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Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering

Sebastian Maerkl, Ekaterina Emilova Petrova, Bruno Emanuel Ferreira De Sousa Correia, Matthew Christopher Blackburn

The capability to rapidly design proteins with novel functions will have a significant impact on medicine, biotechnology and synthetic biology. Synthetic genes are becoming a commodity, but integrated approaches have yet to be developed that take full adva ...

Oxford Univ Press2016

Mathematical models and computational methods for the analysis of genome-scale protein synthesis

Julien Racle

Proteins are a ubiquitous and indispensable element for every living organism, from simple bacteria to mammals. Already in the simplest organisms, there exist some thousands of different protein species that take up a great variety of structures, and thus ...

EPFL2014

In Silico Design of Three-Dimensional Porous Covalent Organic Frameworks via Known Synthesis Routes and Commercially Available Species

Berend Smit, Cory Matthew Simon

Covalent organic frameworks (COFs) are a class of advanced nanoporous polymeric materials which combine the crystallinity of metalorganic frameworks (MOFs) with the stability and potentially low-cost organic chemistry of porous polymer networks (PPNs). Lik ...

Amer Chemical Soc2014

Cell Guidance on Nanogratings: A Computational Model of the Interplay between PC12 Growth Cones and Nanostructures

Silvestro Micera

Background: Recently, the effects of nanogratings have been investigated on PC12 with respect to cell polarity, neuronal differentiation, migration, maturation of focal adhesions and alignment of neurites. Methodology/Principal Findings: A synergistic proc ...

Public Library Science2013

Lack of Enantioselectivity in the SULT1A3-catalyzed Sulfoconjugation of Normetanephrine Enantiomers: An In Vitro and Computational Study

Sandrine Gerber, Jean-Baptiste Gualtierotti

(1R)-Normetanephrine is the natural stereoisomeric substrate for sulfotransferase 1A3 (SULT1A3)-catalyzed sulfonation. Nothing appears known on the enantioselectivity of the reaction despite its potential significance in the metabolism of adrenergic amines ...

Wiley-Blackwell2013

Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Thomas James Penfold, Pablo Campomanes Ramos, Marilisa Neri, Stefano Vanni, Andrey Laktionov

A thorough theoretical description of ultrafast phenomena that occur in complex systems constitutes a formidable challenge. It not only necessitates the use of quantum mechanical methods that can describe ground and possibly even electronically excited sta ...

Schweizerische Chemische Gesellschaft2011

Emergent Properties of in silico Synaptic Transmission in a Model of the Rat Neocortical Column

Srikanth Ramaswamy

The cerebral cortex occupies nearly 80% of the entire volume of the mammalian brain and is thought to subserve higher cognitive functions like memory, attention and sensory perception. The neocortex is the newest part in the evolution of the cerebral corte ...

EPFL2011

Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

Understanding the binding mode of agonists to adrenergic receptors is crucial to enabling improved rational design of new therapeutic agents. However, so far the high conformational flexibility of G protein-coupled receptors has been an obstacle to obtaini ...

Public Library of Science2011

Integration column: Microfluidic high-throughput screening

Sebastian Maerkl

Biology has always been a heavily technology limited field. Burgeoning fields such as systems biology require the development and implementation of new technologies, enabling high-throughput and high-fidelity measurements of large systems. Microfluidics pr ...

2009

Synchronous versus asynchronous modeling of gene regulatory networks

Giovanni De Micheli, Abhishek Garg, Ioannis Xenarios

In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene–gene, ...

2008

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