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Article

Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies

Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA
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Author to whom correspondence should be addressed.
Academic Editors: Filip Jagodzinski, Kevin Molloy and Nino Russo
Molecules 2021, 26(22), 7049; https://doi.org/10.3390/molecules26227049
Received: 16 March 2021 / Revised: 1 November 2021 / Accepted: 15 November 2021 / Published: 22 November 2021
Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. A topology of secondary structures defines the mapping between a set of sequence segments and a set of traces of secondary structures in three-dimensional space. In order to enhance accuracy in ranking secondary structure topologies, we explored a method that combines three sources of information: a set of sequence segments in 1D, a set of amino acid contact pairs in 2D, and a set of traces in 3D at the secondary structure level. A test of fourteen cases shows that the accuracy of predicted secondary structures is critical for deriving topologies. The use of significant long-range contact pairs is most effective at enriching the rank of the maximum-match topology for proteins with a large number of secondary structures, if the secondary structure prediction is fairly accurate. It was observed that the enrichment depends on the quality of initial topology candidates in this approach. We provide detailed analysis in various cases to show the potential and challenge when combining three sources of information. View Full-Text
Keywords: protein structure; cryo-electron microscopy; secondary structure; contact; amino acid; topology; image; constraints protein structure; cryo-electron microscopy; secondary structure; contact; amino acid; topology; image; constraints
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MDPI and ACS Style

Alshammari, M.; He, J. Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies. Molecules 2021, 26, 7049. https://doi.org/10.3390/molecules26227049

AMA Style

Alshammari M, He J. Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies. Molecules. 2021; 26(22):7049. https://doi.org/10.3390/molecules26227049

Chicago/Turabian Style

Alshammari, Maytha, and Jing He. 2021. "Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies" Molecules 26, no. 22: 7049. https://doi.org/10.3390/molecules26227049

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