Results 91 to 100 of about 2,620,413 (304)

Statistical mechanics of transcription-factor binding site discovery using Hidden Markov Models

, 2010
Hidden Markov Models (HMMs) are a commonly used tool for inference of transcription factor (TF) binding sites from DNA sequence data. We exploit the mathematical equivalence between HMMs for TF binding and the "inverse" statistical mechanics of hard rods
A. Drawid, A. Tanay, Anirvan M. Sengupta, D.J. Schwab, David J. Schwab, E. Schneidman, G. Stormo, H. Jeffreys, J.B. Kinney, L.E. Baum, M. Djordjevic, M. Weigt, N. Halabi, O.G. Berg, P. Mahalanobis, Pankaj Mehta, R. Olsen, S. Sinha, T. Mora   +18 more
core   +1 more source

CadC-mediated activation of the cadBA promoter in Escherichia coli [PDF]

, 2005
The transcriptional activator CadC in Escherichia coli, a member of the ToxR-like proteins, activates transcription of the cadBA operon encoding the lysine decarboxylase CadA and the lysine-cadaverine antiporter CadB. cadBA is induced under conditions of
Jung, K., Kuper, C.
core   +1 more source

Calpain small subunit homodimerization is robust and calcium‐independent

FEBS Letters, EarlyView.
Calpains dimerize via penta‐EF‐hand (PEF) domains. Using single‐molecule force spectroscopy, we measured the strength and kinetics of PEF–PEF homodimer binding. The interaction is robust, shows a transient conformational step before dissociation, and remains largely insensitive to Ca2+.
Nesha May O. Andoy, Trina Dykstra‐MacPherson, Mathias A. Bell, Peter L. Davies, Ruby May A. Sullan   +4 more
wiley   +1 more source

Structural insights into an engineered feruloyl esterase with improved MHET degrading properties

FEBS Letters, EarlyView.
A feruloyl esterase was engineered to mimic key features of MHETase, enhancing the degradation of PET oligomers. Structural and computational analysis reveal how a point mutation stabilizes the active site and reshapes the binding cleft, expading substrate scope.
Panagiota Karampa, Konstantinos Makryniotis, Theofani‐Iosifina Sousani, Evangelos Topakas, Vangelis Daskalakis, Maria Dimarogona   +5 more
wiley   +1 more source

Chloride binding to the anion transport binding sites of band 3. A 35Cl NMR study [PDF]

, 1984
Band 3 is an integral membrane protein that exchanges anions across the red cell membrane. Due to the abundance and the high turnover rate of the band 3 transport unit, the band 3 system is the most heavily used ion-transport system in a typical ...
Chan, Sunney I., Falke, Joseph J., Pace, R. J.   +2 more
core  

A methionine‐lined active site governs carbocation stabilization and product specificity in a bacterial terpene synthase

FEBS Letters, EarlyView.
This study reveals a unique active site enriched in methionine residues and demonstrates that these residues play a critical role by stabilizing carbocation intermediates through novel sulfur–cation interactions. Structure‐guided mutagenesis further revealed variants with significantly altered product profiles, enhancing pseudopterosin formation. These
Marion Ringel, Carl P. O. Helmer, Shani Zev, Ronja Driller, Emily Buhr, Markus Reinbold, Renana Schwartz, Gabriel Foley, Mikael Boden, Daniel Garbe, Gerhard Schenk, Dan Thomas Major, Bernhard Loll, Thomas Brück   +13 more
wiley   +1 more source

Many locks to one key: N-acetylneuraminic acid binding to proteins

IUCrJ
Sialic acids play crucial roles in cell surface glycans of both eukaryotic and prokaryotic organisms, mediating various biological processes, including cell–cell interactions, development, immune response, oncogenesis and host–pathogen interactions. This
KanagaVijayan Dhanabalan, YiYang Cheng, Trung Thach, Ramaswamy Subramanian   +3 more
doaj   +1 more source

Valosin‐containing protein counteracts ATP‐driven dissolution of FUS condensates through its ATPase activity in vitro

FEBS Letters, EarlyView.
Biomolecular condensates formed by fused in sarcoma (FUS) are dissolved by high ATP concentrations yet persist in cells. Using a reconstituted system, we demonstrate that valosin‐containing protein (VCP), an AAA+ ATPase, counteracts ATP‐driven dissolution of FUS condensates through its D2 ATPase activity.
Hitomi Kimura, Shin‐ichi Tate, Kyota Yasuda   +2 more
wiley   +1 more source

Structural Analysis of the Drosophila melanogaster GSTome

Biomolecules
Glutathione transferase (GST) is a superfamily of ubiquitous enzymes, multigenic in numerous organisms and which generally present homodimeric structures.
Nicolas Petiot, Mathieu Schwartz, Patrice Delarue, Patrick Senet, Fabrice Neiers, Adrien Nicolaï   +5 more
doaj   +1 more source

Adaptive evolution of transcription factor binding sites

BMC Evolutionary Biology, 2004
Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in ...
Berg Johannes, Willmann Stana, Lässig Michael   +2 more
doaj   +1 more source