Publications (11)
Harnessing Avidity: Quantifying Entropic and Energetic Effects of Linker Length and Rigidity Required for Multivalent Binding of Antibodies to HIV-1 Spikes
Tal Einav, Shahrzad Yazdi, Aaron Coey +2
Due to the low density of envelope (Env) spikes on the surface of HIV-1, neutralizing IgG antibodies rarely bind bivalently using both antigen-binding arms (Fabs) to crosslink betw…
Analysis of Inducer and Operator Binding for Cyclic-AMP Receptor Protein Mutants
Tal Einav, Julia Duque, Rob Phillips
Allosteric transcription factors undergo binding events both at their inducer binding sites as well as at distinct DNA binding domains, and it is often difficult to disentangle the…
Combinatorial Control through Allostery
Vahe Galstyan, Luke Funk, Tal Einav +1
Many instances of cellular signaling and transcriptional regulation involve switch-like molecular responses to the presence or absence of input ligands. To understand how these res…
When Two are Better than One: Modeling the Mechanisms of Antibody Mixtures
Tal Einav, Jesse D Bloom
It is difficult to predict how antibodies will behave when mixed together, even after each has been independently characterized. Here, we present a statistical mechanical model for…
How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene Expression
Tal Einav, Rob Phillips
Although the key promoter elements necessary to drive transcription in Escherichia coli have long been understood, we still cannot predict the behavior of arbitrary novel promoters…
The Energetics of Molecular Adaptation in Transcriptional Regulation
Griffin Chure, Manuel Razo-Mejia, Nathan M. Belliveau +5
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains diffi…
Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants
Tal Einav, Rob Phillips
We present a framework for computing the gating properties of ligand-gated ion channel mutants using the Monod-Wyman-Changeux (MWC) model of allostery. We derive simple analytic fo…
Statistical Mechanics of Allosteric Enzymes
Tal Einav, Linas Mazutis, Rob Phillips
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signalin…
Using Interpretable Machine Learning to Massively Increase the Number of Antibody-Virus Interactions Across Studies
Tal Einav, Rong Ma
A central challenge in every field of biology is to use existing measurements to predict the outcomes of future experiments. In this work, we consider the wealth of antibody inhibi…
Quantitatively visualizing bipartite datasets
Tal Einav, Yuehaw Khoo, Amit Singer
As experiments continue to increase in size and scope, a fundamental challenge of subsequent analyses is to recast the wealth of information into an intuitive and readily-interpret…
Tuning transcriptional regulation through signaling: A predictive theory of allosteric induction
Manuel Razo-Mejia, Stephanie L. Barnes, Nathan M. Belliveau +4
Allosteric regulation is found across all domains of life, yet we still lack simple, predictive theories that directly link the experimentally tunable parameters of a system to its…