Featured Research

from universities, journals, and other organizations

Crowding has big effects on biomolecules

Date:
May 22, 2014
Source:
National Institute of Standards and Technology (NIST)
Summary:
Crowding has notoriously negative effects at large size scales, blamed for everything from human disease and depression to community resource shortages. But relatively little is known about the influence of crowding at the cellular level. A new study shows that a crowded environment has dramatic effects on individual biomolecules.

This is an artist's conception of an RNA molecule (large purplish ladder) in the process of folding as it is crowded by a common polymer, polyethylene glycol (turquoise strands). RNA folds more frequently -- that is, the branch on the left folds upward -- when it is crowded.
Credit: Baxley/JILA and Talbott/NIST

Crowding has notoriously negative effects at large size scales, blamed for everything from human disease and depression to community resource shortages. But relatively little is known about the influence of crowding at the cellular level. A new JILA study shows that a crowded environment has dramatic effects on individual biomolecules.

In the first data on the underlying dynamics (or kinetics)of crowded single biomolecules , reported in Proceedings of the National Academy of Sciences, JILA researchers found that crowding leads to a 35-fold increase in the folding rate of RNA (ribonucleic acid), while the unfolding rate remains relatively stable.

RNA is a long chain-like molecule that contains genetic information, makes proteins and catalyzes biological reactions. It must fold into the correct 3D shape to function properly. The new results show that while RNA usually spends most of its time unfolded, in a crowded situation it folds much more often, although it remains folded for the usual period of time during each round.

"Cells are 25 to 35 percent filled with 'stuff' -- proteins, nucleic acids, lipids, etc. -- and the effect of crowding on simple reactions like folding of nucleic acids and proteins is not well understood," JILA/NIST Fellow David Nesbitt says. "Almost all detailed kinetic data comes from in vitro studies, that is, not in a living cell.

"But our work at the single-molecule level suggests that the rates and equilibrium constants (where folding and unfolding rates are equal) for simple nucleic acid folding processes may be shifted by up to 400,000 percent or more from what one might expect from such uncrowded solution studies."

Nesbitt's group used a specialized microscope to study RNA folding over time in solutions containing various concentrations of a large common polymer, PEG. The size of the PEG molecule constrains the 3D space around the RNA, mimicking the contents of crowded cells better than the typical dilute solutions used in test-tube studies.

Although PEG was previously known to encourage the compactor folded states of biomolecules, the JILA results are the first to determine the underlying processes. The results were not obvious, in that crowding might seem likely to suppress RNA unfolding. JILA researchers suggest that instead, the opposite process is at work: Crowding lowers the energy required for RNA to achieve the transition state for folding, making it easier to fold.

The JILA study also analyzed temperature-related data to show that the boost in the RNA folding rate constant is largely due to the disorder (or entropy) of the mixture, rather than simply the tendency for RNA to stabilize in the shape with the lowest energy.

In addition to collecting experimental data, JILA researchers used a simple particle model to estimate what would happen in the extremely crowded environment of the cell. The results suggest that the RNA folding equilibrium constant could potentially increase more than 4,000-fold -- resulting in a dramatically different biochemical composition -- while the folding rate could increase more than 1,000-fold. JILA researchers speculate that such extreme effects could profoundly influence both the rates and preferred directions of complex biochemical pathways in cells. Further studies are needed to determine whether the model can be extended to other cell contents and other RNA structures.


Story Source:

The above story is based on materials provided by National Institute of Standards and Technology (NIST). Note: Materials may be edited for content and length.


Journal Reference:

  1. N. F. Dupuis, E. D. Holmstrom, D. J. Nesbitt. Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics. Proceedings of the National Academy of Sciences, 2014; DOI: 10.1073/pnas.1316039111

Cite This Page:

National Institute of Standards and Technology (NIST). "Crowding has big effects on biomolecules." ScienceDaily. ScienceDaily, 22 May 2014. <www.sciencedaily.com/releases/2014/05/140522115756.htm>.
National Institute of Standards and Technology (NIST). (2014, May 22). Crowding has big effects on biomolecules. ScienceDaily. Retrieved July 28, 2014 from www.sciencedaily.com/releases/2014/05/140522115756.htm
National Institute of Standards and Technology (NIST). "Crowding has big effects on biomolecules." ScienceDaily. www.sciencedaily.com/releases/2014/05/140522115756.htm (accessed July 28, 2014).

Share This




More Matter & Energy News

Monday, July 28, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Europe's Highest Train Turns 80 in French Pyrenees

Europe's Highest Train Turns 80 in French Pyrenees

AFP (July 25, 2014) Europe's highest train, the little train of Artouste in the French Pyrenees, celebrates its 80th birthday. Duration: 01:05 Video provided by AFP
Powered by NewsLook.com
TSA Administrator on Politics and Flight Bans

TSA Administrator on Politics and Flight Bans

AP (July 24, 2014) TSA administrator, John Pistole's took part in the Aspen Security Forum 2014, where he answered questions on lifting of the ban on flights into Israel's Tel Aviv airport and whether politics played a role in lifting the ban. (July 24) Video provided by AP
Powered by NewsLook.com
Creative Makeovers for Ugly Cellphone Towers

Creative Makeovers for Ugly Cellphone Towers

AP (July 24, 2014) Mobile phone companies and communities across the country are going to new lengths to disguise those unsightly cellphone towers. From a church bell tower to a flagpole, even a pencil, some towers are trying to make a point. (July 24) Video provided by AP
Powered by NewsLook.com
Algonquin Power Goes Activist on Its Target Gas Natural

Algonquin Power Goes Activist on Its Target Gas Natural

TheStreet (July 23, 2014) When The Deal's Amanda Levin exclusively reported that Gas Natural had been talking to potential suitors, the Ohio company responded with a flat denial, claiming its board had not talked to anyone about a possible sale. Lo and behold, Canadian utility Algonquin Power and Utilities not only had approached the company, but it did it three times. Its last offer was for $13 per share as Gas Natural's was trading at a 60-day moving average of about $12.50 per share. Now Algonquin, which has a 4.9% stake in Gas Natural, has taken its case to shareholders, calling on them to back its proposals or, possibly, a change in the target's board. Video provided by TheStreet
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins