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Discrete Exterior Calculus of Proteins and Their cohomology

Open Journal of Discrete Mathematics 2022年第3期12卷 47-63页

作者： Naoto Morikawa Genocript Zama Japan

This paper proposes a novel application of cohomology to protein structure analysis. Since proteins interact each other by forming transient protein complexes, their shape (e.g., shape complementarity) plays an important role in their functions. In our mathematical toy models, proteins are represented as a loop of triangles (2D model) or tetrahedra (3D model), where their interactions are defined as fusion of loops. The purpose of this paper is to describe the conditions for loop fusion using the language of cohomology. In particular, this paper uses cohomology to describe the conditions for “allosteric regulation”, which has been attracted attention in safer drug discovery. I hope that this paper will provide a new perspective on the mechanism of allosteric regulation. Advantages of the model include its topological nature. That is, we can deform the shape of loops by deforming the shape of triangles (or tetrahedra) as long as their folded structures are preserved. Another advantage is the simplicity of the “allosteric regulation” mechanism of the model. Furthermore, the effect of the “post-translational modification” can be understood as a resolution of singularities of a flow of triangles (or tetrahedra). No prior knowledge of either protein science, exterior calculus, or cohomology theory is required. The author hopes that this paper will facilitate the interaction between mathematics and protein science.

关键词： Discrete Differential Geometry Protein Structure Analysis cohomology class Exterior Derivative Allosteric Regulation

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