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Updated: Aug 30, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Functional motions can be extracted from on-lattice construction of protein structures
Pemra Doruker1, Robert L Jernigan
1Chemical Engineering Department and Polymer Research Center, Bogazici University, Bebek 34342, Istanbul, Turkey.
Abstract:
The three-dimensional structure of a 1509-residue protein-hemagglutinin is reconstructed on a simple cubic lattice by retaining all lattice sites that fall within close proximity of the X-ray coordinates. Coarse-grained normal modes analysis is performed using these lattice sites as the nodes of an elastic network. The collective deformations of the protein can still be extracted from such a structure that just mimics the overall shape of the protein but not its mass distribution. These results emphasize that the overall shape rather than the details of the protein fold determines the dynamical domains in proteins. Thus, low-resolution protein structures, even those constructed on a regularly spaced lattice, can provide insights about the functionally important global dynamics around the native state.
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