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MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures
- Source :
- Bioinformatics
- Publication Year :
- 2010
- Publisher :
- Oxford University Press (OUP), 2010.
-
Abstract
- We present a new, first-of-its-kind, fully automated computational tool MOTIF-EM for identifying regions or domains or motifs in cryoEM maps of large macromolecular assemblies (such as chaperonins, viruses, etc.) that remain conformationally conserved. As a by-product, regions in structures that are not conserved are revealed: this can indicate local molecular flexibility related to biological activity. MOTIF-EM takes cryoEM volumetric maps as inputs. The technique used by MOTIF-EM to detect conserved sub-structures is inspired by a recent breakthrough in 2D object recognition. The technique works by constructing rotationally invariant, low-dimensional representations of local regions in the input cryoEM maps. Correspondences are established between the reduced representations (by comparing them using a simple metric) across the input maps. The correspondences are clustered using hash tables and graph theory is used to retrieve conserved structural domains or motifs. MOTIF-EM has been used to extract conserved domains occurring in large macromolecular assembly maps, including as those of viruses P22 and epsilon 15, Ribosome 70S, GroEL, that remain structurally conserved in different functional states. Our method can also been used to build atomic models for some maps. We also used MOTIF-EM to identify the conserved folds shared among dsDNA bacteriophages HK97, Epsilon 15, and ô29, though they have low-sequence similarity. Contact: mitul@cs.stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
Protein Structure and Function
Computational biology
Biology
Bioinformatics
Biochemistry
Chaperonin
03 medical and health sciences
0302 clinical medicine
Molecular Biology
030304 developmental biology
Supplementary data
0303 health sciences
Cryoelectron Microscopy
Cognitive neuroscience of visual object recognition
Computational Biology
Graph theory
biology.organism_classification
Ismb 2010 Conference Proceedings July 11 to July 13, 2010, Boston, Ma, Usa
Original Papers
Hash table
Computer Science Applications
Epsilon 15
Macromolecular assembly
Computational Mathematics
Computational Theory and Mathematics
Motif (music)
Algorithms
Software
030217 neurology & neurosurgery
Subjects
Details
- ISSN :
- 13674811 and 13674803
- Volume :
- 26
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....537b42ad26f085446cb010a5a957e99e