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De novo design of light-responsive protein–protein interactions enables reversible formation of protein assemblies

Light-responsive proteins hold significant potential in biotechnology but naturally occurring examples are scarce and limited in diversity. Now a totally de novo computational approach has been developed to design light-responsive proteins with diverse architectures by precisely incorporating the non-canonical amino acid phenylalanine-4′-azobenzene (AzoF), which is responsive to light.

Bowen Yu
Jiao Liu
Longxing Cao
Research28 Aug 2025
Nature Chemistry

Volume: 17, P: 1910-1919
PTM-Mamba: a PTM-aware protein language model with bidirectional gated Mamba blocks

PTM-Mamba is a post-translational modification-aware protein language model that integrates PTM tokens with bidirectional Mamba blocks and ESM-2 embeddings, enabling modeling of both wild-type and post-translationally modified sequences for diverse downstream applications.

Fred Zhangzhi Peng
Chentong Wang
Pranam Chatterjee
ResearchOpen Access10 Apr 2025
Nature Methods

Volume: 22, P: 945-949
Knocking out OsPht1;9-1;10 genes decreases arsenic accumulation in rice (Oryza sativa) grains

A study provides mechanistic insights into the roles of phosphate transporters OsPht1;9 and OsPht1;10 in arsenic uptake and accumulation in rice and highlights their potential for enhancing food security.

Huayuan Feng
Chentong Chen
Rongliang Qiu
ResearchOpen Access26 Feb 2026
Communications Biology

Volume: 9, P: 1-11
A gain-of-function TPC2 variant R210C increases affinity to PI(3,5)P₂ and causes lysosome acidification and hypopigmentation

TPC2 is an important organellar Na⁺/Ca²⁺ release channel which regulates function of lysosomes and lysosome-related organelles. Here, Wang et al. demonstrate that a gain-of-function mutation (R210C) in TPC2 leads to hypopigmentaion, enlarged endolysosomes, enhanced lysosomal Ca²⁺ release and hyper-acidification.

Qiaochu Wang
Zengge Wang
Wei Li
ResearchOpen Access14 Jan 2023
Nature Communications

Volume: 14, P: 1-16
Liver-specific deletion of Eva1a/Tmem166 aggravates acute liver injury by impairing autophagy

Xin Lin
Ming Cui
Yingyu Chen
ResearchOpen Access10 Jul 2018
Cell Death & Disease

Volume: 9, P: 1-12
Deletion of Pdcd5 in mice led to the deficiency of placenta development and embryonic lethality

Ge Li
Chentong Xu
Yingyu Chen
ResearchOpen Access25 May 2017
Cell Death & Disease

Volume: 8, P: e2811
Monocytic myeloid-derived suppressive cells mitigate over-adipogenesis of bone marrow microenvironment in aplastic anemia by inhibiting CD8⁺ T cells

Ying Qu
Zhengxu Sun
Tong Chen
ResearchOpen Access18 Jul 2022
Cell Death & Disease

Volume: 13, P: 1-14
CRMP2 derived from cancer associated fibroblasts facilitates progression of ovarian cancer via HIF-1α-glycolysis signaling pathway

Yunfeng Jin
Saiyan Bian
Hua Jiang
ResearchOpen Access04 Aug 2022
Cell Death & Disease

Volume: 13, P: 1-13
ZEB2 facilitates peritoneal metastasis by regulating the invasiveness and tumorigenesis of cancer stem-like cells in high-grade serous ovarian cancers

Yiying Li
He Fei
Hua Jiang
ResearchOpen Access01 Jul 2021
Oncogene

Volume: 40, P: 5131-5141
Knockout of MARCH2 inhibits the growth of HCT116 colon cancer cells by inducing endoplasmic reticulum stress

Dan Xia
Wanli Ji
Yingyu Chen
ResearchOpen Access27 Jul 2017
Cell Death & Disease

Volume: 8, P: e2957
TMEM166/EVA1A interacts with ATG16L1 and induces autophagosome formation and cell death

Jia Hu
Ge Li
Yingyu Chen
ResearchOpen Access04 Aug 2016
Cell Death & Disease

Volume: 7, P: e2323

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De novo design of light-responsive protein–protein interactions enables reversible formation of protein assemblies

PTM-Mamba: a PTM-aware protein language model with bidirectional gated Mamba blocks

Knocking out OsPht1;9-1;10 genes decreases arsenic accumulation in rice (Oryza sativa) grains

A gain-of-function TPC2 variant R210C increases affinity to PI(3,5)P₂ and causes lysosome acidification and hypopigmentation

Liver-specific deletion of Eva1a/Tmem166 aggravates acute liver injury by impairing autophagy

Deletion of Pdcd5 in mice led to the deficiency of placenta development and embryonic lethality

Monocytic myeloid-derived suppressive cells mitigate over-adipogenesis of bone marrow microenvironment in aplastic anemia by inhibiting CD8⁺ T cells

CRMP2 derived from cancer associated fibroblasts facilitates progression of ovarian cancer via HIF-1α-glycolysis signaling pathway

ZEB2 facilitates peritoneal metastasis by regulating the invasiveness and tumorigenesis of cancer stem-like cells in high-grade serous ovarian cancers

Knockout of MARCH2 inhibits the growth of HCT116 colon cancer cells by inducing endoplasmic reticulum stress

TMEM166/EVA1A interacts with ATG16L1 and induces autophagosome formation and cell death

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