Nanotechnology Now





Heifer International

Wikipedia Affiliate Button


DHgate

Home > Press > Computer Simulations Yield Clues to How Cells Interact With Surroundings: Berkeley Lab research has implications for cancer, atherosclerosis research

Computer models offer a new look at the molecular machinery that enables cells to interact with their environment. This schematic shows two integrin components (red and blue) protruding from a cell membrane.Credit: Mofrad lab
Computer models offer a new look at the molecular machinery that enables cells to interact with their environment. This schematic shows two integrin components (red and blue) protruding from a cell membrane.

Credit: Mofrad lab

Abstract:
Your cells are social butterflies. They constantly interact with their surroundings, taking in cues on when to divide and where to anchor themselves, among other critical tasks.

This networking is driven in part by proteins called integrin, which reside in a cell's outer plasma membrane. Their job is to convert mechanical forces from outside the cell into internal chemical signals that tell the cell what to do. That is, when they work properly. When they misfire, integrins can cause diseases such as atherosclerosis and several types of cancer.

Computer Simulations Yield Clues to How Cells Interact With Surroundings: Berkeley Lab research has implications for cancer, atherosclerosis research

Berkeley, CA | Posted on March 25th, 2013

Despite their importance—good and bad—scientists don't exactly know how integrins work. That's because it's very difficult to experimentally observe the protein's molecular machinery in action. Scientists have yet to obtain the entire crystal structure of integrin within the plasma membrane, which is a go-to way to study a protein's function. Roadblocks like this have ensured that integrins remain a puzzle despite years of research.

But what if there was another way to study integrin? One that doesn't rely on experimental methods? Now there is, thanks to a computer model of integrin developed by Berkeley Lab researchers. Like its biological counterpart, the virtual integrin snippet is about twenty nanometers long. It also responds to changes in energy and other stimuli just as integrins do in real life. The result is a new way to explore how the protein connects a cell's inner and outer environments.

"We can now run computer simulations that reveal how integrins in the plasma membrane translate external mechanical cues to chemical signals within the cell," says Mohammad Mofrad, a faculty scientist in Berkeley Lab's Physical Biosciences Division and associate professor of Bioengineering and Mechanical Engineering at UC Berkeley. He conducted the research with his graduate student Mehrdad Mehrbod.

They report their research in a recent issue of PLoS Computational Biology.

Their "molecular dynamics" model is the latest example of computational biology, in which scientists use computers to analyze biological phenomena for insights that may not be available via experiment. As you'd expect from a model that accounts for the activities of half a million atoms at once, the integrin model takes a lot of computing horsepower to pull off. Some of its simulations require 48 hours of run time on 600 parallel processors at the U.S. Department of Energy's (DOE) National Energy Research Scientific Computing Center (NERSC), which is located at Berkeley Lab.

The model is already shedding light on what makes integrin tick, such as how they "know" to respond to more force with greater numbers. When activated by an external force, integrins cluster together on a cell's surface and join other proteins to form structures called focal adhesions. These adhesions recruit more integrins when they're subjected to higher forces. As the model indicates, this ability to pull in more integrins on demand may be due to the fact that a subunit of integrin is connected to actin filaments, which form a cell's skeleton.

"We found that if actin filaments sustain more forces, they automatically bring more integrins together, forming a larger cluster," says Mehrbod.

The model may also help answer a longstanding question: Do integrins interact with each other immediately after they're activated? Or do they not interact with each other at all, even as they cluster together?

To find out, the scientists ran simulations that explored whether it's physically possible for integrins to interact when they're embedded in the plasma membrane. They found that interactions are likely to occur only between one compartment of integrin called the β-subunit.

They also discovered an interesting pattern in which integrins fluctuate. Two integrin sections, one that spans the cell membrane and one that protrudes from the cell, are connected by a hinge-like region. This hinge swings about when the protein is forced to vibrate as a result of frequent kicks from other molecules around it, such as water molecules, lipids, and ions.

