Nanotechnology Now

Our NanoNews Digest Sponsors





Heifer International

Wikipedia Affiliate Button


android tablet pc

Home > Press > Folding Funnels Key to Biomimicry: Berkeley Lab Finding that Protein Folding Funnels Also Apply to Self-Assembly Should Benefit Biomimicry and Nanosynthesis

AFM micrograph of 2D S-layers assembled on mica shows two different pathways to crystalization, one in which the domans are 2-3 nanometers taller (white circles). Height differences, measured along the dotted black line, were the result of kinetic trapping. (Image from Molecular Foundry)
AFM micrograph of 2D S-layers assembled on mica shows two different pathways to crystalization, one in which the domans are 2-3 nanometers taller (white circles). Height differences, measured along the dotted black line, were the result of kinetic trapping.

(Image from Molecular Foundry)

Abstract:
Proteins are able to self-assemble into a wide range of highly ordered structures that feature a diverse array of properties. Through biomimicry - technological innovation inspired by nature - humans hope to emulate proteins and produce our own version of self-assembling molecules. A key to accomplishing this is understanding how protein-folding - a process critical to the form and function of a protein - is extended from individual proteins to complex assemblies.

Folding Funnels Key to Biomimicry: Berkeley Lab Finding that Protein Folding Funnels Also Apply to Self-Assembly Should Benefit Biomimicry and Nanosynthesis

Berkeley, CA | Posted on October 31st, 2012

Researchers with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab) have now shown that a concept widely accepted as describing the folding of a single individual protein is also applicable to the self-assembly of multiple proteins. Their findings provide important guidelines for future biomimicry efforts, particularly for device fabrication and nanoscale synthesis.

"We've made the first direct observations that the concept of a folding funnel with kinetic energy traps for individual proteins can be equally applied to the assembly of ordered protein structures," says Jim DeYoreo, a scientist with the Molecular Foundry, a DOE nanoscience center at Berkeley Lab, who led this research along with Berkeley Lab chemist Carolyn Bertozzi. "Our results tell us that efforts to discover and codify the design rules for the self-assembly of complex molecular systems will have to take into account the impact of kinetic traps associated with conformational transformations."

DeYoreo and Bertozzi are the corresponding authors of a paper published by the Proceedings of the National Academy of Sciences (PNAS) that reported this research. The paper is titled "Direct observation of kinetic traps associated with structural transformations leading to multiple pathways of S-layer assembly." Co-authoring the paper were Seong-Ho Shin, Sungwook Chung, Babak Sanii and Luis Comolli.

Proteins are essentially biomolecular nanomachines capable of performing numerous tasks because of their ability to fold themselves into a multitude of shapes and forms. When individual proteins self-assemble into ordered structures the resulting ensemble often adopts conformations that are quite distinct from those of the individual components.

"For example, collagen matrices, which constitute the organic scaffolds of bones and teeth, are constructed from triple helices of individual collagen monomers," DeYoreo says. "These helices will further assemble into highly organized twisted fibrils that exhibit a pseudohexagonal symmetry."

The folding funnel concept explains individual protein folding on the basis of conformational changes to reach a state of minimal free energy. An unfolded protein starts out in a state of high free energy that makes its conformation unstable. Initially, there are a number of possible three-dimensional conformations that would reduce this free energy. However, as the protein starts to fold, the free energy begins to drop and the number of possible conformations begins to decrease like the shrinking width of a funnel. The bottom of the funnel is reached when free energy is minimized and there is only one available conformation. As the free energy drops, however, there may be kinetic traps along the way that can stop the folding process and hold the protein in partially folded conformations, known as molten globules and folding intermediates, for extended periods of time. Eventually these trapped conformational states will be transformed into a stable conformation but the shape and form of that final conformation is influenced by the kinetic traps.

"In a protein folding funnel, the funnel walls are presumed not to be smooth and the resulting bumps and valleys define kinetic traps," DeYoreo says. "This physical picture of folding has been explored in some detail at the single molecule level, but has not been considered for protein self-assembly into extended architectures even though conformational transformations are part and parcel of the self-assembly process."

DeYoreo, Bertozzi and their colleagues took steps to correct this knowledge deficit by studying the surface-layer (S-layer) proteins that self-assemble into a crystalline membrane around the single cells of bacteria and Archaea. This outer membrane serves as the first point of contact between the microbe and its environment and is key to the microbe's ability to survive. Using in situ Atomic Force Microscopy (AFM), the researchers imaged in real time and at the molecular level kinetic trapping during the 2D self-assembly of S-layer protein structures on mica surfaces.

"We observed that self-assembly of S-layer proteins tracks along two different pathways, one leading directly to the low-energy final, ordered state, and the other leading to a kinetic trap occupied by a long-lived transient state that is more disordered," DeYoreo says. "Although either state is easily accessible during crystal nucleation, if the system falls into the high-energy state, escape to the final, low-energy state is strongly impeded at room temperature. This demonstrates the importance of kinetic traps in determining the pathway of S-layer crystallization and suggests that the concept of folding funnels is equally valid for self-assembly of extended protein structures."

