Faculty Project Form - Duquesne University

FACULTY FORM for mentoring a summer URP student.
January 17, 2008
As you know, the REU/ASSURE Site is successful in attracting and training students from
smaller institutions that do not have the infrastructure for research, and provides opportunities for
students from traditionally under represented populations. However, from our past experiences
that are consistent with those reported at the NSF, there are two observations that signal a need
for change in how research experiences are offered and implemented.
PUBLICATION. The number of peer-reviewed publications averaged about two per
year for the summer research students. To have a full experience, the student must
participate in the rewarding, yet painstaking process of manuscript preparation, revision,
and publication. As such, 80% of the students are missing out on one of the most critical
aspects of the research experience. We would like to see this increased.
EXTENSION. A significant number of students expressed desire to continue research on
their projects after the ten-week summer experience. However, the mechanism and
support was not readily available to extend the research experience back to the
LSAMP/PUI institutions. It is clear that students enjoyed the experience, and wanted it to
become a part of their learning community. Thus, collaboration with already identified
faculty from the student’s home institution will facilitate the process. If your research can
be connected to any of the following individuals, then your project will become high
priority for a student. Below are the current connections we have with LSAMP/PUI
Dr. Ayivi Hussio
Optical and quantum electronics
Associate Professor of Physics, Florida Memorial
Dr. Stacie S. Nunes
Assistant Professor of Physics, SUNY at New Paltz
Dr. Remi R. Ok
Tissue engineering
Professor and Chair, Prairie View A&M University
Dr. Ramaiyer Venkatraman
Crystal engineering
Associate Professor, Jackson State University
Please fill out the easy and quick form below. I give an example to illustrate the types of
responses needed. Substitute your responses below.
-------------------------------------------------------------FACULTY FORM for mentoring a summer URP student. Return this part to
Mentor Name: Jeff Evanseck
Date: January 17, 2008
Number of students for project: One
1. Provide the goal of the summer research project:
The goal for the summer research project is to disrupt a critical salt-bridge in the trp-cage
miniprotein to observe its consequences on structure, dynamics and folding.
2. Co-workers/collaborators:
The student will work with one other graduate student on this project. In this particular example,
there is no experimental component. The student will utilize the experimental data published in
the literature. However, in other descriptions, it would be useful to know if there is a
computational component to the project.
3. Instrumentation, techniques, methods learned:
The student will learn how to use Duquesne’s supercomputers to carry out molecular dynamics
simulations using the CHARMM program. A one-microsecond condensed-phase MD simulation
takes less than two-weeks using 8-processors. Thus, the student will have time to learn how to
simulate (2 weeks), carry out the simulation (2 weeks), and have the remaining time for analysis
and writing.
4. Publication aspiration:
The project is designed as part of a larger, on-going effort. Since the salt-bridge is currently
thought to be a key factor in the dynamics of the system, the targeted journal for publication is in
ACS Biochemistry. The data may be published as a stand a lone piece of work submitted to
Biochemistry, or incorporated into a larger more comprehensive J. Am. Chem. Soc. manuscript.
5. LSAMP Collaboration:
It might be possible to connect this research with Prof. Huisso at FMU or one of the faculty in his
Department. I have requested that he consider collaboration or identify the appropriate faculty at
6. Project Description: (helps with recruitment – if I get enough of these, I’d like to post
them on the web)
Impact of Trp-Cage Salt-Bridge on Protein Folding
(Experimental Faculty Mentors: None. Theoretical Faculty Liaison: J. D. Evanseck)
Background: The salt-bridge (bright red in Figure 1) in the smallest
known folding sequence, trp-cage miniprotein (20-residues), will be
studied using all-atom simulations in explicit water to provide a
microscopic interpretation of folding. Despite the extensive
experimental and theoretical work reported on trp-cage, critical issues
surrounding a microscopic understanding remain unanswered. First,
the molecular reasons for stability of trp-cage are not fully
appreciated. Second, the folding process of the miniprotein remains a
mystery. To probe a strong intramolecular force within trp-cage, the
effects of the Asp9Gly mutation on the structure and kinetics will be
Project: This project uses molecular dynamics simulations to
generate a series of one microsecond trajectories to understand the
structure and dynamics of trp-cage folding and unfolding. The student
will use 16 processors on the new supercomputer at Duquesne. A
total of four trajectories will be carried out two at a time, which will take two weeks in total. Thus, the
student will have four independent simulations for analysis and comparison to four natural trp-cage
simulations previously carried out. The student will master the use of the CHARMM program for both data
generation and analysis. In addition to the final URP seminar, the student will be expected to complete a
first draft of a manuscript on this work.
Figure 1. Electrostatic map of trp-cage
Significance: The health relatedness of understanding biomolecular folding and misfolding is critical to
understanding and controlling highly debilitating and increasingly prevalent diseases. Recent research has
shown that these specific diseases depend upon aggregation of misfolded proteins that escape the
cellular quality-control mechanisms. For example, misfolded proteins have been implicated in neurological
disorders, such as Alzheimer’s disease. In this research, the ensembles of intermediates and transition
states sampled during the folding process of trp-cage can lead to understanding the folding code of
biological systems, and provide measures to rectify misfolding events.