peptoids physics 43 santa rosa junior college spring semester 2011 researchers: daniel janiak by...
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PeptoidsPhysics 43 Santa Rosa Junior CollegeSpring Semester 2011
Researchers:Daniel Janiak
By request: a photo of me (at the nanotech forum)
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Ronald Zuckermann, Ph.D
“We’re using nature as our guide to develop functional, stable nanostructures.”
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What are peptoids?
Bio-inspired nanoparticle polymers (a description).
By mimicking natural proteins, these molecules hold the promise of achieving a bottom-up approach, and self-assembly.
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Technical Definition
N-substituted glycine heteropolymers
Example (an octamer):
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Peptoids are Nanotechnology
http://www.daviddarling.info/images/tryptophan.jpg
Tryptophan – the largest amino acid with a length of approximately 1.2 nm. Peptoid monomers are comparable in size.
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Peptoids vs Peptides
• The folding of such chains in a solvent spontaneously creates complex, functional structures.
Peptoid Peptide
http://metamodern.com/2008/12/01/peptoids-at-the-molecular-foundry/
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http://www.chem.purdue.edu/courses/chm333/hemoglobin.JPG
/ http://www.goldbamboo.com/images/content/5530-hemoglobin-t-r-state-ani-hemoglobin.gif
An Illustration of Protein Structure:Hemoglobin
Four separate chains are organized together, making a “dimer of dimers.”
Motifs, such as the many alpha helices seen above are characteristic of secondary structure, their arrangement with other motifs is tertiary structure.
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Plastics simple, useful polymers
Polyvinylidene chloride (cling wrap)
PolyethylenePolystyrene
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?DurabilityEase of manufactureBroad application (flexibility)Variety of physical properties.(many more!)
Achieve complicated physiological tasksSelf-assemblyChemical catalysisBinding of other molecules with high specificity(many more!)
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SignatureStructures
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Alpha-helix (2008*)Magainin-2 in DPPC micelles
[Protein Data Bank (PDB) ID Code 2MAG].
©2008 by National Academy of Sciences
Chongsiriwatana N P et al. PNAS 2008;105:2794-2799
The helical shape is a consequence of the “handedness” of the individual monomers.The result is a structure that is more resilient than one held together by hydrogen bonds.
*The first ever helical peptoid was made in 1997
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Sheets are more difficult to create because both inter- and intra-chain interactions must be considered.
With the right construction, however, sheets self-assemble.
http://byrkeley.blogspot.com/2010_06_01_archive.html
Peptoid sheets
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http://www.nature.com/nmat/journal/v9/n5/fig_tab/nmat2742_F3.html
Magnified:
Aberration-corrected TEM of Peptoid Chains
(*4.5 angstrom = 0.45 nanometers)
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http://www.lbl.gov/publicinfo/newscenter/features/2008/MSD-nano-jaws.html
“Nanojaws”(2008)
Not just shape mimicry, but natural protein function mimicry as well.
Additionally, a synthetic peptoid version is more durable → not limited to a narrow range of temperatures and pH levels.
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A bound molecule of zinc(Recall: Hemoglobin binds Fe)
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How are these structures created / synthesized?
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http://upload.wikimedia.org/wikipedia/commons/3/3e/Peptoid_struc_synth.png
A sub-monomer approach
Peptoid monomers can be individually designed and added one-by-one.Allows for much freedom in achieving a desired end structure.An ideal application for combinatorial chemistry, enabling rational design and quick screening.
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An Example of an Actual peptoid “building
Chirayil S et al. Nucl. Acids Res. 2009;37:5486-5497
© 2009 The Author(s)
Kit.”
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Another Example, this one from the Molecular Foundary in Berkeley, CA.
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Examples of Current Research
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC89291/http://www.thesahara.info/mrsa/staph-bio.jpg
New AntibioticsChiron Corporation, Emeryville, California (1999)
A peptoid termed “CHIR29498 “and others similar to it were affective against a wide spectrum of bacteria, including some antibiotic-resistant strains.
The required concentrations were practical: 3 to 12 μg/ml
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http://topnews.ae/images/alzheimers.jpghttp://www.scientificamerican.com/article.cfm?id=alzheimers-blood-test
A New Diagnosis for Alzheimer's(2011)
(Thomas Kodadek, of Scripps Research Institute ,Jupiter, Florida)
Currently, the disease can only be definitively diagnosed by examining brain plaques .
Kodadek’s group identified 3 antibody-binding peptoids which could identify patients who have the disease with 93% accuracy, requiring only a simple blood test.
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http://newscenter.lbl.gov/wp-content/uploads/nanorope.jpg
Nanorope(at Lawrence Berkeley National Laboratory, 2011)
Self-assembling!Atom-by-atom makeup can be chosenHelices can be engineered to have desired lengths and sequences
Possible Uses:• Scaffolding for nanoscale
construction• Drug delivery• Molecular sensors• Sieve-like devices
Diameter of above example = 600nm
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As Richard Feynman put it ….
There’s plenty of room at the bottom.