Publications by authors named "Nikolay Dokholyan"

Article Synopsis
  • Recent advancements in autonomous technology show promise for revolutionizing areas like nanomedicine by enabling efficient operation of biological therapies without human intervention.
  • Engineering biological nanocomputing agents from nucleic acids and proteins presents challenges, despite two decades of research demonstrating their logical behavior within living cells.
  • The paper discusses the programmability and synergy of nucleic acids and proteins, highlights their versatility in creating new functions, and addresses potential limitations in the field of nanocomputing.
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Copper is an essential element involved in various biochemical processes, such as mitochondrial energy production and antioxidant defense, but improper regulation can lead to cellular toxicity and disease. Copper Transporter 1 (CTR1) plays a key role in copper uptake and maintaining cellular copper homeostasis. Although CTR1 endocytosis was previously thought to reduce copper uptake when levels are high, it was unclear how rapid regulation is achieved.

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  • - RNA-Puzzles is a collaborative project focused on improving the prediction of RNA three-dimensional structures, with predictions made by modeling groups before experimental structures are published.
  • - A significant set of predictions was made by 18 groups for 23 different RNA structures, including various elements like ribozymes and aptamers.
  • - The study highlights key challenges in RNA modeling, such as identifying helix pairs and ensuring proper stacking, and notes that some top-performing groups also excelled in a separate competition (CASP15).
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Therapies for acute myeloid leukemia (AML) face formidable challenges due to relapse, often driven by leukemia stem cells (LSCs). Strategies targeting LSCs hold promise for enhancing outcomes, yet paired comparisons of functionally defined LSCs at diagnosis and relapse remain underexplored. We present transcriptome analyses of functionally defined LSC populations at diagnosis and relapse, revealing significant alterations in IL-1 signaling.

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Chimeric antigen receptor T cell therapies have achieved great success in eradicating some liquid tumors, whereas the preclinical results in treating solid tumors have proven less decisive. One of the principal challenges in solid tumor treatment is the physical barrier composed of a dense extracellular matrix, which prevents immune cells from penetrating the tissue to attack intratumoral cancer cells. Here, we improve immune cell infiltration into solid tumors by manipulating septin-7 functions in cells.

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A complex web of intermolecular interactions defines and regulates biological processes. Understanding this web has been particularly challenging because of the sheer number of actors in biological systems: ∼10 proteins in a typical human cell offer a plausible 10 interactions. This number grows rapidly if we consider metabolites, drugs, nutrients, and other biological molecules.

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c-di-GAMP was first identified in bacteria to promote colonization, while mammalian 2'3'-cGAMP is synthesized by cGAS to activate STING for innate immune stimulation. However, 2'3'-cGAMP function beyond innate immunity remains elusive. Here, we report that 2'3'-cGAMP promotes cell migration independent of innate immunity.

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  • * A study using deep machine learning found that levodopa interacts with important iron transport mechanisms and may disrupt iron regulation in cells.
  • * The findings stress the need to assess levodopa's impact on iron metabolism in Parkinson's treatment, urging further research to balance its benefits with potential side effects.
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  • Understanding how consciousness and behavior are linked to neural activity is crucial for improving treatments for brain disorders.
  • Current research on the medial prefrontal cortex, particularly using existing experimental designs like rodent spike train recordings, lacks the statistical power needed to uncover complex neural processes.
  • This study introduces new methods to analyze neural data which highlights the limitations of current approaches and emphasizes the need for larger, more reliable datasets for meaningful comparisons.
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  • * The study revealed the SOD1 trimer interactome, identifying binding partners in the brain, spinal cord, and skeletal muscle that may affect cellular functions such as synaptic function and metabolism.
  • * Key findings point to specific genes and proteins related to SOD1 trimers, suggesting potential connections between genetic factors and disease mechanisms in ALS.
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Background: with a rich history of traditional medicinal use, has garnered significant attention in contemporary research for its potential therapeutic applications in various human diseases, including pain, inflammation, cancer, and osteoarthritis. However, the specific molecular targets and mechanisms underlying the synergistic effects of its diverse phytochemical constituents remain elusive. Understanding these mechanisms is crucial for developing targeted, effective cannabis-based therapies.

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A series of compounds were designed utilizing molecular modeling and fragment-based design based upon the known protein phosphatase 2A (PP2A) activators, and , and evaluated for their ability to inhibit the viability of colorectal cancer (CRC) and folinic acid, 5-fluorouracil, and oxaliplatin (FOLFOX)-resistant CRC cells. () was identified as the most cytotoxic compound with IC values in the range of 2.36-6.

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Nature continually refines its processes for optimal efficiency, especially within biological systems. This article explores the collaborative efforts of researchers worldwide, aiming to mimic nature's efficiency by developing smarter and more effective nanoscale technologies and biomaterials. Recent advancements highlight progress and prospects in leveraging engineered nucleic acids and proteins for specific tasks, drawing inspiration from natural functions.

