ArticleJournal of the Royal Society, Interface2015
Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?
Article in Journal of the Royal Society, Interface, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Neutral Frustration Landscape Architecture of SARS-CoV-2 Spike-Antibody Interfaces Shapes Immune Evasion Mechanisms for Ultrapotent Neutralizing Antibodies and Determines Pathways of Viral Adaptation: Insights from Integrative Computational Approach.bioRxiv : the preprint server for biology · 2025Article
- Exploring Binding Pockets in the Conformational States of the SARS-CoV-2 Spike Trimers for the Screening of Allosteric Inhibitors Using Molecular Simulations and Ensemble-Based Ligand Docking.International journal of molecular sciences · 2024Article
- Atomic Simulation of the Binding of JAK1 and JAK2 with the Selective Inhibitor Ruxolitinib.International journal of molecular sciences · 2022Article
- BioS2Net: Holistic Structural and Sequential Analysis of Biomolecules Using a Deep Neural Network.International journal of molecular sciences · 2022Article
- Structural communication between the GTPase Sec4p and its activator Sec2p: Determinants of GEF activity and early deformations to nucleotide release.Computational and structural biotechnology journal · 2022Article
- Slowest-first protein translation scheme: Structural asymmetry and co-translational folding.Biophysical journal · 2021Article
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1 author.
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Abstract
The determination of a protein's folding nucleus, i.e. a set of native contacts playing an important role during its folding process, remains an elusive yet essential problem in biochemistry. In this work, we investigate the mechanical properties of 70 protein structures belonging to 14 protein families presenting various folds using coarse-grain Brownian dynamics simulations. The resulting rigidity profiles combined with multiple sequence alignments show that a limited set of rigid residues, which we call the consensus nucleus, occupy conserved positions along the protein sequence. These residues' side chains form a tight interaction network within the protein's core, thus making our consensus nuclei potential folding nuclei. A review of experimental and theoretical literature shows that most (above 80%) of these residues were indeed identified as folding nucleus member in earlier studies.
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