Presenter Information

Madeline SheahanFollow

Major

Neuroscience

Anticipated Graduation Year

2020

Access Type

Open Access

Abstract

The purpose of this research is to gain a further understanding of the biochemical mechanisms involved in the denaturation of small proteins using excess concentrations of chemical denaturant sodium dodecyl sulfate (SDS). This work is significant because it allows for the visualization of how SDS interrupts hydrophobic interactions within a protein at the molecular level. The denaturing of proteins render them completely useless and could relieve negative effects from high concentrations of protein in diseases like Alzheimer’s. All of this will be accomplished by utilizing a visual molecular dynamics (VMD) program for simulation. In VMD, four different proteins, each of which consists of about 100 residues, will be submerged in a water box, and an excess concentration of 2450 SDS molecules will be introduced. All disulfide bonds will be removed in the simulation. Each simulation will be left to run for 200 ns, and results will be calculated using CHARMM 36 parameters. The main goal of this research is to study the functionality of chemical denaturation and virtually represent how a small protein is unfolded when presented with excess denaturant. The potential impact this research possesses cannot be denied, as a molecular level representation of the unfolding of a protein can be useful in drug development and the understanding of biochemistry.

Faculty Mentors & Instructors

Dr. Ken Olsen, PhD, Department of Chemistry and Biochemistry

Creative Commons License

Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.

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Denaturation of Small Proteins In The Presence of Sodium Dodecyl Sulfate

The purpose of this research is to gain a further understanding of the biochemical mechanisms involved in the denaturation of small proteins using excess concentrations of chemical denaturant sodium dodecyl sulfate (SDS). This work is significant because it allows for the visualization of how SDS interrupts hydrophobic interactions within a protein at the molecular level. The denaturing of proteins render them completely useless and could relieve negative effects from high concentrations of protein in diseases like Alzheimer’s. All of this will be accomplished by utilizing a visual molecular dynamics (VMD) program for simulation. In VMD, four different proteins, each of which consists of about 100 residues, will be submerged in a water box, and an excess concentration of 2450 SDS molecules will be introduced. All disulfide bonds will be removed in the simulation. Each simulation will be left to run for 200 ns, and results will be calculated using CHARMM 36 parameters. The main goal of this research is to study the functionality of chemical denaturation and virtually represent how a small protein is unfolded when presented with excess denaturant. The potential impact this research possesses cannot be denied, as a molecular level representation of the unfolding of a protein can be useful in drug development and the understanding of biochemistry.