Shi Yigong and other teams posted on the cover of Science: AI and freeze electron microscope revealed the structure of "atomic level" NPC, a breakthrough in life science

Almost Human reports

edit ： Du Wei 、 Chen Ping

Today, ,《Science》 The magazine published in the form of a cover story 5 Papers , Together, it shows that through AI Technology to reveal the nuclear pore complex of human and Xenopus laevis （NPC） structure .

 

Before you start the text , Let's take a look at a picture first , In the following illustration , It is obvious that , The information represented by the right half of the figure is more abundant , The structure is clearer . And the left half 2016 Year map , The structure is relatively simple , There is less information on behalf of ：

In fact, what is shown above is the nuclear pore complex （NPC） Images . Nuclear pore complex , By about 1000 Protein subunits , It is responsible for the busy transportation of macromolecules between the nucleus and cytoplasm of eukaryotes , It is also the only two-way channel connecting cytoplasm and nucleus . In addition to coordinating transportation ,NPC It also organizes the necessary transcription 、mRNA mature 、 Splicing and ribosome assembly are important life activities .NPC Powerful role , Has become a disease mutation and host - The key point of pathogen interaction .

Thanks to the development of full nuclear pore structure at low resolution and nuclear pore composition structure at high resolution , More and more attention has been paid to the nuclear pore . However , Use this information to assemble correctly 30 Multiple copies of different proteins , And build a high-resolution three-dimensional structure , It has always been a difficult challenge .

today ,《Science》 The magazine published as a cover story 5 Papers , among 3 This paper jointly revealed the structure of the human nuclear pore complex in the near atomic resolution freeze electron microscope , The other two studies presented single particle freeze electron microscopic images of the vertebrate nuclear pore complex through Xenopus laevis . This cover article stitches together a number of research findings , Formed human beings NPC The image is close to atomic level .

 

Address of thesis ：https://www.science.org/doi/pdf/10.1126/science.add2210

This research is based on a number of studies , Including decades of biochemical reconstruction 、X Ray crystallography 、 Mass spectrometry 、 Mutagenesis and cell biology . Reconstruction of human using a substantially improved frozen electron tomography NPC, And use artificial intelligence technology to accurately model components . Other studies have improved the resolution of single particle cryoelectron microscopy , Make vertebrates NPC Visualization of secondary structural elements and residue level details of . Molecular assemblages enrich our understanding of vertebrates and humans NPC Build understanding —— From the old nuclear scaffold to the connexin that holds the parts together , And the cytoplasmic filament anchored from the nuclear membrane to the upper part of the central transport channel .

The research results reported here , It represents the win-win cooperation between experimental structural biology and artificial intelligence , It is another victory for human beings to explore the biological micro world . in addition , It also proves the ongoing resolution revolution , In our quest to understand the construction and design principles of macromolecular components , Have an irreplaceable function .

The following figure for 2022 Cross sectional view of the human nuclear pore complex in , The newly parsed components include symmetric cores （ Orange ） And cytoplasmic filaments （ yellow ）：

Five research papers

The paper 1：《Architecture of the cytoplasmic face of the nuclear pore》

Address of thesis ：https://www.science.org/doi/10.1126/science.abm9129

Nuclear pore complex （NPC） It is the only two-way channel for nuclear and cytoplasmic transport . Although recently it has been clarified that NPC Some progress has been made in symmetrical core structure , But for the mRNA Export and Nucleoporin related diseases are hot spots , The asymmetric distribution of the cytoplasmic surface remains elusive .

Researchers at the California Institute of technology and other institutions have reported that by combining biochemical reconstruction 、 Determination of crystal structure 、 The composite structure of the human cytoplasmic plane obtained from the reconstruction of cryoelectronic tomography and physiological verification . Although species-specific motifs anchor an evolutionarily conserved motif above the central transport pathway 、 about 540 Thousand daltons （kilodalton） Heterohexamer cytoplasmic filament Nucleoporin complex , but NUP358 The attachment of pentamer bundles depends on the double ring arrangement of the mantle Nucleoporin complex . The composite structures they reveal and their predictive power are illustrative mRNA The molecular basis of export and Nucleoporin disease provides a rich basis .

human beings NPC The cytoplasmic surface of .