These computationally obtained insights could guide new experiments designed to uncover how integrins do their job.

"Our research sets up an avenue for future studies by offering a hypothesis that relates integrin activation and clustering," says Mofrad.

The research was supported by a National Science Foundation CAREER award to Mofrad. NERSC is supported by DOE's Office of Science.

####

About Berkeley Lab
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.

For more information, please click here

Contacts:
Dan Krotz

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

Laboratories

Influential Interfaces Lead to Advances in Organic Spintronics July 1st, 2015

NIST ‘How-To’ Website Documents Procedures for Nano-EHS Research and Testing July 1st, 2015

Ultra-stable JILA microscopy technique tracks tiny objects for hours July 1st, 2015

News and information

Leti Announces Launch of First European Nanomedicine Characterisation Laboratory: Project Combines Expertise of 9 Partners in 8 Countries to Foster Nanomedicine Innovation and Facilitate Regulatory Approval July 1st, 2015

Bruker Introduces Second-Generation Inspire Nanochemical Imaging Solution: Featuring Unique PeakForce IR and IR EasyAlign Technology July 1st, 2015

GLOBALFOUNDRIES Completes Acquisition of IBM Microelectronics Business: Transaction adds differentiating technologies, world-class technologists, and intellectual property July 1st, 2015

Samsung's New Graphene Technology Will Double Life Of Your Lithium-Ion Battery July 1st, 2015

Govt.-Legislation/Regulation/Funding/Policy

Influential Interfaces Lead to Advances in Organic Spintronics July 1st, 2015

NIST ‘How-To’ Website Documents Procedures for Nano-EHS Research and Testing July 1st, 2015

Ultra-stable JILA microscopy technique tracks tiny objects for hours July 1st, 2015

Proposed TSCA Nanomaterial Rule ‘Premature’, Says Former EPA Toxicologist July 1st, 2015

Nanomedicine

Leti Announces Launch of First European Nanomedicine Characterisation Laboratory: Project Combines Expertise of 9 Partners in 8 Countries to Foster Nanomedicine Innovation and Facilitate Regulatory Approval July 1st, 2015

Carnegie Mellon chemists characterize 3-D macroporous hydrogels: Methods will allow researchers to develop new 'smart' materials June 30th, 2015

Chitosan coated, chemotherapy packed nanoparticles may target cancer stem cells June 30th, 2015

Researchers from the UCA, key players in a pioneering study that may explain the origin of several digestive diseases June 30th, 2015

Discoveries

Influential Interfaces Lead to Advances in Organic Spintronics July 1st, 2015

Ultra-stable JILA microscopy technique tracks tiny objects for hours July 1st, 2015

Emergence of a 'devil's staircase' in a spin-valve system July 1st, 2015

Measurement of Tiny Amounts of Heavy Metals in Baby Food Samples July 1st, 2015

Announcements

Leti Announces Launch of First European Nanomedicine Characterisation Laboratory: Project Combines Expertise of 9 Partners in 8 Countries to Foster Nanomedicine Innovation and Facilitate Regulatory Approval July 1st, 2015

Bruker Introduces Second-Generation Inspire Nanochemical Imaging Solution: Featuring Unique PeakForce IR and IR EasyAlign Technology July 1st, 2015

GLOBALFOUNDRIES Completes Acquisition of IBM Microelectronics Business: Transaction adds differentiating technologies, world-class technologists, and intellectual property July 1st, 2015

Samsung's New Graphene Technology Will Double Life Of Your Lithium-Ion Battery July 1st, 2015

Nanobiotechnology

Nanometric sensor designed to detect herbicides can help diagnose multiple sclerosis June 23rd, 2015

Newly-Developed Biosensor in Iran Detects Cocaine Addiction June 23rd, 2015

Researchers first to show that Saharan silver ants can control electromagnetic waves over an extremely broad range of the electromagnetic spectrum—findings may lead to biologically inspired coatings for passive radiative cooling of objects June 19th, 2015

Cellulose from wood can be printed in 3-D June 17th, 2015

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