Quantitative Characterization of Domain Motions in Molecular Machines Article Swipe
Suvrajit Maji
,
Rezvan Shahoei
,
Klaus Schulten
,
Joachim Frank
·
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1021/acs.jpcb.6b10732
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1021/acs.jpcb.6b10732
The work of molecular machines such as the ribosome is accompanied by conformational changes, often characterized by relative motions of their domains. The method we have developed seeks to quantify these motions in a general way, facilitating comparisons of results obtained by different researchers. Typically there are multiple snapshots of a structure in the form of pdb coordinates resulting from flexible fitting of low-resolution density maps, from X-ray crystallography, or from molecular dynamics simulation trajectories. Our objective is to characterize the motion of each domain as a coordinate transformation using moments of inertia tensor, a method we developed earlier. What has been missing until now are ancillary tools that make this task practical, general, and biologically informative. We have provided a comprehensive solution to this task with a set of tools implemented on the VMD platform. These tools address the need for reproducible segmentation of domains, and provide a generalized description of their motions using principal axes of inertia. Although this methodology has been specifically developed for studying ribosome motion, it is applicable to any molecular machine.
Related Topics
Concepts
Computer science
Domain (mathematical analysis)
Motion (physics)
Task (project management)
Tensor (intrinsic definition)
Inertia
Algorithm
Coordinate system
Artificial intelligence
Translation (biology)
Transformation (genetics)
Moment of inertia
Set (abstract data type)
Physics
Mathematics
Geometry
Chemistry
Classical mechanics
Messenger RNA
Gene
Programming language
Economics
Biochemistry
Mathematical analysis
Management
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1021/acs.jpcb.6b10732
- OA Status
- green
- Cited By
- 10
- References
- 53
- Related Works
- 10
- OpenAlex ID
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https://openalex.org/W2588246175Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1021/acs.jpcb.6b10732Digital Object Identifier
- Title
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Quantitative Characterization of Domain Motions in Molecular MachinesWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2017Year of publication
- Publication date
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2017-02-15Full publication date if available
- Authors
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Suvrajit Maji, Rezvan Shahoei, Klaus Schulten, Joachim FrankList of authors in order
- Landing page
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https://doi.org/10.1021/acs.jpcb.6b10732Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
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https://doi.org/10.1021/acs.jpcb.6b10732Direct OA link when available
- Concepts
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Computer science, Domain (mathematical analysis), Motion (physics), Task (project management), Tensor (intrinsic definition), Inertia, Algorithm, Coordinate system, Artificial intelligence, Translation (biology), Transformation (genetics), Moment of inertia, Set (abstract data type), Physics, Mathematics, Geometry, Chemistry, Classical mechanics, Messenger RNA, Gene, Programming language, Economics, Biochemistry, Mathematical analysis, ManagementTop concepts (fields/topics) attached by OpenAlex
- Cited by
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10Total citation count in OpenAlex
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2024: 1, 2023: 1, 2021: 2, 2018: 2, 2017: 4Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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