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Peilong Lu Published the First Ever De Novo-Designed Transmembrane Pores on Nature

Qi XU, Tianyu LUAN
16, 2020

PRESS INQUIRIES Yi FENG
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Peilong Lu, principal investigator at School of Life Sciences and his team at Westlake University published their latest research paper, Computational Design of Transmembrane Pores on Nature, in joint effort with the team of Prof. Bill Catterall and Prof. David Baker from Washington University. This is the first project that succeeded in the de novo design of transmembrane protein. 


In this study, Lu Peilong’s laboratory and the cooperative team successfully designed two transmembrane proteins made up by two concentric rings of α-helices (figure 1), which can selectively permeate solutes with different molecular sizes and charges.


Figure 1. Structure models of the transmembrane proteins composed of two concentric rings of α-helices


Patch-clamp electrophysiology experiments show that the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore – but not the 12-helix pore – enables the passage of fluorophores with a molecular weight of about 1000 Daltons. In other words, these pores could work as sieves: molecules would be allowed to pass when they match the size of the pore. This is also consistent with the respective pore sizes of the two pore-containing proteins. Researchers also solved the cryo-electron microscopy structure of the 16-helix transmembrane pore and found it closely matched with the design model, and hence proved the accuracy of the de novo design approach.


Figure 2. The 3D structure model of the 16-helix transmembrane pore designed in this research


This is the first ever de novo designed transmembrane pore, which will help us better understand the cell transport across membrane, that is, the basic principle of substance exchange in cells during metabolism and other life activities. It laid a solid foundation for the artificial design of transmembrane proteins with important functions.


This also opens the door to possible subsequent applications of artificial proteins, and is expected to provide new methods for DNA nanopore sequencing, molecular sensing and other biotechnologies. For example, we can artificially design protein nanopores with special channel structures which can be applied to nanopores sequencing technology and improve the accuracy of DNA nanopore sequencing; another application would be the artificial design of new ligand-gated channel proteins, which could help to build sensors for small molecules.


Protein design is at the core of synthetic biology and an emerging frontier. De novo protein design can explore the entire protein sequence space and offer brand new structures and functions starting from the first principles of biophysics and biochemistry, independently from any existing natural protein. Compared with proteins evolved in nature, artificially designed proteins can better meet with specific needs.


Lu has been devoted to the field of protein design. Back in 2018, he came up with the precise design of the 3D structure of polytopic transmembrane proteins, proving that the computer-designed protein sequence could fold spontaneously in the membrane environment to form a stable 3D structure consistent with the design (the research was published on Science: https://science.sciencemag.org/content/359/6379/1042). The recent paper published on Nature is the latest breakthrough based on previous research results.


Figure 3. Peilong Lu and transmembrane Nanopore model


The challenge is that transmembrane pore-containing protein/channel proteins are membrane proteins with a larger specific surface area and relatively low density of intramolecular interactions. This makes it more difficult to design transmembrane pores from scratch. Another challenge lies with how to realize the functions of selective ion transport and small molecule permeability based on the structure of transmembrane pore-containing protein. In other words, the hard nut to crack in this research is to design the amino acids sequence to spontaneously form specific pore-containing proteins, so that the proteins, in its tiny size, would fold into specific structures and have certain transport functions.


Lu’s team at Westlake University will continue to explore protein design and develop protein tools that do not exist in nature to meet the needs of biotechnology and biomedicine.


The corresponding authors of the paper are Peilong Lu, principal investigater at School of Life Sciences at Westlake University, Professor William A. Catteral and Professor David Baker from Washington University, joining by Chunfu Xu, Postdoc at Washington University and Lu as first authors. Researchers from Osaka University and Cambridge University also contributed to the project. 


To access the paper, please visit https://www.nature.com/articles/s41586-020-2646-5


This research is supported by High Performance Computing Platform, Westlake University, specially from cryo-EM platform and mass spectrum platform. The research is sponsored by National Natural Science Foundation of China, Westlake University and Tencent Foundation.