# Molecular and Structural Studies of Antibody Diversity Mechanisms

> **NIH NIH R01** · APPLIED BIOMEDICAL SCIENCE INSTITUTE · 2020 · $399,418

## Abstract

Abstract
Antibodies are extremely important as the primary mediators of the immune response to
infectious agents and vaccines, but also as recombinant molecules used as therapeutics,
diagnostics, and research reagents. Thus, understanding the mechanisms by which antibodies
form, bind, and neutralize their targets is very important in multiple biomedical areas. Most
vertebrate antibody repertoires form their diversity through V(D)J recombination, where
combinatorial rearrangement of V, D, and J genes form a vast repertoire where the
complementarity determining regions (CDRs) form a relatively flat binding surface for interaction
with antigen. Remarkably, cows appear to have a different mechanism for generating diversity
and binding antigen; cow antibodies have particularly long CDR H3 regions, a subset of which
can be over 70 amino acids long, which form -ribbon “stalk” and disulfide-bonded “knob”
minidomains that protrude far from the typical antibody surface. Remarkably, antibodies from
this repertoire can potently and broadly neutralize HIV, whereas normal human or mouse
antibody repertoires cannot. Therefore, they have unique abilities to bind and neutralize
particularly challenging antigens. Here we propose studies to understand in molecular detail the
genetic mechanisms underlying formation of these antibodies, the binding properties of the stalk
and knob minidomains, and the unique potential of these antibodes to bind bivalently and
bispecifically. These studies will provide insight into mechanisms of viral neutralization
generally, and particularly HIV neutralization. Additionally, given the potential of these
antibodies to bind recessed epitopes, we will generate additional antibodies against particularly
challenging antigens like enzymatic active sites and ion channels. We will employ mutagenesis,
binding, and structural methods, as well as cellular assays to evaluate the unique properties of
these antibodies. Understanding this novel class of antibodies in detail could provide
fundamental insights needed for effective vaccine design as well as discovery and engineering
of antibodies against some of the most challenging targets in biomedicine. Similarly, our unique
antibodies discovered and characterized in this proposal could eventually become therapeutic
candidates themselves.

## Key facts

- **NIH application ID:** 9982985
- **Project number:** 5R01GM105826-08
- **Recipient organization:** APPLIED BIOMEDICAL SCIENCE INSTITUTE
- **Principal Investigator:** Vaughn Vasil Smider
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $399,418
- **Award type:** 5
- **Project period:** 2014-09-30 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9982985

## Citation

> US National Institutes of Health, RePORTER application 9982985, Molecular and Structural Studies of Antibody Diversity Mechanisms (5R01GM105826-08). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9982985. Licensed CC0.

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