NDLI: Interaction simulation of Lipoxygenase with arachidonate acid using NAMD

Content Provider	IEEE Xplore Digital Library
Author	Zhongwei Li Khosravi, E. Shuju Bai
Copyright Year	2011
Description	Author affiliation: Depatrment of Computer Science, Southern University, Baton Rouge, LA 70813 (Zhongwei Li; Khosravi, E.; Shuju Bai)
Abstract	Lipoxygenase (LOX) family is believed as the major cause of pathological symptoms in asthma by biosynthesis of leukotrienes. The physiological function is known as firstly producing 8R-HPETE (derived from arachidonate acid, referred as AA), which is transformed in further enzymatic step into leukotrienes. However, much less detail is known about the role of 5-Lox in the inflammatory reaction. We have used the 1.85Å resolution structure of a wild coral Lipoxygenase (8R-LOX) (with 41% sequence identical to the human arachidonate 5-LOX) as a foundation to model the interactions between 8R-Lox and its substrate AA, and its binding site was identified using ICM. In this research, the 8R-Lox:AA complex obtained was refined and analyzed by molecular dynamic method (NAMD). Parameterization scheme for unknown structure of non-heme iron ligated by a series of residues was developed using VMD paratool plugin. All quantum mechanical calculation were performed by Gaussian03 with the Becke3LYP functional at 6–31G(d) basis set.
Starting Page	973
Ending Page	973
File Size	648939
Page Count	1
File Format	PDF
ISBN	9781457716126
e-ISBN	9781457716133
DOI	10.1109/BIBMW.2011.6112525
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-11-12
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	lipoxygenases arachidonic acid Conferences Biological system modeling Force Physiology Iron Trajectory mocular dynamics force field parameter Substrates NAMD
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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