2 knockout COS-7 cells compared to wild type cells. We propose a model in which Abl2 locally concentrates tubulin and recruits it to MT tips or to defects in the MT lattice to promote MT repair, rescue, and nucleation.

biochemistry↗

bioRxiv2022

Rational evolution of a recombinant DNA polymerase for efficient incorporation of unnatural nucleotides by dual-site boosting

Machine learning modelling assisting function-oriented enzyme engineering is normally built on predefined protein sequence space. However, efficient defining the determinant amino acid positions upon which the combinatorial mutation library is constructed is still a challenge in protein science. Herein, we present a comprehensive investigation of modifying a recombinant DNA polymerase for efficient incorporating one unnatural nucleotide, including the identification of key sites/regions, machine learning-assisted mutants screening, and the underlying mechanism of kinetics boosting. By using hundreds of training points and only dozens of testing samples, we found that one highly engineered enzymes catalytic efficiency can be further improved by one order of magnitude by specific mutation on two sites, 485I and 451L. Compared to the position 485 which is known to dominate local conformation of B-family DNA polymerases, 451 is a split-new active site discovered by our approach. A novel allosteric regulation mechanism is underlying the apparent synergy of 485I and 451L on the kinetics boosting. As a result, a "half-closed" conformation of the binding pocket and a cooperative binding of both primer and template DNA strands on the protein accelerated the processes of substrates incorporation, molecular recognition, and releasing of incorrect nucleotides. These findings have implications in guiding the function-tuning of DNA polymerases for a broad range of biotechnological applications.

biochemistry↗

bioRxiv2021

Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data

With the rapid growth of the number of sequenced ancient genomes, there has been increasing interest in using this new information to study past and present adaptation. Such an additional temporal component has the promise of providing improved power for the estimation of natural selection. Over the last decade, statistical approaches for detection and quantification of natural selection from ancient DNA (aDNA) data have been developed. However, most of the existing methods do not allow us to estimate the timing of natural selection along with its strength, which is key to understanding the evolution and persistence of organismal diversity. Additionally, most methods ignore the fact that natural populations are almost always structured, which can result in overestimation of the effect of natural selection. To address these issues, we introduce a novel Bayesian framework for the inference of natural selection and gene migration from aDNA data with Markov chain Monte Carlo techniques, co-estimating both timing and strength of natural selection and gene migration. Such an advance enables us to infer drivers of natural selection and gene migration by correlating genetic evolution with potential causes such as the changes in the ecological context in which an organism has evolved. The performance of our procedure is evaluated through extensive simulations, with its utility shown with an application to ancient chicken samples.

genetics↗

bioRxiv2021

Moment-based approximations for the Wright-Fisher model of population dynamics under natural selection at two linked loci

Properly modelling genetic recombination and local linkage has been shown to bring significant improvement to the inference of natural selection from time series data of allele frequencies under a Wright-Fisher model. Existing approaches that can account for genetic recombination and local linkage are built on either the diffusion approximation or a moment-based approximation of the Wright-Fisher model. However, methods based on the diffusion approximation are likely to require much higher computational cost, whereas moment-based approximations may suffer from the distribution support issue: for example, the normal approximation can seriously affect computational accuracy. In the present work, we introduce two novel moment-based approximations of the Wright-Fisher model on a pair of linked loci, both subject to natural selection. Our key innovation is to extend existing methods to account for both the mean and (co)variance of the two-locus Wright-Fisher model with selection. We devise two approximation schemes, using a logistic normal distribution and a hierarchical beta distribution, respectively, by matching the first two moments of the Wright-Fisher model and the approximating model. As compared with the diffusion approximation, our approximations enable the approximate computation of the transition probabilities of the Wright-Fisher model at a far smaller computational cost. We can also avoid the distribution support issue found in the normal approximation.

genetics↗

bioRxiv2020

On the accuracy of molecular simulation-based predictions of koff values: a Metadynamics study

Molecular simulations have made great progresses in predicting koff values--the kinetic constant of drug unbinding, a key parameter for modern pharmacology--yet computed values under- or over-estimate experimental data in a system- and/or technique-dependent way. In an effort at gaining insights on this issue, here we used an established method to calculate koff values--frequency-adaptive metadynamics with force field-- and a subsequent QM/MM descriptions of the interactions. First, using force field-based metadynamics, we calculate koff of the Positron Emission Tomography (PET) ligand iperoxo targeting the human muscarinic acetylcholine receptor M2. In line with previously performed in silico studies, the prediction (3.7 {+/-} 0.7 * 10-4 s-1) turned out to differ significantly from the experimentally measured value (1.0 {+/-} 0.2 * 10-2 s-1). Next, we use DFT-based QM/MM simulations to show that this discrepancy arises from erroneous force field energetics at the transition state. It turns out that this discrepancy is partly caused by lack of electronic polarization and/or charge transfer in commonly employed force field. We expect these issues to arise also in other systems where charged portions of the system play a pivotal role, such as protein- or DNA-protein complexes. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/015396v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1ee4e1aorg.highwire.dtl.DTLVardef@49ba0forg.highwire.dtl.DTLVardef@565f25org.highwire.dtl.DTLVardef@80940e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