Nanotechnology Now

Our NanoNews Digest Sponsors

Heifer International

Wikipedia Affiliate Button

Home > Press > Cryo-electron microscopy achieves unprecedented resolution using new computational methods

Complete capsid of bacteriophage P22 generated with validated atomic models that were derived from a high-resolution cryo-electron microscopy density map.
CREDIT
C. Hryc and the Chiu Lab, Baylor College of Medicine
Complete capsid of bacteriophage P22 generated with validated atomic models that were derived from a high-resolution cryo-electron microscopy density map. CREDIT C. Hryc and the Chiu Lab, Baylor College of Medicine

Abstract:
Cryo-electron microscopy (cryo-EM)--which enables the visualization of viruses, proteins, and other biological structures at the molecular level--is a critical tool used to advance biochemical knowledge. Now Lawrence Berkeley National Laboratory (Berkeley Lab) researchers have extended cryo-EM's impact further by developing a new computational algorithm that was instrumental in constructing a 3-D atomic-scale model of bacteriophage P22 for the first time.

Cryo-electron microscopy achieves unprecedented resolution using new computational methods

Berkeley, CA | Posted on March 25th, 2017

Over 20,000 two-dimensional cryo-EM images of bacteriophage P22 (also known as the P22 virus that infects the common bacterium Salmonella) from Baylor College of Medicine were used to make the model. The results were published by researchers from Baylor College of Medicine, Massachusetts Institute of Technology, Purdue University and Berkeley Lab in the Proceedings of the National Academies of Sciences earlier in March.

"This is a great example of how to exploit electron microscopy technology and combine it with new computational methods to determine a bacteriophage's structure," said Paul Adams, Berkeley Lab's Molecular Biophysics & Integrated Bioimaging division director and a co-author of the paper. "We developed the algorithms -- the computational code -- to optimize the atomic model so that it best fit the experimental data."

Pavel Afonine, a Berkeley Lab computational research scientist and paper co-author, took the lead in developing the algorithm using Phenix, a software suite used traditionally in X-ray crystallography for determining macromolecular structures.

The successful rendering of bacteriophage P22's 3-D atomic-scale model allows researchers to peek inside the virus' protein coats at resolution. It is the culmination of several years of work that previously had enabled Baylor College researchers to trace out most of the protein's backbone, but not the fine details, according to Corey Hryc, co-first author and a graduate student of Baylor biochemistry professor Wah Chiu.

"Thanks to this exquisite structural detail, we have determined the protein chemistry of the P22 virus," Chiu said. "I think it is important that we provide detailed annotations with the structure so other researchers can use it for their future experiments," he added. Chiu's lab has been using cryo-EM and computer reconstruction techniques to build 3-D molecular structures for almost 30 years.

And the findings could have valuable biological implications as well.

Thanks to the 3-D atomic-scale model, it's now "possible to see the interactions between the pieces making up the P22 virus, which are critical to making it stable," Adams said. This helps researchers figure out how to make chemicals that can bind to certain proteins. Adams underscores that the ability to understand the configuration of atoms in molecular space can be used to generate new insights into drug design and development.

###

The National Institutes of Health funded this work.

####

About Lawrence Berkeley National Laboratory
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.

DOE's Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

For more information, please click here

Contacts:
Jon Weiner

510-486-4014

Copyright © Lawrence Berkeley National Laboratory

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

Nanobiotix: Update on Head and Neck Phase I/II Trial with NBTXR3 and Other program data presented at ImmunoRad 2018 September 20th, 2018

NUS researchers invent new test kit for quick, accurate and low-cost screening of diseases: Test results are denoted by a color change and could be further analyzed by a smartphone app, making it attractive as a point-of-care diagnostic device September 19th, 2018

Silver nanoparticles are toxic for aquatic organisms: A research team at the UPV/EHU-University of the Basque Country has analysed how zebrafish are affected in the long term by exposure to silver particles September 19th, 2018

Leti Announces EU Project to Develop Powerful, Inexpensive Sensors with Photonic Integrated Circuits: REDFINCH Members Initially Targeting Applications for Gas Detection and Analysis For Refineries & Petrochemical Industry and Protein Analysis for Dairy Industry September 19th, 2018

Imaging

Tiny camera lens may help link quantum computers to network September 14th, 2018

Carbon nanodots do an ultrafine job with in vitro lung tissue: New experiments highlight the role of charge and size when it comes to carbon nanodots that mimic the effect of nanoscale pollution particles on the human lung. September 12th, 2018

Terahertz spectroscopy enters the single-molecule regime September 7th, 2018

Peering into private life of atomic clusters -- using the world's tiniest test tubes September 6th, 2018

Laboratories

Cannibalistic materials feed on themselves to grow new nanostructures September 1st, 2018

A Novel Graphene Quantum Dot Structure Takes the Cake August 24th, 2018

Virginia Tech researchers develop novel process to 3D print one of the strongest materials on Earth August 23rd, 2018

Connecting the (Nano) Dots: NIST Says Big-Picture Thinking Can Advance Nanoparticle Manufacturing August 22nd, 2018

Govt.-Legislation/Regulation/Funding/Policy

Researchers develop microbubble scrubber to destroy dangerous biofilms September 19th, 2018

