Publications by Deniz Aydin | EPFL Graph Search

CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles

Matteo Dal Peraro, Giorgio Elikem Tamo, Deniz Aydin, Martina Audagnotto, Giulia Fonti, Sylvain Träger

Motivation: Proteins are intrinsically dynamic entities. Flexibility sampling methods, such as molecular dynamics or those arising from integrative modeling strategies, are now commonplace and enable the study of molecular conformational landscapes in many ...

OXFORD UNIV PRESS2021

An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis

Matteo Dal Peraro, Deniz Aydin

The biosynthesis of coenzyme Q presents a paradigm for how cells surmount hydrophobic barriers in lipid biology. In eukaryotes, CoQ precursors-among nature's most hydrophobic molecules-must somehow be presented to a series of enzymes peripherally associate ...

CELL PRESS2019

Characterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface

Deniz Aydin

Integral and peripheral membrane proteins account for one-third of the human proteome, and they are estimated to represent the target for over 50% of modern medicinal drugs. Despite their central role in medicine, the complex, heterogeneous and dynamic nat ...

EPFL2019

Overcoming the hydrophobic barrier of the membrane: The role of COQ9 in promoting coenzyme Q biosynthesis

Matteo Dal Peraro, Deniz Aydin

AMER CHEMICAL SOC2019

Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family

Matteo Dal Peraro, Deniz Aydin

2018

A Combined Computational and Experimental Study to Investigate the Role of COQ9 in Promoting COQ Biosynthesis

Matteo Dal Peraro, Deniz Aydin

2018

Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity

Matteo Dal Peraro, Deniz Aydin, Xiao Guo

The UbiB protein kinase-like (PKL) family is widespread, comprising one-quarter of microbial PKLs and five human homologs, yet its biochemical activities remain obscure. COQ8A (ADCK3) is a mammalian UbiB protein associated with ubiquinone (CoQ) biosynthesi ...

Cell Press2016

RoboGen: Robot Generation through Artificial Evolution

Dario Floreano, Ilya Loshchilov, Joshua Evan Auerbach, Andrea Maesani, Ludovic Daler, Przemyslaw Mariusz Kornatowski, Titus Cieslewski, Grégoire Hilaire Marie Heitz, Deniz Aydin, Pradeep Ruben Fernando

Science instructors from a wide range of disciplines agree that hands-on laboratory components of courses are pedagogically necessary (Freedman, 1997). However, certain shortcomings of current laboratory exercises have been pointed out by several authors ( ...

The MIT Press2014