This research was supported by the DOE Office of Science.

####

About DOE/Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. For more, visit www.lbl.gov.

The Molecular Foundry is one of five DOE Nanoscale Science Research Centers (NSRCs), national user facilities for interdisciplinary research at the nanoscale, supported by the DOE Office of Science. Together the NSRCs comprise a suite of complementary facilities that provide researchers with state-of-the-art capabilities to fabricate, process, characterize, and model nanoscale materials, and constitute the largest infrastructure investment of the National Nanotechnology Initiative. The NSRCs are located at DOE’s Argonne, Brookhaven, Lawrence Berkeley, Oak Ridge and Sandia and Los Alamos national laboratories. For more information about the DOE NSRCs, please visit science.energy.gov/bes/suf/user-facilities/nanoscale-science-research-centers/.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit the Office of Science website at science.energy.gov/.

For more information, please click here

Contacts:
Lynn Yarris

510-486-5375

Copyright © DOE/Lawrence Berkeley National Laboratory

If you have a comment, please Contact us.

Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.

Bookmark:
Delicious Digg Newsvine Google Yahoo Reddit Magnoliacom Furl Facebook

Related Links

For more information about the research of Jim DeYoreo go here:

For more information about the Molecular Foundry go here:

For more information about the research of Carolyn Bertozzi go here:

Related News Press

News and information

Nano Ruffles in Brain Matter: Freiburg researchers decipher the role of nanostructures around brain cells in central nervous system function October 31st, 2014

Gold nanoparticle chains confine light to the nanoscale October 31st, 2014

'Nanomotor lithography' answers call for affordable, simpler device manufacturing October 31st, 2014

Device invented at Johns Hopkins provides up-close look at cancer on the move: Microscopic view of metastasis could give insight about how to keep cancer in check October 31st, 2014

Laboratories

Tiny carbon nanotube pores make big impact October 29th, 2014

New evidence for an exotic, predicted superconducting state October 27th, 2014

National Synchrotron Light Source II Achieves 'First Light' October 23rd, 2014

Novel Rocket Design Flight Tested: New Rocket Propellant and Motor Design Offers High Performance and Safety October 23rd, 2014

Govt.-Legislation/Regulation/Funding/Policy

Gold nanoparticle chains confine light to the nanoscale October 31st, 2014

'Nanomotor lithography' answers call for affordable, simpler device manufacturing October 31st, 2014

Device invented at Johns Hopkins provides up-close look at cancer on the move: Microscopic view of metastasis could give insight about how to keep cancer in check October 31st, 2014

'Electronic skin' could improve early breast cancer detection October 29th, 2014

Self Assembly

NYU Researchers Break Nano Barrier to Engineer the First Protein Microfiber October 23rd, 2014

NIST offers electronics industry 2 ways to snoop on self-organizing molecules October 22nd, 2014

‘Designer’ nanodevice could improve treatment options for cancer sufferers October 22nd, 2014

Crystallizing the DNA nanotechnology dream: Scientists have designed the first large DNA crystals with precisely prescribed depths and complex 3D features, which could create revolutionary nanodevices October 20th, 2014

Discoveries

Nano Ruffles in Brain Matter: Freiburg researchers decipher the role of nanostructures around brain cells in central nervous system function October 31st, 2014

Gold nanoparticle chains confine light to the nanoscale October 31st, 2014

'Nanomotor lithography' answers call for affordable, simpler device manufacturing October 31st, 2014

Device invented at Johns Hopkins provides up-close look at cancer on the move: Microscopic view of metastasis could give insight about how to keep cancer in check October 31st, 2014

Announcements

Nano Ruffles in Brain Matter: Freiburg researchers decipher the role of nanostructures around brain cells in central nervous system function October 31st, 2014

Gold nanoparticle chains confine light to the nanoscale October 31st, 2014

'Nanomotor lithography' answers call for affordable, simpler device manufacturing October 31st, 2014

Device invented at Johns Hopkins provides up-close look at cancer on the move: Microscopic view of metastasis could give insight about how to keep cancer in check October 31st, 2014

Nanobiotechnology

Tiny carbon nanotube pores make big impact October 29th, 2014

Molecular beacons shine light on how cells 'crawl' October 27th, 2014

Breakthrough in molecular electronics paves the way for DNA-based computer circuits in the future: DNA-based programmable circuits could be more sophisticated, cheaper and simpler to make October 27th, 2014

NYU Researchers Break Nano Barrier to Engineer the First Protein Microfiber October 23rd, 2014

NanoNews-Digest
The latest news from around the world, FREE





  Premium Products
NanoNews-Custom
Only the news you want to read!
 Learn More
NanoTech-Transfer
University Technology Transfer & Patents
 Learn More
NanoStrategies
Full-service, expert consulting
 Learn More














ASP
Nanotechnology Now Featured Books




NNN

The Hunger Project







© Copyright 1999-2014 7th Wave, Inc. All Rights Reserved PRIVACY POLICY :: CONTACT US :: STATS :: SITE MAP :: ADVERTISE