Researchers managed to prevent the disappearing of quantum information September 14th, 2018

New photonic chip promises more robust quantum computers September 14th, 2018

Could a demon help to create a quantum computer? Physicists implement a version of Maxwell's famous thought experiment for reducing entropy September 5th, 2018

Possible Futures

NUS researchers invent new test kit for quick, accurate and low-cost screening of diseases: Test results are denoted by a color change and could be further analyzed by a smartphone app, making it attractive as a point-of-care diagnostic device September 19th, 2018

Silver nanoparticles are toxic for aquatic organisms: A research team at the UPV/EHU-University of the Basque Country has analysed how zebrafish are affected in the long term by exposure to silver particles September 19th, 2018

Leti Announces EU Project to Develop Powerful, Inexpensive Sensors with Photonic Integrated Circuits: REDFINCH Members Initially Targeting Applications for Gas Detection and Analysis For Refineries & Petrochemical Industry and Protein Analysis for Dairy Industry September 19th, 2018

Researchers develop microbubble scrubber to destroy dangerous biofilms September 19th, 2018

Nanomedicine

Nanobiotix: Update on Head and Neck Phase I/II Trial with NBTXR3 and Other program data presented at ImmunoRad 2018 September 20th, 2018

NUS researchers invent new test kit for quick, accurate and low-cost screening of diseases: Test results are denoted by a color change and could be further analyzed by a smartphone app, making it attractive as a point-of-care diagnostic device September 19th, 2018

Researchers develop microbubble scrubber to destroy dangerous biofilms September 19th, 2018

Halas wins American Chemical Society Award in Colloid Chemistry: Rice University nanophotonics pioneer honored for colloid research September 18th, 2018

Discoveries

NUS researchers invent new test kit for quick, accurate and low-cost screening of diseases: Test results are denoted by a color change and could be further analyzed by a smartphone app, making it attractive as a point-of-care diagnostic device September 19th, 2018

Silver nanoparticles are toxic for aquatic organisms: A research team at the UPV/EHU-University of the Basque Country has analysed how zebrafish are affected in the long term by exposure to silver particles September 19th, 2018

Researchers develop microbubble scrubber to destroy dangerous biofilms September 19th, 2018

New photonic chip promises more robust quantum computers September 14th, 2018

Announcements

Nanobiotix: Update on Head and Neck Phase I/II Trial with NBTXR3 and Other program data presented at ImmunoRad 2018 September 20th, 2018

NUS researchers invent new test kit for quick, accurate and low-cost screening of diseases: Test results are denoted by a color change and could be further analyzed by a smartphone app, making it attractive as a point-of-care diagnostic device September 19th, 2018

Silver nanoparticles are toxic for aquatic organisms: A research team at the UPV/EHU-University of the Basque Country has analysed how zebrafish are affected in the long term by exposure to silver particles September 19th, 2018

Leti Announces EU Project to Develop Powerful, Inexpensive Sensors with Photonic Integrated Circuits: REDFINCH Members Initially Targeting Applications for Gas Detection and Analysis For Refineries & Petrochemical Industry and Protein Analysis for Dairy Industry September 19th, 2018

Tools

Carbon nanodots do an ultrafine job with in vitro lung tissue: New experiments highlight the role of charge and size when it comes to carbon nanodots that mimic the effect of nanoscale pollution particles on the human lung. September 12th, 2018

Terahertz spectroscopy enters the single-molecule regime September 7th, 2018

Mirrorcle Demonstrates MEMS-based Programmable Light Source at CES and PW18 August 30th, 2018

Stress-free ALD from Picosun August 28th, 2018

Nanobiotechnology

Nanobiotix: Update on Head and Neck Phase I/II Trial with NBTXR3 and Other program data presented at ImmunoRad 2018 September 20th, 2018

NUS researchers invent new test kit for quick, accurate and low-cost screening of diseases: Test results are denoted by a color change and could be further analyzed by a smartphone app, making it attractive as a point-of-care diagnostic device September 19th, 2018

Researchers develop microbubble scrubber to destroy dangerous biofilms September 19th, 2018

Halas wins American Chemical Society Award in Colloid Chemistry: Rice University nanophotonics pioneer honored for colloid research September 18th, 2018

Research partnerships

Leti Announces EU Project to Develop Powerful, Inexpensive Sensors with Photonic Integrated Circuits: REDFINCH Members Initially Targeting Applications for Gas Detection and Analysis For Refineries & Petrochemical Industry and Protein Analysis for Dairy Industry September 19th, 2018

Researchers develop microbubble scrubber to destroy dangerous biofilms September 19th, 2018

Leti & EFI Aim to Dramatically Improve Reliability & Speed of Low-Cost Electronic Devices for Autos: Project Will Extend Model Predictive Control Technique to Microcontrollers, Digital Signal Processors and Other Devices that Lack Powerful Computation Capabilities September 18th, 2018

Tiny camera lens may help link quantum computers to network September 14th, 2018

NanoNews-Digest
The latest news from around the world, FREE



  Premium Products
NanoNews-Custom
Only the news you want to read!
 Learn More
NanoStrategies
Full-service, expert consulting
 Learn More











ASP
Nanotechnology Now Featured Books




NNN

The Hunger Project