Biology subjects

Aiyer, S.

Publications and source records attributed to Aiyer, S..

9 recordsLinked to original sources

bioRxiv2025

De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential

Predicting the precise positions of water molecules at the protein interface remains a formidable challenge, fueling active research in this field. Here, we present a novel approach based on molecular dynamics simulations that utilizes statistical thermodynamic signatures of water at protein interfaces to improve the accuracy of water placement in cryo-EM maps, with apoferritin as a model benchmark system. The interaction energy of solvent with the protein is insufficient to distinguish between high- and lower-consensus water positions, consistent with reports of earlier work. Instead, we employ a detailed statistical thermodynamic analysis based on the excess chemical potential (WT) - a measure of the thermodynamic balance between the interaction energy of an interfacial water molecule with the protein and its free energy of interaction with all of the other solvent molecules. WT is proportional to the log ratio of the local density of water molecules at the protein interface to the bulk density. 85% of the top 100 water locations with the most favorable excess chemical potential values are observed in one or more high resolution Cryo-EM maps deposited in the PDB, and 70% of the top 200 water locations indexed by excess chemical potential are observed in the cryo-EM maps. This work paves the way for the development of a cryo-EM refinement tool that integrates molecular dynamics simulations with cryo-EM data for high-resolution modeling of water networks.

biochemistry↗

bioRxiv2025

Nucleosome Engagement Regulates RORγt Structure and Dynamics

ROR{gamma}t is a key transcriptional regulator that supports protective pathogen clearance but also drives autoimmune disorders. Genetic studies have identified ROR{gamma}t mutations that selectively protect from autoimmunity without compromising host defense. Herein, we describe the molecular principles governing how ROR{gamma}t selectively drives these context-dependent gene programs. Structural studies revealed the selectivity-determining mutations lie in an -helix, the C-terminal extension (CTE), which nucleates when ROR{gamma}t engages partially occluded DNA response elements at nucleosome entry/exit sites. In ex vivo Th17 cells, the CTE is required for full genomic occupancy and expression of inflammatory effector genes, while residual DNA binding supports partial occupancy that, alongside context-dependent transcription factors, induces lineage-stabilizing gene expression. These findings support a model where ROR{gamma}t uses distinct chromatin binding modes to engage an expansive chromatin landscape to activate target gene programs, explaining the complex phenotypes of CTE mutant mice.

biophysics↗

bioRxiv2024

An automatic domain-general error signal is shared across tasks and predicts confidence in different sensory modalities

Understanding the ability to self-evaluate decisions is an active area of research. This research has primarily focused on the neural correlates of self-evaluation during visual-tasks, and whether pre- or post-decisional neural correlates capture subjective confidence in that decision. This focus has been useful, yet also precludes an investigation of key every-day features of metacognitive self-evaluation: that decisions are rapid, must be evaluated without explicit feedback, and unfold in a multisensory world. These considerations lead us to hypothesise that an automatic domain-general metacognitive signal may be shared between sensory modalities, which we tested in the present study with multivariate decoding of electroencephalographic (EEG) data. Participants (N=21, 12 female) first performed a visual task with no request for self-evaluations of performance, prior to an auditory task that included rating decision confidence on each trial. A multivariate classifier trained to predict errors in the speeded visual-task generalised to predict errors in the subsequent non-speeded auditory discrimination. This generalisation was unique to classifiers trained on the visual response-locked data, and further predicted subjective confidence on the subsequent auditory task. This evidence of overlapping neural activity across the two tasks provides evidence for automatic encoding of confidence independent of any explicit request for metacognitive reports, and a shared basis for metacognitive evaluations across sensory modalities.

neuroscience↗

bioRxiv2024

Domain consolidation in Bacterial 50S assembly revealed by Anti-Sense Oligonucleotide Probing

Investigating the intricate and rapid folding kinetics of large RNA-protein complexes (RNPs), like the bacterial ribosome, remains a formidable challenge in structural biology. Previous genetic approaches to probe assembly have focused on modulating the expression of either r-proteins or assembly factors. Here, anti-sense oligonucleotides (ASOs) were used to disrupt native RNA/RNA and RNA/protein interactions, in order to generate novel folding intermediates. In an in vitro co-transcriptional assembly assay, 8 assembly inhibitor ASOs were identified. Using cryo-electron microscopy, 38 new intermediate structures were determined resulting from the specific inhibitions. In particular a novel intermediate class provided compelling evidence of independent rRNA domain folding before proper interdomain docking. Three PNAs targeting domain-I of 23S- rRNA further subdivided the previously identified assembly core into smaller blocks representing the earliest steps in assembly. The resulting assembly graph reveals template-directed RNA foldon docking and domain consolidation, which provides a hierarchical view of the RNP assembly process.

