MGOS: A library for molecular geometry and its operating system

Kim, Deok Soo; Ryu, Joonghyun; Cho, Youngsong; Lee, Mokwon; Cha, Jehyun; Song, Chung Kil; Kim, Sang Wha; Laskowski, Roman A.; Sugihara, Kōkichi; Bhak, Jong; Ryu, Seong Eon

doi:10.1016/j.cpc.2019.107101

Cited by 2 publications

(1 citation statement)

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“…For example, although eukaryotic ribosomes are generally larger in size than bacterial ones, their exit tunnel is narrower with heterogeneous variations along it [ 14 , 98 ]. Various algorithms and computational methods adapted to molecular structures, based on tesselation [ 99 , 100 , 101 ] (illustrated in Figure 4 a), or spectral geometry [ 102 ], can be used to encode the structure into geometric objects [ 103 ], and in particular compare ribosome geometric features. For example, by estimating the relative position of residues to the surface, one can separate proteins according to their degree of exposition to the solvent (see Figure 4 b), which has been hypothesized as a key factor for differentiating proteins prone to ribosome repair [ 64 ] or with distinct electrostatic properties [ 104 ].…”

Section: Computational Challenges For Quantifying Heterogeneity Frmentioning

confidence: 99%

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM

Poitevin

Kushner

et al. 2020

Molecules

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The extent of ribosomal heterogeneity has caught increasing interest over the past few years, as recent studies have highlighted the presence of structural variations of the ribosome. More precisely, the heterogeneity of the ribosome covers multiple scales, including the dynamical aspects of ribosomal motion at the single particle level, specialization at the cellular and subcellular scale, or evolutionary differences across species. Upon solving the ribosome atomic structure at medium to high resolution, cryogenic electron microscopy (cryo-EM) has enabled investigating all these forms of heterogeneity. In this review, we present some recent advances in quantifying ribosome heterogeneity, with a focus on the conformational and evolutionary variations of the ribosome and their functional implications. These efforts highlight the need for new computational methods and comparative tools, to comprehensively model the continuous conformational transition pathways of the ribosome, as well as its evolution. While developing these methods presents some important challenges, it also provides an opportunity to extend our interpretation and usage of cryo-EM data, which would more generally benefit the study of molecular dynamics and evolution of proteins and other complexes.

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