Mayton, E. H. | bioRxiv Science

bioRxiv2025

AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications

Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an AI-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 out of 26 antibody sequences into functional single-chain variable fragment (scFv) intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost-effective, and broadly accessible for biological research.

cell biology↗

bioRxiv2019

Age-structured vectorial capacity in a ZIKV-Ae. aegypti model system

The transmission dynamics of arboviruses like Zika virus (ZIKV) are most often evaluated by vector competence and the related extrinsic incubation period (EIP), which represent the proportion of vectors that become infectious given exposure and the time it takes for a vector to become infectious given exposure, respectively. Thus, EIP is the temporality of vector competence, and these measures have been used to evaluate the relative fitness of arbovirus systems. However, another temporal process critical to assessing arbovirus transmission dynamics is the age-structure of vector populations, as studies have demonstrated how vector mortality interplays with vector competence and EIP to alter transmission system efficiency. These and other parameters are critical to vectorial capacity (VC), a measure of transmission potential of a vector-pathogen system. However, how these three components - EIP, vector competence, and age - affect VC still needs to be addressed. We first compared experimentally how vector competence/EIP and mosquito age at the time of infection acquisition (Ageacquisition) interacted in an Aedes aegypti-ZIKV model system. We found that Ageacquisition did not alter the vector competence/EIP using traditional analyses, except in the context of mortality. To capture and quantify this age-dependent context, we developed an age-structured vectorial capacity framework (VCage) by experimentally determining daily mortality and probability of biting, as well as vector competence/EIP parameterized as EIPMin and EIPMax. Like previous studies, we found that arbovirus phenotypes leading to outbreaks are not straightforward and may follow a tortoise and the hare (TotH), whereby slow and steady is as or better than fast and furious phenotypes. Understanding the contributions of these age-dependent life traits as well as VCage allows for quantification and visualization of both the magnitude and temporality of transmission dynamics in an age-dependent manner, which reveals this TotH model that should change how compare and rank arbovirus phenotypes, and perhaps even how we identify highly or negligibly competent vectors.

ecology↗