The association of heavy and light chain variable domains in antibodies: implications for antigen specificity

Chailyan, Anna; Marcatili, Paolo; Tramontano, Anna

doi:10.1111/j.1742-4658.2011.08207.x

Cited by 83 publications

(87 citation statements)

References 45 publications

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“…18 In the following, we focus on an aspect of antibody structure that, in the context of humanization, is often overlooked: the relative orientation of VH and VL domain. A survey of the known repertoire of antibody crystal structures reveals a notable variability in the parameters of VH-VL orientation, [19][20][21] and it seems likely that modulating VH-VL orientation not only is a necessary means to accommodate the diverse antigenic shapes that antibodies are confronted with, but also a mechanism to further diversify the composition (and thus increase the possible number) of antibody paratopes -in addition to the well-known mechanisms of diversification involving variations in length and sequence of the CDRs. It is reasonable to assume that changes in VH-VL orientation (e.g., caused by exchanging the b-sheet framework during humanization) might induce changes with regard to antigen binding.…”

Section: Introductionmentioning

confidence: 99%

VH-VL orientation prediction for antibody humanization candidate selection: A case study

Bujotzek¹,

Lipsmeier²,

Harris³

et al. 2015

mAbs

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Antibody humanization describes the procedure of grafting a non-human antibody's complementaritydetermining regions, i.e., the variable loop regions that mediate specific interactions with the antigen, onto a b-sheet framework that is representative of the human variable region germline repertoire, thus reducing the number of potentially antigenic epitopes that might trigger an anti-antibody response. The selection criterion for the so-called acceptor frameworks (one for the heavy and one for the light chain variable region) is traditionally based on sequence similarity. Here, we propose a novel approach that selects acceptor frameworks such that the relative orientation of the 2 variable domains in 3D space, and thereby the geometry of the antigen-binding site, is conserved throughout the process of humanization. The methodology relies on a machine learning-based predictor of antibody variable domain orientation that has recently been shown to improve the quality of antibody homology models. Using data from 3 humanization campaigns, we demonstrate that preselecting humanization variants based on the predicted difference in variable domain orientation with regard to the original antibody leads to subsets of variants with a significant improvement in binding affinity.

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Section: Introductionmentioning

confidence: 99%

VH-VL orientation prediction for antibody humanization candidate selection: A case study

Bujotzek¹,

Lipsmeier²,

Harris³

et al. 2015

mAbs

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“…This included reports of very small overall changes, side-chain movements, large rearrangement of one or more of the CDRs, change in the VH-VL relative orientation, and, in some cases, combinations of some or all of the above. Recent studies used newer structurecomparison methods (4,36) and used the growing number of available structures (37)(38)(39)(40) to perform comparative research to identify new and more general characteristics of Ab structures. However, many of these studies did not compare free and bound structures of the same Ab (4,37,40), focused only on the VH-VL relative orientation (4,37,38,40), or included only a limited number of structures (4,36,39).…”

mentioning

confidence: 99%

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

Sela-Culang

Alon

Ofran

2012

The Journal of Immunology

104

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To study structural changes that occur in Abs upon Ag binding, we systematically compared free and bound structures of all 141 crystal structures of the 49 Abs that were solved in these two forms. We found that many structural changes occur far from the Ag binding site. Some of them may constitute a mechanism for the recently suggested allosteric effects in Abs. Within the binding site itself, CDR-H3 is the only element that shows significant binding-related conformational changes; however, this occurs in only one third of the Abs. Beyond the binding site, Ag binding is associated with changes in the relative orientation of the H and L chains in both the variable and constant domains. An even larger change occurs in the elbow angle between the variable and the constant domains, and it is significantly larger for binding of big Ags than for binding of small ones. The most consistent and substantial conformational changes occur in a loop in the H chain constant domain. This loop is implicated in the interaction between the H and L chains, is often intrinsically disordered, and is involved in complement binding. Hence, we suggest that it may have a role in Ab function. These findings provide structural insight into the recently proposed allosteric effects in Abs.

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“…Among the ∼500 F V crystal structures they examined, packing angle differed by as much as 30°. Chailyan et al (2011) defined V L -V H orientation differently, via clustering. The resulting description was doi: 10.1093/protein/gzw013…”

Section: Introductionmentioning

confidence: 99%

Improved prediction of antibody V_L–V_Horientation

Marze

Lyskov

Gray

2016

Protein Engineering, Design and Selection

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Antibodies are important immune molecules with high commercial value and therapeutic interest because of their ability to bind diverse antigens. Computational prediction of antibody structure can quickly reveal valuable information about the nature of these antigen-binding interactions, but only if the models are of sufficient quality. To achieve high model quality during complementaritydetermining region (CDR) structural prediction, one must account for the V L -V H orientation. We developed a novel four-metric V L -V H orientation coordinate frame. Additionally, we extended the CDR grafting protocol in RosettaAntibody with a new method that diversifies V L -V H orientation by using 10 V L -V H orientation templates rather than a single one. We tested the multiple-template grafting protocol on two datasets of known antibody crystal structures. During the template-grafting phase, the new protocol improved the fraction of accurate V L -V H orientation predictions from only 26% (12/46) to 72% (33/46) of targets. After the full RosettaAntibody protocol, including CDR H3 remodeling and V L -V H re-orientation, the new protocol produced more candidate structures with accurate V L -V H orientation than the standard protocol in 43/46 targets (93%). The improved ability to predict V L -V H orientation will bolster predictions of other parts of the paratope, including the conformation of CDR H3, a grand challenge of antibody homology modeling.

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The association of heavy and light chain variable domains in antibodies: implications for antigen specificity

Cited by 83 publications

References 45 publications

VH-VL orientation prediction for antibody humanization candidate selection: A case study

VH-VL orientation prediction for antibody humanization candidate selection: A case study

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

Improved prediction of antibody V_L–V_Horientation

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The association of heavy and light chain variable domains in antibodies: implications for antigen specificity

Cited by 83 publications

References 45 publications

VH-VL orientation prediction for antibody humanization candidate selection: A case study

VH-VL orientation prediction for antibody humanization candidate selection: A case study

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

Improved prediction of antibody VL–VHorientation

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Improved prediction of antibody V_L–V_Horientation