SPECS: Integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural models

To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era

Motivation

Protein side-chain packing (PSCP), the problem of predicting side-chain conformation given a fixed backbone structure, has important implications in modeling of structures and interactions. However, despite the groundbreaking progress in protein structure prediction pioneered by AlphaFold, the existing PSCP methods still rely on experimental inputs, and do not leverage AlphaFold-predicted backbone coordinates to enable PSCP at scale.

Results

Here, we perform a large-scale benchmarking of the predictive performance of various PSCP methods on public datasets from multiple rounds of the Critical Assessment of Structure Prediction (CASP) challenges using a diverse set of evaluation metrics. Empirical results demonstrate that the PSCP methods perform well in packing the side-chains with experimental inputs, but they fail to generalize in repacking AlphaFold-generated structures. We additionally explore the effectiveness of leveraging the self-assessment confidence scores from AlphaFold by implementing a backbone confidence-aware integrative approach. While such a protocol often leads to performance improvement by attaining modest yet statistically significant accuracy gains over the AlphaFold baseline, it does not yield consistent and pronounced improvements. Our study highlights the recent advances and remaining challenges in PSCP in the post-AlphaFold era.

Availability

The code and raw data are freely available at https://github.com/Bhattacharya-Lab/PackBench.

Accurate prediction of protein tertiary structural changes induced by single-site mutations with equivariant graph neural networks

Predicting the change of protein tertiary structure caused by singlesite mutations is important for studying protein structure, function, and interaction. Even though computational protein structure prediction methods such as AlphaFold can predict the overall tertiary structures of most proteins rather accurately, they are not sensitive enough to accurately predict the structural changes induced by single-site amino acid mutations on proteins. Specialized mutation prediction methods mostly focus on predicting the overall stability or function changes caused by mutations without attempting to predict the exact mutation-induced structural changes, limiting their use in protein mutation study. In this work, we develop the first deep learning method based on equivariant graph neural networks (EGNN) to directly predict the tertiary structural changes caused by single-site mutations and the tertiary structure of any protein mutant from the structure of its wild-type counterpart. The results show that it performs substantially better in predicting the tertiary structures of protein mutants than the widely used protein structure prediction method AlphaFold.

A Sporothrix spp enolase derived multi-epitope vaccine confers protective response in BALB/c mice challenged with Sporothrix brasiliensis

Sporotrichosis is a cosmopolitan mycosis caused by pathogenic species of Sporothrix genus, that in Brazil is often acquired by zoonotic transmission involved infected cats with S. brasiliensis. Previous studies showed that the Sporothrix spp. recombinant enolase (rSsEno), a multifunctional protein with immunogenic properties, could be a promising target for vaccination against sporotrichosis in cats. Nevertheless, the considerable sequence identity (62%) of SsEno with its feline counterpart is a great concern. Here, we report the identification in silico, chemical synthesis and biological validation of six peptides of SsEno with low sequence identity to its cat orthologue. All synthesized peptides exhibit B-cell epitopes on the molecular surface of SsEno and proved to be highly reactive with the serum of infected mice with S. brasiliensis and sera of cats with sporotrichosis. Interestingly, our study revealed that anti-peptide sera did not react with the recombinant enolase from Felis catus (cats, rFcEno), thus, may not trigger autoimmune response in these felines if used as a vaccine antigen. The immunization with peptide mixture (PeptMix) formulated with Freund adjuvant (FA), induced high levels of antigen-specific IgG, IgG1 and IgG2b antibodies that conferred protection upon passive transference in infected BALB/c mice with S. brasiliensis. We also observed, that the FA + PeptMix formulation induced a Th1/Th2/Th17 cytokine profile ex vivo, associated with protecting effect against the experimental sporotrichosis. Our results suggest that the six SsEno-derived peptides here evaluated, could be used as safe antigens for the development of vaccine strategies against feline sporotrichosis, whether prophylactic or therapeutic.

A conserved residue in the P2X4 receptor has a nonconserved function in ATP recognition

Highly conserved amino acids are generally anticipated to have similar functions across a protein superfamily, including that of the P2X ion channels, which are gated by extracellular ATP. However, whether and how these functions are conserved becomes less clear when neighboring amino acids are not conserved. Here, we investigate one such case, focused on the highly conserved residue from P2X4, E118 (rat P2X4 numbering, rP2X4), a P2X subtype associated with human neuropathic pain. When we compared the crystal structures of P2X4 with those of other P2X subtypes, including P2X3, P2X7, and AmP2X, we observed a slightly altered side-chain orientation of E118. We used protein chimeras, double-mutant cycle analysis, and molecular modeling to reveal that E118 forms specific contacts with amino acids in the "beak" region, which facilitates ATP binding to rP2X4. These contacts are not present in other subtypes because of sequence variance in the beak region, resulting in decoupling of this conserved residue from ATP recognition and/or channel gating of P2X receptors. Our study provides an example of a conserved residue with a specific role in functional proteins enabled by adjacent nonconserved residues. The unique role established by the E118-beak region contact provides a blueprint for the development of subtype-specific inhibitors of P2X4.