Complex DNA binding kinetics of HIV-1 nucleocapsid proteins

Permanent URL: http://hdl.handle.net/2047/d20128367
Title:
Complex DNA binding kinetics of HIV-1 nucleocapsid proteins
Creator:
Li, Jialin (Author)
Contributor:
Williams, Mark (Advisor)
Karma, Alain (Committee member)
Stepanyants, Armen (Committee member)
Israeloff, Nathan E. (Nathan Eli), 1961- (Committee member)
Publisher:
Boston, Massachusetts : Northeastern University, 2014
Date Accepted:
November 2014
Date Awarded:
January 2015
Type of resource:
Text
Genre:
Dissertations
Format:
electronic
Digital origin:
born digital
Abstract/Description:
The Gag polyprotein of human immunodeficiency virus type 1 (HIV-1) plays an important role in the retroviral replication and packaging. It is further processed into matrix (MA), capsid (CA) and nucleocapsid (NC). During the maturation process, Gag is cleaved into three domains, MA, CA and NC and NC is further cleaved from NCp15 to NCp9, and finally NCp7(1). HIV-1 NCp7 is a 55-amino acid polypeptide with two zinc fingers (ZF), each with the invariant CCHC motif and 15 basic residues. The NC protein is the primary region for the interaction of Gag with nucleic acids. NCp7 is a nucleic acid chaperone that can facilitate numerous nucleic acid rearrangements throughout the complex reverse transcription process. The matrix (MA) domain of Gag is also capable of nucleic acid binding. The chaperone activity of these NC proteins has not been fully understood. We use optical tweezers to stretch single ë-DNA molecules through the helix-to-coil transition in the presence of NCp15, NCp9 and NCp7 as a function of pulling rate and solution conditions. The results reveal multiple timescales in the kinetics of interaction among DNA and NC proteins. We also demonstrate that NCp15 exhibits significantly slower kinetics than NCp9 and NCp15, consistent with an important regulatory role for the p6 domain that is cleaved from NCp15 during viral maturation. Previous studies have shown that rapid kinetics between DNA and protein is a major component of protein's chaperone. Here we show that there are additional, slower DNA binding modes that allow NC to remain electrostatically and nonspecifically associated with DNA. In addition, we show that the DNA binding kinetics are also regulated by the cleavage of the p6 domain from NCp15 as retroviral replication proceeds.
Subjects and keywords:
chaperone
kinetics
nucleocapsid
Atomic, Molecular and Optical Physics
Physics
DNA-protein interactions
DNA-binding proteins
Molecular chaperones
Polypeptides
HIV (Viruses)
Retroviruses
DOI:
https://doi.org/10.17760/d20128367
Permanent URL:
http://hdl.handle.net/2047/d20128367
Use and reproduction:
In Copyright: This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the right-holder(s). (http://rightsstatements.org/vocab/InC/1.0/)
Copyright restrictions may apply.

Downloads