Synthetic nanomaterials from standardized protein blocks

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Revision as of 18:11, 10 February 2025

In March, 2024, Huddy, Hsia, Kibler, Xu et al. in the team of David Baker (subsequently a Nobel Laureate) published a wide range of synthetic protein nanostructures self-assembled from standardized, engineered alpha-helical protein "building blocks"^[1] (). The extensively documented report, in Nature, has 32 authors^[1].

The breakthrough here is that instead of designing a single "one-off" desired nanostructure, the Baker group has first designed a series of regular building blocks that can be assembled into diverse nanostructures using straightforward geometric principles. These now enable "construction of protein nanomaterials according to ‘back of an envelope’ architectural blueprints"^[1]. There are many potential applications, such as drug delivery or catalysis, which remain to be explored. For example, in 2025 Brunette et al. (Baker lab)^[2] reported a multivalent ebola virus vaccine synthetic, self-assembling nanoparticle producing immunity in mice to two kinds of ebola virus.

1 Building Blocks
- 1.1 Twistless helix repeat blocks
- 1.2 Five examples of building blocks
2 Assemblies
3 PDB Files

Building Blocks

Twistless helix repeat blocks

Click the green links below to change the molecular scene. Rotate to view the molecule from all sides (drag to rotate). Zoom with your mouse wheel, or Shift-Drag up/down.

In this project, the simplest building blocks consist of anti-parallel alpha helices engineered to be straight and flat, that is twistless helix repeat (THR) protein blocks. A simple example, THR1, is 8g9j, consisting of ^[3]. Each helix is amphipathic, that is, hydrophobic on the side contacting other helixes, and hydrophilic on the side facing outwards (not shown). The 2.5 Å resolution of 8g9j enabled the modeling of all helix side chains. Non-covalent interactions between helices are nearly all apolar, with a few hydrogen bonds, and two salt bridges (not shown). The , making a highly water soluble building block. The edges of the block are "capped" with charges that prevent these blocks from binding to each other, thus enabling crystallization of this block rather than having it precipitate.

The sequences and binding interfaces of building blocks were designed using Rosetta FastDesign and mainly ProteinMPNN^[4]^[5]^[6]. Designed sequences were filtered according to likelihood of desired folding and assembly as predicted by AlphaFold2.

33 linear THRs were tested. 23 were solubly expressed. Of 19 characterized by size exclusion chromatography, 13 were primarily monomeric^[1].

Five examples of building blocks

Dozens of types of building blocks were designed, synthesized, purified, and their structures and assemblies were determined^[1]. ^[7].

Assemblies

Building blocks were designed with precise angles, and with specific points of attachment between blocks. Most self-assembled into the predicted assemblies. The size of the final assembly can be controlled by the number of helices and their lengths in the building blocks. Examples of assemblies include^[8]:

Flat Assemblies

(120_C3_A_design, branch 60°).
(90_C4_A_design, 90°).
(72_C5_A_design, 108°).
(R20A_design).
(strut_C6_21_cryo_fit).
(strut_C6_16_design). Here, the .

Cage Assemblies

Synthetic genes were obtained for 13 nanocage designs; all 13 expressed solubly. Cryo-EM models of seven were symmetric cages resembling the design models^[1]. These included:

(cage_T3_5_+2_design).
(8TL7, 4.1 Å cryo-EM).
(cage_O4_32_design).
(8v2d, 6.8 Å cryo-EM, the initial scene). Here, the .

Inter-Chain Adhesions

In , each chain (block) adheres to three other chains. . The exposed surface of each chain is covered with a mixture of positive + and negative – charges.
Here are four chains in greater detail:

When you hide the three dark colored chains, you will see that they adhere to hydrophobic patches devoid of charges. However, the charges on the edges of these patches may facilitate adhesion.

Animated simulation of self-assembly

This simulation is crude and very oversimplified ... but heuristic, and hopefully fun to watch.

Alternatively, you can click the link below to get the interactive (rotatable, zoomable, and enlargable) simulation.
Please be patient ... Loading this animation may take up to 30 seconds.

The Toggle Animation button works only for the interactive animation in JSMol.

The popout button does not work for this animation.

