crossbetasheets

Crossbetasheets are a data representation used in structural biology to capture and compare the arrangement of beta-sheet elements across proteins. A crossbetasheet encodes the topology of beta strands and their inter-strand hydrogen-bond networks, allowing researchers to compare sheet organization between unrelated proteins or across different conformations of the same protein.

Construction and structure: The representation treats beta strands as elements in a matrix-like schema, with rows corresponding to strands and columns to inter-strand contacts. Each cell records information about interactions, such as the orientation (parallel or antiparallel), strand length, residue ranges, and cross-residue contacts. The approach can be extended to multi-protein assemblies by linking sheets across molecules via interface contacts.

Calculation and analysis: Crossbetasheets support alignment and similarity scoring between sheet topologies using metrics that reflect strand order, hydrogen-bond patterns, and strand length. Algorithms often employ concepts from graph theory and dynamic programming to identify best-fit correspondences, with weighting to accommodate insertions or deletions in sheet regions. Visualization tools may render the grid-like structure alongside three-dimensional coordinates to aid interpretation.

Applications: They are used to study the structural evolution of beta-rich proteins, guide protein design by comparing target sheet topologies, and assist in annotating structures where beta-sheet content is functionally important, including enzymes and amyloid-forming proteins.

Limitations: Depend on accurate annotation of beta strands, can be sensitive to conformational variability, may oversimplify three-dimensional geometry, and can be computationally intensive for large assemblies.

See also: beta sheet, protein structure, contact map, structural alignment.