KIPS Transactions on Software and Data Engineering (정보처리학회논문지:소프트웨어 및 데이터공학)

Korea Information Processing Society (한국정보처리학회)
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Visualization of Geometric Features in the Contact Region of Proteins

단백질 접촉 영역의 기하학적 특성 가시화

  • Received : 2019.04.29
  • Accepted : 2019.06.21
  • Published : 2019.10.31
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Abstract

In this paper, we propose a method to visualize the geometric features of the contact region between proteins in a protein complex. When proteins or ligands are represented as curved surfaces with irregularities, the property that the two surfaces contact each other without intersections is called shape compatibility. Protein-Protein or Protein-Ligand docking researches have shown that shape complementarity, chemical properties, and entropy play an important role in finding contact regions. Usually, after finding a region with high shape complementarity, we can predict the contact region by using residual polarity and hydrophobicity of amino acids belonging to this region. In the research for predicting the contact region, it is necessary to investigate the geometrical features of the contact region in known protein complexes. For this purpose, it is essential to visualize the geometric features of the molecular surface. In this paper, we propose a method to find the contact region, and visualize the geometric features of it as normal vectors and mean curvatures of the protein complex.

본 논문에서는 단백질 복합체에서 단백질 사이의 접촉 영역이 갖는 기하학적 특징을 가시화하는 방법을 제안한다. 단백질 또는 리간드가 요철이 있는 곡면으로 표현될 때, 두 곡면이 서로 접하면서 교차하지 않는 성질을 형태 상보성이라 한다. 단백질-단백질 또는 단백질-리간드 도킹 연구에서 형태 상보성과 화학적인 성질, 엔트로피 등이 접촉 영역의 발견에 중요한 역할을 한다는 것을 볼 수 있다. 일반적으로 형태 상보성이 높은 영역을 발견한 뒤, 이 영역에 속한 아미노산들의 잔기 극성 및 소수성 등을 이용하여 접촉 영역을 예측한다. 접촉 영역을 예측하기 위한 연구에서는 기존에 알려진 복합체에서 접촉 영역이 갖는 기하학적인 특징을 조사하는 작업이 필요하며, 이를 위해 기하학적인 특징을 가시화하는 작업은 필수적이다. 본 논문에서는 단백질 복합체에서 접촉 영역을 발견하고, 두 개의 단백질 각각의 접촉 면에 속한 근거리의 정점들의 기하학적인 특징을 법선 벡터 및 평균 곡률로써 가시화하는 방법을 제안한다.

Keywords

References

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