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Biomacromolecular structure analysis
- channels
Radka Svobodová
CEITEC, Masaryk University

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Tunnels, pores, pockets, cavities: Locations of key biochemical processes
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MOLEonline
Use case: Transient receptor potential mucolipin 1
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(A)The channel (closed conformation) of TRPML1 (PDB ID: 5WJ5). The blue and red dashed lines
delimit the membrane region. The profiles depict polarity and charge along the pore.
(B)The channel in open conformation (PDB ID: 5WJ9). The pore is divided into three main parts:
Activation gate; Central cavity and Selectivity filter. The figure was generated using Pymol
software.

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MOLEonline
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§MOLEonline: Web application for detection of channels and pores and calculation of their
geometrical and physico-chemical properties
§New features:
§Automatic detection of transmembrane pores
§Visualization of properties on the channel’s profile
§Interconnection with other bioinformatics tools (PDBe, CSA, ChannelsDB, OPM, UniProt) and data
transfer from them
§Integration of LiteMol suite
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Pravda L., Sehnal D., Toušek D., Navrátilová V., Bazgier V., Berka K., ... & Koča J., Otyepka M.
(2018). MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).
Nucleic acids research.

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MOLEonline - Initialization
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MOLEonline
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Channels mode
§Identification of channels and other types of pores
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§Origins of channels:
§Origins - Automatic Start points definition in the deepest points within cavities
§CSA origins - Catalytic site residues from Catalytic Site Atlas
§Start and end points user definition
§List of residues (selectable from sequence or 3D stucture)
§Cofactors
§XYZ coordinates
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MOLEonline
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MOLEonline
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MOLEonline
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MOLEonline
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MOLEonline
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Pore mode
§transmembrane pores
•membrane position from Orientations of Proteins in Membranes (OPM) database or calculated with
MEMEMBED program. •Membrane region parameter - calculate pore in transmembrane region only •Beta
structure parameter is recommended for transmembrane regions formed by β-barrel structure
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MOLEonline
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MOLEonline
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MOLEonline
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ChannelsDB
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§ChannelDB – interactive database of channels with expected and annotated biological relevancy.
§Pathways were calculated using an algorithms CAVER and MOLE
§Channel visualisation via LiteMol
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Pravda L., Sehnal D., Svobodová R., Navrátilová V., Toušek D., Berka K., ... & Koča J. (2017).
ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic acids research, 46(D1),
D399-D405.

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ChannelsDB – Search
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ChannelsDB
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ChannelsDB
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4nm9 - Proline utilization A protein (PutA)

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ChannelsDB
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Thank you for your attention!