Related Experiment Video
Updated: Aug 24, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
Published on: January 26, 2024
Intramolecular orbital alignments in serine protease/protein inhibitor complexes
Yun-Hua Fan1, Claire-Anne Grégoire, John Haseltine
1School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.
Abstract:
By an analysis of PDB crystal structures, the mean conformations of protein strands bound in serine protease active sites are shown to contain extensively aligned atomic orbitals. The active-serine-bearing segment of each enzyme (subtilisin BPN' and beta-trypsin) also contains such alignments. The participating orbitals are almost identical in each system. All of the alignments converge on the targeted linkage. They suggest that a kind of through-strand polarizability is being optimized by evolution, presumably due to corresponding benefits in proteolysis rate. Such polarizability would help to explain the high values of kcat seen for long oligopeptide substrates. The idea predicts long substrates to be relatively reactive even under non-enzymatic conditions, which in fact they are.
More Related Videos
Related Concept Videos
Protein-protein Interfaces
Protein-Protein Interfaces
Ligand Binding and Linkage
Ligand Binding Sites
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein Organization
The primary structure of a protein is its amino acid sequence.
Cooperative Allosteric Transitions

