title: Toward Modular Analysis of Supramolecular Protein Assemblies.
abstract: Despite recent advances in molecular simulation technologies, analysis of high-molecular-weight structures is still challenging. Here, we propose an automated model reduction procedure aiming to enable modular analysis of these structures. It employs a component mode synthesis for the reduction of finite element protein models. Reduced models may consist of real biological subunits or artificial partitions whose dynamics is described using the degrees of freedom at the substructural interfaces and a small set of dominant vibrational modes only. Notably, the proper number of dominant modes is automatically determined using a novel estimator for eigenvalue errors without calculating the reference eigensolutions of the full model. The performance of the proposed approach is thoroughly investigated by analyzing 50 representative structures including a crystal structure of GroEL and an electron density map of a ribosome.
authors.forename: Jaehoon
authors.initials: J
authors.lastname: Kim
authors.affiliation: Mechanical Systems Safety Research Division, Korea Institute of Machinery & Materials , Gajeongbuk-ro 156, Yuseong-gu, Daejeon 34103, Republic of Korea.
authors.forename: Jin-Gyun
authors.initials: JG
authors.lastname: Kim
authors.forename: Giseok
authors.initials: G
authors.lastname: Yun
authors.affiliation: Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology , Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea.
authors.forename: Phill-Seung
authors.initials: PS
authors.lastname: Lee
authors.forename: Do-Nyun
authors.initials: DN
authors.lastname: Kim
mesh_terms: D018834:Chaperonin 60 / Q000737:chemistry*; D004583:Electrons; D004926:Escherichia coli / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D012270:Ribosomes / Q000737:chemistry*; D014732:Vibration
chemical_list: D018834:Chaperonin 60