Results 71 to 80 of about 2,620,413 (304)

Sequence determinants of RNA G‐quadruplex unfolding by Arg‐rich regions

FEBS Letters, EarlyView.
We show that Arg‐rich peptides selectively unfold RNA G‐quadruplexes, but not RNA stem‐loops or DNA/RNA duplexes. This length‐dependent activity is inhibited by acidic residues and is conserved among SR and SR‐related proteins (SRSF1, SRSF3, SRSF9, U1‐70K, and U2AF1).
Naiduwadura Ivon Upekala De Silva, Puspa Kunwar, Md Ibnul Rifat Rahman, Joanna Koryo Kwao, Nathan Lehman, Zihan Zhang, Trenton Paul, Claire Cheng, Nicholas Truex, Hui‐Ting Lee, Jun Zhang   +10 more
wiley   +1 more source

Tuning genetic clocks employing DNA binding sites. [PDF]

PLoS ONE, 2012
Periodic oscillations play a key role in cell physiology from the cell cycle to circadian clocks. The interplay of positive and negative feedback loops among genes and proteins is ubiquitous in these networks.
Shridhar Jayanthi, Domitilla Del Vecchio
doaj   +1 more source

Structural instability impairs function of the UDP‐xylose synthase 1 Ile181Asn variant associated with short‐stature genetic syndrome in humans

FEBS Letters, EarlyView.
The Ile181Asn variant of human UDP‐xylose synthase (hUXS1), associated with a short‐stature genetic syndrome, has previously been reported as inactive. Our findings demonstrate that Ile181Asn‐hUXS1 retains catalytic activity similar to the wild‐type but exhibits reduced stability, a looser oligomeric state, and an increased tendency to precipitate ...
Tuo Li, Pedro A. Sánchez‐Murcia, Bernd Nidetzky   +2 more
wiley   +1 more source

PocketPicker: analysis of ligand binding-sites with shape descriptors [PDF]

, 2007
Background Identification and evaluation of surface binding-pockets and occluded cavities are initial steps in protein structure-based drug design.
Weisel, Martin, Proschak, Ewgenij, Schneider, Gisbert (Prof. Dr.)   +2 more
core   +2 more sources

Cell wall target fragment discovery using a low‐cost, minimal fragment library

FEBS Letters, EarlyView.
LoCoFrag100 is a fragment library made up of 100 different compounds. Similarity between the fragments is minimized and 10 different fragments are mixed into a single cocktail, which is soaked to protein crystals. These crystals are analysed by X‐ray crystallography, revealing the binding modes of the bound fragment ligands.
Kaizhou Yan, Mathew Stanley, Olawale Raimi, Andrew T. Ferenbach, Helge C Dorfmueller, Daan M. F. van Aalten   +5 more
wiley   +1 more source

Structural Plasticity and Noncovalent Substrate Binding in the GroEL Apical Domain. A study using electrospray ionization mass spectrometry and fluorescence binding studies [PDF]

, 2002
Advances in understanding how GroEL binds to non-native proteins are reported. Conformational flexibility in the GroEL apical domain, which could account for the variety of substrates that GroEL binds, is illustrated by comparison of several independent ...
Adams, Boisvert, Braig, Braig, Brinker, Brocchierei, Brunger, Brunger, Buckle, Bukau, Chatellier, Chatellier, Chatellier, Chen, Collaborative Computational Project, N., Coyle, Dessauer, Ewalt, Feltham, Fenton, Ferrige, Grallert, Hartl, Hartl, HayerHartl, Hemmingsen, Hlodan, Houry, Hunt, Hutchinson, Jancarik, Jones, Jones, Kobayashi, Konermann, Kraunsoe, Kusmierczyk, Landry, Landry, Leslie, Loo, Ma, Murshudov, Navaza, Pace, Pflugrath, Ploegman, Raftery, Ranson, Robinson, Romano, Roseman, Rye, Sigler, Smith, Smote, Tanaka, Wang, Weber, Weber, Weissman, Xu, Zahn   +62 more
core   +1 more source

DBSI: DNA-binding site identifier [PDF]

Nucleic Acids Research, 2013
In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30 ...
Zhu, Xiaolei, Ericksen, Spencer S., Mitchell, Julie C.   +2 more
openaire   +2 more sources

The (Glg)ABCs of cyanobacteria: modelling of glycogen synthesis and functional divergence of glycogen synthases in Synechocystis sp. PCC 6803

FEBS Letters, EarlyView.
We reconstituted Synechocystis glycogen synthesis in vitro from purified enzymes and showed that two GlgA isoenzymes produce glycogen with different architectures: GlgA1 yields denser, highly branched glycogen, whereas GlgA2 synthesizes longer, less‐branched chains.
Kenric Lee, Dimitrios Bekiari, Sofia Doello, Karl Forchhammer   +3 more
wiley   +1 more source

Polyphenol Interactions with Amyloid Fibrils: A Molecular Docking Study

East European Journal of Physics
Polyphenols, a versatile group of naturally occurring compounds with many favorable biological properties currently attract increasing research interest in the context of their ability to inhibit the formation and to destabilize special protein ...
Uliana Malovytsia, Valeriya Trusova, Mette Thomsen, Kateryna Vus, Olga Zhytniakivska, Galyna Gorbenko   +5 more
doaj   +1 more source

Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision

Journal of Cheminformatics, 2021
Rationalizing the identification of hidden similarities across the repertoire of druggable protein cavities remains a major hurdle to a true proteome-wide structure-based discovery of novel drug candidates.
Merveille Eguida, Didier Rognan
doaj   +1 more source