1 toxic effects of pristine and carboxyl functionalized graphene on p53 protein case study
TRANSCRIPT
1
Toxic Effects of Pristine and Carboxyl Functionalized Graphene on p53 Protein
CASE STUDY
Size of Different Objects
Bhasma, Metal ion (Cd, Pb etc.)
In Ayurvedic Medicine
DNA DamageCell Cycle Arrest
Hypoxia
Cell Cycle Arrest
DNA Repair
Cell Cycle Restart
Apoptosis and Senescence
Death & elimination of damaged cells
Guardian of Genome
P53MDM2Active form P53
Angiogenesis
Cellular and Genetic Stability
4
How graphene and its functionalized form (COOH) interact with p53 tumor suppressor protein? A Computational Nanotoxicology study.
Structure of Human p53 protein in complex with 1 nm Graphene
p53 _grap1nm -12 Kcal/mol
Crystal structure of Human p53 protein
BINDING STUDIES OF GRAPHENE OF SIZE 1 nm, 6 nm and 10 nm WITH HUMAN p53 TETRAMER
How graphene of different sizes effect the normal functioning of the p53 protein?
BE -20.7 kcal/mol
BE -20.7 kcal/mol
General Mode of binding of human p53 tetramer and DNA
Mode of binding of human p53 tetramer with Graphene of 1 nm size and DNA
Mode of Binding of Graphene of 1 nm size do not have any influence on p53-DNA complexes.
Interestingly this preliminary result suggest that Graphene of 1 nm size can be used as a Drug delivery agent.
p53_grap6nm -34.0 Kcal/mol
p53_grap6nm_DNA -25.5 Kcal/mol
A-chain
π-π perpendicular stacking (2.5 Å) interaction ofGraphene with Phe212 residue of p53
Mechanism of Binding of p53 and Graphene of size 6 nm (a) and p53-graphene (6 nm)-DNA complexes (b)
(a)
(b)
Target Ligand Binding energy
(Kcal/mol) 5 Å ligand interacting residues
p53 (2OCJ-human p53
crystal structure )
Graphene
6 nm -34.0
A Chain: SER 99, LYS 101, ARG 158, LEU 206, ASP 208, SER 261, ASN 263, LEU 264, ARG 267
C Chain: GLN 167, HIS 168, THR 170, GLU 171, PRO 177, ARG 181, PHE 212, MET 243, ASN 247, ARG 249
Human p53 tetramer-
Graphene
6 nm
DNA
-25.5
B Chain: TYR 107, SER 149, THR 150, PRO 151, PRO 152, ARG 202, GLU 221, GLU 224, VAL 225
C Chain: PRO 177, GLU 180, ARG 181, SER 185, ASP 186, LEU 188, PRO 199, GLN 192, LEU 201, ARG 202, VAL 203, PHE 212
Binding energy and interacting amino acids of p53-graphene 6 nm complexesand also its interaction with DNA
The interaction (binding) energy, the binding pattern and the dynamic conformational changes of the p53-graphene (6 nm) complexes revealed potential interference of graphene with the functional aspects of p53.
A-chain
C-chainB-chain
D-chain
Human p53 tetramer interaction with 5% COOH group functionalized graphene of 6 nm size
BE -25.3 kcal/mol
CONCLUSIONS
• Normal DNA repair mechanism -- DNA makes contact with four domains (A, B, C and D) of p53 protein.
• Possible effects of graphene of different sizes on the molecular structure and function of p53 revealed.
• 1 nm pristine and COOH functionalized graphene sheets did not interfere with the normal p53 functioning.
• Pristine graphene of size 6 nm (and its COOH functionalized sheet) and 10 nm blocks the binding of DNA to two domains (A and D) of p53.
• This indicates the graphene intervention with the DNA binding mechanism and thereby halting the DNA repair mechanism Tumorigenesis (graphene toxicity).
• This may be due to the strong adsorbing property of graphene sheet that pulls the DNA towards itself restricting DNA’s interaction towards p53’s A and D-chains.
11
Acknowledgements
Director, Amrita Centre for Nanosciences and Molecular Medicine, Kochi, Kerala State
Dr. Shikhar Gupta, NIPER M.Tech. Students: Ph.D. Students: Faiza B, Sneha P, Shruthy K,Ms. Anju CP, ACNSMM Shraddha P, Aathira B, Geetha PMs. Jane Jose, ACNSMMMs. Anu R. Melge, JRF, ACNSMM
Indo-Finland Collaborators:Dr. Adyary Fallareo and Prof. Pia Vuorela
University of Helsinki, Finland
Department of Biotechnology (DBT) - India under Nanotoxicology and Nanomedicine-Phase-II Program to ACNSMM
12
13
14
Representative Database of 1200 Ayurvedic, Unani and Siddha Formulations.
Access to 2.50 Lakh (0.250 million) Medicinal Formulations is available to Patent Offices only under TKDL Access Agreement.
Tool to understand the codified knowledge existing for the Indian Systems of Medicine including Ayurveda, Siddha, Unani and Yoga as prior art. It is not a diagnostic or usage database.
Collaborative Project of :Council of Scientific & Industrial Research (CSIR)
Department of Ayurveda, Yoga & Naturopathy, Unani, Siddha and Homeopathy (AYUSH)
Traditional Knowledge Digital Library
Super Natural II provides a highly curated online database for natural products. This database contains 325,508 natural products extracted from various resources.
Super Natural II offers additional search and analysis options. It also provides the toxicity prediction for the database compounds.
For instance, a substructure search can be performed to identify compounds containing this substructure.
Additionally, possible target proteins and pathways are predicted for the natural compounds, based on 2D structural similarity search to known drug molecules.
Super Natural II Database
http://bioinf-applied.charite.de/supernatural_new/index.php?site=home
http://nlam.in/search_module.phpNational Library of Ayurved Medicine (NLAM)
The NLAM database contains botanical information about 700 plants which form an integral part of Ayurveda formulations. These herbs can be searched through the SEARCH BOX or can be accessed through individual formulation descriptions.
http://www.dharaonline.org/Forms/Home.aspx
Digital Helpline for Ayurveda Research Articles
http://www.instituteofayurveda.org/plants/
http://www.ayurvedahealthcare.info/content/ayurveda-research-database-ard
QUESTIONS OR COMMENTS
THANK YOU