Protein carpentry - Revision history

Apm: improvements

2026-04-26T08:15:39Z

improvements

@@ Line 20: / Line 20: @@
 * possibly even vacuum stability
-'''Difficult to compare trade-offs versus SDN: protein …'''
+'''Main disadvantaged compared to SDN:'''
 * primary structure (backbone & sidechains) is smaller than DNA (thus the much more dense attachment points)
 * secondary structure (local [[molecular motif]]s like alpha helices & beta sheets) – used for stiffness
@@ Line 28: / Line 37: @@
 Particularly of interest: Especially stiff classes of proteins <br>
 which reuse the secondary structure as the tertiary structure. <br>
 = Discovered branches =

Apm: /* Overview */

2026-04-26T08:11:22Z

Overview

← Older revision		Revision as of 10:11, 26 April 2026
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	The basic idea is to get something similar to [[Structural DNA nanotechnology]] (SDN) but with proteins.		The basic idea is to get something similar to [[Structural DNA nanotechnology]] (SDN) but with proteins.

	Most critical and most difficult being the attainment of		Most critical and most difficult being the attainment of <br>
	[[termination control]] and [[Hierarchical selfassembly]] on the [[upward and outward]] scaling aspect.		[[termination control]] and [[Hierarchical selfassembly]] on the [[upward and outward]] scaling aspect.

Apm at 08:09, 26 April 2026

2026-04-26T08:09:40Z

← Older revision		Revision as of 10:09, 26 April 2026
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	'''Main advantaged compared to SDN:'''		'''Main advantaged compared to SDN:'''
	* Hard to get decently large [[orthogonally binding sets of proteins]]		* Hard to get decently large [[orthogonally binding sets of proteins]]
	* The ~~doubel~~ edged sword of brick stiffness prevent gradual unzipping on faulty selfassembly increasing the difficulty of the fist point		* The double edged sword of brick stiffness prevent gradual unzipping on faulty selfassembly increasing the difficulty of the fist point
	* generic voxels assembly with termination control like with SDN still not achieved (as of 2026)		* generic voxels assembly with termination control like with SDN still not achieved (as of 2026)
	* de-novo protein interface design is challenging, but this got way better in recent years (as of 2026)		* de-novo protein interface design is challenging, but this got way better in recent years (as of 2026)

Apm at 08:08, 26 April 2026

2026-04-26T08:08:56Z

← Older revision		Revision as of 10:08, 26 April 2026
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	* possibly even vacuum stability		* possibly even vacuum stability

	'''Difficult to compare ~~tradeoffs~~: protein …'''		'''Difficult to compare trade-offs versus SDN: protein …'''
	* primary structure (backbone & sidechains) is smaller than DNA (thus the much more dense attachment points)		* primary structure (backbone & sidechains) is smaller than DNA (thus the much more dense attachment points)
	* secondary structure (local [[molecular motif]]s like alpha helices & beta sheets) – used for stiffness		* secondary structure (local [[molecular motif]]s like alpha helices & beta sheets) – used for stiffness

Apm: /* Discovered branches */

2026-04-26T08:08:20Z

Discovered branches

← Older revision		Revision as of 10:08, 26 April 2026
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	=== Just building blocks without side-chain functionalities ===		=== Just building blocks without side-chain functionalities ===

			Not yet [[downward and inward]]. Also barely [[upward & outwart]]. Just bare-bones beginning. <br>
	Funding issue: High cost & no near term economic value.		Funding issue: High cost & no near term economic value.

	=== Functional block construction kit approach ===		=== Functional block construction kit approach ===

	Main page: [[Functional block construction kit approach]]		Main page: [[Functional block construction kit approach]] <br>
			'''This one is especially important as [[APM:About\|this wikis author]] had experience within related startup.'''

	~~Basic "Protein LEGO":~~
	* Focus on binding/sensing not catalyzing		* Focus on binding/sensing not catalyzing
	* No active or passive motion here		* No active or passive motion here

Apm: /* Overview */ significant improvement and extension

2026-04-26T08:03:52Z

Overview: significant improvement and extension

← Older revision		Revision as of 10:03, 26 April 2026
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	= Overview =		= Overview =

	~~Basically getting~~ something similar to [[Structural DNA nanotechnology]] (SDN) but with proteins.		The basic idea is to get something similar to [[Structural DNA nanotechnology]] (SDN) but with proteins.

	Main advantaged compared to SDN:		Most critical and most difficult being the attainment of
			[[termination control]] and [[Hierarchical selfassembly]] on the [[upward and outward]] scaling aspect.

			There is also some focus on integration and increase of capabilities of functionalization <br>
			and slimbing the [[technology levels]] of increasingly advanced materials. <br>
			The [[downward and inward]] capability increase.

			'''Main advantaged compared to SDN:'''
	* higher stiffness (core backbone possibly even [[positionally atomically precise]] at 300K)		* higher stiffness (core backbone possibly even [[positionally atomically precise]] at 300K)
	* much higher density for functional attachment points		* much higher density for functional attachment points
	* possibly even vacuum stability		* possibly even vacuum stability

	~~difficult~~ to compare tradeoffs: protein …		'''Difficult to compare tradeoffs: protein …'''
	* primary structure (backbone & sidechains) is smaller than DNA (thus the much more dense attachment points)		* primary structure (backbone & sidechains) is smaller than DNA (thus the much more dense attachment points)
	* secondary structure (local [[molecular motif]]s like alpha helices & beta sheets) – used for stiffness		* secondary structure (local [[molecular motif]]s like alpha helices & beta sheets) – used for stiffness
Line 19:		Line 26:
	* qaternary structure (inter protein assembly) is larger than SDN voxels		* qaternary structure (inter protein assembly) is larger than SDN voxels