biochemistry↗

bioRxiv2024

Assembly of the Bacterial Ribosome with Circularly Permuted rRNA

Co-transcriptional assembly is an integral feature of the formation of RNA-protein complexes that mediate translation. For ribosome synthesis, prior studies have indicated that the strict order of transcription of rRNA domains may not be obligatory during bacterial ribosome biogenesis, since a series of circularly permuted rRNAs are viable. In this work, we report the insights into assembly of the bacterial ribosome large subunit (LSU) based on cryo-EM density maps of intermediates that accumulate during in vitro ribosome synthesis using a set of circularly permuted (CiPer) rRNAs. The observed ensemble of twenty-three resolved ribosome large subunit intermediates reveals conserved assembly routes with an underlying hierarchy among cooperative assembly blocks. There are intricate interdependencies for the formation of key structural rRNA helices revealed from the circular permutation of rRNA. While the order of domain synthesis is not obligatory, the order of domain association does appear to proceed with a particular order, likely due to the strong evolutionary pressure on efficient ribosome synthesis. This work reinforces the robustness of the known assembly hierarchy of the bacterial large ribosomal subunit, and offers a coherent view of how efficient assembly of CiPer rRNAs can be understood in that context.

biophysics↗

bioRxiv2024

Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding

Integrase (IN) performs dual essential roles during HIV-1 replication. During ingress, IN functions within an oligomeric "intasome" assembly to catalyze viral DNA integration into host chromatin. During late stages of infection, tetrameric IN binds viral RNA and orchestrates the condensation of ribonucleoprotein complexes into the capsid core. The molecular architectures of HIV-1 IN assemblies that mediate these distinct events remain unknown. Furthermore, the tetramer is an important antiviral target for allosteric IN inhibitors. Here, we determined cryo-EM structures of wildtype HIV-1 IN tetramers and intasome hexadecamers. Our structures unveil a remarkable plasticity that leverages IN C-terminal domains and abutting linkers to assemble functionally distinct oligomeric forms. Alteration of a newly recognized conserved interface revealed that both IN functions track with tetramerization in vitro and during HIV-1 infection. Collectively, our findings reveal how IN plasticity orchestrates its diverse molecular functions, suggest a working model for IN-viral RNA binding, and provide atomic blueprints for allosteric IN inhibitor development.

biochemistry↗

bioRxiv2023

Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection

Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60{degrees} are virtually indistinguishable. These strategies allowed the reconstruction to 3 [A] resolution of a bacterial RNA polymerase with preferred orientation. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle for dataset acquisition. These data reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.

biophysics↗

bioRxiv2020

A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins

The extra-terminal (ET) domain of BRD3 is conserved among BET proteins (BRD2, BRD3, BRD4), interacting with multiple host and viral protein-protein networks. Solution NMR structures of complexes formed between BRD3-ET domain with either the 79-residue murine leukemia virus integrase (IN) C-terminal domain (IN329-408), or its 22-residue IN tail peptide (TP) (IN386-407) alone, reveal similar intermolecular three-stranded {beta}-sheet formation. 15N relaxation studies reveal a 10-residue linker region (IN379-388) tethering the SH3 domain (IN329-378) to the ET-binding motif (IN389-405)-ET complex. This linker has restricted flexibility, impacting its potential range of orientations in the IN - nucleosome complex. The complex of the ET-binding peptide of host NSD3 protein (NSD3148-184) and BRD3-ET domain includes a similar three-stranded {beta}-sheet interaction, but the orientation of the {beta}-hairpin is flipped compared to the two IN : ET complexes. These studies expand our understanding of molecular recognition polymorphism in complexes of ET-binding motifs with viral and host proteins. HighlightsO_LIThe BRD3 ET domain binds to key peptide motifs of diverse host and viral proteins. C_LIO_LIThese complexes reveal conformational plasticity in molecular recognition. C_LIO_LINMR studies demonstrate restricted interdomain motion in the IN CTD / ET complex. C_LIO_LIA cost-effective approach is described for producing isotopically-labeled peptides. C_LI Etoc BlurbWe address structurally how the MLV Integrase (IN) usurps the host function of the BET protein through comparative studies of the IN : Brd3 ET complex with that of the host NSD3. MLV integration and thus its pathogenesis is driven through protein interactions of the IN : BET family.

microbiology↗

bioRxiv2018

Sub-2 A Ewald Curvature Corrected Single-Particle Cryo-EM

Single-particle cryogenic electron microscopy (cryo-EM) provides a powerful methodology for structural biologists, but the resolutions typically attained with experimentally determined structures have lagged behind microscope capabilities. Here, we have exploited several technical solutions to improve resolution, including sub-Angstrom pixelation, per-particle CTF refinement, and most notably a correction for Ewald sphere curvature. The application of these methods on micrographs recorded on a base model Titan Krios enabled structure determination at [~]1.86-[A] resolution of an adeno-associated virus serotype 2 variant (AAV2), an important gene-delivery vehicle.

biophysics↗