Better computer modeling provides a new look at large biomolecules

A new method for studying the electrical landscape of large biological molecules may enable researchers to make a leap from modeling molecules of 50,000 atoms to those of more than a million atoms.

The technique, developed by Howard Hughes Medical Institute (HHMI) researchers at the University of California, San Diego (UCSD), was used to model the electrostatic properties of microtubules, which are part of the cell's structural and transport systems, and ribosomes, which are the cell's protein-making factories. The scientists say their new computer modeling method, called parallel focusing, will provide molecular biologists with a useful tool for exploring the dynamic behavior of complex biomolecules. The scientists plan to make their software widely available to the scientific community.

Electrostatic models portray how the charges on individual atoms of a molecule interact to produce a distribution of electric fields throughout the molecule. Such models have proven useful in analyzing the stability and dynamic motions of biological molecules such as proteins, DNA, RNA and ligands, as well as how they interact.

In an article published online on August 21, 2001, in Proceedings of the National Academy of Sciences, researchers led by HHMI investigator J. Andrew McCammon report that parallel focusing is a new approach to solving the Poisson-Boltzmann equation (PBE), a fundamental equation in the field of electrostatics.

"One of the problems with traditional molecular dynamics methods for simulating large systems, is that they require considerable computational effort to simulate the surrounding atoms of the aqueous solvent," said McCammon. "The Poisson-Boltzmann equation circumvents this by treating the solvent as one featureless polarizable medium -- essentially a big cloud of charge around a molecule such as a protein," he said.

According to McCammon, the effectiveness of the PBE, which is called an "implicit solvent method

Contact: Jim Keeley
Howard Hughes Medical Institute

Page: 1 2 3 4

Related biology news :

1. Better living through urban ecology
2. Better techniques needed to predict earthquake hazards, UC study finds
3. Better model of cancer development sheds light on potential angiogenesis target
4. Natural Science and Public Health: Prescription for a Better Environment
5. UF nutritionist: Better to vow to eat healthy for new year
6. Better "bugs" lead to cheaper ethanol from biomass
7. Diet and cancer prevention: a sampler of story ideas for 5-a-Day for Better Health Week
8. Some Atlantic Coast Beaches Are Shrinking While Floridas Beaches Better Off Than Most
9. New Polyester Products Perform Better And Are Easy To Recycle
10. Better Binding Through Chemistry
11. Urine Tests Will Do Better Than Pelvic Exams To Save Teens From Serious Effects Of Sexually Transmitted Diseases, UCSF Analysis Shows

Post Your Comments:

(Date:8/5/2020)... ... August 05, 2020 , ... Regenative Labs has received approval from the Centers ... making them the first Wharton’s jelly allografts to be assigned a Q code and ... are the first Wharton’s jelly allograft product to be recognized as a 361 HCT/P ...
(Date:7/31/2020)... (PRWEB) , ... July 30, 2020 , ... ... Research (SBIR) Phase II contract awarded by the Joint Science & Technology Office—Chemical ... this project is to develop, optimize, and scale-up a highly efficient mammalian cell ...
(Date:7/22/2020)... Calif. (PRWEB) , ... July 21, 2020 , ... ... driving digital transformation and innovation in technology and compliance, announces a new solution ... device companies must ensure every layer of their technology stack complies with FDA ...
Breaking Biology News(10 mins):
(Date:8/12/2020)... ... August 11, 2020 , ... The FSHD Society announced ... Dystrophy Clinical Trial Research Network (FSHD CTRN), with consideration of follow-on ... consortium of academic research centers in the United States and Europe with expertise ...
(Date:8/12/2020)... ... August 12, 2020 , ... ... (EMMA International), a global leader in FDA compliance consulting has been named on ... private companies. The list represents a unique look at the most successful companies ...
(Date:8/3/2020)... ... August 03, 2020 , ... ERT, the ... CEO has been named one of the 100 most inspiring individuals in the ... honorees are selected based on how they have inspired their colleagues and affected ...
(Date:7/31/2020)... ... July 29, 2020 , ... R3 Stem Cell International is now offering patients ... million stem cells total, patients may choose which extremities they would like treated. , ... (BMC Musculoskelet Disord. 2016). At R3 International, umbilical cord tissue is obtained from a ...
Breaking Biology Technology:
Cached News: