Molecular Biosciences Scholarly Works: Recent submissions
Now showing items 1-20 of 590
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Branched actin networks are assembled on microtubules by adenomatous polyposis coli for targeted membrane protrusion
(Rockefeller University Press, 2020-06-29)Cell migration is driven by pushing and pulling activities of the actin cytoskeleton, but migration directionality is largely controlled by microtubules. This function of microtubules is especially critical for neuron ... -
Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning
(Frontiers Media, 2023-01-17) -
GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling
(American Chemical Society, 2022-02-24)We introduce a Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and free energy profiling workflow (GLOW) to predict molecular determinants and map free energy landscapes of biomolecules. All-atom ... -
Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex
(Oxford University Press, 2022-07-06)Sex chromosomes frequently differ from the autosomes in the frequencies of genes with sexually dimorphic or tissue-specific expression. Multiple hypotheses have been put forth to explain the unique gene content of the X ... -
Docking-based long timescale simulation of cell-size protein systems at atomic resolution
(National Academy of Sciences, 2022-10-03)Computational methodologies are increasingly addressing modeling of the whole cell at the molecular level. Proteins and their interactions are the key component of cellular processes. Techniques for modeling protein ... -
Septate junction proteins are required for cell shape changes, actomyosin reorganization and cell adhesion during dorsal closure in Drosophila
(Frontiers Media, 2022-09-27)Septate junctions (SJs) serve as occluding barriers in invertebrate epithelia. In Drosophila, at least 30 genes are required for the formation or maintenance of SJs. Interestingly, loss-of-function mutations in core SJ ... -
Analytical Approaches for Deriving Friction Coefficients for Selected α‑Helical Peptides Based Entirely on Molecular Dynamics Simulations
(American Chemical Society, 2022-10-27)In this paper we derive analytically from molecular dynamics (MD) simulations the friction coefficients related to conformational transitions within several model peptides with α-helical structures. We study a series of ... -
Size of the protein-protein energy funnel in crowded environment
(Frontiers Media, 2022-11-08)Association of proteins to a significant extent is determined by their geometric complementarity. Large-scale recognition factors, which directly relate to the funnel-like intermolecular energy landscape, provide important ... -
Discovery of malathion resistance QTL in Drosophila melanogaster using a bulked phenotyping approach
(Oxford University Press, 2022-10-17)Drosophila melanogaster has proved an effective system with which to understand the evolutionary genetics and molecular mechanisms of insecticide resistance. Insecticide use has left signatures of selection in the fly ... -
Genetic variation in P-element dysgenic sterility is associated with double-strand break repair and alternative splicing of TE transcripts
(Public Library of Science, 2022-12-07)The germline mobilization of transposable elements (TEs) by small RNA mediated silencing pathways is conserved across eukaryotes and critical for ensuring the integrity of gamete genomes. However, genomes are recurrently ... -
QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs
(Elsevier, 2021-02-23)The number of available protein sequences in public databases is increasing exponentially. However, a significant percentage of these sequences lack functional annotation, which is essential for the understanding of how ... -
Linearized Siderophore Products Secreted via MacAB Efflux Pump Protect Salmonella enterica Serovar Typhimurium from Oxidative Stress
(American Society for Microbiology, 2020-05-05)Nontyphoidal salmonellae (NTS) are exposed to reactive oxygen species (ROS) during their residency in the gut. To survive oxidative stress encountered during infection, salmonellae employ several mechanisms. One of these ... -
Oncogenic Serine 45-Deleted β-Catenin Remains Susceptible to Wnt Stimulation and APC Regulation in Human Colonocytes
(MDPI, 2020-07-30)The Wnt/β-catenin signaling pathway is deregulated in nearly all colorectal cancers (CRCs), predominantly through mutation of the tumor suppressor Adenomatous Polyposis Coli (APC). APC mutation is thought to allow a ... -
APC controls Wnt-induced β-catenin destruction complex recruitment in human colonocytes
(Nature Research, 2020-02-19)Wnt/β-catenin signaling is essential for intestinal homeostasis and is aberrantly activated in most colorectal cancers (CRC) through mutation of the tumor suppressor Adenomatous Polyposis Coli (APC). APC is an essential ... -
Coronavirus infection and PARP expression dysregulate the NAD metabolome: An actionable component of innate immunity
(Elsevier, 2020-12-25)Poly(ADP-ribose) polymerase (PARP) superfamily members covalently link either a single ADP-ribose (ADPR) or a chain of ADPR units to proteins using NAD as the source of ADPR. Although the well-known poly(ADP-ribosylating) ... -
PARP14: A key ADP-ribosylating protein in host–virus interactions?
(Public Library of Science, 2022-06-09)Over 300 posttranslational modifications (PTMs) are known to modify the functions of proteins by affecting processes ranging from activation, degradation, localization, secretion, recognition, and regulation [1]. One such ... -
Efficacy of an HSV-1 Neuro-Attenuated Vaccine in Mice Is Reduced by Preventing Viral DNA Replication
(MDPI, 2022-04-22)We previously isolated an HSV-1 mutant, KOS-NA, that contains two non-synonymous mutations in UL39. One of the mutations, resulting in an R950H amino acid substitution in ICP6, renders KOS-NA severely neuro-attenuated and ... -
Inter-species lateral gene transfer focused on the Chlamydia plasticity zone identifies loci associated with immediate cytotoxicity and inclusion stability
(Wiley, 2021-11-04)Chlamydia muridarum actively grows in murine mucosae and is a representative model of human chlamydial genital tract disease. In contrast, C. trachomatis infections in mice are limited and rarely cause disease. The factors ... -
CRC-derived exosomes containing the RNA binding protein HuR promote lung cell proliferation by stabilizing c-Myc mRNA
(Taylor and Francis, 2022-02-07)HuR overexpression is related to poor survival in patients with colon cancer. HuR overexpression leads to stabilization of tumor-promoting mRNAs by binding to 3′UTR-resident AREs. Exosomes, nanosized lipid bilayer vesicles, ... -
Pseudomonas aeruginosa Bacterioferritin Is Assembled from FtnA and BfrB Subunits with the Relative Proportions Dependent on the Environmental Oxygen Availability
(MDPI, 2022-02-25)Ferritins are iron storage proteins assembled from 24 subunits into a spherical and hollow structure. The genomes of many bacteria harbor genes encoding two types of ferritin-like proteins, the bacterial ferritins (Ftn) ...
