Results 71 to 80 of about 1,386,749 (339)

The Caenorhabditis elegans DPF‐3 and human DPP4 have tripeptidyl peptidase activity

FEBS Letters, EarlyView.
The dipeptidyl peptidase IV (DPPIV) family comprises serine proteases classically defined by their ability to remove dipeptides from the N‐termini of substrates, a feature that gave the family its name. Here, we report the discovery of a previously unrecognized tripeptidyl peptidase activity in DPPIV family members from two different species.
Aditya Trivedi, Rajani Kanth Gudipati
wiley   +1 more source

CHCHD4 Oxidoreductase Activity: A Comprehensive Analysis of the Molecular, Functional, and Structural Properties of Its Redox-Regulated Substrates

Molecules
The human CHCHD4 protein, which is a prototypical family member, carries a coiled–coil–helix–coiled–coil–helix motif that is stabilized by two disulfide bonds.
Nicole Balasco, Nazanine Modjtahedi, Alessandra Monti, Menotti Ruvo, Luigi Vitagliano, Nunzianna Doti   +5 more
doaj   +1 more source

A probabilistic fragment-based protein structure prediction algorithm.

PLoS ONE, 2012
Conformational sampling is one of the bottlenecks in fragment-based protein structure prediction approaches. They generally start with a coarse-grained optimization where mainchain atoms and centroids of side chains are considered, followed by a fine ...
David Simoncini, Francois Berenger, Rojan Shrestha, Kam Y J Zhang   +3 more
doaj   +1 more source

Current successes and remaining challenges in protein function prediction

Frontiers in Bioinformatics, 2023
In recent years, improvements in protein function prediction methods have led to increased success in annotating protein sequences. However, the functions of over 30% of protein-coding genes remain unknown for many sequenced genomes.
Constance J. Jeffery
doaj   +1 more source

Molecular bases of circadian magnesium rhythms across eukaryotes

FEBS Letters, EarlyView.
Circadian rhythms in intracellular [Mg2+] exist across eukaryotic kingdoms. Central roles for Mg2+ in metabolism suggest that Mg2+ rhythms could regulate daily cellular energy and metabolism. In this Perspective paper, we propose that ancestral prokaryotic transport proteins could be responsible for mediating Mg2+ rhythms and posit a feedback model ...
Helen K. Feord, Gerben van Ooijen
wiley   +1 more source

Accurate prediction of protein catalytic residues by side chain orientation and residue contact density. [PDF]

PLoS ONE, 2012
Prediction of protein catalytic residues provides useful information for the studies of protein functions. Most of the existing methods combine both structure and sequence information but heavily rely on sequence conservation from multiple sequence ...
Yu-Tung Chien, Shao-Wei Huang
doaj   +1 more source

Peptide‐based ligand antagonists block a Vibrio cholerae adhesin

FEBS Letters, EarlyView.
The structure of a peptide‐binding domain of the Vibrio cholerae adhesin FrhA was solved by X‐ray crystallography, revealing how the inhibitory peptide AGYTD binds tightly at its Ca2+‐coordinated pocket. Structure‐guided design incorporating D‐amino acids enhanced binding affinity, providing a foundation for developing anti‐adhesion therapeutics ...
Mingyu Wang, Grace Du, Charity Yongo‐Luwawa, Angelina Lu, Brett Kinrade, Kim Munro, Karl E. Klose, William D. Lubell, Peter Davies, Shuaiqi Guo   +9 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

Fast and accurate protein structure search with Foldseek

bioRxiv, 2022
Foldseek speeds up protein structural search by four to five orders of magnitude. As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming a bottleneck.
Michel van Kempen, Stephanie Kim, Charlotte Tumescheit, M. Mirdita, Jeongjae Lee, C. Gilchrist, J. Söding, Martin Steinegger   +7 more
semanticscholar   +1 more source

Disordered but rhythmic—the role of intrinsic protein disorder in eukaryotic circadian timing

FEBS Letters, EarlyView.
Unstructured domains known as intrinsically disordered regions (IDRs) are present in nearly every part of the eukaryotic core circadian oscillator. IDRs enable many diverse inter‐ and intramolecular interactions that support clock function. IDR conformations are highly tunable by post‐translational modifications and environmental conditions, which ...
Emery T. Usher, Jacqueline F. Pelham
wiley   +1 more source