Nanotechnology Now

Our NanoNews Digest Sponsors

Heifer International

Wikipedia Affiliate Button

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

News and information

Spin current detection in quantum materials unlocks potential for alternative electronics October 15th, 2017

Quantum manipulation power for quantum information processing gets a boost: Improving the efficiency of quantum heat engines involves reducing the number of photons in a cavity, ultimately impacting quantum manipulation power October 14th, 2017

Injecting electrons jolts 2-D structure into new atomic pattern: Berkeley Lab study is first to show potential of energy-efficient next-gen electronic memory October 13th, 2017

The secret to improving liquid crystal's mechanical performance: Better lubricating properties of lamellar liquid crystals could stem from changing the mobility of their structural dislocations by adding nanoparticles October 13th, 2017

Rice U. lab surprised by ultraflat magnets: Researchers create atom-thick alloys with unanticipated magnetic properties October 13th, 2017

Physics

The secret to improving liquid crystal's mechanical performance: Better lubricating properties of lamellar liquid crystals could stem from changing the mobility of their structural dislocations by adding nanoparticles October 13th, 2017

What can be discovered at the junction of physics and chemistry October 6th, 2017

Energy against the current on a quantum scale, without contradicting the laws of physics: A piece of research in which the UPV/EHU-University of the Basque Country has participated confirms that merely observing a flow of energy or particles can change its direction October 6th, 2017

Tungsten offers nano-interconnects a path of least resistance: Crystalline tungsten shows insight and promise in addressing the challenges of electrical interconnects that have high resistivity at the nanoscale October 4th, 2017

Chemistry

What can be discovered at the junction of physics and chemistry October 6th, 2017

Copper catalyst yields high efficiency CO2-to-fuels conversion: Berkeley Lab scientists discover critical role of nanoparticle transformation September 20th, 2017

Videos/Movies

Columbia engineers invent breakthrough millimeter-wave circulator IC October 6th, 2017

DNA triggers shape-shifting in hydrogels, opening a new way to make 'soft robots' September 21st, 2017

Researchers printed graphene-like materials with inkjet August 17th, 2017

Freeze-dried foam soaks up carbon dioxide: Rice University scientists lead effort to make novel 3-D material August 16th, 2017

Software

Leti Launches Emulator Service to Boost ROI and Speed Time to Market for European Chipmakers: Anchored by Mentor Veloce Emulator Machine, Leti’s Offer Includes Support for Design, Debug and Analysis of Results August 31st, 2017

Technology Companies Join Forces for TEM Imaging and Analysis August 3rd, 2017

Govt.-Legislation/Regulation/Funding/Policy

Spin current detection in quantum materials unlocks potential for alternative electronics October 15th, 2017

Injecting electrons jolts 2-D structure into new atomic pattern: Berkeley Lab study is first to show potential of energy-efficient next-gen electronic memory October 13th, 2017

Rice U. lab surprised by ultraflat magnets: Researchers create atom-thick alloys with unanticipated magnetic properties October 13th, 2017

On the road to fire-free, lithium-ion batteries made with asphalt October 12th, 2017

Academic/Education

Two Scientists Receive Grants to Develop New Materials: Chad Mirkin and Monica Olvera de la Cruz recognized by Sherman Fairchild Foundation August 16th, 2017

Moving at the Speed of Light: University of Arizona selected for high-impact, industrial demonstration of new integrated photonic cryogenic datalink for focal plane arrays: Program is major milestone for AIM Photonics August 10th, 2017

Graduate Students from Across the Country Attend Hands-on NanoCamp: Prominent scientists Warren Oliver, Ph.D., and George Pharr, Ph.D., presented a weeklong NanoCamp for hand-picked graduate students across the United States July 26th, 2017

The Physics Department of Imperial College, London, uses the Quorum Q150T to deposit metals and ITO to make plasmonic sensors and electric contact pads July 13th, 2017

Announcements

Spin current detection in quantum materials unlocks potential for alternative electronics October 15th, 2017

Quantum manipulation power for quantum information processing gets a boost: Improving the efficiency of quantum heat engines involves reducing the number of photons in a cavity, ultimately impacting quantum manipulation power October 14th, 2017

Injecting electrons jolts 2-D structure into new atomic pattern: Berkeley Lab study is first to show potential of energy-efficient next-gen electronic memory October 13th, 2017

The secret to improving liquid crystal's mechanical performance: Better lubricating properties of lamellar liquid crystals could stem from changing the mobility of their structural dislocations by adding nanoparticles October 13th, 2017

Tools

Nanometrics Announces Preliminary Results for the Third Quarter of 2017: Quarterly Results Impacted by Delays in Revenue Recognition on Multiple Systems into Japan October 12th, 2017

Seeing the next dimension of computer chips: Researchers image perfectly smooth side-surfaces of 3-D silicon crystals with a scanning tunneling microscope, paving the way for smaller and faster computing devices October 11th, 2017

Quorum announces new customer support and demonstration facilities for users worldwide October 10th, 2017

Graphene forged into three-dimensional shapes September 26th, 2017

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