Electrostatics of the GABA(A) receptor pore

Project Title: Electrostatics of the GABA(A) receptor pore
Program:
CAREERS (323)

Project Image: https://support.access-ci.org/system/files/webform/project/109/eprotein.jpg
Tags:
bash (242), molecular-dynamics (288), namd (290), programming (5), programming-best-practices (49), scripting (243), slurm (71)

Status: Complete
Project Leader
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Project Leader:
Grace Brannigan

Email: grace.brannigan@rutgers.edu
Mobile Phone: {Empty}
Work Phone: {Empty}

Project Personnel
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Mentor(s):
Galen Collier (420)

Student-facilitator(s):
Jesse Sandberg (559)

Mentee(s):
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Project Information
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Project Description:
The coronavirus E protein is an ion channel in the membrane envelope that is important for maintaining viral shape as well as conducting ions. We aim to run coarse-grained and atomistic  molecular dynamics simulation of E proteins, in order to test two distinct hypotheses for how the protein shapes the membrane.  The student would both run simulations using open-source, highly developed existing packages, and write their own analysis and signal processing code.

Project Information Subsection
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Project Deliverables:
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Project Deliverables:
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Student Research Computing Facilitator Profile:
Grad or undergrad
Interested in structural biology research
Experienced Linux or Unix user
Comfortable working in a remote Linux environment (HPC cluster)
Some experience with Python programming
Structural modeling experience (understanding general concepts) will be helpful

Mentee Research Computing Profile:
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Student Facilitator Programming Skill Level: Some hands-on experience
Mentee Programming Skill Level: {Empty}
Project Institution: Rutgers University–Camden
Project Address:
303 Cooper St
Camden, New Jersey. 08102

Anchor Institution: CR-Rutgers
Preferred Start Date: 11/01/2020
Start as soon as possible.: No
Project Urgency: Already behind3Start date is flexible
Expected Project Duration (in months): 6
Launch Presentation: https://support.access-ci.org/system/files/webform/project/109/Jesse.Sandberg-Brannigan.Lab-Project.Launch.2021_1.pdf
Launch Presentation Date: 02/10/2021
Wrap Presentation: {Empty}
Wrap Presentation Date: 11/19/2021
Project Milestones:
- Milestone Title: Run simulations
  Milestone Description: Run coarse-grained simulations of the E protein in 8 different lipid bilayers
  Completion Date Goal: 2021-02-10
  Actual Completion Date: 2021-02-10
- Milestone Title: Analyze results for deformations
  Milestone Description: Analyze elastic deformations of membranes for different systems
  Completion Date Goal: 2021-03-10
  Actual Completion Date: 2021-03-10
- Milestone Title: Analyze results for lipid sorting
  Milestone Description: Analyze lipid sorting in each bilayer
  Completion Date Goal: 2021-04-14
  Actual Completion Date: 2021-04-14
- Milestone Title: Run follow-up sorting simulations
  Milestone Description: Based on results from milestones 1-3, run additional simulations to test role of lipid chains vs headgroups in sorting
  Completion Date Goal: 2021-05-12
- Milestone Title: Run general interactions simulations
  Milestone Description: Run atomistic simulations to confirm potential interactions are stable
  Completion Date Goal: 2021-06-09

Github Contributions: {Empty}
Planned Portal Contributions (if any):
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Planned Publications (if any):
One publication on the role of hydrophobic mismatch in driving the effect of E proteins on membrane shape.

What will the student learn?:
The student will learn how to run coarse-grained and atomistic simulations, analyze simulations using VMD and python, and the underlying elastic theory for the proposed mechanism. 

What will the mentee learn?:
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What will the Cyberteam program learn from this project?:
Effort involved in recruiting and training junior-level research software engineers.

HPC resources needed to complete this project?:
We will apply for time on the State of New Jersey's "Caliburn" system at Rutgers University

Notes:
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Final Report
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What is the impact on the development of the principal discipline(s) of the project?:
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What is the impact on other disciplines?:
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Is there an impact physical resources that form infrastructure?:
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Is there an impact on the development of human resources for research computing?:
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Is there an impact on institutional resources that form infrastructure?:
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Is there an impact on information resources that form infrastructure?:
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Is there an impact on technology transfer?:
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Is there an impact on society beyond science and technology?:
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Lessons Learned:
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Overall results:
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