Biology subjects

zhou, k.

Publications and source records attributed to zhou, k..

3 recordsLinked to original sources

bioRxiv2025

Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction

In this technical report, we present Protenix, a comprehensive reproduction of AlphaFold3 (AF3), aimed at advancing the field of biomolecular structure prediction. Protenix tackles the challenges of predicting complex interactions involving proteins, ligands, and nucleic acids, while enhancing accessibility and reproducibility. Across diverse benchmarks, including PoseBusters V2, low-homology PDB sets, and CASP15 RNA, Protenix achieves state-of-the-art performance in protein-ligand, protein-protein, and protein-nucleic acid predictions. We also address limitations, such as potential memorization effects, and outline future directions for improvement. By open-sourcing Protenix, we aim to democratize advanced structure prediction tools and accelerate interdisciplinary research in computational biology and drug discovery.

bioinformatics↗

bioRxiv2022

Cryo-EM structure of amyloid fibril formed by α-synuclein familial A53E mutation

Synucleinopathies, including Parkinsons disease (PD), dementia with Lewy bodies (DLB), and multiple systems atrophy (MSA) have the same hallmark pathologic feature of misfolded -synuclein protein accumulation in the brain. PD patients who carry -syn hereditary mutations tend to have an earlier onset and more severe clinical symptoms and pathology than sporadic PD patients who carry wild-type (WT) -syn. Therefore, revealing the structural effect of -syn hereditary mutations on the wild-type fibril structure can help us understand synucleinopathies structural basis. Here, we present a 3.38 [A] cryo-electron microscopy structure of -synuclein fibrils containing the hereditary A53E mutation. The A53E fibril is symmetrically composed of two protofilaments, as are many other synucleopathic structures - including WT. Interestingly, the interface between the protofilaments in A53E has significantly less buried surface area than all other documented fibril structures of -syn and its other mutants. The A53E fibril also exhibits slower formation/growth in in vitro fibrillation experiment compared to other mutants. This implies that the structural differences - both in the protofilament and between each protofilament of A53E - change the aggregation mechanism, or in the least, its kinetics of formation. These differences influence the molecular characteristics of each fibril mutant and likely plays a macro-scale role in progressing one clinical pathology over another.

biophysics↗

bioRxiv2019

SKU5-Similar3 gene could be alternatively spliced into two variants at an unreported splicing site in Arabidopsis

Alternative splicing largely enhanced the diversity of transcriptome and proteome in eukaryas. Along with technical development, more and more alternatively splicing was demonstrated. Here, we report an unexpected alternative splicing of SKU5-Similar 3 (SKS3) within a special splicing site in Arabidopsis. Based on bioinformatics database, SKS3 was predicted to be alternatively transcribed into two variants, SKS3.1 and SKS3.2, which encoded a GPI-anchored protein and a soluble secretory protein respectively. But, instead of SKS3.2, a novel variant, SKS3.3, which encoded a protein with transmembrane region at its C-terminus, was demonstrated based on our experimental data. Interestingly, it exhibited a different organ-specific expression pattern from SKS3.1, and its intron splicing site did not follow GT-AG rule or any reported rules.

plant biology↗