Submission information
Submission Number: 173
Submission ID: 3942
Submission UUID: 73f73831-3131-42b1-a998-b2f42ab40cc7
Submission URI: /form/project
Created: Mon, 08/21/2023 - 06:03
Completed: Mon, 08/21/2023 - 06:10
Changed: Wed, 09/04/2024 - 15:23
Remote IP address: 146.75.253.174
Submitted by: Gaurav Khanna
Language: English
Is draft: No
Webform: Project
| Project Title | Steered Molecular Dynamics Simulations on Human beta Defensin Crossing Model Bacterial Lipid Membranes |
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| Program | CAREERS |
| Project Image | |
| Tags | molecular-dynamics (288) |
| Status | Complete |
| Project Leader | Liqun Zhang |
| zhangl@uri.edu | |
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| Work Phone | |
| Mentor(s) | Liqun Zhang |
| Student-facilitator(s) | Cole Pepin |
| Mentee(s) | |
| Project Description | Human beta defensins (hBDs) are an important family of natural antimicrobial peptides (AMPs). They belong to the human innate immune system and have broad-spectrum of antimicrobial activities against yeast, fungi, and both Gram-positive and Gram-negative bacteria. It is widely accepted that hBDs kill bacteria by directly binding, disrupting bacterial lipid membrane, then forming pores. But the exact functional mechanism in molecular details is still elusive. Human beta defensins type 1 to 3 (abbreviated as hBD-1, hBD-2, and hBD-3) are the typical members in hBD family and they have distinct membrane crossing capabilities. In this project, steered molecular dynamics simulations will be applied to predict the translocation of those three hBDs through explicit model Gram-negative membranes. The result will supply insight designing novel AMP based antibiotics in the future. |
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| Student Research Computing Facilitator Profile | |
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| Project Institution | University of Rhode Island |
| Project Address | |
| Anchor Institution | CR-University of Rhode Island |
| Preferred Start Date | |
| Start as soon as possible. | No |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | 6 |
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| What will the student learn? | |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | |
| HPC resources needed to complete this project? | |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | Working on Steered Molecular Dynamics aids in showing the importance of biophysics research when it comes to the medical field. Although the biochemistry aspect of knowing how the human beta-defensin’s work with the human body is extremely important, it is also important to gain an understanding of how the peptides may move through the human body as well as bacterial cell membranes. To efficiently use the peptides biochemical properties to its potential, the biophysical properties must be understood. Working with the online programs also provided insight on how efficient it can be to simulate an experiment rather than testing an experiment in a lab. Although using actual peptides shows how they act in reality, that can cost a lot of money and time to secure the samples and run tests. Online simulations allows for many tests to be ran, at a fraction of the price of a real experiment, while still providing accurate results. |
| What is the impact on other disciplines? | Working with the online programs also provided insight on how efficient it can be to simulate an experiment rather than testing an experiment in a lab. |
| Is there an impact physical resources that form infrastructure? | |
| Is there an impact on the development of human resources for research computing? | |
| Is there an impact on institutional resources that form infrastructure? | |
| Is there an impact on information resources that form infrastructure? | |
| Is there an impact on technology transfer? | |
| Is there an impact on society beyond science and technology? | |
| Lessons Learned | A lesson I learned throughout my project was that it is important to do outside research on your own to solve problems. Unlike classes, there is not a known solution to find, so it is important to do additional research to find needed information such as creating a code that simplifies the simulations. |
| Overall results | Overall, the results from the project showed that the dimer forms of the hBD’s performed better than the monomer forms. Each human beta-defensin had advantages over others in certain experiments, however the dimers always performed better than the monomers. |