A novel 3D visualization approach: A proof-of-concept study on the histidine residues in myoglobin

We present a proof-of-concept study towards the development of a novel 3D visualization method, based on the existence in proteins — in addition to the extrinsic geometry — of two independent intrinsic geometric structures determined by the peptide planes and the side chains. The method makes use of the construction of a series of orthonormal coordinate frames along the protein side chains and mapping the atoms positions onto a unit sphere. We apply our method to analyze distal and proximal histidine residues in myoglobin. The results are in good agreement with biological data and provide a new perspective for further understanding of structure and function of histidine in myoglobin. This suggests the method can reliably depict the spatial orientation of side-chain covalent bonds in a protein and may eventually be advanced into a valuable visual tool for protein-structure prediction, validation and refinement, complementary to widely used visualization suits like VMD, Jmol, PyMOL and others.We present a proof-of-concept study towards the development of a novel 3D visualization method, based on the existence in proteins — in addition to the extrinsic geometry — of two independent intrinsic geometric structures determined by the peptide planes and the side chains. The method makes use of the construction of a series of orthonormal coordinate frames along the protein side chains and mapping the atoms positions onto a unit sphere. We apply our method to analyze distal and proximal histidine residues in myoglobin. The results are in good agreement with biological data and provide a new perspective for further understanding of structure and function of histidine in myoglobin. This suggests the method can reliably depict the spatial orientation of side-chain covalent bonds in a protein and may eventually be advanced into a valuable visual tool for protein-structure prediction, validation and refinement, complementary to widely used visualization suits like VMD, Jmol, PyMOL and others.