PDBTM

PDBTM#

TMKit is very powerful for obtaining different kinds of topologies from an XML file retrieved from the PDBTM database[1]. Together with TMDET algorithm[2], they constitute a nice community for managing the data source of transmembrane (TM) protein topologies. PDBTM defines 9 topologies:

Open dropdown

  • Side1

  • Side2

  • Beta-strand

  • Alpha-helix

  • Coil

  • Membrane-inside

  • Membrane-loop

  • Interfacial helix

  • Unknown

When working with an XML file that documents transmembrane topologies, it is essential to efficiently access each type of topology. In this tutorial, we demonstrate how to achieve this using an example XML file.

Hint

Technically, we implement the tmkit.topo module by using aspect-oriented programming (AOP), which makes it easier to use the topological information in other functions.

Reminder of data

Please make sure that the build-in example dataset has been downloaded before you walk through the tutorial.

Example usage#

First, we can define all types of topologies of transmembrane proteins used in PDBTM in the following way.

topos = {
    'Side1': 'side1',
    'Side2': 'side2',
    'Beta': 'strand',
    'Alpha': 'tmh',
    'Coil': 'coil',
    'Membrane-inside': 'inside',
    'Membrane-loop': 'loop',
    'Interfacial ': 'interfacial',
    'Unknown': 'Unknown',
}

Then, we can scan a protein’s XML file to see if it contains all types of the topologies. By default, we still use 1xqf.xml. If we open this file, in chain A, there are only Side1, Side2, Alpha helix, and Unknown types. Using the following codes, we can get the results expected.

for topo, i in topos.items():
    print('Topology: {}'.format(topo))
    try:
        lower_ids, upper_ids = tmk.topo.from_pdbtm(
            xml_fp='data/xml/',
            prot_name='1xqf',
            seq_chain='A',
            topo=i,
        )
        if lower_ids:
            print('---lower bounds', lower_ids)
            print('---upper bounds', upper_ids)
    except:
        continue
    else:
        print('It does not has this topology.\n')

Attributes#

Attribute

Description

xml_fp

path where a target XML file is placed

xml_name

name of the XML file

seq_chain

chain of a protein

topo

a topology code. It can be one of side1, side2, strand, tmh, coil, inside, loop, interfacial, and Unknown, which correspond to Side1, Side2, Beta strand, Alpha helix, Coil, Membrane-inside, Membrane-loop, Interfacial, Unknown topologies

See also

Please see here for better understanding the file-naming system.

Output#

Finally, you will see the following output showing which one type of topology that protein 1xqf chain A has.

In the output, lower bounds are the set of starting positions of residues in the PDB structure while upper bounds are the set of ending positions of residues in the PDB structure. They match each other this way. For example, for topology Side2, the first continuous segment is from residue 3 to residue 14, and the second one is from residue 65 to residue 101, …, and the last one is from residue 333 to residue 352.

Topology: Side1
---lower bounds [33, 119, 179, 195, 249, 300, 311, 378]
---upper bounds [45, 126, 181, 201, 260, 301, 313, 386]
It does not has this topology.

Topology: Side2
---lower bounds [3, 65, 148, 220, 277, 333]
---upper bounds [14, 101, 160, 230, 281, 352]
It does not has this topology.

Topology: Beta strand
It does not has this topology.

Topology: Alpha helix
---lower bounds [15, 46, 102, 127, 161, 202, 231, 261, 282, 314, 353]
---upper bounds [32, 64, 118, 147, 178, 219, 248, 276, 299, 332, 377]
It does not has this topology.

Topology: Coil
It does not has this topology.

Topology: Membrane-inside
It does not has this topology.

Topology: Membrane-loop
It does not has this topology.

Topology: Interfacial
It does not has this topology.

Topology: Unknown
---lower bounds [1, 3, 15, 33, 46, 65, 102, 119, 127, 148, 161, 179, 182, 195, 202, 220, 231, 249, 261, 277, 282, 300, 302, 311, 314, 333, 353, 378, 387]
---upper bounds [2, 14, 32, 45, 64, 101, 118, 126, 147, 160, 178, 181, 194, 201, 219, 230, 248, 260, 276, 281, 299, 301, 310, 313, 332, 352, 377, 386, 418]
It does not has this topology.
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