Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model.

Biophysical Journal
Takeshi Kawabata

Abstract

Recently, electron microscopy measurement of single particles has enabled us to reconstruct a low-resolution 3D density map of large biomolecular complexes. If structures of the complex subunits can be solved by x-ray crystallography at atomic resolution, fitting these models into the 3D density map can generate an atomic resolution model of the entire large complex. The fitting of multiple subunits, however, generally requires large computational costs; therefore, development of an efficient algorithm is required. We developed a fast fitting program, "gmfit", which employs a Gaussian mixture model (GMM) to represent approximated shapes of the 3D density map and the atomic models. A GMM is a distribution function composed by adding together several 3D Gaussian density functions. Because our model analytically provides an integral of a product of two distribution functions, it enables us to quickly calculate the fitness of the density map and the atomic models. Using the integral, two types of potential energy function are introduced: the attraction potential energy between a 3D density map and each subunit, and the repulsion potential energy between subunits. The restraint energy for symmetry is also employed to build symmetric...Continue Reading

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Citations

Mar 16, 2012·The Journal of Physical Chemistry. B·Juan Esquivel-Rodríguez, Daisuke Kihara
Apr 2, 2016·Proceedings of the National Academy of Sciences of the United States of America·Tzviya Zeev-Ben-MordehaiKay Grünewald
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Apr 9, 2021·Nature Communications·Xusi HanDaisuke Kihara
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Aug 24, 2021·Frontiers in Molecular Biosciences·Bhaskar DasguptaFlorence Tama
Aug 22, 2021·Molecular & Cellular Proteomics : MCP·Daniel S ZiemianowiczDavid C Schriemer

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Methods Mentioned

BETA
x-ray crystallography
electron microscopy

Software Mentioned

qdock
SITUS
gmfit
gmfit FITting
colores

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