Nanotechnology Now

Our NanoNews Digest Sponsors


Heifer International

Wikipedia Affiliate Button


DHgate

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

GLOBALFOUNDRIES to Expand Presence in China with 300mm Fab in Chongqing: Company plans new manufacturing facility and additional design capabilities to serve customers in China May 31st, 2016

Nanobiotix establishes promising preclinical proof-of-concept in Immuno Oncology May 31st, 2016

UK NANOSAFETY GROUP publishes 2nd Edition of guidance to support safe working with nanomaterials May 30th, 2016

Fast, stretchy circuits could yield new wave of wearable electronics May 30th, 2016

Physics

Doubling down on Schrödinger's cat May 27th, 2016

Thermal modification of wood and a complex study of its properties by magnetic resonance May 26th, 2016

Theorists smooth the way to modeling quantum friction: New paradigm offers a strategy for solving one of quantum mechanics' oldest problems May 18th, 2016

Videos/Movies

Revealing the nature of magnetic interactions in manganese oxide: New technique for probing local magnetic interactions confirms 'superexchange' model that explains how the material gets its long-range magnetic order May 25th, 2016

Programmable materials find strength in molecular repetition May 23rd, 2016

Graphene makes rubber more rubbery May 23rd, 2016

ORNL demonstrates large-scale technique to produce quantum dots May 21st, 2016

Technique improves the efficacy of fuel cells: Research demonstrates a new phase transition from metal to ionic conductor May 18th, 2016

Chemistry

Syracuse University chemists add color to chemical reactions: Chemists in the College of Arts and Sciences have come up with an innovative new way to visualize and monitor chemical reactions in real time May 19th, 2016

Technique improves the efficacy of fuel cells: Research demonstrates a new phase transition from metal to ionic conductor May 18th, 2016

Software

Los Alamos National Laboratory Expands Scope to Locus Technologies SaaS Contract: Los Alamos National Laboratory Adds Two New Applications to Locus SaaS Platform May 7th, 2016

The intermediates in a chemical reaction photographed 'red-handed' Researchers at the UPV/EHU-University of the Basque Country have for the first time succeeded in imaging all the steps in a complex organic reaction and have resolved the mechanisms that explain it May 4th, 2016

University of Illinois researchers create 1-step graphene patterning method April 27th, 2016

The reliability of material simulations put to test April 26th, 2016

Govt.-Legislation/Regulation/Funding/Policy

Scientists illuminate a hidden regulator in gene transcription: New super-resolution technique visualizes important role of short-lived enzyme clusters May 27th, 2016

Doubling down on Schrödinger's cat May 27th, 2016

Harnessing solar and wind energy in one device could power the 'Internet of Things' May 26th, 2016

Thermal modification of wood and a complex study of its properties by magnetic resonance May 26th, 2016

Academic/Education

Graphene: Progress, not quantum leaps May 23rd, 2016

Smithsonian Science Education Center and National Space Society Team Up for Next-Generation Space Education Program "Enterprise In Space" May 11th, 2016

The University of Colorado Boulder, USA, combines Raman spectroscopy and nanoindentation for improved materials characterisation May 9th, 2016

Albertan Science Lab Opens in India May 7th, 2016

Announcements

GLOBALFOUNDRIES to Expand Presence in China with 300mm Fab in Chongqing: Company plans new manufacturing facility and additional design capabilities to serve customers in China May 31st, 2016

Nanobiotix establishes promising preclinical proof-of-concept in Immuno Oncology May 31st, 2016

UK NANOSAFETY GROUP publishes 2nd Edition of guidance to support safe working with nanomaterials May 30th, 2016

Fast, stretchy circuits could yield new wave of wearable electronics May 30th, 2016

Tools

Scientists illuminate a hidden regulator in gene transcription: New super-resolution technique visualizes important role of short-lived enzyme clusters May 27th, 2016

Light can 'heal' defects in new solar cell materials: Defects in some new electronic materials can be removed by making ions move under illumination May 24th, 2016

More light on cancer: Scientists created nanoparticles to highlight cancer cells May 21st, 2016

Nanotubes are beacons in cancer-imaging technique: Rice University researchers use spectral triangulation to pinpoint location of tumors May 21st, 2016

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







Car Brands
Buy website traffic