Peppytides: 3D printed, scaled, foldable model of the polypeptide chain for protein folding
Created by
Dr. Promita Chakraborty
Created:
7/1/15
Submitted:
3/6/23
Published:
3/6/23
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Category
Description
For a brief History of invention, Citation details and Contact details, please refer to Attribution.
Peppytide is a scaled, flexible protein model to explore protein folding with hands. It is a 3D printed, physical model with a scaling factor of 1A=0.3676", and focuses on accuracy of scale and dynamic behavior of protein chains. With assembly instructions provided, build an accurate, scaled 3D-model of a polypeptide chain that can be folded into all the basic protein secondary structures, like α-helices, β-sheets, and β-turns. Small tertiary structures can also be made with Peppytides. I have explored folding into beta-beta-alpha motif and fish osteocalcin with Peppytides. The model is made by linking together many 3D-printed molecular subunits with a series of precisely placed magnets and screws. Once built, the Peppytide chain faithfully reproduces the size, shape and flexibility of proteins. When it is carefully folded into the protein helix and sheet structures, the model becomes locked in by all the hydrogen-bond magnets and bond-bias magnets, and becomes rigid as alpha helix and beta sheet should be, thus demonstrating how a floppy, flexible chain can fold into stable structures. Peppytide enables a great way to learn about protein folding and protein structures.
The model consists of three repeating elements: an amide unit, an alpha carbon unit and a side chain methyl unit, and is a poly-alanine chain. All .STL files are provided for each of these parts, holders for drilling and assembly, and helix-folding template. I have all the .STL files optimally positioned for best resolution along Z-axis of 3D-printer. These parts require assembly and access to a drill press and basic tools. For more information on how to assemble these parts into the final model, please go to http://www.peppytides.org
Citation:
Promita Chakraborty, A Computational Framework for Interacting with Physical Molecular Models of the Polypeptide Chain, PhD Dissertation, Virginia Tech., 2014
For later versions, please go to http://www.peppytides.org
If you have made a model and would like to contact Promita to send a picture or to collaborate, contact details can be found at http://www.peppytides.org
Most recent collaboration:
https://www.youtube.com/watch?v=POk2iETe0OE
Title: Peppytide as a tangible molecular interface based on camera-tracking
Commercialization info: http://www.quezylab.com/
a super accurate, scaled 3D-model of a polypeptide chain that can be folded into all the basic protein structures, like α-helices, β-sheets, and β-turns. The model, called a Peppytide, is made by linking together many 3D-printed molecular subunits with a series of precisely placed magnets and screws. Once built, the Peppytide chain faithfully reproduces the size, shape and flexibility of proteins. When it is carefully folded into the protein helix and sheet structures, the model becomes locked in by all the magnets and becomes quite rigid. A great way to learn about protein folding and protein secondary structures!
The model consists of three repeating elements: an amide unit, an alpha carbon unit and a side chain methyl unit. There is a separate stl file provided for each of these parts. These parts require assembly and access to a drill press and basic tools is required. For more information on how to assemble these parts into the final model, please see the following article: http://makezine.com/projects/peppytide
- See more at: http://3dprint.nih.gov/discover/3dpx-000914#sthash.Ry6z3Sv4.dpufBuild a super accurate, scaled 3D-model of a polypeptide chain that can be folded into all the basic protein structures, like α-helices, β-sheets, and β-turns. The model, called a Peppytide, is made by linking together many 3D-printed molecular subunits with a series of precisely placed magnets and screws. Once built, the Peppytide chain faithfully reproduces the size, shape and flexibility of proteins. When it is carefully folded into the protein helix and sheet structures, the model becomes locked in by all the magnets and becomes quite rigid. A great way to learn about protein folding and protein secondary structures!
The model consists of three repeating elements: an amide unit, an alpha carbon unit and a side chain methyl unit. There is a separate stl file provided for each of these parts. These parts require assembly and access to a drill press and basic tools is required. For more information on how to assemble these parts into the final model, please see the following article: http://makezine.com/projects/peppytide
- See more at: http://3dprint.nih.gov/discover/3dpx-000914#sthash.Ry6z3Sv4.dpufBuild a super accurate, scaled 3D-model of a polypeptide chain that can be folded into all the basic protein structures, like α-helices, β-sheets, and β-turns. The model, called a Peppytide, is made by linking together many 3D-printed molecular subunits with a series of precisely placed magnets and screws. Once built, the Peppytide chain faithfully reproduces the size, shape and flexibility of proteins. When it is carefully folded into the protein helix and sheet structures, the model becomes locked in by all the magnets and becomes quite rigid. A great way to learn about protein folding and protein secondary structures!
The model consists of three repeating elements: an amide unit, an alpha carbon unit and a side chain methyl unit. There is a separate stl file provided for each of these parts. These parts require assembly and access to a drill press and basic tools is required. For more information on how to assemble these parts into the final model, please see the following article: http://makezine.com/projects/peppytide
- See more at: http://3dprint.nih.gov/discover/3dpx-000914#sthash.Ry6z3Sv4.dpuf