Biology subjects

Dokholyan, N. V.

Publications and source records attributed to Dokholyan, N. V..

32 records · Page 2Linked to original sources

bioRxiv2022

Predicting 3D RNA structure from solely the nucleotide sequence using Euclidean distance neural networks

Fast and accurate 3D RNA structure prediction remains a major challenge in structural biology, mostly due to the size and flexibility of RNA molecules, as well as lack of diverse experimentally determined structures of RNA molecules. Unlike DNA structure, RNA structure is far less constrained by base pair hydrogen bonding, resulting in an explosion of potential stable states. Here, we propose a convolutional neural network which predicts all pairwise distances between residues in an RNA, using a recently described smooth parametrization of Euclidean distance matrices. We achieve high accuracy predictions on RNAs up to 100 nucleotides in length in fractions of a second, a factor of 107 faster than existing molecular dynamics-based methods. We also convert our coarse-grained machine learning output into an all-atom model using discrete molecular dynamics with constraints. Our proposed computational pipeline accurately predicts all-atom RNA models solely from the nucleotide sequence.

biophysics↗

bioRxiv2022

Allosteric inactivation of an engineered optogenetic GTPase

Optogenetics is a technique for establishing direct spatiotemporal control over molecular function within living cells using light. Light application induces conformational changes within targeted proteins that produce changes in function. One of the applications of optogenetic tools is an allosteric control of proteins via light-sensitive LOV2 domain, which allows direct and robust control of protein function. Computational studies supported by cellular imaging demonstrated that application of light allosterically controlled signaling proteins Vav2, ITSN, and Rac1, but the structural and dynamic basis of such control has yet to be elucidated by experiment. Here, using NMR spectroscopy, we discover principles of action of allosteric control of cell division control protein 42 (CDC42), a small GTPase involved in cell signaling. Both LOV2 and Cdc42 employ flexibility in their function to switch between "dark"/ "lit" or active/inactive states, respectively. By conjoining Cdc42 and LOV2 domains into the bi-switchable fusion Cdc42Lov, application of light - or alternatively, mutation in LOV2 to mimic light absorption - allosterically inhibits Cdc42 downstream signaling. The flow and patterning of allosteric transduction in this flexible system is well-suited to observation by NMR. Close monitoring of the structural and dynamic properties of dark versus lit states of Cdc42Lov revealed lit-induced allosteric perturbations. Chemical shift perturbations for lit mimic, I539E, have distinct regions of sensitivity and both the domains are coupled together leading to bi-directional interdomain signaling. Insights gained from this optoallosteric design will increase our ability to control response sensitivity in future designs. Significance StatementControl of cell signaling activity in proteins by light is one of the primary goals of optogenetics. The hybrid light-receptor/cell-signaling protein Cdc42Lov was engineered recently as an optogenetic tool, employing a novel allosteric strategy that results in photoinhibition. In contrast to previous activation designs, the mechanism of inhibition of GTPase signaling activity in Cdc42 is only apparent at a detailed structural and dynamic level. NMR characterization of dark and mutationally "lit" forms reveals the allosteric interdomain perturbations, knowledge of which will enhance future applications of this design strategy.

biophysics↗

bioRxiv2022

Septin-Mediated Mechanobiological Reprogramming of T Cell Transmigration and 3D Motility

