Turina Paola, Dal Cortivo Giuditta, Enriquez Sandoval Carlos A, Alexov Emil, Ascher David B, Babbi Giulia, Bakolitsa Constantina, Casadio Rita, Fariselli Piero, Folkman Lukas, Kamandula Akash, Katsonis Panagiotis, Li Dong, Lichtarge Olivier, Martelli Pier Luigi, Panday Shailesh Kumar, Pires Douglas E V, Portelli Stephanie, Pucci Fabrizio, Rodrigues Carlos H M, Rooman Marianne, Savojardo Castrense, Schwersensky Martin, Shen Yang, Strokach Alexey V, Sun Yuanfei, Woo Junwoo, Radivojac Predrag, Brenner Steven E, Dell'Orco Daniele, Capriotti Emidio
Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
Department of Neurosciences, Biomedicine, and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134, Verona, Italy.
Hum Genet. 2025 Mar;144(2-3):113-125. doi: 10.1007/s00439-024-02720-y. Epub 2024 Dec 23.
Recent thermodynamic and functional studies have been conducted to evaluate the impact of amino acid substitutions on Calmodulin (CaM). The Critical Assessment of Genome Interpretation (CAGI) data provider at University of Verona (Italy) measured the melting temperature (T) and the percentage of unfolding (%unfold) of a set of CaM variants (CaM challenge dataset). Thermodynamic measurements for the equilibrium unfolding of CaM were obtained by monitoring far-UV Circular Dichroism as a function of temperature. These measurements were used to determine the T and the percentage of protein remaining unfolded at the highest temperature. The CaM challenge dataset, comprising a total of 15 single amino acid substitutions, was used to evaluate the effectiveness of computational methods in predicting the T and unfolding percentages associated with the variants, and categorizing them as destabilizing or not. For the sixth edition of CAGI, nine independent research groups from four continents (Asia, Australia, Europe, and North America) submitted over 52 sets of predictions, derived from various approaches. In this manuscript, we summarize the results of our assessment to highlight the potential limitations of current algorithms and provide insights into the future development of more accurate prediction tools. By evaluating the thermodynamic stability of CaM variants, this study aims to enhance our understanding of the relationship between amino acid substitutions and protein stability, ultimately contributing to more accurate predictions of the effects of genetic variants.
最近开展了热力学和功能研究，以评估氨基酸取代对钙调蛋白（CaM）的影响。意大利维罗纳大学的基因组解释关键评估（CAGI）数据提供者测量了一组CaM变体（CaM挑战数据集）的解链温度（T）和去折叠百分比（%去折叠）。通过监测远紫外圆二色性随温度的变化，获得了CaM平衡去折叠的热力学测量结果。这些测量用于确定T以及在最高温度下仍未折叠的蛋白质百分比。CaM挑战数据集包含总共15个单氨基酸取代，用于评估计算方法在预测与变体相关的T和去折叠百分比以及将它们分类为不稳定或非不稳定方面的有效性。对于CAGI的第六版，来自四大洲（亚洲、澳大利亚、欧洲和北美）的九个独立研究小组提交了超过52组源自各种方法的预测。在本手稿中，我们总结了评估结果，以突出当前算法的潜在局限性，并为更准确的预测工具的未来发展提供见解。通过评估CaM变体的热力学稳定性，本研究旨在加深我们对氨基酸取代与蛋白质稳定性之间关系的理解，最终有助于更准确地预测遗传变体的影响。
