Protein structure prediction in the era of AI: challenges and limitations when applying toin-silicoforce spectroscopy

Abstract

Mechanoactive proteins are essential for a myriad of physiological and pathological processes. Guided by the advances in single-molecule force spectroscopy (SMFS), we have reached a molecular-level understanding of how several mechanoactive proteins respond to mechanical forces. However, even SMFS has its limitations, including the lack of detailed structural information during force-loading experiments. That is where molecular dynamics (MD) methods shine, bringing atomistic details with femtosecond time-resolution. However, MD heavily relies on the availability of high-resolution structures, which is not available for most proteins. For instance, the Protein Data Bank currently has 192K structures deposited, against 231M protein sequences available on Uniprot. But many are betting that this gap might become much smaller soon. Over the past year, the AI-based AlphaFold created a buzz on the structural biology field by being able to, for the first time, predict near-native protein folds from their sequences. For some, AlphaFold is causing the merge of structural biology with bioinformatics. In this perspective, using an in silico SMFS approach, we investigate how reliable AlphaFold structure predictions are to investigate mechanical properties of staph bacteria adhesins proteins. Our results show that AlphaFold produce extremally reliable protein folds, but in many cases is unable to predict high-resolution protein complexes accurately. Nonetheless, the results show that AlphaFold can revolutionize the investigation of these proteins, particularly by allowing high-throughput scanning of protein structures. Meanwhile, we show that the AlphaFold results need to be validated and should not be employed blindly, with the risk of obtaining an erroneous protein mechanism.

Bridging the gap between in vitro and in silico single-molecule force spectroscopy

“…1 This methodology has been used by our group to investigate a myriad of systems, including cytoplasmic proteins, 2,3 as well as extracellular proteins that are remarkably resistant to shear forces, including cellulosomal proteins, [4][5][6][7] coronavirus proteins, 8 and bacterial adhesins. 9,10 Beside those, we have also investigated the mechanical properties of the widely employed streptavidin-biotin complex. 11,12 Among the highly mechanostable protein complexes, adhesins are particularly interesting.…”