The all-terrain motility of lymphocytes in tissues and tissue-like gels is best described as amoeboid motility. For amoeboid motility, lymphocytes do not require specific biochemical or structural modifications to the surrounding extracellular matrix. Instead, they rely on changing shape and steric interactions with the microenvironment. However, the exact mechanism of amoeboid motility remains elusive. Here we report that septins shape T cells for amoeboid motility. Specifically, septins form F-actin and alpha-actinin-rich cortical rings at the sites of cortex-indenting collisions of T cells with the extracellular matrix. Cortical rings compartmentalize cells into chains of spherical segments that are spatially conformed to the available lumens, forming transient hourglass-shaped steric locks onto the surrounding collagen fibers. The steric lock facilitates pressure-driven peristaltic propulsion of cytosolic content by individually contracting cell segments. Our results demonstrate that septins provide microenvironment-guided partitioning of actomyosin contractility and steric pivots for amoeboid motility of T cells in tissue-like microenvironments. GLOSSARYO_LISteric interactions - interactions by the means of their spatial collision dependent on objects shapes. C_LIO_LISteric guidance - cell navigation within crowded 3D environments, determined by the available passages around and between steric hindrances. C_LIO_LIPeristaltic treadmilling - locomotion mode by the means of a repeated sequence of polarized cell cortex extension, stabilization, and retraction, accompanied by translocation of nucleus and cytoplasm via circumferential cortex contractility. C_LI Significance StatementT cells can be highly motile, searching for cognate antigens or better yet targets in chimeric antigen receptor therapy settings. However, mechanisms of motility remain elusive for T cells migrating in structurally and biochemically diverse tissues. Here we address one pivotal question of basic and clinical immunology - How T cells achieve the all-terrain motility? Here we decipher and report septin-based T cell motility in a 3D tissue-like environment. Specifically, we show that septins facilitate cell morphological responsiveness to the steric obstacles, i.e., collagen fiber-wise partitioning of actomyosin cortex contractility and cell-obstacle steric interactions. These responses coordinate peristaltic propulsion of the lymphocytes cytosolic content along its individually contracting cell segments, forming the obstacle-avoiding motility, i.e., circumnavigation, shared across various tested lymphocytes.

biophysics↗

bioRxiv2021

Robust and Efficient Assessment of Potency (REAP): A Quantitative Tool for Dose-response Curve Estimation

The median-effect equation has been widely used to describe the dose-response relationship and identify compounds that activate or inhibit specific disease targets in contemporary drug discovery. However, the experimental data often contain extreme responses, which may significantly impair the estimation accuracy and impede valid quantitative assessment in the standard estimation procedure. To improve the quantitative estimation of the dose-response relationship, we introduce a novel approach based on robust beta regression. Substantive simulation studies under various scenarios demonstrate solid evidence that the proposed approach consistently provides robust estimation for the median-effect equation, particularly when there are extreme outcome observations. Moreover, simulation studies illustrate that the proposed approach also provides a narrower confidence interval, suggesting a higher power in statistical testing. Finally, to efficiently and conveniently perform common lab data analyses, we develop a freely accessible web-based analytic tool to facilitate the quantitative implementation of the proposed approach for the scientific community.

pharmacology and toxicology↗

bioRxiv2021

AlphaFold Models Illuminate Half of Dark Human Proteins

We investigate the use of confidence scores to predict the accuracy of a given AlphaFold model for drug discovery. Predicted accuracy is improved by eliminating confidence scores below 80, due to effects of disorder. 95% of models corresponding to a set of recent crystal structures are accurate at the fold level. Conformational discordance in the training set has a more significant effect on accuracy than sequence divergence. We propose criteria for models and residues that are possibly useful for virtual screening, by which AlphaFold provides models for half of understudied (dark) human proteins and two-thirds of residues in those models.

pharmacology and toxicology↗

bioRxiv2021

NeuralDock: Rapid and conformation-agnostic docking of small molecules

Virtual screening is a cost- and time-effective alternative to traditional high-throughput screening in the drug discovery process. Both virtual screening approaches, structure-based molecular docking and ligand-based cheminformatics, suffer from computational cost, low accuracy, and/or reliance on prior knowledge of a ligand that binds to a given target. Here, we propose a neural network framework, NeuralDock which accelerates the process of high-quality computational docking by a factor of 106, and does not require prior knowledge of a ligand that binds to a given target. By approximating both protein-small molecule conformational sampling and energy-based scoring, NeuralDock accurately predicts the binding energy and affinity of a protein-small molecule pair, based on protein pocket 3D structure and small molecule topology. We use NeuralDock and 25 GPUs to dock 937 million molecules from the ZINC database against superoxide dismutase-1 in 21 hours, which we validate with physical docking using MedusaDock. Due to its speed and accuracy, NeuralDock may be useful in brute-force virtual screening of massive chemical libraries and training of generative drug models.

biophysics↗

bioRxiv2021

Toxic SOD1 trimers are off-pathway in the formation of amyloid-like fibrils in ALS

