Nanotechnology Now

Our NanoNews Digest Sponsors





Heifer International

Wikipedia Affiliate Button


android tablet pc

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

HP Supercomputer at NREL Garners Top Honor October 19th, 2014

First Canada Excellence Research Chair gets $10 million from the federal government for oilsands research at the University of Calgary: Federal government announces prestigious research chair to study improving oil production efficiency October 19th, 2014

Ucore's McKenzie to Deliver Presentation to Rare Earths Conference in Singapore as Highlight of Fall 2014 Marketplace Schedule October 19th, 2014

Non-Toxic Nanocatalysts Open New Window for Significant Decrease in Reaction Process October 19th, 2014

Superconducting circuits, simplified: New circuit design could unlock the power of experimental superconducting computer chips October 18th, 2014

Videos/Movies

Ucore's McKenzie to Deliver Presentation to Rare Earths Conference in Singapore as Highlight of Fall 2014 Marketplace Schedule October 19th, 2014

Australian teams set new records for silicon quantum computing October 12th, 2014

Chemistry

Non-Toxic Nanocatalysts Open New Window for Significant Decrease in Reaction Process October 19th, 2014

QD Vision Wins Prestigious Presidential Green Chemistry Challenge Award from the U.S. Environmental Protection Agency October 16th, 2014

The Körber Foundation congratulates Stefan Hell on winning the 2014 Nobel Prize October 10th, 2014

Physics

Solid nanoparticles can deform like a liquid: Unexpected finding shows tiny particles keep their internal crystal structure while flexing like droplets October 12th, 2014

Unconventional photoconduction in an atomically thin semiconductor: New mechanism of photoconduction could lead to next-generation excitonic devices October 9th, 2014

Software

How things coil: Researchers discover that simulation technology designed for Hollywood can be used as a predictive tool for understanding fundamental engineering problems September 29th, 2014

Terabyte Photonic Dataset Sale July 30th, 2014

A*STAR and industry form S$200M semiconductor R&D July 25th, 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

Govt.-Legislation/Regulation/Funding/Policy

HP Supercomputer at NREL Garners Top Honor October 19th, 2014

First Canada Excellence Research Chair gets $10 million from the federal government for oilsands research at the University of Calgary: Federal government announces prestigious research chair to study improving oil production efficiency October 19th, 2014

Superconducting circuits, simplified: New circuit design could unlock the power of experimental superconducting computer chips October 18th, 2014

QD Vision Wins Prestigious Presidential Green Chemistry Challenge Award from the U.S. Environmental Protection Agency October 16th, 2014

Academic/Education

First Canada Excellence Research Chair gets $10 million from the federal government for oilsands research at the University of Calgary: Federal government announces prestigious research chair to study improving oil production efficiency October 19th, 2014

Raytheon, UMass Lowell open on-campus research institute: Industry leader’s researchers to collaborate with faculty, students to move key technologies forward through first-of-its-kind partnership October 11th, 2014

SUNY Colleges of Nanoscale Science and Engineering and National Institute for Occupational Safety and Health Announce Expanded Partnership October 2nd, 2014

Yale University and Leica Microsystems Partner to Establish Microscopy Center of Excellence: Yale Welcomes Scientists to Participate in Core Facility Opening and Super- Resolution Workshops October 20 Through 31, 2014 September 30th, 2014

Announcements

HP Supercomputer at NREL Garners Top Honor October 19th, 2014

First Canada Excellence Research Chair gets $10 million from the federal government for oilsands research at the University of Calgary: Federal government announces prestigious research chair to study improving oil production efficiency October 19th, 2014

Ucore's McKenzie to Deliver Presentation to Rare Earths Conference in Singapore as Highlight of Fall 2014 Marketplace Schedule October 19th, 2014

Non-Toxic Nanocatalysts Open New Window for Significant Decrease in Reaction Process October 19th, 2014

Tools

New Grand ARM Transmission Electron Microscope Offers Highest Commercially-Available Atomic Resolution of 63 Picometers October 17th, 2014

Nanodevices for clinical diagnostic with potential for the international market: The development is based on optical principles and provides precision and allows saving vital time for the patient October 15th, 2014

Nanotronics Imaging Releases nSPEC® 3D, Powerful Microscope That Captures 3D Images at Nanoscale, in Lightning Speed: Company Unveils Design at American Chemical Society 2014 International Elastomer Conference October 14th, 2014

Unique catalysts for hydrogen fuel cells synthesized in ordinary kitchen microwave oven October 14th, 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