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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

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Published on: October 15, 2018

GISA: using Gauss Integrals to identify rare conformations in protein structures.

Christian Grønbæk^1,2, Thomas Hamelryck³, Peter Røgen⁴

¹Department of Biology, University of Copenhagen, Copenhagen, Denmark.

|June 23, 2020

Summary

We developed GISA, a general method using knot theory to create protein structure fingerprints. This approach identifies unusual topological-geometric features, like knots and links, across all scales, aiding protein analysis.

Keywords:

Database scan Fast algorithm Gauss integrals Geometry Knots and links Protein structure analysis Rare conformations Sub-chains Topology

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Structural Bioinformatics
Biophysics
Computational Biology

Background:

Protein structure is crucial for function, driving research into structure determination methods.
Existing methods often lack sensitivity to complex topological-geometric features (e.g., knots, links).
Current approaches are typically limited to specific predefined topologies or geometries.

Purpose of the Study:

To introduce a general method for analyzing protein topological-geometric features.
To develop a computational tool (GISA) that generates a "fingerprint" of protein structures using knot theory descriptors.
To enable the identification of unusual or novel protein conformations on multiple scales.

Main Methods:

Developed the GISA algorithm to compute Gauss integrals (knot theory descriptors) for all protein sub-chains.
Generated topological-geometric "fingerprints" for protein structures.
Applied GISA to analyze thousands of high-resolution protein structures.

Main Results:

GISA successfully identified known topological features like pokes and links using the basic writhe descriptor.
Unrestricted analysis revealed previously undescribed entangled configurations and knotted conformations.
Identified 10 known knots and 14 cis-trans isomerases with a potentially overlooked spatial motif.

Conclusions:

GISA provides a general, scale-independent method for analyzing protein topology.
The tool can identify known and novel complex protein conformations, aiding in fold classification and error detection.
GISA offers significant potential benefits to the structural bioinformatics community.