Accumulation of insoluble amyloid fibrils is widely studied as a critical factor in the pathology of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease. Misfolded Cu, Zn superoxide dismutase (SOD1) was the first protein linked to ALS, and non-native SOD1 trimeric oligomers were recently linked to cytotoxicity, while larger oligomers were protective to cells. The balance between trimers and larger aggregates in the process of SOD1 aggregation is, thus, a critical determinant of potential therapeutic approaches to treat ALS. Yet, it is unknown whether these trimeric oligomers are a necessary intermediate for larger aggregate formation or a distinct off-pathway species competing with fibril formation. Depending on the on- or off-pathway scenario of trimer formation, we expect drastically different therapeutic approaches. Here, we show that the toxic SOD1 trimer is an off-pathway intermediate competing with protective fibril formation. We design mutant SOD1 constructs that remain in a trimeric state (super stable trimers) and show that stabilizing the trimeric SOD1 prevents formation of fibrils in vitro and in a motor neuron like cell model (NSC-34). Using size exclusion chromatography we track the aggregation kinetics of purified SOD1 and show direct competition of trimeric SOD1 with larger oligomer and fibril formation. Finally, we show the trimer is structurally independent of both larger soluble oligomers and insoluble fibrils using circular dichroism spectroscopy and limited proteolysis. Significance StatementProtein aggregation into large insoluble species is a hallmark of many neurodegenerative diseases, but recent evidence suggests that smaller soluble aggregates are responsible for neuronal death. Depending on whether these toxic oligomers appear on- or off-pathway to larger aggregates, which is currently unknown, the strategies for pharmaceutic intervention would be drastically different. Here, we determine that stabilizing the trimeric form of SOD1 reduces larger aggregate formation while increasing toxicity to cells. Trimeric and larger aggregate concentrations have a strong negative correlation over time, and the structure of the trimer is significantly different from larger soluble and insoluble aggregates. Our findings show that formation of trimeric SOD1 is directly competing with that of larger aggregates.

molecular biology↗

bioRxiv2021

GM1 mediates the formation and maintenance of cytotoxic Aβ oligomers

The aggregation of amyloid beta (A{beta}) peptide is associated with Alzheimers disease (AD) pathogenesis. Cell membrane composition, especially monosialotetrahexosylganglioside (GM1), is known to promote the formation of A{beta} fibrils, yet little is known about the roles of GM1 in the early steps of A{beta} oligomer formation. Here, by using GM1-contained liposomes as a mimic of neuronal cell membrane, we demonstrate that GM1 is a critical trigger of A{beta} oligomerization and aggregation. We find that GM1 not only promotes the formation of A{beta} fibrils, but also facilitates the maintenance of A{beta} oligomers on liposome membranes. We structurally characterize the A{beta} oligomers formed on the membrane and find that GM1 captures A{beta} by binding to its arginine-5 residue. To interrogate the mechanism of A{beta} oligomer toxicity, we design a new liposome-based Ca2+-encapsulation assay and provide new evidence for the A{beta} ion channel hypothesis. Finally, we conduct cell viability assay to determine the toxicity of A{beta} oligomers formed on membranes. Overall, by uncovering the roles of GM1 in mediating early A{beta} oligomer formation and maintenance, our work provides a novel direction for pharmaceutical research for AD.

biophysics↗

bioRxiv2021

Yuel: Compound-Protein Interaction Prediction with High Generalizability

Virtual drug screening has the potential to revolutionize the stagnant drug discovery field due to its low cost and fast speed. Predicting binding affinities between small molecules and the protein target is at the core of computational drug screening. Deep learning-based approaches have recently been adapted to predict binding affinities and claim to achieve high prediction accuracy in their tests, however, we show that current approaches are not reliable for virtual drug screening due to the lack of generalizability, i.e. the ability to predict interactions between unknown proteins and unknown small molecules. To address this shortcoming, we develop a compound-protein interaction predictor, Yuel. Upon comprehensive tests on various datasets, we find that out of all the deep-learning approaches surveyed, only Yuel can predict interactions between unknown compounds and unknown proteins. Additionally, Yuel can also be utilized to identify compound atoms and proteins residues that are involved in the binding.

