Download Poster - Center for BioMolecular Modeling

NO S-nitrosylation, NO Memorization
Whitefish Bay High School SMART Team:
Sam Broadnax, Jieun Heo, Michelle Shin, Ryan Davis, Brenna Grych, Brianna Donaldson Morton, Camille Middleton, Frank Zhang,Grant Von Paumgartten, Jamelah Johnson, John Schroeder, Koobmeej Xiong, Laura
Prekosovich, Morgan Phillips, Nick Longo, Philip Flejsierowicz
Teachers: Katie Brown, Paula Krukar
Mentors: Dmitry G. Khomyakov, Ph.D. Candidate and Qadir K. Timerghazin, Ph.D., Department of Chemistry, Marquette University
Abstract
The Molecular Story
How S-nitrosylation Works
• S-nitrosylation is an essential nitric oxide dependent process that is found in
almost every part of cellular biology
• This is a reversible process of the covalent addition of nitric oxide to the
thiol group of a cysteine
• A study by researchers at UPenn revealed that S-nitrosylation truly is
omnipresent, as the process of was found in 328 peptides in 192 proteins
endogenously modified WT mouse liver
• Researchers, including our mentors, determined that S-nitrosylation was
found in areas near negatively charged and positively charged amino acids,
indicating that S-nitrosylation’s site location might be influenced by protein
environment
• Scientists and researchers acknowledge the significance of the process, but
they do not know why the process occurs at the specific cysteine that it does
as opposed to the many other cysteine that are present
• Presence or absence, and also specific spatial arrangement of such residues
creates an active site of potential nitrosylase or denitrosylase – an enzyme,
responsible for addition or removal of NO fragment as a post-translational
modification of given protein
• S-nitrosylation via S-nitrosoglutathione, or GSNO, represents a simplified
model of NO group transfer between two proteins
• Combination of experimental protein science (X-ray crystallography, mass
spectrometry) and computational chemistry (electronic structure
calculations, molecular dynamics) allows future understanding of the
complexity of S-nitrosylation
Nitrogen and oxygen are two components of the air we breathe. Bonded
together as nitric oxide, they are an important signaling molecule that is
involved in numerous physiological processes including S-nitrosylation. The
human body cannot function without this effective process, and if the
regulation of this process breaks down, it can lead to common diseases such as
Parkinson’s and Alzheimer's. Irregular nitrosylase and denitrosylase activities
may be involved in these diseases, so they are important therapeutic targets.
This important process also allows blood vessels to expand, so they can
transport more blood and retain more oxygen. The key component, nitric oxide
(NO), attaches to glutathione to give the S-nitrosoglutathione molecule
(GSNO). The NO from the GSNO then travels to a specific cysteine in a protein,
which can affect the properties of that protein. Using 3D printing technology,
the Whitefish Bay SMART Team is aiding its mentors as they research and try to
figure out why the NO attaches to one cysteine specifically and what exactly
this process does. Doctor Timerghazin and Dmitry G. Khomyakov hypothesize
that a positive amino acid, such as arginine, catalyzes the NO transfer and
causes it to jump to the specific cysteine. Figuring out what S-nitrosylation’s
physiological role as well as why one cysteine is chosen over others could lead
to developments in our understanding of certain diseases that are linked to the
erratic regulations of S-nitrosylation in the human body.
The Big Picture:
S-nitrosylation in Our World Today
Dysfunctional S-nitrosylation has been linked to various medical complications,
including stroke, Alzheimer’s, Lou Gehrig’s disease, and potentially cancer.
Understanding the selectivity of S-nitrosylation will help scientists to better
understand the reaction between the NO molecule and proteins found in the
human body. This breakthrough could potentially lead to more effective
treatments for detrimental diseases, for pinpointing the exact location that this
process occurs at may aid in the creation of treatments that target this binding
site more directly.
Background of the Process
The process of S-nitrosylation is so remarkable because it is ubiquitous in
nature and has connections with the nervous and cardiovascular systems in the
human body as well as other organisms. Although little is known about where
and why this process occurs in almost every living organism's body, researchers
do know that without it, the human body would not function properly. When
the process of S-nitrosylation is not operating properly in the body scientists
have found that it may lead to a variety of different cardiovascular diseases.
Process of Science: Molecular Dynamics Computational Experiment
Conclusion
Computational Modeling Methods
The Whitefish Bay SMART Team uses a computer modeling system called Jmol
to visualize our molecule and biological process. Jmol presents a 3-D
visualization of the molecule. The 3-D model is then printed at MSOE as a
physical representation of the molecule. Having a physical model of the
process allows researchers to better understand the “whats” and “whys” of
the S-nitrosylation.
Citations: Nakamura, Lipton Antiox. Redox. Signal. 2013
Researchers at the University of Pennsylvania are experimenting with the mice livers in order to investigate
the process of S-nitrosylation in that protein. Dr. Timerghazin’s lab, working collaboratively with the University
of Pennsylvania, is responsible for the computational experiments in order to further develop their scope of Snitrosylation. Computational data has been found that supports their hypothesis on S-nitrosylation. This data
shows that the vibration of nuclei of the molecules they hypothesized is associated with the S-nitrosylation
process. Examination of the graph (above left) reveals there is a high probability of finding electrons where
the bond length is 4 angstroms. This data corresponds to the bond length of the S-glutathione molecule,
supporting the hypothesis that S-nitrosylation happens near the S-glutathione molecule. This crucial data
serves as the basis for the location of S-nitrosylation and the associated molecules.
Smith, Marletta Curr. Opin. Chem. Biol. 2012
S-nitrosylation is one of the most crucial physiological processes enabling
survival and healthy living. The process mainly utilizes nitric oxide which bonds
with the glutathione molecule and then transports to a specific cysteine in the
form of S-nitrosoglutathione. The function and behavior of that protein is
impacted by this process. Researchers hypothesize that the lack or the excess
of S-nitrosylation is linked to many of the pressing diseases today, including
Parkinson's and Alzheimer's. Cooperating with the University of Pennsylvania,
Doctor Timerghazin and Dmitry G. Khomyakov are working on the
computational model of S-nitrosylation and hypothesize that an arginine
catalyzes the NO transfer to a specific cysteine. Computational experiments
clearly support their hypothesis by showing that there is a high probability to
find Arg 706 near the docked S-nitrosoglutathione molecule, which helps to
nitrosate the target cysteine. Currently, they are conducting further research
to find more data to support and explain their hypotheses. Alongside the
researchers, the Whitefish Bay SMART Team is also learning more about this
process by creating a model of the S-nitrosylation active site using Jmol
software and physical 3D model of protein. Understanding this process and
finding its links to physiological processes can help develop future medications
and treatments for common diseases.
"What Happens To The Brain in Alzheimer’s Disease?" Fisher Center for Alzheimer's Research Foundation, n.d. Web. 05 Mar. 2014.
SMART Teams are supported by the National Center for Advancing Translational Sciences, National Institutes of Health, through Grant Number 8UL1TR000055. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.
Prof. Harry Ischiropoulos, Upenn.