Results 91 to 100 of about 180,875 (351)

The ubiquitin ligase RNF115 is required for the clearance of damaged lysosomes

FEBS Letters, EarlyView.
Upon lysosomal rupture, an E3 ubiquitin ligase RNF115 translocates from the cytosol to the damaged lysosomal membrane. Moreover, RNF115 depletion impairs the clearance of damaged lysosomes, identifying it as a key regulator of lysosomal quality control.
Sae Nakanaga, Toshiki Takahashi, Akiko Kuma, Hiroyuki Kawahara   +3 more
wiley   +1 more source

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

Proteins: Structure, Function, and Bioinformatics, 2019
We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure Prediction round 13 (CASP13). The analysis includes (a) assignment and discussion of best models through scores‐aided visual inspection of ...
L. Abriata, G. Tamò, M. dal Peraro
semanticscholar   +1 more source

In silico characterization and structural modeling of bacterial metalloprotease of family M4

Journal of Genetic Engineering and Biotechnology, 2021
Background The M4 family of metalloproteases is comprised of a large number of zinc-containing metalloproteases. A large number of these enzymes are important virulence factors of pathogenic bacteria and therefore potential drug targets.
Rajnee Hasan, Md. Nazmul Haq Rony, Rasel Ahmed   +2 more
doaj   +1 more source

Organizing the interface—Plasma membrane architecture and receptor dynamics in virus‐cell interactions

FEBS Letters, EarlyView.
Plasma membranes contain dynamic nanoscale domains that organize lipids and receptors. Because viruses operate at similar scales, this architecture shapes early infection steps, including attachment, receptor engagement, and entry. Using influenza A virus and HIV‐1 as examples, we highlight how receptor nanoclusters, multivalent glycan interactions ...
Jan Schlegel, Christian Sieben
wiley   +1 more source

Epigenetic blind spots – the role of DNA methylation dynamics in stem cell‐based models of embryogenesis

FEBS Letters, EarlyView.
Embryo‐like structures (stembryos) are an innovative tool, but they are hindered by experimental variability and limited developmental potential. DNA methylation is crucial for mammalian development, but its status in stembryo models is poorly characterized.
Sara Canil, Anna Corrà, Annalisa Scapolatiello, Chengxiang Qiu, Gianluca Amadei   +4 more
wiley   +1 more source

Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data

Nature Methods
The DeepMSA2 pipeline employs iterative alignment search against large genomic and metagenomic sequence databases to construct single- and multichain multiple-sequence alignment (MSA) for proteins.
Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, L. Freddolino, Yang Zhang   +5 more
semanticscholar   +1 more source

Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics

Structure, 2014
Summary The relationship between protein sequence, structure, and dynamics has been elusive. We report one of the first comprehensive analyses using an in-solution experimental approach to study how the conservation of tertiary structure correlates with ...
J. Fang, P. Nevin, V. Kairys, Č. Venclovas, J. Engen, P. Beuning   +5 more
semanticscholar   +1 more source

The k-junction motif in RNA structure [PDF]

, 2014
The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP ...
Daldrop, Peter, Jia Wang, Lilley, David M. J.; id_orcid, Peter Daldrop, David M. J. Lilley, Wang, Jia, Huang, Lin, Lin Huang   +7 more
core   +1 more source

Neural network‐derived Potts models for structure‐based protein design using backbone atomic coordinates and tertiary motifs

, 2023
Designing novel proteins to perform desired functions, such as binding or catalysis, is a major goal in synthetic biology. A variety of computational approaches can aid in this task.
Mindren Lu, Lu, Mindren, Li, Alex J., Gevorg Grigoryan, Keating, Amy E., Vikram Sundar, Grigoryan, Gevorg, Amy E. Keating, Israel Desta, Keating, Amy E, Sundar, Vikram, Alex J. Li, Desta, Israel, Li, Alex J   +13 more
core   +1 more source

A hybrid variational autoencoder and WGAN with gradient penalty for tertiary protein structure generation

Scientific Reports
Elucidating the tertiary structure of proteins is important for understanding their functions and interactions. While deep neural networks have advanced the prediction of a protein’s native structure from its amino acid sequence, the focus on a single ...
Aalaa I. Sehsah, Afaf Mousa, Gamal Farouk   +2 more
doaj   +1 more source