In vitro studies on non-canonical DNA binding specificities of KAP6 and HMO1 and mechanistic insights into DNA bound and unbinding dynamics of KAP6

Rajakumara, Eerappa and Satish, Mutyala and Abhishek, Suman (2020) In vitro studies on non-canonical DNA binding specificities of KAP6 and HMO1 and mechanistic insights into DNA bound and unbinding dynamics of KAP6. International Journal of Biological Macromolecules, 160. pp. 925-933. ISSN 01418130

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Abstract

High mobility group box (HMGB) members are DNA binding proteins with varied functions present across kingdoms. The mechanism by which HMGBs with varying number of HMG boxes are able to carry out similar functions, are poorly understood. Moreover, how non-canonical DNAs are recognized by HMGB proteins is not clear. To address these, we carried out detailed biochemical and computational studies to characterize two HMGB members- Kinetoplast associated protein (KAP6) of Trypanosoma and High mobility group protein 1 (HMO1) from yeast. Here, we report that KAP6 binds non-canonical DNAs tighter than B-form DNA. Among non-canonical DNAs, KAP6 has the highest affinity for splayed and flap structures, but least for Holliday Junction (HJ). In contrast, HMO1 binds tighter to HJ. Computational analysis show that the secondary structural elements involved in DNA interaction are conserved in HMGB members KAP6 and mitochondrial transcription factor A. Simulation analyses revealed that the ~90° bend in DNA induced by KAP6 HMG box is a result of two ~45° bends, by Helix 1 and Helix 2 of the protein. Our data also suggests that the orthologs of HMO1 and KAP6 are oligomers in solution, which could be necessary for their functioning such as DNA bending and looping.

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IITH Creators:

IITH Creators	ORCiD
Rajakumara, Eerappa	UNSPECIFIED
Satish, Mutyala	UNSPECIFIED
Abhishek, Suman	UNSPECIFIED

Item Type:

Article

Uncontrolled Keywords:

rossover junction endodeoxyribonuclease; curved DNA; DNA binding protein; high mobility group B protein; high mobility group B1 protein; kinetoplast associated protein; mitochondrial transcription factor A; oligomer; unclassified drug; DNA; DNA binding protein; high mobility group protein; protein binding; analysis; Article; binding affinity; Candida albicans; computational analysis; controlled study; correlational study; dissociation constant; DNA binding; helix 1; helix 2; in vitro study; Lachancea kluyveri; nonhuman; oligomerization; protein DNA binding; protein DNA interaction; protein function; protein structure; simulation; Trypanosoma; amino acid sequence; chemistry; conformation; metabolism; protein conformation; protein multimerization; structure activity relation

Subjects:

Others > Biotechnology

Divisions:

Department of Biotechnology

Depositing User:

. LibTrainee 2021

Date Deposited:

29 Jun 2021 05:57

Last Modified:

29 Jun 2021 05:57

URI:

http://raiithold.iith.ac.in/id/eprint/8040