	Particularly ~~interesting (a especially~~ stiff) classes of proteins		Particularly of interest: Especially stiff classes of proteins <br>
	reuse the secondary structure as the tertiary structure		which reuse the secondary structure as the tertiary structure. <br>

			'''Main advantaged compared to SDN:'''
			* Hard to get decently large [[orthogonally binding sets of proteins]]
			* The doubel edged sword of brick stiffness prevent gradual unzipping on faulty selfassembly increasing the difficulty of the fist point
			* generic voxels assembly with termination control like with SDN still not achieved (as of 2026)
			* de-novo protein interface design is challenging, but this got way better in recent years (as of 2026)
			* more expensive production/syntehsis than DNA oligomers? May depend on the specifics.

	= Discovered branches =		= Discovered branches =

Apm at 07:49, 26 April 2026

2026-04-26T07:49:59Z

← Older revision		Revision as of 09:49, 26 April 2026
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	"Protein carpentry", term coined by Eric K Drexler. <br>		"Protein carpentry", term coined by Eric K Drexler. <br>
	High stiffness high symmetry protein construction kits. <br>		High stiffness high symmetry (high density functionalizabe) protein construction kits. <br>

	= Overview =		= Overview =

Apm: basic page

2026-04-26T07:49:10Z

basic page

New page

{{stub}}

"Protein carpentry", term coined by Eric K Drexler. 
High stiffness high symmetry protein construction kits. 

= Overview =

Basically getting something similar to [[Structural DNA nanotechnology]] (SDN) but with proteins.

Main advantaged compared to SDN:
* higher stiffness (core backbone possibly even [[positionally atomically precise]] at 300K)
* much higher density for functional attachment points
* possibly even vacuum stability

difficult to compare tradeoffs: protein …
* primary structure (backbone & sidechains) is smaller than DNA (thus the much more dense attachment points)
* secondary structure (local [[molecular motif]]s like alpha helices & beta sheets) – used for stiffness
* tertiary structure (protein shape) is similar or bigger) – used for geometry
* qaternary structure (inter protein assembly) is larger than SDN voxels

Particularly interesting (a especially stiff) classes of proteins
reuse the secondary structure as the tertiary structure

= Discovered branches =

== Basic protein LEGO ==

'''Just small sets of still small size [[orthogonally binding proteins]].''' 
Overall focus: [[Expanding the kinematic loop]] – [[downward and inward]].

=== Just building blocks without side-chain functionalities ===

Funding issue: High cost & no near term economic value.

=== Functional block construction kit approach ===

Main page: [[Functional block construction kit approach]]

Basic "Protein LEGO":
* Focus on binding/sensing not catalyzing
* No active or passive motion here

=== Catalysis construction kit approach ===

* Main page: [[Catalysis construction kit approach]] 

The Functional block construction kit approach but extended.
* aiming at not just binding/sensing but also catalysis
* possibly focus on passive or active motion here (role of actively driven motion on catalysis still contended in Sic community)

== Foldamer robot approach (incremental path) ==

Main page: [[Foldamer robot approach (incremental path)]] 
Overall focus: [[Expanding the kinematic loop]] – [[upward and outward]]. 

'''Aiming to scale capability to bigger sets of bigger size [[orthogonally binding proteins]] before focus on functionalization.''' 

Seems (2019 … 2026 …) this is gradually and accidentally happening in research that is 
not dedicatedly focused towards advanced [[APM]] i.e. not dedicatedly focused on 
usage of proteins to get beyond the material of just proteins ASAP.

== Advanced function carrying protein carpentry ==

For [[expanding the kinematic loop]] this
very pushingly and relatively early tries to combines:
The "[[upward and outward]]" and "[[downward and inward]]" scaling aspects.

=== Foldamer printer ===

Main page: [[Foldamer printer approach (incremental path)]]

A concept of xyz assembly satage like a 3D printer but simplifies by
site activation an flow in flush by feedstock to avert complexities of feedstock delivery and pickup.

Intended usage is in solution.
These devices may or may not be surface bound.

Challenges:
* Still way beyond current capabilities (2026)
* Way past suspense of disbelief of scientific community (experience 2019)

=== Modular molecular composite nanosystem ===
Main page: [[Modular molecular composite nanosystem]]

A distributed system of protein (foldamer) mechanisms. 
Most likely on a flat chip (but it could be surface anchored or free floating 3D aggregates too.

Flat on chip for:
– analytic access (e.g. confocal microscopy) 
– '''eventual pass-over to a [[mixed path]] that is critically dependent on flat on surface architectures''' 
… The direct path analog to join up with is the [[Early diamondoid nanosystem pixel (direct path)]] 

It may contain other foldamer techologies than just proteins. 
Eventually transitioning to better stiffer aterials up the [[technology levels]]. 

Some parts may eventually more or less resemble the precedingly described [[foldamer printers]].

Still in solution maybe transitioning to dry. 
[[SDN]] is mist likely breaking when dry so that would be out by then. 

= Related =

* [[Expanding the kinematic loop]]
----
* Turn left later: [[Foldamer robot approach (incremental path)]]
* Turn left here: [[Foldamer printer approach (incremental path)]]
* Turn left earlier: [[Catalysis construction kit approach]] & [[Functional block construction kit approach]]
* Diagram for these directions is here: [[Positional assembly redundancy blockade]]
----
* [[Incremental path]]
* [[Positional assembly]]
* [[Pathways]]

[[category:Incremental path]]