A Structural-informatics Approach for Tracing β-Sheets: Building Pseudo-Cα Traces for β-Strands in Intermediate-resolution Density Maps

Kong, Ying; Zhang, Xing; Baker, Timothy S.; Ma, Jianpeng

doi:10.1016/j.jmb.2004.03.038

Cited by 80 publications

(74 citation statements)

References 49 publications

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“…They were also tested on skeletons in which one or more secondary structure was purposely removed and an eight-stranded skeleton obtained from an experimental 7.6 Å cryo-EM density map using Sheetminer 12 and Sheettracer. 13 In most cases, the native topology was identified as the most energetically favorable one for a given skeleton. These results strongly suggest it is indeed plausible to derive reliably protein native topology from secondary-structural skeletons.…”

Section: Introductionmentioning

confidence: 99%

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Determining Protein Topology from Skeletons of Secondary Structures

Chen

et al. 2005

Journal of Molecular Biology

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Section: Introductionmentioning

confidence: 99%

“…13 The outputs of these methods outline the skeletons of secondary structures that describe the location of a-helices and b-strands. But, the information of the directionality of the secondary structures and loop connectivity among them is not available.…”

Section: Introductionmentioning

confidence: 99%

Determining Protein Topology from Skeletons of Secondary Structures

Chen

et al. 2005

Journal of Molecular Biology

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“…Procedures to detect alpha helices (Jiang et al, 2001) and beta sheets (Kong, et al, 2004) in intermediate-resolution density maps can be used to create tentative atomic models. A procedure to recognize structural homologues of protein domains in intermediate-resolution maps and to construct quasi-atomic models of the assembly has been demonstrated (Lasker, et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

YUP.SCX: Coaxing atomic models into medium resolution electron density maps

Tan

Devkota

Harvey

2008

Journal of Structural Biology

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The structures of large macromolecular complexes in different functional states can be determined by cryo-electron microscopy, which yields electron density maps of low to intermediate resolutions.The maps can be combined with high-resolution atomic structures of components of the complex, to produce a model for the complex that is more accurate than the formal resolution of the map. To this end, methods have been developed to dock atomic models into density maps rigidly or flexibly, and to refine a docked model so as to optimize the fit of the atomic model into the map. We have developed a new refinement method called YUP.SCX. The electron density map is converted into a component of the potential energy function to which terms for stereochemical restraints and volume exclusion are added. The potential energy function is then minimized (using simulated annealing) to yield a stereochemically-restrained atomic structure that fits into the electron density map optimally. We used this procedure to construct an atomic model of the 70S ribosome in the pre-accommodation state. Although some atoms are displaced by as much as 33 Å, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments.

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“…Most helices longer than two turns can be detected. Most of the major β-sheets can also be detected using various methods such as SheetTracer, SSEhunter, SSELearner and SSETracer [29][30][31][32]. By analyzing the twist of β-sheet density, the position of β-strands can be predicted [31].…”

Section: Introductionmentioning

confidence: 99%

Deriving Protein Backbone Using Traces Extracted from Density Maps at Medium Resolutions

Nasr

2015

Bioinformatics Research and Applications

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Abstract. Electron cryomicroscopy is an experimental technique that is capable to produce three dimensional gray-scale images for protein molecules, called density maps. At medium resolution, the atomic details of the molecule cannot be visualized from density maps. However, some features of the molecule can be seen such as the locations of major secondary structures and the skeleton of the molecule. In addition, the order and direction of the detected secondary structure traces can be inferred. We introduce a method to construct the entire model of a protein directly for traces extracted from the density map. The initial results show that this method has good potential. A single model was built for each of the 12 proteins used in the test. The RMSD 100 of the models is slightly improved from our previous method. Keywords:Cryo-EM · Volume image · Skeletonization · Protein modeling · Loop modeling IntroductionElectron cryomicroscopy (cryo-EM) is an emerging technique that produces threedimensional (3D) electron density maps at a wide-range of resolutions [1][2][3][4]. When the resolution of density maps is higher than 4Å, the atomic structure can often be derived [5][6][7][8][9]. At the medium resolutions, such as 5-10Å, the backbone and the characteristic features of amino acids are not resolved. It is still challenging to derive the atomic structure from such a density map. When a component of the protein has atomic structure available, fitting can be performed to derive the atomic structure [10][11][12]. When a homologous model is available, rigid or flexible fitting can be used to derive the atomic structure [13][14][15][16][17][18]. However, it is still challenging to find a suitable template for many proteins. De novo modeling is an alternative method to derive atomic structures without relying on template structures [19][20][21][22][23][24]. It relies on the detection of secondary structure positions and the connection patterns encoded in the skeleton of the density map. A number of computational methods have been developed to detect α-helices from the density maps [25][26][27][28][29][30][31]. Most helices longer than two turns can be detected. Most of the major β-sheets can also be detected using various methods such as SheetTracer, SSEhunter,. By analyzing the twist of β-sheet

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A Structural-informatics Approach for Tracing β-Sheets: Building Pseudo-Cα Traces for β-Strands in Intermediate-resolution Density Maps

Cited by 80 publications

References 49 publications

Determining Protein Topology from Skeletons of Secondary Structures

Determining Protein Topology from Skeletons of Secondary Structures

YUP.SCX: Coaxing atomic models into medium resolution electron density maps

Deriving Protein Backbone Using Traces Extracted from Density Maps at Medium Resolutions

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