Posts tagged as:

protein engineering

An advance in atomically precise
building-block assembly

May 27, 2011

A paper in Science reports a design method that substantially advances the macromolecular technology base for building atomically precise nanosystems.
Background: foldamer engineering
As many readers know, biology shows an effective way build large, intricate, atomically precise systems: Use covalent chemistry to build chains of small building blocks, and design these chains to fold into nanoscale building [...]

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Electron cryomicroscopy
reaches landmark molecular resolution

October 17, 2010

Electron microscopes can image biological macromolecules in cryogenic ice, but it shows them as low-contrast features in a grainy image (see below). Using enough electrons to reduce the graininess would first destroy the specimen.
The trick to getting enough information without frying the molecules is to image many specimens that are known to be identical, and [...]

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Evolutionary refinement of engineered molecules

October 5, 2010

Blind variation and focused selection have made the biosphere, and they’re being used in the lab to make functional biomolecular components. The laboratory methods often go under the names of “directed evolution” and (in single-round versions) “high-throughput screening”, and they hold promise as partners for rational design in macromolecular systems engineering.
As background, here are [...]

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Ribo-Q1: Genetic manufacturing expanded

March 1, 2010

All ribosomes read genetic data as three-letter words that encode 20 standard amino acids (give or take a few anomalies). This is equally true of the ribosomes in deep-sea bacteria living at 120°C, and the ones in your thumb. This universal code has been a wall that bounds the scope of biosynthetic polypeptide engineering — [...]

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The Molecular Machine Path
to Molecular Manufacturing (2):
Exploiting Improved Methods and Building Blocks

December 27, 2009

Part 4 of a series on the history and prospects of advanced nanotechnology concepts, prompted by the upcoming 50th anniversary of Feynman’s historic talk, “There’s Plenty of Room at the Bottom”.

Rigid, structurally diverse bis-peptide oligomers C. Schafmeister, JACS, 2006

In this post, I’d like to outline the promise of fabrication technologies that are within reach of [...]

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The Molecular Machine Path
to Molecular Manufacturing (1):
Foldamers and Brownian Assembly

December 25, 2009

Part 3 of a series prompted by the upcoming 50th anniversary of Feynman’s historic talk, “There’s Plenty of Room at the Bottom”.

Lathe, 1911 A machine tool, used to make machines

In my view, the most attractive way forward in developing advanced molecular machine systems is by exploiting the molecular machine systems that are available today. Historically, [...]

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Molecular Manufacturing: Where’s the progress?

December 19, 2009

Part 2 of a series on the history and prospects of advanced nanotechnology concepts, prompted by the upcoming 50th anniversary of Feynman’s historic talk, “There’s Plenty of Room at the Bottom”.

John Stewart Mill Debugging defects in human thought

As cognitive psychologists know, we human beings suffer from multiple, systematic cognitive biases, aberrations of intellectual vision that [...]

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Molecular Nanomachines: Physical Principles and Implementation Strategies

October 1, 2009

I’ve migrated another paper to E-drexler.com:

Drexler, KE. “Molecular Nanomachines: Physical Principles and Implementation Strategies”, Annual Review of Biophysics and Biomolecular Structure, 23:377-405 (1994).
(With thanks to Robert Bradbury for the original HTML conversion.)

Click to read.

See also:

The Physical Basis of Atomically Precise Manufacturing
A Telescope Aimed at the Future
Productive nanosystems: the physics of molecular fabrication [pdf] (from [...]

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Slides for Berkeley Talk
on Molecular Nanosystems

May 6, 2009

Framework-directed self assembly
I’ve now posted the slides for my Berkeley talk on objectives and experimental directions in biomolecular/inorganic composite nanosystems: Click here to download.
The talk was a keynote at the 2009 Berkeley Nanotechnology Forum.
I’ve described some of the concepts and motivations in an earlier post, and this technology direction is also discussed in the report [...]

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Machines Evolving to the Brink of Failure

April 30, 2009

While writing a post on molecular engineering for the Macromolecular Modeling Blog, I came across an EMBO Reports paper that provided new guidelines for protein engineering; It also illustrates a general principle that should be taken to heart by anyone thinking about molecular engineering from a biomolecular perspective:
Molecular machines tend to evolve toward the [...]

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Macromolecular Modeling
for Molecular Systems Engineering

April 16, 2009

Nir London of the Macromolecular Modeling Blog has invited me to offer my perspective on the field. After patiently waiting for me to complete it, he’s posted the resulting essay, which I have cross-posted below.
The Macromolecular Modeling Blog is hosted by the Rosetta Design Group, which offers molecular modeling services based on the Rosetta protein [...]

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A Revolution
in de novo Protein Engineering Methodology

March 30, 2009

In a recent Nature article, researchers describe the design of a peptide foldamer device (a.k.a. “protein”) that binds and releases oxygen in a way that resembles the heme protein, neuroglobin — and they focus more on the design process than on the design product. They advocate an engineering approach that explicitly rejects aspects of the [...]

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