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

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...

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Autores principales:	Maytha Alshammari, Jing He
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	protein structure cryo-electron microscopy secondary structure contact amino acid topology Organic chemistry QD241-441
Acceso en línea:	https://doaj.org/article/eb148b4b36bc4166b3023e7b1eae5f30
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spelling	oai:doaj.org-article:eb148b4b36bc4166b3023e7b1eae5f302021-11-25T18:29:26ZCombining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies10.3390/molecules262270491420-3049https://doaj.org/article/eb148b4b36bc4166b3023e7b1eae5f302021-11-01T00:00:00Zhttps://www.mdpi.com/1420-3049/26/22/7049https://doaj.org/toc/1420-3049Although 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.Maytha AlshammariJing HeMDPI AGarticleprotein structurecryo-electron microscopysecondary structurecontactamino acidtopologyOrganic chemistryQD241-441ENMolecules, Vol 26, Iss 7049, p 7049 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	protein structure cryo-electron microscopy secondary structure contact amino acid topology Organic chemistry QD241-441
spellingShingle	protein structure cryo-electron microscopy secondary structure contact amino acid topology Organic chemistry QD241-441 Maytha Alshammari Jing He Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies
description	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.
format	article
author	Maytha Alshammari Jing He
author_facet	Maytha Alshammari Jing He
author_sort	Maytha Alshammari
title	Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies
title_short	Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies
title_full	Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies
title_fullStr	Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies
title_full_unstemmed	Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies
title_sort	combining cryo-em density map and residue contact for protein secondary structure topologies
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/eb148b4b36bc4166b3023e7b1eae5f30
work_keys_str_mv	AT maythaalshammari combiningcryoemdensitymapandresiduecontactforproteinsecondarystructuretopologies AT jinghe combiningcryoemdensitymapandresiduecontactforproteinsecondarystructuretopologies
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Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies

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