Students Modeling A Research Topic: SMART TEAM Students Modeling A Research Topic: The Journey Explained

What is SMART Team? Team Definition: science program where high school students learn about a specific protein and construct a three-dimensional model of that protein. Team Anna Grim Bryan Lampkin Dua Her Rachel Babiarz

Milwaukee School Of Engineering The University’s Center for BioMolecular Modeling is the center for SMART Team. Funding: NIH National Center for Research Resources, Department of Education for Educational Sciences and Howard Hughes Medical Institute.

Purpose Focus: to tell the “molecular story” of NS1 protein and influenza infections. In addition, modeling the NS1 protein. Modeling Tool: Rasmol

Rasmol Definition: computer modeling program. Models are created by using commands to highlight specific parts of the protein. Proteins were downloaded from a national data bank.

Virus Background Information Part 1 Virus Background Information & The NS1 Protein

“So What?” Learning how viruses/influenzas invade (such as H5N1 and H1N1) Understanding how our immune system battles against the flu Increased knowledge of NS1 can help avoid future viruses Relates to stronger and nastier influenzas (such as swine flu)

The branch of medicine that focuses on the study of viruses Virology The branch of medicine that focuses on the study of viruses

Micro-Anatomy of Virus -Nucleic acid enclosed in a protein shell. -Approximately 15-20 nanometers in diameter. -May have DNA or RNA that is double-stranded or single-stranded . -Genetic material is covered by a protein coat. Viruses: Structure A virus particle, also known as a virion, is essentially a nucleic acid (DNA or RNA) enclosed in a protein shell or coat. Viruses are extremely small, approximately 15 - 25 nanometers in diameter. Viruses: Genetic Material Viruses may have double-stranded DNA, double-stranded RNA, single-stranded DNA or single-stranded RNA. The type of genetic material found in a particular virus depends on the nature and function of the specific virus. The genetic material is not typically exposed but covered by a protein coat. The viral genome can consist of a very small number of genes or up to hundreds of genes depending on the type of virus. Note that the genome is typically organized as a long molecule that is usually straight or circular. Viruses are incapable of replicating independently. They are also not able to produce their own energy, nor can they make proteins All viruses contain a core which is comprised of either DNA, or RNA, but never both. DNA or RNA found in the center of a virus and have either a single strand, or a double strand. The central core of genetic material is then covered up in a protective protein coat. As a protein coat is known as capsid. A capsid contains several subunits which are known as capsomers. http://www.google.com/images?q=anatomy+of%20a%20virus&um=1&hl=en&client=

How Does a Virus Invade? 1. Virus enters body. 2. Virus’s Antigen binds to cell through hemagglutinin. Antigens “keys” in interaction. 5. This allows the cell to move freely. 3. Virus enters the cell through endocytosis. 4. A clathrin-coated vesicle is formed around the virus. http://www.invivogen.com/images/RLR_pathway.jpg

How Does a Virus Invade? 5. Once inside the cell, the vesicle breaks apart. 6. Virus’ RNA passes through the nucleus and is replicated. -Lysogenic Cycle -Lytic Cycle 7. The replicated viruses leave the cell. Fact: One virus enters the cell and results in the replication of millions of viruses that leave the cell.

The NS1 Protein NS1 protein (non- structural protein) Found in a virus Encoded within an influenza virus http://web5.cns.utexas.edu/news/wp-content/uploads/2009/12/NS1A-PNAS_cover4.jpg

Taking a Closer Look The NS1 protein is a gene segment located in the inside of a virus Influenza A, B, and C viruses contain the NS1 protein Viruses with NS1 protein are H5N1 (bird flu) and H1N1 (swine flu)

NS1’s Role Binds RNA messengers of host cell from activation Attacks TRIM-25 protein TRIM-25 assists RIG-1 protein RIG-1 sends out alarm signals throughout cell Slows down pre-mRNA production of a cell http://focus.hms.harvard.edu/2007/051807/images/RIG-I-TRIM25.gif

