Biology subjects

Guloglu, B.

Publications and source records attributed to Guloglu, B..

7 recordsLinked to original sources

bioRxiv2024

Protein Sequence Modelling with Bayesian Flow Networks

Exploring the vast and largely uncharted territory of amino acid sequences is crucial for understanding complex protein functions and the engineering of novel therapeutic proteins. Whilst generative machine learning has advanced protein sequence modelling, no existing approach is proficient for both unconditional and conditional generation. In this work, we propose that Bayesian Flow Networks (BFNs), a recently introduced framework for generative modelling, can address these challenges. We present ProtBFN, a 650M parameter model trained on protein sequences curated from UniProtKB, which generates natural-like, diverse, structurally coherent, and novel protein sequences, significantly outperforming leading autoregressive and discrete diffusion models. Further, we fine-tune ProtBFN on heavy chains from the Observed Antibody Space (OAS) to obtain an antibody-specific model, AbBFN, which we use to evaluate zero-shot conditional generation capabilities. AbBFN is found to be competitive with, or better than, antibody-specific BERT-style models, when applied to predicting individual framework or complimentary determining regions (CDR).

bioinformatics↗

bioRxiv2024

T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity

T-cell receptor (TCR) structures are currently under-utilised in early-stage drug discovery and repertoire-scale informatics. Here, we leverage a large dataset of solved TCR structures from Immunocore to evaluate the current state-of-the-art for TCR structure prediction, and identify which regions of the TCR remain challenging to model. Through clustering analyses and the training of a TCR-specific model capable of large-scale structure prediction, we find that the alpha chain VJ-recombined loop (CDRA3) is as structurally diverse and correspondingly difficult to predict as the beta chain VDJ-recombined loop (CDRB3). This differentiates TCR variable domain loops from the genetically analogous antibody loops and supports the conjecture that both TCR alpha and beta chains are deterministic of antigen specificity. We hypothesise that the larger number of alpha chain joining genes compared to beta chain joining genes compensates for the lack of a diversity gene segment. Overall, our study demonstrates that valuable structure-function relationships can lie in alpha chains despite their simpler junctions. We also provide over 1.5M predicted TCR structures to enable repertoire structural analysis and elucidate strategies towards improving the accuracy of future TCR structure predictors.

immunology↗

bioRxiv2023

Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling

Antibodies with lambda light chains ({lambda}-antibodies) are generally considered to be less developable than those with kappa light chains ({kappa}-antibodies), leading to substantial systematic biases in drug discovery pipelines. This has contributed to kappa dominance amongst clinical-stage therapeutics. However, the identification of increasing numbers of epitopes preferentially engaged by{lambda} -antibodies shows there is a functional cost to neglecting them as potential lead candidates during discovery campaigns. Here, we update our Therapeutic Antibody Profiler (TAP) tool to use the latest data and machine learning-based structure prediction methods, and apply this new protocol to evaluate developability risk profiles for{kappa} -antibodies and{lambda} -antibodies based on their surface physicochemical properties. We find that{lambda} -antibodies are on average at a higher risk of poor developability -- as an indication, over 40% of single-cell sequenced human{lambda} -antibodies are flagged by TAP for risk-prone patches of surface hydrophobicity (PSH), compared to around 11% of human{kappa} -antibodies. Nonetheless, a substantial proportion of natural{lambda} -antibodies are assigned more moderate risk profiles by TAP and should therefore represent more tractable candidates for therapeutic development. We also analyse the populations of high and low risk antibodies, highlighting opportunities for strategic design that TAP suggests would enrich for more developable{lambda} -based candidates. Overall, we provide context to the differing developability of{kappa} - and{lambda} -antibodies, enabling a rational approach to incorporate more diversity into the initial pool of immunotherapeutic candidates.

