Difference between revisions of "Foldamer R&D"
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(→External links: added link to a presentation of Christian Schafmeister + some discussion of that) |
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* spiroligomers | * spiroligomers | ||
| − | = | + | = Some possibly relevant papers = |
| + | == Critical advances in structural DNA nanotechnology == | ||
| + | |||
| + | '''Electrostatics actuation demo (fast data injection)''' | ||
| + | * Official name: "A self-assembled nanoscale robotic arm controlled by electric fields" | ||
| + | * Authords: "Enzo Kopperger1,*, Jonathan List1,*, Sushi Madhira2, Florian Rothfischer1, Don C. Lamb2,3,4, Friedrich C. Simmel1,4,†" | ||
| + | * Weblink (walled access): http://science.sciencemag.org/content/359/6373/296 | ||
| + | |||
| + | '''Scaling of structural DNA origami to higher self-assebly convergent assembly-levels''' | ||
| + | * Official Name: "Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components" | ||
| + | * Authors: "Thomas Gerling, Klaus F. Wagenbauer, Andrea M. Neuner, Hendrik Dietz*" | ||
| + | * Places: "Physik Department, Walter Schottky Institute, Technische Universität München Am Coulombwall 4a, 85748 Garching near Munich, Germany" | ||
| + | * MainPublisherInfo: "Science 27 Mar 2015: <br> Vol. 347, Issue 6229, pp. 1446-1452 <br> DOI: 10.1126/science.aaa5372" | ||
| + | *Weblink (walled access): http://science.sciencemag.org/content/347/6229/1446 | ||
| + | |||
| + | '''Demonstration of atomic resolution (but very likely AP only in an statistical average yet!!)''' | ||
| + | * Official Name: "Placing molecules with Bohr radius resolution using DNA origami" | ||
| + | * Web (walled access): https://www.nature.com/articles/nnano.2015.240 | ||
| + | |||
| + | '''Proof of atoimic precision (topoligical) in structural DNA origami (no atomic resolution yet)''' | ||
| + | *Official Name: "Cryo-EM structure of a 3D DNA-origami object" | ||
| + | *Authors: "Xiao-chen Bai a, Thomas G. Martin b, Sjors H. W. Scheres a,1, and Hendrik Dietz b,1" | ||
| + | * Places: "a Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; and b Physics Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany" | ||
| + | * MainPublisherInfo: "PNAS December 4, 2012 109 (49) 20012-20017; https://doi.org/10.1073/pnas.1215713109 " | ||
| + | * Weblink (open access): https://www.pnas.org/content/109/49/20012 | ||
| + | * Direct link: https://www.pnas.org/content/pnas/109/49/20012.full.pdf | ||
| + | |||
| + | == Advances in de-novo protein engineering == | ||
| + | |||
| + | '''de novo protein design demo''' | ||
| + | * Official Name: "Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces." | ||
| + | * Authors: "Shane Gonen1,2,3,4, Frank DiMaio2,3, Tamir Gonen1,*, David Baker2,3,4,*" | ||
| + | * Places: (see link) | ||
| + | * Weblink (walled access): http://science.sciencemag.org/content/348/6241/1365.figures-only | ||
| + | * Open: https://cryoem.ucla.edu/uploads/image/pdfs/2015_gonen.pdf | ||
| + | |||
| + | = Related = | ||
| + | |||
| + | * This is part of [[Present-forward development]] as opposed to [[Future-backward development]] | ||
* [[Incremental path]] | * [[Incremental path]] | ||
* [[Reached milestones in foldamer R&D]] | * [[Reached milestones in foldamer R&D]] | ||
| Line 15: | Line 53: | ||
* Microfluidics | * Microfluidics | ||
| − | + | = External links = | |
* Wikipedia: [https://en.wikipedia.org/wiki/Foldamer Foldamer] | * Wikipedia: [https://en.wikipedia.org/wiki/Foldamer Foldamer] | ||
| Line 29: | Line 67: | ||
* Iterative design of early forms of [[Kaehler bracket]]s <br>optimization of a stiff backbone to get functional groups as close as possible to a fixed predefined configuration (that may have been stolen from a natural protein) | * Iterative design of early forms of [[Kaehler bracket]]s <br>optimization of a stiff backbone to get functional groups as close as possible to a fixed predefined configuration (that may have been stolen from a natural protein) | ||
* [[General software issues]] – programming language limitations, the dreaded interface problem, <br>"deforresting" unnecessary computer algebra reevaluations (a problem also showing up in volumetric 3D modelling aka distance field based [[3D modelling]]; [[Design levels]]),<br> the need for derivation towers (scalar,vector,tensor) (automatic derivation - links to Conal Elliotts work) | * [[General software issues]] – programming language limitations, the dreaded interface problem, <br>"deforresting" unnecessary computer algebra reevaluations (a problem also showing up in volumetric 3D modelling aka distance field based [[3D modelling]]; [[Design levels]]),<br> the need for derivation towers (scalar,vector,tensor) (automatic derivation - links to Conal Elliotts work) | ||
| − | * The waste problem with POPs (persistent organic pollutants) -- See: [[Recycling]] | + | * Going deep down the rabbit-hole to reach a far term target (in an highly non-obvious way for outsiders).<br> Sidenote: That's exactly where natural [[evolution]] has severe limitations. |
