Cisneros de la Rosa, E. | bioRxiv Science

bioRxiv2025

IRIS Integrates Sparse Sequence, Experimental, and AI-Predicted Structures for Protein-RNA Affinity Prediction and Motif Discovery

Protein-RNA interactions are fundamental to numerous cellular processes, yet quantitatively characterizing their binding specificity remains a major challenge. We present IRIS (Integrative RNA-protein interaction prediction Informed by Structure and sequence), a biophysical framework that integrates residue-level sequence and structural features without relying on large-scale affinity data to predict binding affinities and identify binding motifs. Applied across different protein-RNA systems, IRIS predicts relative binding free energies ({Delta}{Delta}G) with consistent correlations and competitive error metrics, and its performance is further improved by incorporating additional high-affinity sequences into the training set. By leveraging predicted structural complexes, IRIS reveals alternative binding modes not observed in experimental structures, extends applicability to systems lacking experimental protein-RNA complexes, and generates a library of favorable RNA-binding motifs at protein-RNA interfaces. Collectively, these results establish IRIS as a versatile framework that leverages increasingly accurate structural predictions to enable quantitative modeling and rational engineering of protein-RNA interactions.

biophysics↗

bioRxiv2018

HCMV glycoprotein B subunit vaccine efficacy was mediated by non-neutralizing antibody effector functions

Human cytomegalovirus (HCMV) is the most common congenital infection worldwide, frequently causing hearing loss and brain damage in afflicted infants. A vaccine to prevent maternal acquisition of HCMV during pregnancy is necessary to reduce the incidence of infant disease. The glycoprotein B (gB) + MF59 adjuvant subunit vaccine platform is the most successful HCMV vaccine tested to-date, demonstrating approximately 50% efficacy in preventing HCMV acquisition in phase II trials. However, the mechanism of vaccine protection remains unknown. Plasma from 33 gB/MF59 vaccinees at peak immunogenicity was tested for gB epitope specificity as well as neutralizing and non-neutralizing anti-HCMV effector functions, and compared to an HCMV-seropositive cohort. gB/MF59 vaccination elicited IgG responses with gB-binding magnitude and avidity comparable to natural infection. Additionally, IgG subclass distribution was similar with predominant IgG1 and IgG3 responses induced by gB vaccination and HCMV infection. However, vaccine-elicited antibodies exhibited limited neutralization of the autologous virus, negligible neutralization of multiple heterologous strains, and limited binding responses against gB structural motifs targeted by neutralizing antibodies including AD-1, AD-2, and Domain I. Interestingly, vaccinees had high-magnitude IgG responses against AD-3 linear epitopes, demonstrating immunodominance against this non-neutralizing, cytosolic region. Finally, vaccine-elicited IgG robustly bound trimeric, membrane-associated gB on the surface of transfected or HCMV-infected cells and mediated virion phagocytosis, though were poor mediators of NK cell activation. Altogether, these data suggest that non-neutralizing antibody functions, including virion phagocytosis, likely played a role in the observed 50% vaccine-mediated protection against HCMV acquisition.\n\nSignificanceThe CDC estimates that every hour, a child is born in the United States with permanent neurologic disability resulting from human cytomegalovirus (HCMV) infection - more than is caused by Down syndrome, fetal alcohol syndrome, and neural tube defects combined. A maternal vaccine to block transmission of HCMV to the developing fetus is a necessary intervention to prevent these adverse outcomes. The gB/MF59 vaccine is the most successful tested clinically to-date, achieving 50% reduction in HCMV acquisition. This manuscript establishes the function and epitope specificity of the humoral response stimulated by this vaccine that may explain the partial vaccine efficacy. Understanding the mechanism of gB/MF59-elicited protective immune responses will guide rational design and evaluation of the next generation of HCMV vaccines.

immunology↗