Nanotechnology Now

Our NanoNews Digest Sponsors
Heifer International



Home > Press > Dancing in the dark: how proteins and salts interact

Simulation of the interaction between triglycine and dissolved sodium sulfite in water shows the long chain-like triglycine molecule (center) interacting directly with sulfite anions (tripods of yellow and red atoms) while also interacting via multiple hydrogen bonds (thin red or blue lines) with the surrounding water molecules (red and white sticks). Courtesy Berkeley Lab
Simulation of the interaction between triglycine and dissolved sodium sulfite in water shows the long chain-like triglycine molecule (center) interacting directly with sulfite anions (tripods of yellow and red atoms) while also interacting via multiple hydrogen bonds (thin red or blue lines) with the surrounding water molecules (red and white sticks). Courtesy Berkeley Lab

Abstract:
Scientists are getting a new look at how proteins interact with simple salts in water, and what impacts these interactions may have on protein structures at the atomic level.

Dancing in the dark: how proteins and salts interact

Berkeley, CA | Posted on August 13th, 2010

To study nanostructures in real environments, Berkeley Lab scientists have combined theoretical and experimental approaches to glimpse into a protein's interaction with simple salts in water. Enabled by x-ray absorption simulation software developed at Berkeley Lab's Molecular Foundry, these findings shed new light on how salts impact protein structure at the atomic level.

Traditional crystallographic techniques, such as x-ray diffraction, provide a profile of ordered materials with static structures. However, for dynamic or complex systems in which the atomic structure is rapidly changing, more sophisticated methods are needed. Now, Berkeley Lab scientists have applied x-ray absorption spectroscopy to study a model protein, triglycine—a short chain of three molecules of the simplest amino acid, glycine. By simulating this molecule's x-ray absorption spectrum the team has show how its chain kinks and straightens in response to ions in solution.

"Watching a molecule in solution is like watching a marionette—you can see it bending in response to making and breaking of hydrogen bonds," said David Prendergast, a staff scientist in the Theory of Nanostructures Facility at the Molecular Foundry. "A concrete knowledge of how ions influence this behavior comes from using molecular dynamics simulations, which show persistent differences in structure on nanosecond timescales. From this data we can generate x-ray absorption spectra which can then be compared with experimental results."

In a specialized x-ray absorption experiment called near edge x-ray absorption fine structure (NEXAFS), x-rays are used to probe the chemical bonding and environment of specific elements in a molecule or nanostructure, such as the nitrogen atoms in a triglycine molecule. Coupled with a liquid microjet technology developed at Berkeley Labs, NEXAFS has been previously used to examine how proteins dissolve and crystallize in the presence of various ions .

Prendergast's software can now simulate NEXAFS data by averaging a series of snapshots taken from a molecular dynamics simulation of a given molecule. This software is a critical tool for interpreting NEXAFS data from complex, dynamic systems, as the probe times in these measurements are too slow—seconds rather than nanoseconds—to reveal structural differences at the nanoscale.

"Previous studies from our group have shown the development of x-ray absorption spectroscopy of liquid microjets provides a new atom-sensitive probe of the interactions between aqueous ions, but it is the advent of this new theory that provides the first reliable molecular-level interpretation of these data," said Richard Saykally, a Berkeley Lab chemist and professor of chemistry at the University of California at Berkeley. "Here we see this new combination of theory and experiment applied to one of the most important problems in biophysical chemistry."

Prendergast says his molecular dynamics technique can be used to model x-ray spectra of a biological system with known structure to determine its local interactions, what causes it to form a particular structure, and why it takes on a particular conformation—all by simulating the spectra of a series of individual snapshots and comparing with experimental results. These simulations are computationally intensive and rely heavily on the large-scale supercomputing infrastructure provided by Berkeley Lab's National Energy Research Scientific Computing Center (NERSC).

"Although these effects are a fundamental part of nature, they are still poorly understood," said Craig Schwartz, a researcher working with Prendergast and Saykally, whose graduate work led to this publication. "The experimental sensitivity of NEXAFS, coupled with a breakthrough in theory, gave us new insight into how these molecules interact."

The researchers anticipate demand from other groups exploring water (or other solvent) interactions, as well as both soft materials (such as polymers) and inorganic materials (oxides and metal surfaces) that are directly relevant to energy-related applications in catalysis, battery technology and photovoltaics. In addition, as x-ray free electron laser sources become available to scientists, a richer experimental data set will be available to augment theoretical findings.

A paper reporting this research titled, "Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy," appears in Proceedings of the National Academy of Sciences and is available to subscribers online (*). Co-authoring the paper with Schwartz, Prendergast and Saykally were Janel Uejio, Andrew Duffin, Alice England and Daniel Kelly.