| − | * The lignin pileup in the [https://en.wikipedia.org/wiki/Carboniferous Carboniferous] epoch of earths history. | + | * Invention (and market introduction) of covalent protein crosslinking technology |
| + | * Bootstrapping of the synthesis of the fundamental spiroligomer building blocks | ||
| + | * The "indestructibility" of spiroligomers raise the issue of the waste problem with POPs (persistent organic pollutants) -- See: [[Recycling]] | ||
| + | * The suspected lignin pileup in the [https://en.wikipedia.org/wiki/Carboniferous Carboniferous] epoch of earths history. | ||
| + | * The talk doesn't look beyond towards gemstone based systems as far term goal. Partially [[brownian technology path]]? | ||
Latest revision as of 12:33, 13 March 2021
- structural DNA nanotechnology
- de-novo protein engineering
- peptidomimetics like peptoids (& beta-peptides)
- spiroligomers
Contents
Some possibly relevant papers
Critical advances in structural DNA nanotechnology
Electrostatics actuation demo (fast data injection)
- Official name: "A self-assembled nanoscale robotic arm controlled by electric fields"
- Authords: "Enzo Kopperger1,*, Jonathan List1,*, Sushi Madhira2, Florian Rothfischer1, Don C. Lamb2,3,4, Friedrich C. Simmel1,4,†"
- Weblink (walled access): http://science.sciencemag.org/content/359/6373/296
Scaling of structural DNA origami to higher self-assebly convergent assembly-levels
- Official Name: "Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components"
- Authors: "Thomas Gerling, Klaus F. Wagenbauer, Andrea M. Neuner, Hendrik Dietz*"
- Places: "Physik Department, Walter Schottky Institute, Technische Universität München Am Coulombwall 4a, 85748 Garching near Munich, Germany"
- MainPublisherInfo: "Science 27 Mar 2015:
Vol. 347, Issue 6229, pp. 1446-1452
DOI: 10.1126/science.aaa5372" - Weblink (walled access): http://science.sciencemag.org/content/347/6229/1446
Demonstration of atomic resolution (but very likely AP only in an statistical average yet!!)
- Official Name: "Placing molecules with Bohr radius resolution using DNA origami"
- Web (walled access): https://www.nature.com/articles/nnano.2015.240
Proof of atoimic precision (topoligical) in structural DNA origami (no atomic resolution yet)
- Official Name: "Cryo-EM structure of a 3D DNA-origami object"
- Authors: "Xiao-chen Bai a, Thomas G. Martin b, Sjors H. W. Scheres a,1, and Hendrik Dietz b,1"
- Places: "a Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; and b Physics Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany"
- MainPublisherInfo: "PNAS December 4, 2012 109 (49) 20012-20017; https://doi.org/10.1073/pnas.1215713109 "
- Weblink (open access): https://www.pnas.org/content/109/49/20012
- Direct link: https://www.pnas.org/content/pnas/109/49/20012.full.pdf
Advances in de-novo protein engineering
de novo protein design demo
- Official Name: "Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces."
- Authors: "Shane Gonen1,2,3,4, Frank DiMaio2,3, Tamir Gonen1,*, David Baker2,3,4,*"
- Places: (see link)
- Weblink (walled access): http://science.sciencemag.org/content/348/6241/1365.figures-only
- Open: https://cryoem.ucla.edu/uploads/image/pdfs/2015_gonen.pdf
Related
- This is part of Present-forward development as opposed to Future-backward development
- Incremental path
- Reached milestones in foldamer R&D
- Self folding
- covalent cross interlinking (increasing stiffness)
- POPs (persistant organic pollutants) -- See: "Soil pollutants"
- Microfluidics
External links
- Wikipedia: Foldamer
- Wikipedia: De_novo_protein_structure_prediction
- Wikipedia: PeptidomimeticPeptoidBeta-peptide
Video:
"Clasp: Common Lisp using LLVM and C++ for Molecular Metaprogramming" [1]
Published on Jun 15, 2015 – Google Tech Talk – June 9, 2015 – Presented by Christian Schafmeister.
This video also brings up topics like:
- The importance of stiffness – double linked backbones prevent rotations making resulting structures much easier to desing and more predictable
- Iterative design of early forms of Kaehler brackets
optimization of a stiff backbone to get functional groups as close as possible to a fixed predefined configuration (that may have been stolen from a natural protein) - General software issues – programming language limitations, the dreaded interface problem,
"deforresting" unnecessary computer algebra reevaluations (a problem also showing up in volumetric 3D modelling aka distance field based 3D modelling; Design levels),
the need for derivation towers (scalar,vector,tensor) (automatic derivation - links to Conal Elliotts work) - Going deep down the rabbit-hole to reach a far term target (in an highly non-obvious way for outsiders).
Sidenote: That's exactly where natural evolution has severe limitations. - Invention (and market introduction) of covalent protein crosslinking technology
- Bootstrapping of the synthesis of the fundamental spiroligomer building blocks
- The "indestructibility" of spiroligomers raise the issue of the waste problem with POPs (persistent organic pollutants) -- See: Recycling
- The suspected lignin pileup in the Carboniferous epoch of earths history.
- The talk doesn't look beyond towards gemstone based systems as far term goal. Partially brownian technology path?
