[bioundgrd] Fwd: Five New UROP Openings in the Sasisekharan Lab for IAP/Spring'11

[MacKenzie Outlund]

--
Venkataramanan Soundararajan, PhD
Postdoctoral Associate, Harvard-MIT Division of Health Sciences & Technology
Massachusetts Institute of Technology, Cambridge, MA 02139
Website -- http://web.mit.edu/venk/www


IAP and Spring 2011
Multiple Openings
UROP Department/Lab/Center: Harvard-MIT Division of Health Sciences and
Technology (HST)and MIT Biological Engineering (BE)
Faculty Supervisor: Prof. Ram Sasisekharan

Project #1
Project Title: A Novel Approach to Structure-based Protein Design and
Engineering

Project Description: The rational design of proteins is central to the
engineering of novel molecules for a broad-spectrum of biotechnology and
medical
applications. However, design-based protein engineering has been rife with
challenges arising from misfolding, instability, and dysfunction of the
designed molecules. In recent years, our group has been actively decoding
the
rules governing folding, stability, and function for diverse human and
pathogen
proteins, owing to our development of powerful in-house structural and
sequence
analysis tools (e.g. see our recent publications in Nature Biotechnology
2009
and PLoS ONE 2010 at the following links --
http://www.nature.com/nbt/journal/v27/n6/full/nbt0609-510.html and
http://dx.plos.org/10.1371/journal.pone.0009391). Towards furthering the
decoding of rules governing design-based protein engineering and applying
such
knowledge for creating novel proteins with important therapeutic
applications,
we are currently seeking an undergraduate student with keen interest in both
the computational and experimental aspects of molecular structural biology.
Specifically, this UROP is ideally suited for students with interest in both
(i.) learning state-of-the-art molecular modeling (e.g. Discovery Studio,
PyMol) and programming (e.g. MATLAB) tools for the de novo design of novel
proteins; and (ii.) performing guided bench work for experimental validation
of
the designed protein's functions. The UROP student will benefit from working
with senior researchers in a fast-paced group and is expected to co-author
significant journal publications emerging from this research (as has been
the
norm with all of our past and present UROPs). The UROP engagement is
expected
to commence during the IAP/Spring 2011 term, or earlier if a suitable
candidate
expresses interest.

Prerequisites: Strong analytical abilities and an active interest in
computational/molecular biology are both desirable skills for this UROP
research.

Contact: Dr. Venky Soundararajan (http://web.mit.edu/venk/www/) by e-mail at
venk at mit.edu


Project #2
Project Title: Engineering a Database of Virus Surface Protein Molecular
Models
to Decode Patterns of Antigenic and Functional Site Evolution towards
Developing Novel Therapeutic Solutions

Project Description: This UROP will involve the use of in-house molecular
modeling tools to compute a database of viral surface protein molecular
structures from NCBI bioinformatics databases. The main goal of this
constructed massive database will be to develop protocols for analysis and
mining of novel biomedical signatures that will facilitate important
biomedical
and biotechnological applications. Specifically for influenza virus, the
determinants of (i.) glycan receptor-binding specificity of viral
hemagglutinin
protein and (ii.) antigenic evolution; will be determined by utilizing
techniques from our recently published studies (see our Innate Immunity 2010
and Nature Biotechnology 2009 papers at the following links --
http://ini.sagepub.com/content/early/2010/08/09/1753425910377099.abstract and
http://www.nature.com/nbt/journal/v27/n6/full/nbt0609-510.html ).
Significant
biological and therapeutic value is anticipated for the results emerging
this
analysis, which is expected to lead to important scientific publications.
The
UROP engagement is expected to commence during the IAP/Spring 2011 term, or
earlier if a suitable candidate expresses interest.

Prerequisites: Strong analytical abilities, with an active interest in
database
construction and data mining, are desirable for this UROP research.

