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New Methods for Simulating, Refining, and Modeling Supramolecular Complexes at Multi‐resolution and Multi‐length Scales
Author(s) -
Ma Jianpeng
Publication year - 2006
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.20.5.a889-d
Subject(s) - scale (ratio) , substructure , small angle x ray scattering , biological system , computer science , resolution (logic) , folding (dsp implementation) , length scale , algorithm , physics , scattering , artificial intelligence , optics , mechanical engineering , engineering , biology , structural engineering , quantum mechanics
A set of new computational methods has been developed for simulating, refining, and modeling supermolecular complexes at multi‐resolution and length scales. On the resolution scale, quantized elastic deformational model (QEDM) was designed to reliably describe large‐scale protein motions without sequence and atomic coordinates. QEDM yields an accurate description of protein dynamics even as low as 30 Å. On the length scale, substructure synthesis method (SSM) was developed to derive the motions of a given structure from those of its substructures. Its application to F‐actin, clearly demonstrated its capability of scaling the atomic motions to a macroscopic length scale. QEDM and SSM have been used to assist structural refinement against cryo‐EM and fibre diffraction data, respectively. Thus, under the scheme of harmonic modal analysis, structural refinement for seemingly remote experimental techniques can be unified for systems involving large‐scale structural flexibility. In order to improve one's ability to interpret low‐ to intermediate‐resolution density maps, a set of methods have been developed, such as sheetminer and sheettracer to extract secondary structural features, and methods to derive protein topology based only on secondary structural skeletons. Methods were also developed for protein folding assisted by SAXS. Results have shown that SAXS data carry sufficient information to derive the fold of proteins. Such methods will make SAXS an attractive technique for structural study of small, soluble, and noncrystalizable proteins.