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Computational Protein Topographics for Health Improvement

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Title: Computational Protein Topographics for Health Improvement


1
Computational Protein Topographics for Health
Improvement Jie Liang, Ph.D. Bioengineering Prim
e Grant Support National Science Foundation
Career Award, National Institutes of Health R01,
Office of Naval Research, and the
Whitaker Foundation.
Protein surface matching
Problem Statement and Motivation
  • The structure of proteins provide rich
    information about how cells work. With the
    success of structural genomics, soon we will have
    all human proteins mapped to structures.
  • However, we need to develop computational tools
    to extract information from these structures to
    understand how cell works and how new diseases
    can be treated.
  • Therefore, the development of computational tools
    for surface matching and for function prediction
    will open the door for many new development for
    health improvement.

Evolution of function
Key Achievements and Future Goals
Technical Approach
  • We have developed a web server CASTP (cast.engr.
    uic.edu) that identify and measures protein
    surfaces. It has been used by thousands of
    scientists world wide.
  • We have built a protein surface library for
    gt10,000 proteins, and have developed models to
    characterize cross reactivities of enzymes.
  • We also developed methods for designing phage
    library for discovery of peptide drugs.
  • We have developed methods for predicting
    structures of beta-barrel membrane proteins.
  • Future Understand how protein fold and
    assemble, and designing method for engineering
    better proteins and drugs.
  • We use geometric models and fast algorithm to
    characterize surface properties of over thirty
    protein structures.
  • We develop evolutionary models to understand how
    proteins overall evolve to acquire different
    functions using different combination of surface
    textures.
  • Efficient search methods and statistical models
    allow us to identify very similar surfaces on
    totally different proteins
  • Probablistc models and sampling techniques help
    us to understand how protein works to perform
    their functions.

2
Fluid Physics and Transport Phenomena in the
Human Brain Laboratory for Product and Process
Design, Director A. A. LINNINGER College of
Engineering, University of Illinois, Chicago, IL,
60607, U.S.A. Grant Support NSF, Susman and
Asher Foundation
  • Problem Statement
  • Prediction of large deformations of the brain
    parenchyma based on Fluid-Structure Interaction
    modeling.
  • Coupling of the brain parenchyma, vascular and
    ventricular system in the human brain.
  • Motivation
  • The therapeutic approach for hydrocephalus
    treatment is very brutal (shunting) and many
    revisions are needed.
  • Ultimate goal precise model of human brain
    dynamics to design treatments without in vivo
    test.
  • Key Achievements
  • 3D geometric reconstruction of patient-specific
    brain dimensions based on MRI data
  • 3D patient-specific dynamic analysis of CSF flow
    in the human brain
  • Future Goals
  • Optimal Drug Delivery to the Human Brain.
  • Feedback control systems to better treat
    Hydrocephalus.
  • Data from Magnetic Resonance Imaging.
  • Use of MRI reconstruction tools for generation of
    3D patient specific brain geometry.
  • Introduction of the geometry to Finite Volumes or
    Finite Elements advanced solvers.
  • Post processing of the obtained results.

3
Integrating Nanostructures with Biological
Structures Investigators M. Stroscio, ECE and
BioE M. Dutta, ECE Prime Grant Support ARO,
NSF, AFOSR, SRC, DARPA
Problem Statement and Motivation
Quantum Dot
  • Coupling manmade nanostructures with biological
    structures to monitor and control biological
    processes.
  • For underlying concepts see Biological
    Nanostructures and Applications of Nanostructures
    in Biology Electrical, Mechanical, Optical
    Properties, edited by Michael A. Stroscio and
    Mitra Dutta (Kluwer, New York, 2004).

Cellular Membrane
Integrin
Technical Approach
Key Achievements and Future Goals
  • Synthesis of nanostructures
  • Binding nanostructures to manmade structures
  • Modeling electrical, optical and mechanical
  • properties of nanostructures
  • Experimental characterization of intergated
    manmade
  • nanostructure-biological structures
  • Numerous manmade nanostructures have been
    functionalized with biomolecules
  • Nanostructure-biomolecule complexes have been
    used to study a variety of biological structures
    including cells
  • Interactions between nanostructures with
    biomolecules and with biological environments
    have been modeled for a wide variety of systems
  • Ultimate goal is controlling biological systems
    at the nanoscale

4
Multimode Sonic Ultrasonic Diagnostic
Imaging Investigators Thomas J. Royston
Francis Loth, Mechanical Industrial
Engineering Prime Grant Support NIH
Problem Statement and Motivation
Bimodal image.
  • Ultrasonic (US) imaging provides detailed
    geometry
  • Geometric changes may indicate disease or injury
  • Sonic imaging provides unique functional
    information
  • Sounds associated with disease are sonic, not US
  • Merge US and Sonics to harness strengths of each
  • Initial application peripheral vascular
    pathologies vessel constrictions (plaque and
    intimal hyperplasia)

Blood vessel with constriction in soft tissue
phantom Grayscale of geometry from US
imaging Color overlay of acoustic field generated
by turbulence downstream of the constriction
Key Achievements and Future Goals
Technical Approach
  • Sonic wave propagation in biological tissue is
    more complex than US.
  • Requires new acoustic modeling developments
  • Inverse modeling to extract acoustic image from
    array
  • Novel acoustic sensor development
  • Prototype US/Sonic system has been developed
  • - conventional US system retrofitted with
  • - electromagnetic position device for true
    3D imaging
  • - acoustic sensor array pad that is
    transparent to US so US imaging can be conducted
    with the pad in place
  • Calibration of system on phantom models in
    progress
  • Turbulence imaged downstream of vessel
    constriction
  • Future plans Human subject studies, improved
    prototype, better sensor array, improved imaging
    software

Prototype 15 sensor sonic array pad on arm
  • Merging multiple imaging modalities on same
    platform

Biomedical Biotechnology
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