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

News and information

Scientific breakthrough in rechargeable batteries: Researchers from Singapore and Québec Team Up to Develop Next-Generation Materials to Power Electronic Devices and Electric Vehicles February 28th, 2015

First detailed microscopy evidence of bacteria at the lower size limit of life: Berkeley Lab research provides comprehensive description of ultra-small bacteria February 28th, 2015

Leti to Offer Updates on Silicon Photonics Successes at OFC in LA February 27th, 2015

Moving molecule writes letters: Caging of molecules allows investigation of equilibrium thermodynamics February 27th, 2015

Laboratories

First detailed microscopy evidence of bacteria at the lower size limit of life: Berkeley Lab research provides comprehensive description of ultra-small bacteria February 28th, 2015

Govt.-Legislation/Regulation/Funding/Policy

First detailed microscopy evidence of bacteria at the lower size limit of life: Berkeley Lab research provides comprehensive description of ultra-small bacteria February 28th, 2015

Warming up the world of superconductors: Clusters of aluminum metal atoms become superconductive at surprisingly high temperatures February 25th, 2015

SUNY Poly CNSE Researchers and Corporate Partners to Present Forty Papers at Globally Recognized Lithography Conference: SUNY Poly CNSE Research Group Awarded Both ‘Best Research Paper’ and ‘Best Research Poster’ at SPIE Advanced Lithography 2015 forum February 25th, 2015

European roadmap for graphene science and technology published February 25th, 2015

Nanomedicine

Untangling DNA with a droplet of water, a pipet and a polymer: With the 'rolling droplet technique,' a DNA-injected water droplet rolls like a ball over a platelet, sticking the DNA to the plate surface February 27th, 2015

Graphene shows potential as novel anti-cancer therapeutic strategy: University of Manchester scientists have used graphene to target and neutralise cancer stem cells while not harming other cells February 26th, 2015

Cutting-edge technology optimizes cancer therapy with nanomedicine drug combinations: UCLA bioengineers develop platform that offers personalized approach to treatment February 24th, 2015

Optical nanoantennas set the stage for a NEMS lab-on-a-chip revolution February 24th, 2015

Discoveries

First detailed microscopy evidence of bacteria at the lower size limit of life: Berkeley Lab research provides comprehensive description of ultra-small bacteria February 28th, 2015

Leti to Offer Updates on Silicon Photonics Successes at OFC in LA February 27th, 2015

Moving molecule writes letters: Caging of molecules allows investigation of equilibrium thermodynamics February 27th, 2015

Untangling DNA with a droplet of water, a pipet and a polymer: With the 'rolling droplet technique,' a DNA-injected water droplet rolls like a ball over a platelet, sticking the DNA to the plate surface February 27th, 2015

Announcements

Scientific breakthrough in rechargeable batteries: Researchers from Singapore and Québec Team Up to Develop Next-Generation Materials to Power Electronic Devices and Electric Vehicles February 28th, 2015

First detailed microscopy evidence of bacteria at the lower size limit of life: Berkeley Lab research provides comprehensive description of ultra-small bacteria February 28th, 2015

Leti to Offer Updates on Silicon Photonics Successes at OFC in LA February 27th, 2015

Moving molecule writes letters: Caging of molecules allows investigation of equilibrium thermodynamics February 27th, 2015

Nanobiotechnology

Untangling DNA with a droplet of water, a pipet and a polymer: With the 'rolling droplet technique,' a DNA-injected water droplet rolls like a ball over a platelet, sticking the DNA to the plate surface February 27th, 2015

Bacteria network for food: Bacteria connect to each other and exchange nutrients February 23rd, 2015

Building tailor-made DNA nanotubes step by step: New, block-by-block assembly method could pave way for applications in opto-electronics, drug delivery February 23rd, 2015

Better batteries inspired by lowly snail shells: Biological molecules can latch onto nanoscale components and lock them into position to make high performing Li-ion battery electrodes, according to new research presented at the 59th annual meeting of the Biophysical Society February 12th, 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







© Copyright 1999-2015 7th Wave, Inc. All Rights Reserved PRIVACY POLICY :: CONTACT US :: STATS :: SITE MAP :: ADVERTISE