Background. All life forms are supported by the work of proteins, very large macromolecules that exert their function through interactions and dynamic activity. Protein structures are determined through a growing number of techniques (based on X-ray, Cryo-EM and NMR), providing data on the general shape of proteins (and sometimes on their movements), deposited in the dataBank as atomic coordinates. Reading 3D coordinates is accomplished through one of few software that transform them into virtual images, using techniques of 3D computer graphics. Some authors have proposed the fabrication of protein models using direct printing or other techniques, but a general method for producing models that can be adopted in most settings was still lacking. Results. We propose a general pipeline for casting flexible protein models in soft silicone, based on the PDB files and on the design and printing of a two-pieces mold. The bipartite mold is automatically generated by an algorithm taking into account the geometrical and topological properties of the protein, so that the latter can easily be extracted once it is cast. We have evaluated our pipeline on We present our results multimeric Actin, tetrameric Hemoglobin and the Histone Octamer. All models can be fabricated as monomers (dimers in the case of Histones) and their assembly can be facilitated by the insertion of magnets at the protein-protein interfaces. Conclusions. The availability of physical models of proteins produced as soft, flexible objects makes it possible to handle the monomers and combine them to show their biological assemblies. The procedure for designing the mold, the printing, and the casting details are described; the STL files for the three selected proteins are freely available and deposited on the NIH database. The use of soft protein models will allow a better understanding of the way proteins work, facilitate teaching at high and superior grade courses and possibly inspire biologically based reasoning in any interested people, both scholars and lay persons.
Assembly of protein complexes using 3D models printed in soft silicone
Luigi Malomo;
2020-01-01
Abstract
Background. All life forms are supported by the work of proteins, very large macromolecules that exert their function through interactions and dynamic activity. Protein structures are determined through a growing number of techniques (based on X-ray, Cryo-EM and NMR), providing data on the general shape of proteins (and sometimes on their movements), deposited in the dataBank as atomic coordinates. Reading 3D coordinates is accomplished through one of few software that transform them into virtual images, using techniques of 3D computer graphics. Some authors have proposed the fabrication of protein models using direct printing or other techniques, but a general method for producing models that can be adopted in most settings was still lacking. Results. We propose a general pipeline for casting flexible protein models in soft silicone, based on the PDB files and on the design and printing of a two-pieces mold. The bipartite mold is automatically generated by an algorithm taking into account the geometrical and topological properties of the protein, so that the latter can easily be extracted once it is cast. We have evaluated our pipeline on We present our results multimeric Actin, tetrameric Hemoglobin and the Histone Octamer. All models can be fabricated as monomers (dimers in the case of Histones) and their assembly can be facilitated by the insertion of magnets at the protein-protein interfaces. Conclusions. The availability of physical models of proteins produced as soft, flexible objects makes it possible to handle the monomers and combine them to show their biological assemblies. The procedure for designing the mold, the printing, and the casting details are described; the STL files for the three selected proteins are freely available and deposited on the NIH database. The use of soft protein models will allow a better understanding of the way proteins work, facilitate teaching at high and superior grade courses and possibly inspire biologically based reasoning in any interested people, both scholars and lay persons.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