PDB Files

PDB files for the nano structures illustrated above are available in the supplementary materials of Huddy et al., 2024^[1], or below. PDB files obtained from Huddy et al., 2024 or derived from those files are re-distributed here under the terms of the original Creative Commons Attribution 4.0 International License.

8v2b cubic cage with ring faces, 48 blocks, alpha carbons only Image:Huddy2024-8v2d-cao.pdb.gz
Simple twistless helix repeat block THR1 8g9j
Five examples of building blocks in a single PDB file Image:Huddy2024-5-building-blocks.pdb
Triangle Image:Huddy2024-triangle-60deg-120-c3-a.pdb.gz
Square Image:Huddy2024-square-90-c4-a.pdb.gz
Pentagon Image:Huddy2024-pentagon-108deg-72-c5-a.pdb.gz
Circle Image:Huddy2024-circle-r20a.pdb.gz
Concentric circles with struts, six blocks Image:Huddy2024-concentric-6pcs-strut-c6-21-cryofit.pdb.gz
Concentric circles with struts, 12 blocks Image:Huddy2024-concentric-12pcs-strut-c6-16.pdb.gz
Tetrahedron A Image:Huddy2024-tetrahedron-cage-t3-5-plus2.pdb.gz
Tetrahedron B 8tl7, alpha carbons only Image:Huddy2024-8tl7-cao.pdb. Four chains IUXY Image:Huddy2024-8tl7-iuxy.pdb.gz.
Cube with no vertices Image:Huddy2024-cube-noverts-cage-o4-32.pdb.gz used in the assembly simulation.
Simulation of self assembly ((60 models) Image:Huddy-cage-o4-32-assembly-morf.pdb.gz

Method of simulating assembly

The cage model (Cube with no vertices Image:Huddy2024-cube-noverts-cage-o4-32.pdb.gz) has about 272,000 atoms including hydrogens. It was simplified to alpha carbon atoms only (17,256) using the Jmol.jar Java application using Jmol commands "select *.ca; write 0.pdb;". The assembled cage has 24 protein chains.

In Jmol.jar, 4 chains were dragged out of the assembly to the periphery of the viewport, and each was rotated arbitrarily using the Jmol setting "set picking dragmolecule" (holding down Alt enables rotation). The resulting state was written into a PDB file.

Repeating this drag/rotate save process six times produced a final model in which none of the protein chains were in their original assembled positions. This resulted in six PDB files 1.pdb, ... 6.pdb.

The linear morph server by Karsten Theis was used on each pair of PDB files to morph in reverse (towards assembly), producing six morphs 6->5, 5->4, ... 1->0 (where 0 is the fully assembled cube).

