ACCORD: An assessment tool to determine the orientation of homodimeric coiled-coils

Byeong Won Kim, Yang Ouk Jung, Min Kyung Kim, Do Hoon Kwon, Si Hoon Park, Jun Hoe Kim, Yong Boo Kuk, Sun Joo Oh, Leehyeon Kim, Bong Heon Kim, Woo Seok Yang, Hyun Kyu Song

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)

Abstract

The coiled-coil (CC) domain is a very important structural unit of proteins that plays critical roles in various biological functions. The major oligomeric state of CCs is a dimer, which can be either parallel or antiparallel. The orientation of each α-helix in a CC domain is critical for the molecular function of CC-containing proteins, but cannot be determined easily by sequence-based prediction. We developed a biochemical method for assessing differences between parallel and antiparallel CC homodimers and named it ACCORD (Assessment tool for homodimeric Coiled-Coil ORientation Decision). To validate this technique, we applied it to 15 different CC proteins with known structures, and the ACCORD results identified these proteins well, especially with long CCs. Furthermore, ACCORD was able to accurately determine the orientation of a CC domain of unknown directionality that was subsequently confirmed by X-ray crystallography and small angle X-ray scattering. Thus, ACCORD can be used as a tool to determine CC directionality to supplement the results of in silico prediction.

Original languageEnglish
Article number43318
JournalScientific reports
Volume7
DOIs
Publication statusPublished - 2017 Mar 7

Bibliographical note

Funding Information:
This work was supported by National Research Foundation of Korea (NRF) grants from the Korean government (MEST) (NRF-2016R1E1A1A01942623 and BRL grant: No. 2015041919) and by a grant from the Institute for Basic Science (IBS-R023-D1). This research was also supported by a Korea University Grant and by the Basic Science Research Program of the NRF funded by the Ministry of Education (NRF-2013R1A6A3A04063675 to YOJ).

Publisher Copyright:
© 2017 The Author(s).

ASJC Scopus subject areas

  • General

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