Analysis of AlphaFold and molecular dynamics structure predictions of mutations in serpins

Abstract

Serine protease inhibitors (serpins) include thousands of structurally conserved proteins playing key roles in many organisms. Mutations affecting serpins may disturb their conformation, leading to inactive forms. Unfortunately, conformational consequences of mutations affecting serpins are difficult to predict. In this study we integrate experimental data of patients with mutations affecting one serpin with the predictions obtained by AlphaFold and molecular dynamics. Five SERPINC1 mutations causing antithrombin deficiency, the strongest congenital thrombophilia, (p.Arg79Cys; p.Pro112Ser, p.Met283Val; p.Pro352insValPheLeuPro, and p.Glu241_Leu242delinsValLeuValLeuValAsnThrArgThrSer) were selected from a cohort of 350 unrelated patients based on functional, biochemical, and crystallographic evidence supporting a folding defect. AlphaFold gave an accurate prediction for the wild-type antithrombin structure. However, it only produced native structures for all variants, regardless of its complexity and in-vivo conformational consequences. Similarly, molecular dynamics of up to 1000 ns at temperatures that caused conformational transitions did not show significant changes in the native structure of wild-type or variants. In conclusion, one predictive tool of protein folding, AlphaFold, and a simulation method for analyzing the physical movements of atoms and molecules, molecular dynamics, force predictions into the native stressed conformation at conditions with experimental evidence supporting a conformational change to relaxed structures. It is necessary to improve predictive strategies for serpins that consider the conformational sensitivity of these molecules.

Computational Tools to Assist in Analyzing Effects of the SERPINA1 Gene Variation on Alpha-1 Antitrypsin (AAT)

“…Recently, attempts have been made to harness AlphaFold’s structure prediction capabilities to determine the effect of SNVs [ 96 , 105 ]. Efforts to apply this approach to investigate mutations in proteins belonging to the SERPIN family did not give the expected outcomes, as AlphaFold tended to generate native structures for all variants, irrespective of their complexity and potential in vivo conformational effects [ 106 ]. Hence, there is a clear imperative for research to enhance the accuracy of AlphaFold’s predictions regarding the structural implications of SNVs in AAT and other proteins that maintain their function via conformational changes.…”