bioinformatics↗

bioRxiv2020

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

The intrinsically disordered protein, -synuclein, implicated in synaptic vesicle homeostasis and neurotransmitter release, is also associated with several neurodegenerative diseases. The different roles of -synuclein are characterized by distinct structural states (membrane-bound, dimer, tetramer, oligomer, and fibril), which are originated from its various monomeric conformations. The pathological states, determined by the ensemble of -synuclein monomer conformations and dynamic pathways of interconversion between dominant states, remain elusive due to their transient nature. Here, we use inter-dye distance distributions from bulk time-resolved Forster resonance energy transfer as restraints in discrete molecular dynamics simulations to map the conformational space of the -synuclein monomer. We further confirm the generated conformational ensemble in orthogonal experiments utilizing far-UV circular dichroism and cross-linking mass spectrometry. Single-molecule protein-induced fluorescence enhancement measurements show that within this conformational ensemble, some of the conformations of -synuclein are surprisingly stable, exhibiting conformational transitions slower than milliseconds. Our comprehensive analysis of the conformational ensemble reveals essential structural properties and potential conformations that promote its various functions in membrane interaction or oligomer and fibril formation.

biophysics↗

bioRxiv2020

Prefusion spike protein stabilization through computational mutagenesis

A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) has emerged as a human pathogen, causing global pandemic and resulting in over 400,000 deaths worldwide. The surface spike protein of SARS-CoV-2 mediates the process of coronavirus entry into human cells by binding angiotensin-converting enzyme 2 (ACE2). Due to the critical role in viral-host interaction and the exposure of spike protein, it has been a focus of most vaccines developments. However, the structural and biochemical studies of the spike protein are challenging because it is thermodynamically metastable1. Here, we develop a new pipeline that automatically identifies mutants that thermodynamically stabilize the spike protein. Our pipeline integrates bioinformatics analysis of conserved residues, motion dynamics from molecular dynamics simulations, and other structural analysis to identify residues that significantly contribute to the thermodynamic stability of the spike protein. We then utilize our previously developed protein design tool, Eris, to predict thermodynamically stabilizing mutations in proteins. We validate the ability of our pipeline to identify protein stabilization mutants through known prefusion spike protein mutants. We finally utilize the pipeline to identify new prefusion spike protein stabilization mutants.

biophysics↗

bioRxiv2020

Rational design and implementation of a chemically inducible hetero-trimerization system

Chemically inducible dimerization (CID) uses a small molecule to induce binding of two different proteins. CID tools exemplified by the FKBP/FRB/rapamycin system have been widely employed to probe molecular events inside and outside cells. While various CID tools are available, chemically inducible trimerization (CIT) has not been developed, due to inherent challenges in designing or identifying a chemical that simultaneously binds three proteins with high affinity and target specificity. Nevertheless, by introducing a third recruitable component, CIT could enable versatile applications. Here, we devised the CIT by rationally splitting FRB and FKBP. Based on cellular and structural datasets, select split pairs of FRB or FKBP underwent efficient trimerization with full length FKBP or FRB, respectively, upon addition of rapamycin. We also demonstrated its potential for cellular applications by rapidly inducing tri-organellar plasma membrane-ER-mitochondria junctions, and by perturbing intended membrane lipids exclusively at the plasma membrane-ER membrane contact sites. By conferring one additional condition to what is achievable with CID, CIT expands the types of manipulation in single live cells, to address cell biology questions otherwise intractable, and engineer cell functions for future synthetic biology applications.

