Results 71 to 80 of about 6,347,071 (258)

Prediction of Calmodulin-Binding Proteins Using Short-Linear Motifs

, 2017
Prediction of Calmodulin-binding (CaM-binding) proteins plays a very important role in the fields of biology and biochemistry, because Calmodulin binds and regulates a multitude of protein targets affecting different cellular processes. Short linear motifs (SLiMs), on the other hand, have been effectively used as features for analyzing protein-protein ...
Yixun Li, Mina Maleki, Nicholas J. Carruthers, Luis Rueda 0001, Paul M. Stemmer, Alioune Ngom   +5 more
openaire   +3 more sources

Exploiting the endogenous yeast nuclear proteome to identify short linear motifs in vivo

Cell Reports Methods, 2023
Peptide-domain interactions mediated by short linear motifs (SLiMs) play crucial roles in cellular biology. The simplicity of SLiMs poses challenges in their computational identification. Existing high-throughput methods for discovering SLiMs lack cellular context as they are typically performed in vitro.
Tanner M. Tessier, Cason R. King, Joe S. Mymryk   +2 more
openaire   +3 more sources

Potential of known and short prokaryotic protein motifs as a basis for novel peptide-based antibacterial therapeutics: a computational survey.

Frontiers in Microbiology, 2014
Short linear motifs are functional stretches of protein sequence that are of crucial importance for numerous biological processes by mediating protein-protein interactions.
Heini eRuhanen, Heini eRuhanen, Heini eRuhanen, Daniel eHurley, Daniel eHurley, Daniel eHurley, Ambarnil eGhosh, Kevin T O'Brien, Kevin T O'Brien, Kevin T O'Brien, Catrióna R Johnston, Denis Colum Shields, Denis Colum Shields, Denis Colum Shields   +13 more
doaj   +1 more source

ELM-the eukaryotic linear motif resource in 2020 [PDF]

, 2019
The eukaryotic linear motif (ELM) resource is a repository of manually curated experimentally validated short linear motifs (SLiMs). Since the initial release almost 20 years ago, ELM has become an indispensable resource for the molecular biology ...
Gibson, TJ, Samano-Sanchez, Hugo, Gouw, M, Sámano-Sánchez, H, Čalyševa, J, Kumar, Manjeet, Gibson, Toby J., Gibson, Toby J, Pancsa, R, Palopoli, N, Pancsa, Rita, Palopoli, Nicolas, Valverde, Jesús Alvarado, Calyseva, Jelena, Glavina, J, Chemes, LB, Chemes, Lucia Beatriz, Alvarado Valverde, Jesús, Davey, NE, Valverde, JA, Bukirova, D, Bukirova, Dayana, Davey, Norman E., Diakogianni, Athina, Michael, S, Gouw, Marc, Chemes, Lucía B., Kumar, M, Diakogianni, A, Michael, Sushama, Glavina, Juliana   +30 more
core   +1 more source

Hypocoercivity and hypocontractivity concepts for linear dynamical systems

, 2023
For linear dynamical systems (in continuous-time and discrete-time), we revisit and extend the concepts of hypocoercivity and hypocontractivity and give a detailed analysis of the relations of these concepts to (asymptotic) stability, as well as (semi ...
Achleitner, Franz; orcid:, Arnold, Anton; orcid:, Mehrmann, Volker; orcid:   +2 more
core   +1 more source

Golgi enzymes are retrieved from the plasma membrane to the trans‐Golgi network

FEBS Letters, EarlyView.
Golgi enzymes are traditionally considered resident proteins retained within the Golgi apparatus. Here, we demonstrate that a subset transiently reaches the cell surface and is subsequently retrieved to the trans‐Golgi network via retrograde transport. Using a nanobody‐based toolkit, we uncover a dynamic trafficking cycle of several Golgi enzymes.
Dominik P. Buser, Tina Junne
wiley   +1 more source

From junk to function — How weak selection in eukaryotes builds new parts and drives genomic complexity

FEBS Letters, EarlyView.
How do genomes gain new functional parts? In eukaryotes, which tend to evolve under weak selection, much of the genome is junk. Palazzo and Qiu borrow the logic of Markov chains to show how non‐functional DNA becomes functional through the appearance of intermediate states, which arise due to epistasis, buffering, and biochemical messiness, allowing ...
Alexander F. Palazzo, Yi Qiu
wiley   +1 more source

SLIDER: Mining correlated motifs in protein-protein interaction networks [PDF]

, 2009
—Correlated motif mining (CMM) is the problem to find overrepresented pairs of patterns, called motif pairs, in interacting protein sequences. Algorithmic solutions for CMM thereby provide a computational method for predicting binding sites for protein ...
Boyen, P., Dijk, A.D.J., van, Ham, R.C.H.J., van, Neven, F.   +3 more
core  

The Shewanella oneidensis Fic enzyme SoFic targets the switch‐I region of EF‐Tu for AMPylation

FEBS Letters, EarlyView.
Fic enzymes mediate diverse post‐translational modifications across all domains of life, including AMPylation. Prokaryotic EF‐Tu can be AMPylated and deAMPylated by the conserved Fic enzyme SoFic. Structural and biochemical approaches were used to characterize the effect of AMPylation on EF‐Tu, SoFic's enzymatic activities, and the enzyme‐target ...
Svenja Runge, Vivian Pogenberg, Alexander Baumgart, Bente Siebels, Hartmut Schlüter, Michael Hecht‐Bucher, Aymelt Itzen   +6 more
wiley   +1 more source

Evolutionary Conserved Short Linear Motifs Provide Insights into the Cellular Response to Stress

Antioxidants, 2022
Short linear motifs (SLiMs) are evolutionarily conserved functional modules of proteins composed of 3 to 10 residues and involved in multiple cellular functions. Here, we performed a search for SLiMs that exert sequence similarity to two segments of alpha-fetoprotein (AFP), a major mammalian embryonic and cancer-associated protein.
Sergey P. Zavadskiy, Denis S. Gruzdov, Susanna S. Sologova, Alexander A. Terentiev, Nurbubu T. Moldogazieva   +4 more
openaire   +3 more sources