Contact: Dr. Venky Soundararajan (http://web.mit.edu/venk/www/) by e-mail at
venk at mit.edu

Project #3
Project Title: Construction of a Universal Protein Sequence-to-Structure
Database for High-throughput Mining of Structure-Function Relationships

Project Description: This UROP research will commence with building on the
in-house, high-throughput sequence-to-structure mapping protocol developed
recently by our group published in PLoS ONE and Innate Immunity
(http://dx.plos.org/10.1371/journal.pone.0009391  and
http://ini.sagepub.com/content/early/2010/08/09/1753425910377099.abstract),
to
enable the construction of a universal protein structural database. Post
construction of the database, an appropriate Graphical User Interface (GUI)
is
to be developed, to showcase the bioinformatics information content relating
to
the modeled protein structures. Our vision is to create an easy-to-mine
database
of the universal set of molecular models built, using which resource,
specific
biological applications such as sequence-to-function mapping will be
explored.
There is a rich plethora of protocols already implemented by our past and
present UROPs, and the new UROP is expected to quickly adapt to working with
our group to further these goals. Based on the interests of the UROP,
several
follow-up applications may be explored, in the post-database-construction
phase, including de novo identification of glycan-binding properties from
amino
acid sequence. This project will involve significant analytical and
computational skills. Journal publications are already being compiled and it
is
expected that this UROP student will contribute to these papers as a
co-author.
The UROP engagement is expected to commence during the IAP/Spring 2011 term,
or
earlier if a suitable candidate expresses interest.

Prerequisites: Strong analytical abilities, with a vivid and creative
imagination, general appreciation of structures/geometry, and an active
interest in molecular modeling and computational biology are all desirable
traits for this UROP research.

Contact: Dr. Venky Soundararajan (http://web.mit.edu/venk/www/) by e-mail at
venk at mit.edu


Project #4
Project Title: Pattern Recognition on Protein Structural Surfaces:
Applications
to Decode the Glycosylation Machinery

Project Description: This UROP is a very fundamental biological project with
broad applications that are expected to provide significant insight into the
biomolecular mechanisms facilitating the glycosylation of proteins.
Glycosylation is one of the most common post-translational modifications and
is
performed by numerous enzymes with poorly defined specificity. The goal of
this
UROP is to build on the in-house protein structural analysis protocols
developed by us recently (e.g. see our recent publications in Nature
Biotechnology 2009 and PLoS ONE 2010 at the following links --
http://www.nature.com/nbt/journal/v27/n6/full/nbt0609-510.html and
http://dx.plos.org/10.1371/journal.pone.0009391 ) for recognition of
'signature
glycosylation patterns' on the molecular surfaces of diverse protein
structures. The findings that emerge from this analysis are expected to have
major implications for furthering our understanding of the glycosylation
machinery, thus opening the doors for novel biotechnological applications
involving prediction and modulation of these fundamental processes. If
successful, similar protocols may be more broadly explored for predicting
signatures of other biologically and biomedically important
post-translational
modifications, as well. The advances enabled by this UROP study are expected
to
result in major publications in pioneering journals that will have a
profound
impact on molecular biology at large.

Prerequisites: Strong analytical abilities with some previous MATLAB
experience
is desirable for this UROP research.

Contact: Dr. Venky Soundararajan (http://web.mit.edu/venk/www/) by e-mail at
venk at mit.edu

Project #5
Project Title: Mining Protein-Protein Interfaces for Understanding
Biomolecular
Interaction Specificity and Furthering Design-based Therapeutic Engineering

Project Description: This UROP research involves the development of a
protocol
for mining of protein-protein interfaces from the PDB, by building on our
recently-showcased and novel protein structural analysis tools (e.g. see our
recent publications in Nature Biotechnology 2009 and PLoS ONE 2010 at the
following links --
http://www.nature.com/nbt/journal/v27/n6/full/nbt0609-510.html and
http://dx.plos.org/10.1371/journal.pone.0009391 ). The goal is to compute
the
signatures of protein-protein interaction specificity and affinity. Novel
analytical approaches have been envisioned to enable the mining and analysis
aspects of this research. The ideal UROP student would have an inherent
ability
to recognize patterns from analysis of data-rich signals. Prediction of
protein-protein interactions is a significant biological advancement with
major
biotechnological implications. Important scientific and technological
publications are hence expected from this UROP research.

Prerequisites: Strong analytical abilities with some previous MATLAB
experience
is desirable for this UROP research.

Contact: Dr. Venky Soundararajan (http://web.mit.edu/venk/www/) by e-mail at
venk at mit.edu
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