cell biology↗

bioRxiv2020

Various miRNAs are involved in efficient HCV replication

One of the determinants for tissue tropism of hepatitis C virus (HCV) is miR-122, a liver-specific microRNA. Recently, it has been reported that interaction of miR-122 to HCV RNA induces a conformational change of the 5UTR internal ribosome entry site (IRES) structure to form stem-loop II structure (SLII) and hijack of translating 80S ribosome through the binding of SLIII to 40S subunit, which leads to efficient translation. On the other hand, low levels of HCV-RNA replication have also been detected in some non-hepatic cells; however, the details of extrahepatic replication remain unknown. These observations suggest the possibility that miRNAs other than miR-122 can support efficient replication of HCV-RNA in non-hepatic cells. Here, we identified a number of such miRNAs and show that they could be divided into two groups: those that bind HCV-RNA at two locations (miR-122 binding sites I and II), in a manner similar to miR-122 (miR-122-like), and those that target a single site that bridges sites I and II and masking both G28 and C29 in the 5UTR (non-miR-122-like). Although the enhancing activity of these non-hepatic miRNAs were lower than those of miR-122, substantial expression was detected in various normal tissues. Furthermore, structural modeling indicated that both miR-122-like and non-miR-122-like miRNAs not only can facilitate the formation of an HCV IRES SLII but also can stabilize IRES 3D structure in order to facilitate binding of SLIII to the ribosome. Together, these results suggest that HCV facilitates miR-122-independent replication in non-hepatic cells through recruitment of miRNAs other than miR-122. And our findings can provide a more detailed mechanism of miR-122-dependent enhancement of HCV-RNA translation by focusing on IRES tertiary structure. Author summaryOne of the determinants for tissue tropism of hepatitis C virus (HCV) is miR-122, a liver-specific microRNA, which is required for efficient propagation. Recently, it has been reported that interaction of miR-122 with the 5UTR of HCV contributes to the folding of a functional IRES structure that is required for efficient translation of viral RNA. In this study, we examined the minimum motifs in the seed region of miRNAs required for the enhancement of HCV replication. As a result, we found two groups of non-hepatic miRNAs: "miR-122-like miRNAs" that can bind HCV-RNA at two locations in a manner similar to miR-122, and "non-miR-122-like miRNAs" that target a single site that masking both G28 and C29 in the 5UTR. The interaction of these non-hepatic miRNAs with the 5UTR can facilitate not only the folding of active HCV IRES but also the stabilization of IRES 3D structure in order to facilitate binding to the ribosome. These results suggest the possibility of replication of HCV in non-hepatic cells through interaction with miRNAs other than miR-122 and provide insight into the establishment of persistent infection of HCV in non-hepatic tissues that lead to the development of extrahepatic manifestations.

microbiology↗

bioRxiv2019

Mapping Co-regulation Pathways among Ligand Binding sites in RyR1

Ryanodine receptor 1 (RyR1) is an intracellular calcium (Ca2+) release channel required for skeletal muscle contraction. RyR1 is co-regulated by multiple activators - Ca2+, ATP and caffeine (CFF), yet the mechanism of co-regulation and the action synergy of these activators is unknown. Here, we report the detailed network of allosteric connections between the three ligand sites and the pore region in (i) Ca2+ bound - closed, (ii) ATP/CFF bound - closed, (iii) Ca2+/ATP/CFF bound - closed and (iv) Ca2+/ATP/CFF bound - open RyR1 states. We find that two dominant paths mediate the communication between the Ca2+ binding site and pore region in Ca2+-only state. ATP/CFF-only occupied - closed RyR1 has two additional paths with CFF-but not ATP-occupied path using part of the closed Ca2+-only pathway. In the presence of Ca2+, ATP and CFF, major differences between the open and closed states are identified with both using part of the paths of the closed Ca2+-only and ATP/CFF-only states. We find that the three activators Ca2+, ATP, and CFF propagate their effects to the pore region through a network of partially overlapping pathways. Such coordination of allosteric pathway underlies the molecular basis of synergy of channel regulation by multiple activators.\n\nStatement of SignificanceRyRs are a group of Ca2+ channels that bind to several endogenous modulators and regulate Ca2+ release through closed-to-open gating transition. Despite the high-resolution structural data available for RyR1, the allosteric mechanism of RyR1 gating remains elusive. In this study, we employed graph-theoretical approach to demonstrate the allosteric network of synergistic interaction among various activators in RyR1. To our knowledge, for the first time we were able to identify the co-regulation among ligand sites in RyR1 to regulate the closed-to-open gating transition. The explored allosteric coupling in RyR1 may assist in designing advanced therapeutics for several debilitating diseases. Our findings in this study will assist to design new strategies for controlled allosteric regulation of RyR1 functionality in future.

biophysics↗