bioinformatics↗

bioRxiv2023

A comparison of the binding sites of antibodies and single-domain antibodies

Antibodies are the largest class of biotherapeutics. However, in recent years, single-domain antibodies have gained traction due to their smaller size and comparable binding affinity. Antibodies (Abs) and single-domain antibodies (sdAbs) differ in the structures of their binding sites: most significantly, single-domain antibodies lack a light chain and so have just three CDR loops. Given this inherent structural difference, it is important to understand whether Abs and sdAbs are distinguishable in how they engage a binding partner and thus, whether they are suited to different types of epitopes. In this study, we use non-redundant sequence and structural datasets to compare the paratopes, epitopes and antigen interactions of Abs and sdAbs. We demonstrate that even though sd-Abs have smaller paratopes, they target epitopes of equal size to those targeted by Abs. To achieve this, the paratopes of sdAbs contribute more interactions per residue than the paratopes of Abs. Additionally, we find that conserved framework residues are of increased importance in the paratopes of sd-Abs, suggesting that they include non-specific interactions to achieve comparable affinity. Further-more, the epitopes of sdAbs and Abs cannot be distinguished by their shape. For our datasets, sd-Abs do not target more concave epitopes than Abs: we posit that this may be explained by differences in the orientation and compaction of sdAb and Ab CDR-H3 loops. Overall, our results have important implications for the engineering and humanization of sdAbs, as well as the selection of the best modality for targeting a particular epitope.

immunology↗

bioRxiv2023

Specific attributes of the VL domain influence both the structure and structural variability of CDR-H3 through steric effects

Antibodies, through their ability to target virtually any epitope, play a key role in driving the adaptive immune response in jawed vertebrates. The binding domains of standard antibodies are their variable light (VL) and heavy (VH) domains, both of which present analogous complementarity-determining region (CDR) loops. It has long been known that the VH CDRs contribute more heavily to the antigen-binding surface (paratope), with the CDR-H3 loop providing a major modality for the generation of diverse paratopes. Here, we provide evidence for an additional role of the VL domain as a modulator of CDR-H3 structure, using a diverse set of antibody crystal structures and a large set of molecular dynamics simulations. We show that specific attributes of the VL domain such as CDR canonical forms and genes can influence the structural diversity of the CDR-H3 loop, and provide a physical model for how this effect occurs through inter-loop contacts and packing of CDRs against each other. Our study provides insights into the interdependent nature of CDR conformations, an understanding of which is important for the rational antibody design process.

bioinformatics↗

bioRxiv2023

Structural basis for DARC binding in reticulocyte invasion by Plasmodium vivax

The symptoms of malaria occur during the blood stage of infection, when the parasite replicates within human red blood cells. The human malaria parasite, Plasmodium vivax, selectively invades reticulocytes in a process which requires an interaction between the ectodomain of the human DARC receptor and the Plasmodium vivax Duffy-binding protein, PvDBP. Previous studies have revealed that a small helical peptide from DARC binds to region II of PvDBP (PvDBP-RII). However, it is also known that sulphation of tyrosine residues on DARC affects its binding to PvDBP and these residues were not observed in previous structures. We have therefore determined the structure of PvDBP-RII bound to sulphated DARC peptide, showing that a sulphate on tyrosine 41 binds to a charged pocket on PvDBP-RII. We use molecular dynamics simulations, affinity measurements and growth-inhibition experiments in parasites to confirm the importance of this interaction. We also reveal the epitope for vaccine-elicited growth-inhibitory antibody, DB1. This provides a complete understanding of the binding of PvDBP-RII to DARC and will guide the design of vaccines and therapeutics to target this essential interaction.

microbiology↗

bioRxiv2022

Structure of the malaria vaccine candidate Pfs48/45 and its recognition by transmission blocking antibodies

An effective malaria vaccine remains a global health priority and vaccine immunogens which prevent transmission of the parasite will have important roles in multi-component vaccines. One of the most promising candidates for inclusion in a transmission-blocking malaria vaccine is the gamete surface protein Pfs48/45, which is essential for development of the parasite in the mosquito midgut. Indeed, antibodies which bind Pfs48/45 can prevent transmission if ingested with the parasite as part of the mosquito bloodmeal. Here we present the first structure of full-length Pfs48/45, revealing its three domains to form a dynamic, planar, triangular arrangement. From this, we show where transmission-blocking and non-blocking antibodies bind on Pfs48/45. Finally, we demonstrate that antibodies which bind across this molecule can be transmission-blocking. These studies will guide the development of future Pfs48/45-based vaccine immunogens.

microbiology↗