Comprehensive Analysis of the Factors Contributing to the Stability and Solubility of Autonomous Human VH Domains

Abstract

We report a comprehensive analysis of sequence features that allow for the production of autonomous human heavy chain variable (V H ) domains that are stable and soluble in the absence of a light chain partner. Using combinatorial phage-displayed libraries and conventional biophysical methods, we analyzed the entire former light chain interface and the third complementarity determining region (CDR3). Unlike the monomeric variable domains of camelid heavy chain antibodies (V H H domains), in which autonomous behavior depends on interactions between the hydrophobic former light chain interface and CDR3, we find that the stability of many in vitro evolved V H domains is essentially independent of the CDR3 sequence and instead derives from mutations that increase the hydrophilicity of the former light chain interface by replacing exposed hydrophobic residues with structurally compatible hydrophilic substitutions. The engineered domains can be expressed recombinantly at high yield, are predominantly monomeric at high concentrations, unfold reversibly, and are even more thermostable than typical camelid V H H domains. Many of the stabilizing mutations are rare in natural V H and V H H domains and thus could not be predicted by studying natural sequences and structures. The results demonstrate that autonomous V H domains with structural properties beyond the scope of natural frameworks can be derived by using non-natural mutations, which differ from those found in camelid V H H domains. These findings should enable the development of libraries of synthetic V H domains with CDR3 diversities unconstrained by structural demands.It was long believed that all antibodies are composed of heavy and light chains and consequently that the simplest antigenbinding unit is the variable fragment (Fv), 2 a heterodimer of heavy and light chain variable domains (V H and V L , respectively) (1). This supposition has held true for most species, but members of the Camelidae family have proven to be notable exceptions (2, 3). Camelids produce not only conventional antibodies but also "heavy chain antibodies" that are devoid of light chains (4). Consequently, the antigen-binding site of a heavy chain antibody is contained within a monomeric variable domain (V H H, for heavy chain variable domain of a heavy chain antibody), which has evolved to be autonomously stable in the absence of a light chain partner.The simplicity of the V H H domain architecture has attracted interest from protein engineers concerned with developing novel antibodies for biotechnological and therapeutic applications. V H H domains are well suited for use as modular building blocks that can be linked together to assemble multivalent or bispecific antibodies (5). The third complementarity determining loop (CDR3) of camelid V H H domains is often unusually long, and it has been suggested that these protruding loops may be especially effective for targeting active site clefts (6) and cryptic viral epitopes (7). Furthermore, because of their small size, V H H domains are r...

Mitigation of reversible self-association and viscosity in a human IgG1 monoclonal antibody by rational, structure-guided Fv engineering

“…This resulted in increased hydrophilicity of the VH surface, which is normally interfaced with the VL. 16 A similar result was observed in another study on the VH single domain antibodies HEL4 and DP47d, which are highly and poorly soluble, respectively. 40 In contrast to DP47d, HEL4 has a glycine at position 35.…”

“…A structural study of a VH single domain antibody revealed that mutation of H35 to glycine or alanine increased solubility, expression, and thermostability. 16 The H35 glycine mutation created a cavity into which an adjacent tryptophan at position 95 became buried. This resulted in increased hydrophilicity of the VH surface, which is normally interfaced with the VL.…”

“…14 A number of studies have illustrated the diversity of structural mechanisms by which self-association can occur. 9,[15][16][17][18][19][20][21][22] Antibodies have been found to self-interact through sites within both the variable fragment (Fv) and constant regions of the antigen-binding fragment (Fab) domains, as well as the crystallizable fragment (Fc) domain. 9,15,[18][19][20] In addition to the multitude of distinct domain surfaces that can compose the binding interfaces, the nature of the driving forces behind antibody selfassociation can also be diverse, with both electrostatic and hydrophobic interactions playing key roles.…”

Rational design of potent domain antibody inhibitors of amyloid fibril assembly

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Structure-based design of conformation- and sequence-specific antibodies against amyloid β

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