Trends in Antibody Sequence Changes during the Somatic Hypermutation Process

Abstract

Probable germline gene sequences from thousands of aligned mature Ab sequences are inferred using simple computational matching to known V(D)J genes. Comparison of the germline to mature sequences in a structural region-dependent fashion allows insights into the methods that nature uses to mature Abs during the somatic hypermutation process. Four factors determine the residue type mutation patterns: biases in the germline, accessibility from single base permutations, location of mutation hotspots, and functional pressures during selection. Germline repertoires at positions that commonly contact the Ag are biased with tyrosine, serine, and tryptophan. These residue types have a high tendency to be present in mutation hotspot motifs, and their abundance is decreased during maturation by a net conversion to other types. The heavy use of tyrosines on mature Ab interfaces is thus a reflection of the germline composition rather than being due to selection during maturation. Potentially stabilizing changes such as increased proline usage and a small number of double cysteine mutations capable of forming disulfide bonds are ascribed to somatic hypermutation. Histidine is the only residue type for which usage increases in each of the interface, core, and surface regions. The net overall effect is a conversion from residue types that could provide nonspecific initial binding into a diversity of types that improve affinity and stability. Average mutation probabilities are ∼4% for core residues, ∼5% for surface residues, and ∼12% for residues in common Ag-contacting positions, excepting the those coded by the D gene.

The Protein-Protein Interface Evolution Acts in a Similar Way to Antibody Affinity Maturation

“…Capturing the Key Evolutionary Information of the Antibody Binding Site during Affinity Maturation-The trends in antibody sequence changes during the somatic hypermutation process were systematically studied by Clark et al (9). They illuminated the strategies that nature uses to bias immature Ab properties and subsequently refines them during the affinity maturation process.…”

“…They found that the frequency of somatic hypermutation and the diversity of the germline sequences are highest in the CDRs. Rather than focus on the mutation frequencies, Clark et al (9) examined the type of mutation and its functional implications deduced from the location in the structure. Their results indicated that residue type changes during the somatic hypermutation process were significant and had underlying functional rationales.…”

A Systematic Comparison of Free and Bound Antibodies Reveals Binding-Related Conformational Changes

“…Notably, this change is significantly lower than that of the other CDRs and is even smaller than the change in the FR and the constant domain (the baseline). It is not the shortest CDR, but it has the lowest number of contacts with the Ag (53), a low number of mutations during affinity maturation (55), and low structural diversity in different Abs (56). These observations may suggest that the conformational change that a CDR undergoes is related to its role in Ag binding.…”

Immunoglobulin Classification Using the Colored Antibody Graph

“…In this simple case, the most popular color can be selected as the reference label. The V gene segments frequently contain many mutations, some having known associated motifs (Rogozin and Kolchanov, 1992;Dörner et al, 1998;Clark et al, 2006). Rogozin and Kolchanov (1992) first exposed the RGYW motif, and Doerner et.…”