Computer-aided NMR assay for detecting natively folded structural domains

Protein Science : a Publication of the Protein Society
Takayuki HondohYutaka Kuroda

Abstract

Structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of proteins into structural domains that form stable native structures. However, protein dissection essentially remains an empirical and often a tedious process. Here, we describe a simple strategy for rapidly identifying structural domains and assessing their structures. This approach combines the computational prediction of sequence regions corresponding to putative domains with an experimental assessment of their structures and stabilities by NMR and biochemical methods. We tested this approach with nine putative domains predicted from a set of 108 Thermus thermophilus HB8 sequences using PASS, a domain prediction program we previously reported. To facilitate the experimental assessment of the domain structures, we developed a generic 6-hour His-tag-based purification protocol, which enables the sample quality evaluation of a putative structural domain in a single day. As a result, we observed that half of the predicted structural domains were indeed natively folded, as judged by their HSQC spectra. Furthermore, two of the natively...Continue Reading

Citations

Jun 15, 2007·Extremophiles : Life Under Extreme Conditions·Francis E Jenney, Michael W W Adams
May 30, 2013·Journal of Computer-aided Molecular Design·Teppei EbinaYutaka Kuroda
Jun 14, 2013·PloS One·N Laila HuqEric C Reynolds
Apr 3, 2007·Protein Science : a Publication of the Protein Society·Jason CellittiSusan Marqusee
Feb 14, 2015·Computational Biology and Chemistry·Maad Shatnawi, Nazar Zaki
Dec 29, 2016·Journal of Computer-aided Molecular Design·Tambi RichaYutaka Kuroda

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