Title

Steered Molecular Dynamics Hydrogen Bond Analysis on CE8k12 Peptide

Poster Number

56

Lead Author Major

Chemistry

Format

Poster Presentation

Faculty Mentor Name

Michael McCallum

Faculty Mentor Department

Chemistry

Abstract/Artist Statement

Secondary structure of proteins includes alpha helices (the most common), beta sheets, and other coils such as π helices and 310 helices—all held together by hydrogen bonds. Hydrogen bonds can occur between the helices and sheets, between side chains, or other backbone groups. Some proteins also contain salt bridges (a form of ion pairing), which tends to increase stability of the overall structure. Salt bridges form from neutralization of an acid and amine within the side chains of the protein. Molecular dynamics (MD) simulations permit thorough investigations of the physical structure and intramolecular forces of small proteins & peptides by integrating Newton’s equations of motion. Protein simulations are run in silico with optimal thermodynamic settings automated by the program. Steered molecular dynamics (SMD) simulations are an extension of MD, whereby forces are applied through constant velocity pulling or constant force pulling. Though the latter does not give the force and total work done from pulling on a molecule, it is useful in order to identify important structural features, and possibly lead to knowledge about how secondary structural features form. In our simulations, the alpha carbon atom of the first residue remains fixed, and an applied force pulls the last residue. In this way, the velocity changes in order to keep the force constant. Results were obtained to study the number of hydrogen bonds within the protein as a function of extension, allowing the observation of the breakage of hydrogen bonds by distance versus time. We thus try to identify the ordering and importance of hydrogen bond breaking.

Location

DeRosa University Center, Ballroom

Start Date

20-4-2013 1:00 PM

End Date

20-4-2013 3:00 PM

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Apr 20th, 1:00 PM Apr 20th, 3:00 PM

Steered Molecular Dynamics Hydrogen Bond Analysis on CE8k12 Peptide

DeRosa University Center, Ballroom

Secondary structure of proteins includes alpha helices (the most common), beta sheets, and other coils such as π helices and 310 helices—all held together by hydrogen bonds. Hydrogen bonds can occur between the helices and sheets, between side chains, or other backbone groups. Some proteins also contain salt bridges (a form of ion pairing), which tends to increase stability of the overall structure. Salt bridges form from neutralization of an acid and amine within the side chains of the protein. Molecular dynamics (MD) simulations permit thorough investigations of the physical structure and intramolecular forces of small proteins & peptides by integrating Newton’s equations of motion. Protein simulations are run in silico with optimal thermodynamic settings automated by the program. Steered molecular dynamics (SMD) simulations are an extension of MD, whereby forces are applied through constant velocity pulling or constant force pulling. Though the latter does not give the force and total work done from pulling on a molecule, it is useful in order to identify important structural features, and possibly lead to knowledge about how secondary structural features form. In our simulations, the alpha carbon atom of the first residue remains fixed, and an applied force pulls the last residue. In this way, the velocity changes in order to keep the force constant. Results were obtained to study the number of hydrogen bonds within the protein as a function of extension, allowing the observation of the breakage of hydrogen bonds by distance versus time. We thus try to identify the ordering and importance of hydrogen bond breaking.