This work at the Molecular Foundry and Advanced Light Source was supported by DOE's Office of Science. Computational resources were provided by NERSC, a DOE advanced scientific computing research user facility.

(*) www.pnas.org/content/107/32/14008.abstract

####

About Berkeley Lab
Berkeley Lab is a U.S. Department of Energy national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California.

For more information, please click here

Contacts:
Aditi Risbud (510)486-4861

Copyright © Berkeley Lab

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 News Press

Chemistry

Quantum interference in molecule-surface collisions February 28th, 2025

Chainmail-like material could be the future of armor: First 2D mechanically interlocked polymer exhibits exceptional flexibility and strength January 17th, 2025

Breaking carbon–hydrogen bonds to make complex molecules November 8th, 2024

News and information

Researchers are cracking the code on solid-state batteries: Using a combination of advanced imagery and ultra-thin coatings, University of Missouri researchers are working to revolutionize solid-state battery performance February 28th, 2025

Unraveling the origin of extremely bright quantum emitters: Researchers from Osaka University have discovered the fundamental properties of single-photon emitters at an oxide/semiconductor interface, which could be crucial for scalable quantum technology February 28th, 2025

Closing the gaps — MXene-coating filters can enhance performance and reusability February 28th, 2025

Rice researchers harness gravity to create low-cost device for rapid cell analysis February 28th, 2025

Physics

Department of Energy announces $71 million for research on quantum information science enabled discoveries in high energy physics: Projects combine theory and experiment to open new windows on the universe January 17th, 2025

‘Brand new physics’ for next generation spintronics: Physicists discover a unique quantum behavior that offers a new way to manipulate electron-spin and magnetization to push forward cutting-edge spintronic technologies, like computing that mimics the human brain January 17th, 2025

Videos/Movies

New X-ray imaging technique to study the transient phases of quantum materials December 29th, 2022

Solvent study solves solar cell durability puzzle: Rice-led project could make perovskite cells ready for prime time September 23rd, 2022

Scientists prepare for the world’s smallest race: Nanocar Race II March 18th, 2022

Visualizing the invisible: New fluorescent DNA label reveals nanoscopic cancer features March 4th, 2022

Software

Visualizing nanoscale structures in real time: Open-source software enables researchers to see materials in 3D while they're still on the electron microscope August 19th, 2022

Luisier wins SNSF Advanced Grant to develop simulation tools for nanoscale devices July 8th, 2022

Govt.-Legislation/Regulation/Funding/Policy

Rice researchers harness gravity to create low-cost device for rapid cell analysis February 28th, 2025

Department of Energy announces $71 million for research on quantum information science enabled discoveries in high energy physics: Projects combine theory and experiment to open new windows on the universe January 17th, 2025

Quantum engineers ‘squeeze’ laser frequency combs to make more sensitive gas sensors January 17th, 2025

Chainmail-like material could be the future of armor: First 2D mechanically interlocked polymer exhibits exceptional flexibility and strength January 17th, 2025

Academic/Education

Rice University launches Rice Synthetic Biology Institute to improve lives January 12th, 2024

Multi-institution, $4.6 million NSF grant to fund nanotechnology training September 9th, 2022

National Space Society Helps Fund Expanding Frontier’s Brownsville Summer Entrepreneur Academy: National Space Society and Club for the Future to Support Youth Development Program in South Texas June 24th, 2022

How a physicist aims to reduce the noise in quantum computing: NAU assistant professor Ryan Behunin received an NSF CAREER grant to study how to reduce the noise produced in the process of quantum computing, which will make it better and more practical April 1st, 2022

Announcements

Development of 'transparent stretchable substrate' without image distortion could revolutionize next-generation displays Overcoming: Poisson's ratio enables fully transparent, distortion-free, non-deformable display substrates February 28th, 2025

Unraveling the origin of extremely bright quantum emitters: Researchers from Osaka University have discovered the fundamental properties of single-photon emitters at an oxide/semiconductor interface, which could be crucial for scalable quantum technology February 28th, 2025

Closing the gaps — MXene-coating filters can enhance performance and reusability February 28th, 2025

Rice researchers harness gravity to create low-cost device for rapid cell analysis February 28th, 2025

Tools

Rice researchers harness gravity to create low-cost device for rapid cell analysis February 28th, 2025

New 2D multifractal tools delve into Pollock's expressionism January 17th, 2025

New material to make next generation of electronics faster and more efficient With the increase of new technology and artificial intelligence, the demand for efficient and powerful semiconductors continues to grow November 8th, 2024

Turning up the signal November 8th, 2024

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




  Premium Products
NanoNews-Custom
Only the news you want to read!
 Learn More
NanoStrategies
Full-service, expert consulting
 Learn More











ASP
Nanotechnology Now Featured Books




NNN

The Hunger Project