A Sign of Hope? An Antiviral Target against Influenza? NS1 binds to the CPSF30 human protein CPSF30 protects our cells from infections Within the binding site, zinc fingers (F2,F3) from the CPSF30 protein cuts down the virus’s ability to duplicate by blocking the binding between CPSF30 and the NS1 protein This binding site can suggest a potential antiviral target against the influenza virus http://web5.cns.utexas.edu/news/wp-content/uploads/2009/12/NS1A-PNAS_cover4.jpg

Protein Modeling

NS1 Protein Before

NS1 Protein After

Orange: Hydrogen Bonds NS1 Protein Guide Yellow: Active Site Green: 7 Beta Sheets Blue: 3 Alpha Helices Orange: Hydrogen Bonds

Immunology The branch of medicine concerned with the ability of an organism to resist a infection by the action of antibodies.

Immunity Innate Immunity: defends the host from infection by an immediate nonspecific respond to pathogens. Adaptive Immunity: antigen-specific immune response and includes a "memory" that makes future responses against a specific antigen. Acquired Immunity: acquired by the vaccination of the transfer of antibody .

Innate vs. Adaptive Immunity Innate immunity Innate immunity refers to nonspecific defense mechanisms that come into play immediately or within hours of an antigen's appearance in the body. These mechanisms include physical barriers such as skin, chemicals in the blood, and immune system cells that attack foreign cells in the body. The innate immune response is activated by chemical properties of the antigen. Adaptive immunity Adaptive immunity refers to antigen-specific immune response. The adaptive immune response is more complex than the innate. The antigen first must be processed and recognized. Once an antigen has been recognized, the adaptive immune system creates an army of immune cells specifically designed to attack that antigen. Adaptive immunity also includes a "memory" that makes future responses against a specific antigen more efficient.

Immunology T-cells: identify, directly attack and destroy infectious agents. Interferons: proteins made and released by lymphocytes in response to the presence of pathogens - such as viruses, bacteria, or parasites. RIG-1: required for the production of interferons in response to RNA viruses.

Immunology Tumor Necrosis Factor: cytokine involved in a systemic inflammation and is a member of a group of cytokines that stimulate the acute phase reaction. Cytokines: signaling molecules that are used in cellular communication. Macrophages: molecules that engulf antigens and other necrotic tissue. http://www.itb.cnr.it/flex/images/D.0ce220a1911164afd50b/boraschi_1.jpg

In 1962 they were awarded the Nobel Prize in Chemistry. Crystallography Definition: method of determining the arrangement of atoms within a crystal, in which a beam of X-ray strikes a crystal and diffracts into many specific directions. Began in the 1950s when Max Perutz and Sir John Cowdery Kendrew used it to study the structure of sperm whale myoglobin. http://ysm.research.yale.edu/images/78.4/articles-structures-crystallography.jpg In 1962 they were awarded the Nobel Prize in Chemistry.

relation with NS1 Protein Part 2 The Interferon (IFN) & relation with NS1 Protein

Interferon Detects and fights off infections invading our body Classified as a Cytokines Cytokines are from the immune system Purpose is to warn the cells of invasions Role of Interferon: Triggers other immunity cells to activate Builds up other uninfected cells’ resistant towards the new infections Forms interferon-stimulated genes (ISGs) to fight off viruses

Types of Interferons Type I IFN (alpha and beta) Produces cells resistant against viral infections Produced from cells in the body Type II IFN (gamma) Control how the immune system functions Produced from T lymphocytes and natural killer cells

Connection with NS1 Interferons decrease the virus’s ability to spread Unfortunately, not all viruses are affected by interferons Example: H1N1 influenza virus is encoded with a Non-Structural Protein 1 (NS1) NS1 resists the presence of interferons…not good

Conclusions Viruses that contain NS1 protein are harder to get rid of Our immune systems are not familiar with new viruses Immune systems takes longer to destroy viruses with NS1 protein Knowing about NS1 now can aware us of future nastier viruses Studies are being done to shut down NS1 protein receptor

Acknowledgements Dr. Shannon Colton (SMART team coordinator) MSOE - Center of Biomolecular modeling SMART team program Rasmol program Mr. Heeren (assisting DCE SMART team)

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