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Molecular Modeling J-Term 08. By: Laura Megorden. Goals and Objectives Learn how to use computational programs like gaussian03, Unix, Linux, webMO, and webAMBER, and VMD Create a webpage that details my work in class and on my project

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Goals and Objectives
  • Learn how to use computational programs like gaussian03, Unix, Linux, webMO, and webAMBER, and VMD
  • Create a webpage that details my work in class and on my project
  • Create a research project that utilizes my knowledge on the computational programs
  • Present my project to the class

What do these people have in common?



All of these Professional Athletes and Performers have been linked to steroid abuse.

Anabolic steroids
  • A class of steroid hormones related to testosterone
  • Known to increase protein synthesis within cells which results in buildup of cellular tissue, especially in muscles.
  • Have 2 properties:
    • Androgenic: Responsible for control of “male” characteristics
    • Anabolic: Regulate anabolic processes like synthesis of protein in muscle, formation of blood cells, and the emotional and physical aspects of sexual function
Medicinal use of Steroids
  • Used to stimulate bone growth
  • Stimulate appetite
  • Induce male puberty
  • Have been used to treat cancer and AIDS
  • Increase muscle mass and physical strength
  • **This characteristic makes them so attractive to athletes
Risks and Side Effects
  • Changes in cholesterol levels
  • Acne
  • High blood pressure
  • Liver damage
  • Changes of the left ventricle of the heart
  • Testosterone is closely related to anabolic steroids. It is usually taken by males since it is produced naturally by the testes and circulates through the blood acting on cells throughout the body.
  • It is transported inside carrier proteins in the blood. The carrier proteins then slowly release testosterone which can then slip through cell membranes and into cells.
  • Once it is inside the cells it finds a way to get into the nucleus and binds to the androgen receptor and changes the expression of many genes turning on the anabolic and androgenic functions
Testosterone Continued
  • Testosterone is created step-by-step by a process of collection of enzymes.
  • 17-beta-hydroxysteroid dehydrogenase is the enzyme that performs the last step in converting androstenedione into testosterone
  • Androstenedione
  • 19-carbon steroid hormone produced in the adrenal glands and the gonads, that acts as the intermediate step in the pathway that produces testosterone.
Structures of Androstenedione and Testosterone

Crystal structure of human estrogenic 17beta-hydroxysteroid dehydrogenase complex with androstanedione and NADP

Crystal structure of human androgen receptor ligand binding domain in complex with testosterone

My ultimate goal for this project is to compare the structures of Androstenedione and Testosterone using a variety of tools including webMO, webAMBER, and VMD.
Works Cited
  • Pereira de Jesus-Tran, K.,  Cote, P.-L.,  Cantin, L.,  Blanchet, J.,  Labrie, F.,  Breton, R. (2006) Comparison of crystal structures of human androgen receptor ligand-binding domain complexed with various agonists reveals molecular determinants responsible for binding affinity. Protein Sci. 15: 987-999
  • Shi, R.,  Lin, S.X. (2004) Cofactor hydrogen bonding onto the protein main chain is conserved in the short chain dehydrogenase/reductase family and contributes to nicotinamide orientation. J.Biol.Chem. 279: 16778-16785
  • D. H. Catlin (2006) Anabolic Steroids. Chapter 176 in the textbook: Endocrinology, edited by DeGroot and Jameson, Elsevier.C. Saudan, N. Baume, N. Robinson, L. Avois, P. Mangin and M. Saugy (2006) Testosterone and Doping Control. Journal of Sports Medicine 40(supplement 1), i21-i24.