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• W2891867890 abstract "Ubiquitin is a small model protein, commonly used in protein folding experiments and simulations. We simulated ubiquitin using a well-tested structure-based model coarse-grained to a Cα level (Cα-SBM) and found that the simulated folding route did not agree with the experimentally observed one. Simulating the Cα-SBM with a cutoff contact map, instead of a screened contact map, switched the folding route with the new route matching the experimental route. Thus, the simulated folding of ubiquitin is sensitive to contact map definition. The screened contact map, which is used in folding simulations because it captures protein folding cooperativity, removes contacts in which the atoms in contact are occluded by a third atom and is less sensitive to the value of the cutoff distance in well-packed regions of the protein. In sparsely packed regions, the larger cutoff distance creates bridging contacts between atoms which are separated by voids. Such contacts do not seem to affect the folding of most proteins, including those of the ubiquitin fold. However, the surface of ubiquitin has several protruding functional side chains which naturally create bridging contacts. Together, our results show that subtle structural features of a protein that may not be apparent by mere observation can be identified by comparing folding simulations of SBMs in which these features are differently encoded. When such structural features are preserved for functional reasons, differences in computational folding can be leveraged to identify functional features. Notably, such features are accessible to a gradation of SBMs even in commonly studied proteins such as ubiquitin." @default.
• W2891867890 created "2018-09-27" @default.
• W2891867890 creator A5056115805 @default.
• W2891867890 creator A5059941545 @default.
• W2891867890 date "2018-09-20" @default.
• W2891867890 modified "2023-09-26" @default.
• W2891867890 title "The Sensitivity of Computational Protein Folding to Contact Map Perturbations: The Case of Ubiquitin Folding and Function" @default.
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• W2891867890 doi "https://doi.org/10.1021/acs.jpcb.8b07409" @default.
• W2891867890 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/30234303" @default.
• W2891867890 hasPublicationYear "2018" @default.
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