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  • Researchers are creating a new version of the ACE2 receptor, called miniature ACE2 (mACE2), which can bind tightly to the spike protein of SARS-CoV-2.
  • This engineered mACE2 is used in a novel detection method for the virus, utilizing magnetic nanoparticles for sensitivity and specificity.
  • The study demonstrates that mACE2 could be a promising tool for not only diagnosing but also neutralizing SARS-CoV-2, paving the way for similar approaches against other viral diseases.
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Apolipoprotein E (APOE) is responsible for lipid transport, including cholesterol transport and clearance. While the ε4 allele of APOE (APOE4) is associated with a significant genetic risk factor for late-onset Alzheimer's disease (AD), no mechanistic understanding of its contribution to AD etiology has been established yet. In addition to cholesterol, monosialotetrahexosylganglioside (GM1) is a crucial lipid component in cell membranes and has been implicated in promoting the aggregation of amyloid beta protein (Aβ), a key protein associated with AD.

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  • The study highlights the potential of microRNAs (miRNAs) as disease-specific biomarkers for Amyotrophic Lateral Sclerosis (ALS), which could improve diagnosis, treatment monitoring, and drug discovery.
  • Despite extensive research over the last decade, no miRNA candidates have yet advanced to clinical use.
  • The systematic review analyzed 807 miRNA observations from 31 studies, identifying key dysregulated miRNAs across various biological sources, providing insights for future ALS biomarker research.
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Fibrous nanomaterials containing silica, titanium oxide, and carbon nanotubes are notoriously known for their undesirable inflammatory responses and associated toxicities that have been extensively studied in the environmental and occupational toxicology fields. Biopersistance and inflammation of "hard" nanofibers prevent their broader biomedical applications. To utilize the structural benefits of fibrous nanomaterials for functionalization with moieties of therapeutic significance while preventing undesirable immune responses, researchers employ natural biopolymers─RNA and DNA─to design "soft" and biodegradable nanomaterials with controlled immunorecognition.

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contains minor cannabinoids that have potential therapeutic value in pain management. However, detailed experimental evidence for the antinociceptive effects of many of these minor cannabinoids remains lacking. Here, we employed artificial intelligence (AI) to perform compound-protein interaction estimates with cannabichromene (CBC) and receptors involved in nociceptive signaling.

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The ability of cells and tissues to respond differentially to mechanical forces applied in distinct directions is mediated by the ability of load-bearing proteins to preferentially maintain physical linkages in certain directions. However, the molecular basis and biological consequences of directional force-sensitive binding remain unclear. Vinculin (Vcn) is a load-bearing linker protein that exhibits directional catch bonding due to interactions between the Vcn tail domain (Vt) and filamentous (F)-actin.

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  • Molecular dynamics (MD) is widely used in structural biology to study the structure and function of macromolecules.
  • Boltzmann generators offer a new method by using generative neural networks to simulate molecular systems more quickly than traditional MD, but they currently face theoretical and computational challenges.
  • This study establishes a solid mathematical basis for Boltzmann generators, proving they can effectively replace MD in certain scenarios involving complex macromolecules like proteins, and introduces tools for navigating molecular energy landscapes with neural networks.
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REAP-2 is an interactive dose-response curve estimation tool for Robust and Efficient Assessment of drug Potency. It provides user-friendly dose-response curve estimation for studies and conducts statistical testing for model comparisons with a redesigned user interface. We also make a major update of the underlying estimation method with penalized beta regression, which demonstrates great reliability and accuracy in dose estimation and uncertainty quantification.

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The dysregulation of protein kinases is associated with multiple diseases due to the kinases' involvement in a variety of cell signaling pathways. Manipulating protein kinase function, by controlling the active site, is a promising therapeutic and investigative strategy to mitigate and study diseases. Kinase active sites share structural similarities, making it difficult to specifically target one kinase, and allosteric control allows specific regulation and study of kinase function without directly targeting the active site.

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  • Fast and accurate 3D RNA structure prediction is challenging due to RNA's size, flexibility, and a lack of diverse experimental structures, which complicates identifying stable states compared to DNA.
  • A convolutional neural network has been developed to predict all pairwise distances between RNA residues, achieving high accuracy for RNA sequences up to 100 nucleotides in length and performing predictions significantly faster than traditional methods.
  • The method converts predictions into all-atom RNA models based on nucleotide sequences but faces limitations due to the shortage of available RNA crystal structures for training purposes.
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Lymphocytes exit circulation and enter in-tissue guided migration toward sites of tissue pathologies, damage, infection, or inflammation. By continuously sensing and adapting to the guiding chemo-mechano-structural properties of the tissues, lymphocytes dynamically alternate and combine their amoeboid (non-adhesive) and mesenchymal (adhesive) migration modes. However, which mechanisms guide and balance different migration modes are largely unclear.

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Cell invasion is an important process in cancer progression and recurrence. Invasion and implantation of cancer cells from their original place to other tissues, by disabling vital organs, challenges the treatment of cancer patients. Given the importance of the matter, many molecular treatments have been developed to inhibit cancer cell invasion.

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