Feb
20
2014
0
Mar
14
2012
0

Tezcan-RDG supramolecular design collab in the news

Stu Borman wrote a nice piece in Chemical & Engineering News (CEN) highlighting a recent paper in Nature Chemistry that presents the work of a collaboration between the Tezcan Lab at UCSD and the Rosetta Design Group. In this work, a monomeric protein was redesigned to become capable of forming metal and pH tunable nano- to micro- scale sheets, tubes, and other assemblies.


Mr. McGuire: I just want to say one word to you. Just one word.

Benjamin: Yes, sir.

Mr. McGuire: Are you listening?

Benjamin: Yes, I am.

Mr. McGuire: Plastics. Proteins.

Benjamin: Exactly how do you mean?

Written by Xavier Ambroggio in: Literature Reviews | Tags: , , , ,
Nov
09
2011
0

Protein design: breaks gluten, wins iGEM2011

An undergraduate group of students from the University of Washington, managed to redesign an enzyme to efficiently break down a model peptide for Gluten, achieving an increase in activity of hundreds fold over the only current clinically tested treatment for Gluten intolerance – Winning iGEM2011. All this, over the summer. Oh, and they also managed to produce Diesel in E. Coli.

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Written by Nir London in: News,Weird science | Tags: , , , , , ,
Feb
16
2010
0

Tradeoff between stability and multispecificity in the design of promiscuous proteins

Traditionally, computational protein design efforts have been directed at calculating a single sequence predicted to fold to a particular target structure. Recently, however, a number of conceptual generalizations have been pursued, ranging from the use of backbone flexibility, off-rotamer side chain flexibility, negative design, multi-body potentials, conformational free energy, and prediction of sequence profiles. Below I present our state-of-the-art research whose goal is to understand how protein sequences are optimized to be compatible with binding multiple partners with high affinity. – By Menachem Fromer.

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Apr
16
2009
8

Macromolecular Modeling for Molecular Systems Engineering

Macromolecular systems engineering can help us meet some of the most important technological challenges in the world today, ranging from medicine to renewable energy, and the development of better-integrated computational design tools will accelerate progress. Macromolecular modeling capabilities are advancing rapidly, but much of their potential for supporting systems engineering has yet to be exploited. In this post, I’d like to describe the fundamental nature of the problems and outline some of what needs to be done to make their potential a reality. By Dr. Eric Drexler.

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Apr
14
2009
0

Design and engineering of an O2 transport protein

In a recent Nature paper Koder & Anderson et al. describe the procedure for creating an O2 transport protein from first principals. The paper is somewhat technical and may appeal to the biochemists amongst our readers, here we present the main ideas, findings and conclusions. 

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Written by Nir London in: Literature Reviews | Tags: , , , ,
Dec
18
2008
0

Model for the Peptide-Free Conformation of Class II MHC Proteins

Although numerous structures of peptide bound MHC-II molecules were solved, no one knows how does the peptide free MHC look like. Painter et al. elegantly use molecular dynamics to model the conformational changes upon peptide removal. Most interestingly a helix from the peptide binding domain adopts the binding mode of the antigen peptide. They successfully validate their model using antibodies and superantigens, predicted to differentially bind peptide-bound/free molecules according to their model. We take the validation one step further and propose mutations based on Painter’s model that would stabilize the free MHC. Will it work? Who will pick up the gauntlet?

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