Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study DOI Creative Commons
Sebastian Bittrich, Alexander Rose, David Sehnal

и другие.

Protein Science, Год журнала: 2025, Номер 34(4)

Опубликована: Март 18, 2025

Abstract The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three‐dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed RCSB Protein Data Bank (RCSB PDB, RCSB.org ) in Europe (PDBe, PDBe.org as an open‐source, web‐based, 3D software suite for examination analyses biostructures. It capable displaying atomic coordinates related experimental data biomolecular together variety annotations, facilitating basic applied research, training, education, information dissemination. Across , the PDB research‐focused web portal, has been implemented support single‐mouse‐click atomic‐level (e.g., proteins, nucleic acids, carbohydrates) bound cofactors, small‐molecule ligands, ions, water molecules, other macromolecules. can seamlessly display from various sources, allowing structure interrogation, superimposition, comparison. Using influenza A H5N1 virus topical case study important pathogen, we exemplify how embedded within tools—allowing users view polymer sequence structure‐based annotations integrated trusted bioinformatics resources, assess patterns trends groups structures, any size compositional complexity. In addition being linked every biostructure Computed Structure Model made available at Standalone freely visualizing multi‐scale rcsb.org/3d-view .

Язык: Английский

Discovery of widespread activating mutations in a compact RNA-guided endonuclease DOI Creative Commons
Brittney W. Thornton, Rachel F. Weissman,

Ryan Tran

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 12, 2025

TnpB is an evolutionarily diverse family of RNA-guided endonucleases associated with prokaryotic transposons. Due to their small size and putative evolutionary relationship Cas12s, holds significant potential for genome editing mechanistic exploration. However, most TnpBs lack robust gene-editing activity, unbiased profiling mutational effects on activity has not been experimentally explored. Here, we mapped comprehensive sequence-function landscapes a ribonucleoprotein discovered many activating mutations in both the protein RNA. Single-position changes RNA outperform existing variants, highlighting utility systematic scaffold mutagenesis. Leveraging landscape protein, identified enhanced variants from combinatorial library mutations. These increased human cells N. benthamiana by over two-fold fifty-fold relative wild-type TnpB, respectively. In total, this study highlights unknown elements critical regulation endonuclease RNA, reveals surprising amount latent accessible through mutation.

Язык: Английский

Процитировано

0
Gene novelty and gene family expansion in the early evolution of Lepidoptera DOI Creative Commons

Asia E. Hoile,

Peter W. H. Holland, Peter O. Mulhair

и другие.

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Фев. 19, 2025

Abstract Background Almost 10% of all known animal species belong to Lepidoptera: moths and butterflies. To understand how this incredible diversity evolved we assess the role gene gain in driving early lepidopteran evolution. Here, compared complete genomes 115 insect species, including 99 Lepidoptera, search for novel genes coincident with emergence Lepidoptera. Results We find 217 orthogroups or families which emerged on branch leading Lepidoptera; these 177 likely arose by duplication followed extensive sequence divergence, 2 are candidates origin horizontal transfer, 38 have no homology outside Lepidoptera possibly via de novo genesis. focus two new that conserved across underwent duplication, suggesting important roles biology. One encodes a family sugar ion transporter molecules, potentially involved evolution diverse feeding behaviours The second unusual propeller-shaped proteins originated transfer from Spiroplasma bacteria; name propellin genes. Conclusion provide first insights into genetic novelty This gives insight rate during order as well providing context mechanisms origin. describe examples were retained duplicated further their importance

Язык: Английский

Процитировано

0
Mining yeast diversity unveils novel targets for improved heterologous laccase production in Saccharomyces cerevisiae DOI Creative Commons
Ryan Wong, Marissa Foo,

Jasmine R. S. Lay

и другие.

Microbial Cell Factories, Год журнала: 2025, Номер 24(1)

Опубликована: Март 10, 2025

Язык: Английский

Процитировано

0
Harnessing Ogataea parapolymorpha DL-1 alcohol oxidase in Komagataella phaffii for recombinant xylanase expression DOI
Shoufeng Wang,

Wenjie Cong,

Mingxuan Wang

и другие.

Food Bioscience, Год журнала: 2025, Номер unknown, С. 106346 - 106346

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study DOI Creative Commons
Sebastian Bittrich, Alexander Rose, David Sehnal

и другие.

Protein Science, Год журнала: 2025, Номер 34(4)

Опубликована: Март 18, 2025

Abstract The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three‐dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed RCSB Protein Data Bank (RCSB PDB, RCSB.org ) in Europe (PDBe, PDBe.org as an open‐source, web‐based, 3D software suite for examination analyses biostructures. It capable displaying atomic coordinates related experimental data biomolecular together variety annotations, facilitating basic applied research, training, education, information dissemination. Across , the PDB research‐focused web portal, has been implemented support single‐mouse‐click atomic‐level (e.g., proteins, nucleic acids, carbohydrates) bound cofactors, small‐molecule ligands, ions, water molecules, other macromolecules. can seamlessly display from various sources, allowing structure interrogation, superimposition, comparison. Using influenza A H5N1 virus topical case study important pathogen, we exemplify how embedded within tools—allowing users view polymer sequence structure‐based annotations integrated trusted bioinformatics resources, assess patterns trends groups structures, any size compositional complexity. In addition being linked every biostructure Computed Structure Model made available at Standalone freely visualizing multi‐scale rcsb.org/3d-view .

Язык: Английский

Процитировано

0