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EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.

Dror O, Lasker K, Nussinov R, Wolfson H - Acta Crystallogr. D Biol. Crystallogr. (2006)

Bottom Line: Structural analysis of biological machines is essential for inferring their function and mechanism.Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process.The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel. oranit@post.tau.ac.il

ABSTRACT
Structural analysis of biological machines is essential for inferring their function and mechanism. Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process. In contrast, structural data at lower resolution is becoming more and more available owing to recent advances in cryo-electron microscopy (cryo-EM) techniques. Once a cryo-EM map is acquired, one of the basic questions asked is what are the folds of the components in the assembly and what is their configuration. Here, a novel knowledge-based computational method, named EMatch, towards tackling this task for cryo-EM maps at 6-10 A resolution is presented. The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly. The strengths of EMatch are demonstrated on a cryo-EM map of native GroEL at 6 A resolution.

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A priori known domain reconstruction. (a–c) The matched helices of the top-ranking alignment for the intermediate (blue), equatorial (red) and apical (yellow) domains, respectively. (d) A quasi-atomic structural model of a GroEL ring as revealed from the cryo-EM map (depicted in grey). This figure and subsequent figures were prepared using Chimera (Pettersen et al., 2004 ▶).
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fig2: A priori known domain reconstruction. (a–c) The matched helices of the top-ranking alignment for the intermediate (blue), equatorial (red) and apical (yellow) domains, respectively. (d) A quasi-atomic structural model of a GroEL ring as revealed from the cryo-EM map (depicted in grey). This figure and subsequent figures were prepared using Chimera (Pettersen et al., 2004 ▶).

Mentions: Each of the three input domains was aligned with the set of detected EM helices in less than 30 s (27, 12 and 9 s for the equatorial, apical and intermediate domains, respectively). Figs. 2 ▶(a), 2 ▶(b) and 2 ▶(c) present the matched helices of the top-ranking alignment for the three domains. The top-ranking alignment for the equatorial domain consists of six matched helices with an r.m.s.d. of 3.40 Å between their axial midpoints. For the apical domain, the top-ranking alignment consists of three matched helices with an r.m.s.d. of 0.68 Å between their axial midpoints. Finally, the top-ranking alignment for the intermediate domain has four matched helices with an r.m.s.d. of 3.40 Å between their axial midpoints. Further details of the alignments (including Z scores and additional data on the matched helices) are available in Table 1 ▶ and at the EMatch website (http://bioinfo3d.cs.tau.ac.il/EMatch).


EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.

Dror O, Lasker K, Nussinov R, Wolfson H - Acta Crystallogr. D Biol. Crystallogr. (2006)

A priori known domain reconstruction. (a–c) The matched helices of the top-ranking alignment for the intermediate (blue), equatorial (red) and apical (yellow) domains, respectively. (d) A quasi-atomic structural model of a GroEL ring as revealed from the cryo-EM map (depicted in grey). This figure and subsequent figures were prepared using Chimera (Pettersen et al., 2004 ▶).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483490&req=5

fig2: A priori known domain reconstruction. (a–c) The matched helices of the top-ranking alignment for the intermediate (blue), equatorial (red) and apical (yellow) domains, respectively. (d) A quasi-atomic structural model of a GroEL ring as revealed from the cryo-EM map (depicted in grey). This figure and subsequent figures were prepared using Chimera (Pettersen et al., 2004 ▶).
Mentions: Each of the three input domains was aligned with the set of detected EM helices in less than 30 s (27, 12 and 9 s for the equatorial, apical and intermediate domains, respectively). Figs. 2 ▶(a), 2 ▶(b) and 2 ▶(c) present the matched helices of the top-ranking alignment for the three domains. The top-ranking alignment for the equatorial domain consists of six matched helices with an r.m.s.d. of 3.40 Å between their axial midpoints. For the apical domain, the top-ranking alignment consists of three matched helices with an r.m.s.d. of 0.68 Å between their axial midpoints. Finally, the top-ranking alignment for the intermediate domain has four matched helices with an r.m.s.d. of 3.40 Å between their axial midpoints. Further details of the alignments (including Z scores and additional data on the matched helices) are available in Table 1 ▶ and at the EMatch website (http://bioinfo3d.cs.tau.ac.il/EMatch).

Bottom Line: Structural analysis of biological machines is essential for inferring their function and mechanism.Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process.The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel. oranit@post.tau.ac.il

ABSTRACT
Structural analysis of biological machines is essential for inferring their function and mechanism. Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process. In contrast, structural data at lower resolution is becoming more and more available owing to recent advances in cryo-electron microscopy (cryo-EM) techniques. Once a cryo-EM map is acquired, one of the basic questions asked is what are the folds of the components in the assembly and what is their configuration. Here, a novel knowledge-based computational method, named EMatch, towards tackling this task for cryo-EM maps at 6-10 A resolution is presented. The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly. The strengths of EMatch are demonstrated on a cryo-EM map of native GroEL at 6 A resolution.

Show MeSH
Related in: MedlinePlus