One of the challenges of modern structural biology is to account for protein structural dynamics. Intrinsically disordered proteins (IDPs), which do not fold spontaneously into a defined conformation, existing, instead, as highly heterogeneous conformational ensembles, provide an extreme and challenging example of prot...
S. Brocca, E. Ponzini, C. Santambrogio et al.· Frontiers in Biophysics· 0 citations
In this work, we focus on predicting fold-switching phenomena observed in certain protein structures. Proteins that undergo fold-switching are called metamorphic proteins. We model fold-switch prediction in proteins as a position/residue-wise classification task. We use various features extracted from a protein’s seque...
Pranav Machingal, N. Hemachandra, P. V. Balaji· bioRxiv· 0 citations
Oxidative folding, involving disulfide (SS) bond formation and isomerization, is essential for the maturation of many secreted and membrane proteins. Although numerous small-molecule mimics of protein disulfide isomerase, a key enzyme that catalyzes oxidative folding, have been developed, most require superstoichiome...
Y. Iwata, Shunpei Iwamoto, Hiroki Takeda et al.· Biomacromolecules· 0 citations
Proteostasis is essential for cellular health, with its disruption contributing to aging, neurodegeneration, and metabolic disorders. While the upstream proteotoxic stress-sensing and protein-folding mechanisms in the ER and cytosol are well studied, the transcriptional regulation of proteostasis remains incompletely u...
Syeda Kubra, Michelle Sun, William Dion et al.· PLoS Biology· 0 citations
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Although antineoplastic agents target diverse proteins, whether they converge on conserved cellular response states remains unclear. Here, we generate a TMTpro 18-plex quantitative proteomics atlas of 367 antineoplastic agents in HepG2 cells and identify recurrent drug response phenotypes (DRPs). The higher-order organ...
Serum amyloid A (SAA) is one of the most abundant acute-phase proteins that exerts a key role in the inflammatory response, and is considered a clinically significant biomarker in many pathologies. Under inflammatory conditions, plasma SAA levels can rise over 1000- fold due to rapid hepatic production, which is largel...
Salena Abdulabbas Naser· Jana Nexus: Journal of Healt...· 0 citations
This study addresses a major bottleneck in dairy waste management by engineering a highly efficient, thermophilic enzyme for lactose hydrolysis, transforming the cheese manufacturing by-product whey into a high-value resource. While traditional glycoside hydrolase family 2 (GH2) enzymes suffer from poor industrial ther...
Molecular chaperones are central regulators of the proteostasis network, ensuring proteome integrity through protein folding, the prevention of aggregation, and targeted degradation. These mechanisms are essential for limiting proteotoxic stress and preventing the accumulation of pathogenic proteins. Consequently, ch...
Adna Berilo, Naida Odobašić, Merjem Husić et al.· Journal of Physical Chemistr...· 0 citations
Large-scale mining of public transcriptomic datasets can reveal viral diversity that remains invisible to conventional virus-surveillance approaches, while increasingly powerful structure-prediction methods provide a complementary route to characterizing highly divergent viral proteins. Here, we combine sequence detect...
Nicolás Bejerman, David Nicolas Giuseppe Huebert, Robert A. Alvarez‐Quinto et al.· Viruses· 0 citations
Motif scaffolding builds a protein around a prescribed structural motif -- an active site, a binding epitope, a metal site -- so that the motif is presented in its required geometry. The task is usually posed with the motif pinned down: its position along the sequence is given, and several rigid fragments inherit their...
Ivan Permyakov, Elizaveta Geraseva, Andrey V. Golovin· bioRxiv (Cold Spring Harbor...· 0 citations
The 240 E8 root vectors, when partitioned into the 120 antipodal pairs that define minimal closed-shell conformational states, predict that protein folding proceeds not through sequential collapse but through a discrete sequence of 240-fold-encoded soliton states. Each state corresponds to a unique E8 node whose projec...
Andrew Stewart Caldin· Zenodo (CERN European Organi...· 0 citations
Abstract Biogenesis of the bacterial outer membrane is key to bacterial survival and antibiotic resistance. Central to this is the β-barrel assembly machine (Bam) complex and its associated chaperones, which are responsible for transport, folding and insertion of outer membrane proteins (OMPs). The Escherichia coli Bam...
Jack Alfred Bryant, Kara A Staunton, Hannah M. Doherty et al.· eLife· 1 citation
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