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Weidle C, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, Han HL, Carr KD, Li Z, McHugh R, Reggiano G, Kang A, Sankaran B, Dickinson MS, Coventry B, Brunette TJ, Liu Y, Dauparas J, Borst AJ, Ekiert D, Kollman JM, Bhabha G, Baker D. Blueprinting extendable nanomaterials with standardized protein blocks. Nature. 2024 Mar;627(8005):898-904. PMID:38480887 doi:10.1038/s41586-024-07188-4
↑ Brunette et al. (David Baker lab), [https://doi.org/10.1101/2025.01.29.635581 A Multivalent Pan-Ebolavirus Nanoparticle Vaccine Provides Protection in Rodents from Lethal Infection by Adapted Zaire and Sudan Viruses], bioRXiv Preprint, February, 2005.
↑ An amino-terminal histidine tag was not resolved in the electron density map of 8g9j, and thus is missing in the structure depicted.
↑ de Haas RJ, Brunette N, Goodson A, Dauparas J, Yi SY, Yang EC, Dowling Q, Nguyen H, Kang A, Bera AK, Sankaran B, de Vries R, Baker D, King NP. Rapid and automated design of two-component protein nanomaterials using ProteinMPNN. Proc Natl Acad Sci U S A. 2024 Mar 26;121(13):e2314646121. PMID:38502697 doi:10.1073/pnas.2314646121
↑ Sumida KH, Núñez-Franco R, Kalvet I, Pellock SJ, Wicky BIM, Milles LF, Dauparas J, Wang J, Kipnis Y, Jameson N, Kang A, De La Cruz J, Sankaran B, Bera AK, Jiménez-Osés G, Baker D. Improving Protein Expression, Stability, and Function with ProteinMPNN. J Am Chem Soc. 2024 Jan 9. PMID:38194293 doi:10.1021/jacs.3c10941
↑ Dauparas J, Anishchenko I, Bennett N, Bai H, Ragotte RJ, Milles LF, Wicky BIM, Courbet A, de Haas RJ, Bethel N, Leung PJY, Huddy TF, Pellock S, Tischer D, Chan F, Koepnick B, Nguyen H, Kang A, Sankaran B, Bera AK, King NP, Baker D. Robust deep learning-based protein sequence design using ProteinMPNN. Science. 2022 Sep 15:eadd2187. doi: 10.1126/science.add2187. PMID:36108050 doi:http://dx.doi.org/10.1126/science.add2187
↑ The five modules shown are from the following assemblies that can be downloaded as PDB files from supplementary materials of Huddy et al,, 2024: 90° from strut_C6_16. Branch from TT_rail+_tie+. Curve from R20A. Handshake 90° from cage_O4_32. Handshake obtuse angle from cage_I3_8.
↑ The assemblies shown can be downloaded as PDB files from supplementary materials of Huddy et al,, 2024.
↑ Wang S, Favor A, Kibler R, Lubner J, Borst AJ, Coudray N, Redler RL, Chiang HT, Sheffler W, Hsia Y, Li Z, Ekiert DC, Bhabha G, Pozzo LD, Baker D. Bond-centric modular design of protein assemblies. bioRxiv [Preprint]. 2024 Oct 12:2024.10.11.617872. PMID:39416012 doi:10.1101/2024.10.11.617872

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

Retrieved from "http://52.214.119.220/wiki/index.php/Synthetic_nanomaterials_from_standardized_protein_blocks"

@@ Line 112: / Line 112: @@
 </StructureSection>
 ==Method of simulating assembly==
-The cage model (Cube with no vertices [[Image:Huddy2024-cube-noverts-cage-o4-32.pdb.gz]]) has about 272,000 atoms including hydrogens. It was simplified to alpha carbon atoms only (17,256) using the [[Jmol/Application|Jmol.jar Java application]]. The assembled cage has 24 protein chains. In Jmol.jar, 4 chains were dragged out of the assembly to the periphery of the viewport, and each was rotated arbitrarily.
+The cage model (Cube with no vertices [[Image:Huddy2024-cube-noverts-cage-o4-32.pdb.gz]]) has about 272,000 atoms including hydrogens. It was simplified to alpha carbon atoms only (17,256) using the [[Jmol/Application|Jmol.jar Java application]] using Jmol commands "select *.ca; write 0.pdb;". The assembled cage has 24 protein chains.
+#In Jmol.jar, 4 chains were dragged out of the assembly to the periphery of the viewport, and each was rotated arbitrarily using the Jmol setting "set picking dragmolecule" (holding down Alt enables rotation). The resulting state was written into a PDB file.
+#Repeating this drag/rotate save process six times produced a final model in which none of the protein chains were in their original assembled positions. This resulted in six PDB files 1.pdb, ... 6.pdb.
+# The [https://www.bioinformatics.org/pdbtools/morph2 linear morph server by Karsten Theis] was used on each pair of PDB files to morph in reverse (towards assembly), producing six morphs 6->5, 5->4, ... 1->0 (where 0 is the fully assembled cube).
 ==See Also==
 *Related work from the Baker group includes <i>Bond-centric modular design of protein assemblies</i> by Wang <i>et al.</i>, 2024<ref name="wang">PMID: 39416012</ref>.

Synthetic nanomaterials from standardized protein blocks

From Proteopedia

Revision as of 18:11, 10 February 2025

Contents

Building Blocks

Twistless helix repeat blocks

Five examples of building blocks

Assemblies

Flat Assemblies

Cage Assemblies

Inter-Chain Adhesions

Animated simulation of self-assembly

PDB Files

Method of simulating assembly

See Also

References

Proteopedia Page Contributors and Editors (what is this?)

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