The paper 2：《Architecture of the linker-scaffold in the nuclear pore》

Address of thesis ：https://www.science.org/doi/10.1126/science.abm9798

Although one can already be certain NPC Arrangement of structural scaffold Nucleoporin in symmetric core , However, their cohesiveness through multivalent unstructured linker Nucleoporin remains elusive .

By combining biochemical reconstruction 、 High resolution structure determination 、 Cryoelectronic tomography reconstruction and physiological verification , Researchers at the California Institute of technology have elucidated the evolutionarily conservative joint scaffold structure , Human beings were born NPC About 64 Megadalton （megadalton） Symmetric near atomic compound nuclei . Although joints are usually rigid , but NPC The connector bracket of the utility model provides the necessary plasticity and robustness for the reversible contraction and expansion of the central transport channel and the emergence of the transverse channel . Their results have greatly advanced NPC Structural characterization of symmetric cores , It lays a foundation for future functional research .

human beings NPC Symmetrical core joint support structure .

The paper 3：《AI-based structure prediction empowers integrative structural analysis of human nuclear pores》

 

Address of thesis ：https://www.science.org/doi/10.1126/science.abm9506

Although the nuclear pore complex （NPC） Mediate nucleocytoplasmic transport , They are intricate 120 The mega Dalton architecture is not yet fully understood . Marx · Researchers from Planck Institute of Biophysics and other institutions have reported that humans with explicit membrane and multi conformational states NPC Support 70 Megadalton model .

They will be based on AI The structure was predicted with in situ and cell freeze electron tomography 、 Integrated modeling . It turns out that , Junctional Nucleoporin in subcomplex and intercomplex tissue scaffold , To establish a higher-order structure . Microsecond molecular dynamics simulations show that , The scaffold does not need to stabilize the fusion of inner and outer nuclear membranes , Instead, enlarge the center hole . They give examples of how to base AI The modeling is combined with in situ structural biology , To understand the subcellular structure at the level of cross spatial organization .

human beings NPC Support structure 70 Megadalton model .

The paper 4：《Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex》

Address of thesis ：https://www.science.org/doi/10.1126/science.abl8280

West Lake University and Tsinghua University 3.7-4.7 Egyptian （angstrom） The resolution of Xenopus laevis NPC Single particle cryoelectron microscopy reconstruction of the cytoplasmic cyclic subunits . among ,Nup358 The structure of the amino terminal domain of is resolved as 3.0 Egyptian , This helps to identify five of each cytoplasmic cyclic subunit Nup358 molecular .

The researchers' final model of the cytoplasmic cyclic subunit includes five Nup358、 Two Nup205 And two Nup93 molecular , And two previously characterized Y complex .Nup160 The carboxyl terminal fragment of each Y The organizational center at the apex of the complex . Structural analysis reveals Nup93、Nup205 and Nup358 How to promote and strengthen mainly consists of two layers Y Assembly of the cytosolic ring scaffold formed by the complex .

Xenopus Laevis NPC Of a double cytoplasmic ring Cryo-EM structure .

The paper 5：《Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold》

 

Address of thesis ：https://www.science.org/doi/10.1126/science.abm9326

Researchers at Harvard Medical School and other institutions used single particle cryoelectron microscopy and AlphaFold forecast , Almost complete oocytes were identified from Xenopus laevis oocytes NPC Cytoplasmic ring structure . In particular , They use AlphaFold Predict the structure of Nucleoporin , And use the prominent secondary structure density as a guide to adapt to the medium resolution map .

Besides , Some molecules interact by using AlphaFold The complex prediction of is further established or confirmed . The researchers identified five Nup358 The combination mode of , It's the biggest NPC Subunits , Have... For transshipment Phe-Gly Repetitive sequence . They predicted Nup358 Contains a coiled coil domain , It can provide activity to help it function under certain conditions NPC Nucleation centers formed .

Xenopus Laevis NPC Of the cytoplasmic ring Cryo-EM structure .