Rapid solution of the cryo-EM reconstruction problem by frequency marching

Alex Barnett, Leslie Greengard, Andras Pataki, Marina Spivak

Research output: Contribution to journalArticle

Abstract

Determining the three-dimensional (3D) structure of proteins and protein complexes at atomic resolution is a fundamental task in structural biology. Over the last decade, remarkable progress has been made using “single particle” cryo-electron microscopy (cryo-EM) for this purpose. In cryo-EM, hundreds of thousands of two-dimensional (2D) images are obtained of individual copies of the same particle, each held in a thin sheet of ice at some unknown orientation. Each image corresponds to the noisy projection of the particle’s electron-scattering density. The reconstruction of a high-resolution image from this data is typically formulated as a nonlinear, nonconvex optimization problem for unknowns which encode the angular pose and lateral offset of each particle. Since there are hundreds of thousands of such parameters, this leads to a very CPU-intensive task|limiting both the number of particle images which can be processed and the number of independent reconstructions which can be carried out for the purpose of statistical validation. Moreover, existing reconstruction methods typically require a good initial guess to converge. Here, we propose a deterministic method for high-resolution reconstruction that operates in an ab initio manner|that is, without the need for an initial guess. It requires a predictable and relatively modest amount of computational effort, by marching out radially in the Fourier domain from low to high frequency, increasing the resolution by a fixed increment at each step.

Original languageEnglish (US)
Pages (from-to)1170-1195
Number of pages26
JournalSIAM Journal on Imaging Sciences
Volume10
Issue number3
DOIs
StatePublished - 2017

Fingerprint

Electron Microscopy
Electron microscopy
Proteins
Electron scattering
Image resolution
Program processors
Ice
Guess
High Resolution
Protein
Unknown
Nonconvex Optimization
Nonconvex Problems
Increment
Biology
Lateral
Limiting
Scattering
Projection
Electron

Keywords

  • Cryo-EM
  • Frequency marching
  • Protein structure
  • Recursive linearization
  • Single particle reconstruction

ASJC Scopus subject areas

  • Mathematics(all)
  • Applied Mathematics

Cite this

Rapid solution of the cryo-EM reconstruction problem by frequency marching. / Barnett, Alex; Greengard, Leslie; Pataki, Andras; Spivak, Marina.

In: SIAM Journal on Imaging Sciences, Vol. 10, No. 3, 2017, p. 1170-1195.

Research output: Contribution to journalArticle

Barnett, Alex ; Greengard, Leslie ; Pataki, Andras ; Spivak, Marina. / Rapid solution of the cryo-EM reconstruction problem by frequency marching. In: SIAM Journal on Imaging Sciences. 2017 ; Vol. 10, No. 3. pp. 1170-1195.
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