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Field-portable optofluidic plasmonic biosensor for wide-field and label-free monitoring of molecular interactions

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Amelogenin refers to a class of intrinsically disordered proteins that are the major constituents of enamel matrix derivative (EMD), an extract of porcine fetal teeth used in regenerative periodontal therapy. Modifications in molecular conformation induced ...

Taylor & Francis Inc2017

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based ...

Wiley-Blackwell2016

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We present the crystal structures of the SEC14-like domain of supernatant protein factor (SPF) in complex with squalene and 2,3-oxidosqualene. The structures were resolved at 1.75 angstrom (complex with squalene) and 1.6 angstrom resolution (complex with 2 ...

Academic Press Inc Elsevier Science2015

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

Matteo Dal Peraro, Luciano Andres Abriata

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dime ...

Nature Publishing Group2015

Mono layer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enz ...

Amer Chemical Soc2015

Real-Time Monitoring of Protein Conformational Changes Using a Nano-Mechanical Sensor

Giovanni Dietler, Paolo De Los Rios, Sandor Kasas, Giovanni Longo, Dusan Vobornik, Fabrizio Benedetti, Livan Bladimir Alonso Sarduy

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center ...

Public Library of Science2014

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Ligands that have an affinity for protein targets can be screened very effectively by exploiting favorable properties of long-lived states (LLS) in NMR spectroscopy. In this work, we describe the use of LLS for competitive binding experiments to measure ac ...

Wiley-Blackwell2014

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

Matteo Dal Peraro, Marco Stenta, Thomas Lemmin, Matteo Thomas Degiacomi, Christophe Bovigny

The stereospecific oxidative decomposition of urate into allantoin is the core of purine catabolism in many organisms. The spontaneous decomposition of upstream intermediates and the nonenzymatic racemization of allantoin lead to an accumulation of (R)-all ...

Amer Chemical Soc2014

The allosteric communication pathways in KIX domain of CBP

Alessandro Barducci, Michele Parrinello

Allosteric regulation plays an important role in a myriad of bio-macromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the ...

National Academy of Sciences2013

Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics

Geoffrey Bodenhausen, Daniel Abergel

Nuclear magnetic resonance is used to investigate the backbone dynamics in 6-phosphogluconolactonase from Trypanosoma brucei (Tb6PGL) with (holo-) and without (apo-) 6-phosphogluconic acid as ligand. Relaxation data were analyzed using the model-free appro ...

2012