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

Haydale and Goodfellow Announce Major Distribution Agreement for Functionalised Graphene Materials July 21st, 2014

Relaunch of the Nanoscribe Website New design, optimized research, and impressive gallery of applications July 21st, 2014

Dongbu HiTek Unveils Low-Voltage BCDMOS Process for Efficient Power Management in Smart Phones and Tablet Computers July 21st, 2014

Iran to Host 1st Asian Congress on Nanostructures on Kish Island July 21st, 2014

Laboratories

Sono-Tek Corporation Announces New Clean Room Rated Laboratory Facility in China July 18th, 2014

Fundamental Chemistry Findings Could Help Extend Moore’s Law: A Berkeley Lab-Intel collaboration outlines the chemistry of photoresist, enabling smaller features for future generations of microprocessors July 15th, 2014

Labs characterize carbon for batteries: Rice, Lawrence Livermore scientists calculate materials’ potential for use as electrodes July 14th, 2014

Ribosome Research in Atomic Detail Offers Potential Insights into Cancer, Anemia, Alzheimer’s: New movement during decoding occurs in humans, not in bacteria July 3rd, 2014

Govt.-Legislation/Regulation/Funding/Policy

Oregon chemists eye improved thin films with metal substitution: Solution-based inorganic process could drive more efficient electronics and solar devices July 21st, 2014

More than glitter: Scientists explain how gold nanoparticles easily penetrate cells, making them useful for delivering drugs July 21st, 2014

Carbyne morphs when stretched: Rice University calculations show carbon-atom chain would go metal to semiconductor July 21st, 2014

Tiny laser sensor heightens bomb detection sensitivity July 19th, 2014

Self Assembly

Berkeley Lab researchers create nanoparticle thin films that self-assemble in 1 minute June 9th, 2014

Design of self-assembling protein nanomachines starts to click: A nanocage builds itself from engineered components June 5th, 2014

Molecular self-assembly scales up from nanometers to millimeters June 5th, 2014

Nano world: Where towers construct themselves: How physicists get control on the self-assembly process June 2nd, 2014

Discoveries

Oregon chemists eye improved thin films with metal substitution: Solution-based inorganic process could drive more efficient electronics and solar devices July 21st, 2014

Steam from the sun: New spongelike structure converts solar energy into steam July 21st, 2014

More than glitter: Scientists explain how gold nanoparticles easily penetrate cells, making them useful for delivering drugs July 21st, 2014

Carbyne morphs when stretched: Rice University calculations show carbon-atom chain would go metal to semiconductor July 21st, 2014

Announcements

Oxford Instruments Asylum Research Opens an Atomic Force Microscopy Demonstration Lab in Mumbai, India July 21st, 2014

Steam from the sun: New spongelike structure converts solar energy into steam July 21st, 2014

More than glitter: Scientists explain how gold nanoparticles easily penetrate cells, making them useful for delivering drugs July 21st, 2014

Iran to Host 1st Asian Congress on Nanostructures on Kish Island July 21st, 2014

Nanobiotechnology

Production of Non-Virus Nanocarriers with Highest Amount of Gene Delivery July 17th, 2014

Physicists Use Computer Models to Reveal Quantum Effects in Biological Oxygen Transport: The team solved a long-standing question by explaining why oxygen – and not deadly carbon monoxide – preferably binds to the proteins that transport it around the body. July 17th, 2014

Tiny DNA pyramids enter bacteria easily -- and deliver a deadly payload July 9th, 2014

Artificial cilia: Scientists from Kiel University develop nano-structured transportation system July 4th, 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