Antibody-Antigen Binding Interface Analysis in the Big Data Era

Reis, Pedro B. P. S.; Barletta, German Patricio; Gagliardi, Luca; Fortuna, Sara; Soler, Miguel A.; Rocchia, Walter

doi:10.3389/fmolb.2022.945808

Cited by 11 publications

(8 citation statements)

References 36 publications

(76 reference statements)

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“…1b-1f). The BSA on antigen-antibody complex formation is 923.2 A ˚2 on average for the two BRIL-SRP2070Fab complexes in the asymmetric unit (Supplementary Table S2a), which is larger than the average for known antigen-antibody interfaces of 534 AE 157 A ˚ (Reis et al, 2022). Hydrophilic interactions such as hydrogen bonds and salt bridges play major roles in BRIL recognition: seven hydrogen bonds and one salt bridge are formed between the H chain and BRIL.…”

Section: Resultsmentioning

confidence: 93%

Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone

Miyagi¹,

Suzuki²,

Yasunaga³

et al. 2023

Acta Cryst Sect D Struct Biol

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Structure determination of G-protein-coupled receptors (GPCRs) is key for the successful development of efficient drugs targeting GPCRs. BRIL is a thermostabilized apocytochrome b 562 (with M7W/H102I/R106L mutations) from Escherichia coli and is often used as a GPCR fusion protein for expression and crystallization. SRP2070Fab, an anti-BRIL antibody Fab fragment, has been reported to facilitate and enhance the crystallization of BRIL-fused GPCRs as a crystallization chaperone. This study was conducted to characterize the high-resolution crystal structure of the BRIL–SRP2070Fab complex. The structure of the BRIL–SRP2070Fab complex was determined at 2.1 Å resolution. This high-resolution structure elucidates the binding interaction between BRIL and SRP2070Fab. When binding to BRIL, SRP2070Fab recognizes conformational epitopes, not linear epitopes, on the surface of BRIL helices III and IV, thereby binding perpendicularly to the helices, which indicates stable binding. Additionally, the packing contacts of the BRIL–SRP2070Fab co-crystal are largely due to SRP2070Fab rather than BRIL. The accumulation of SRP2070Fab molecules by stacking is remarkable and is consistent with the finding that stacking of SRP2070Fab is predominant in known crystal structures of BRIL-fused GPCRs complexed with SRP2070Fab. These findings clarified the mechanism of SRP2070Fab as a crystallization chaperone. Moreover, these data will be useful in the structure-based drug design of membrane-protein drug targets.

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Section: Resultsmentioning

confidence: 93%

Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone

Miyagi¹,

Suzuki²,

Yasunaga³

et al. 2023

Acta Cryst Sect D Struct Biol

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“…This led to the removal of three pairs of mutations (highlighted in Table S1). The frequency of the mutation type is represented in Figure b, with mutation to/from alanine being the most frequent due to the common experimental alanine scanning procedures, and followed by mutation to tyrosine, which is one of the ubiquitous residues in CDR loops …”

Section: Resultsmentioning

confidence: 99%

“…The second most frequent amino acid mutated in our database is tyrosine, which is the most frequent residue in therapeutic Ab CDRs. 49 Another limitation is that this study focuses on only a single Ag (HEL). While this allowed us to eliminate Ag-dependent variables from our investigation, it is possible that some results are specific to this Ag and its epitopes.…”

Section: Discussionmentioning

confidence: 99%

“…This problem is common to many protein–protein databases , and can only be overcome by a much broader experimental effort. The second most frequent amino acid mutated in our database is tyrosine, which is the most frequent residue in therapeutic Ab CDRs . Another limitation is that this study focuses on only a single Ag (HEL).…”

Section: Discussionmentioning

confidence: 99%

“…The frequency of the mutation type is represented in Figure 1b, with mutation to/from alanine being the most frequent due to the common experimental alanine scanning procedures, and followed by mutation to tyrosine, which is one of the ubiquitous residues in CDR loops. 49 3.2. Binding Interface Conservation upon Single Mutation.…”

Section: Reconstructed Data Setmentioning

confidence: 99%

See 2 more Smart Citations

Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions

Tandiana,

Barletta,

Soler

et al. 2024

J. Chem. Theory Comput.

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The development of highly potent antibodies and antibody fragments as binding agents holds significant implications in fields such as biosensing and biotherapeutics. Their binding strength is intricately linked to the arrangement and composition of residues at the binding interface. Computational techniques offer a robust means to predict the three-dimensional structure of these complexes and to assess the affinity changes resulting from mutations. Given the interdependence of structure and affinity prediction, our objective here is to disentangle their roles. We aim to evaluate independently six side-chain reconstruction methods and ten binding affinity estimation techniques. This evaluation was pivotal in predicting affinity alterations due to single mutations, a key step in computational affinity maturation protocols. Our analysis focuses on a data set comprising 27 distinct antibody/hen egg white lysozyme complexes, each with crystal structures and experimentally determined binding affinities. Using six different side-chain reconstruction methods, we transformed each structure into its corresponding mutant via in silico single-point mutations. Subsequently, these structures undergo minimization and molecular dynamics simulation. We therefore estimate ΔΔG values based on the original crystal structure, its energy-minimized form, and the ensuing molecular dynamics trajectories. Our research underscores the critical importance of selecting reliable side-chain reconstruction methods and conducting thorough molecular dynamics simulations to accurately predict the impact of mutations. In summary, our study demonstrates that the integration of conformational sampling and scoring is a potent approach to precisely characterizing mutation processes in single-point mutagenesis protocols and crucial for computational antibody design.

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Understanding the Specific Implications of Amino Acids in the Antibody Development

Gavade,

Nagraj,

Patel

et al. 2024

Protein J

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Antibody-Antigen Binding Interface Analysis in the Big Data Era

Cited by 11 publications

References 36 publications

Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone

Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone

Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions

Understanding the Specific Implications of Amino Acids in the Antibody Development

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