Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Computer Simulation Renders Transient Chemical Structures Visible

14.07.2016

Chemists at the University of Basel have succeeded in using computer simulations to elucidate transient structures in proteins. In the journal Angewandte Chemie, the researchers set out how computer simulations of details at the atomic level can be used to understand proteins’ modes of action.

Using computational chemistry, it is possible to characterize the motion of individual atoms of a molecule. Today, the latest simulation techniques allow scientists to quantitatively describe the dynamics of molecules and systems containing hundreds of thousands of atoms.


Structure of the protein myoglobin (silver) with the embedded active site (in color). In this image, the nitrogen molecule (red/blue) is bonded to the iron atom (green ball).

University of Basel / Department of Chemistry

These techniques are important, above all, for characterizing molecular states that are difficult to observe directly in experiments due to their short lifetime. Here, computer simulations are a source of valuable complementary insight.

A protein’s function is determined by its structure and dynamics. It is particularly important that information relevant to the nature of structures and molecular processes in the active site – i.e. the place where chemical reactions take place – is known. The formation and breaking of chemical bonds is a dynamic process that results in structural changes.

The observable dynamics usually result in stable (low energy) states that are reached via one or more metastable (higher energy) intermediate steps. Whether a metastable state can be detected directly in an experiment depends on its lifetime. If it is too short, only indirect detection methods are available.

Computer determines atomic geometry

Now, a research team led by Prof. Markus Meuwly from the Department of Chemistry at the University of Basel has used molecular dynamics simulations to characterize the spatial and temporal behavior of the protein myoglobin.

Myoglobin plays an important role in the transport of oxygen within cells and is found mainly in muscle tissue. Nitrogen monoxide, which is formed in the cells, is a short-lived and reactive messenger that is important in regulating vasodilation under hypoxia.

“The process by which nitrogen monoxide binds to myoglobin is already well characterized experimentally, which is important for the calibration of computer simulations,” explains Meuwly. “There is also experimental evidence for the existence of metastable intermediates, but our simulations provide insights into the underlying chemical structure and the dynamics of these intermediates, and thus the function of the protein.

Together with experimental observations, therefore, computer simulations are the basis for an understanding of complex chemical and biological systems. Accordingly, this combined approach also provides a starting point for further questions to be addressed; for example, the adaptation and optimization of proteins or active pharmaceutical agents. This requires an understanding of the underlying processes at the molecular and atomic level.

Original source

Maksym Soloviov, Akshaya K. Das, Markus Meuwly
Structural Interpretation of Metastable States in MbNO
Angew. Chem. Int. Ed. (2016), doi: 10.1002/ange.201604552

Further information

Prof. Dr. Markus Meuwly, University of Basel, Department of Chemistry, Tel. +41 61 267 38 21, email: m.meuwly@unibas.ch

Reto Caluori | Universität Basel
Further information:
http://www.unibas.ch

More articles from Life Sciences:

nachricht New application for acoustics helps estimate marine life populations
16.01.2018 | University of California - San Diego

nachricht Unexpected environmental source of methane discovered
16.01.2018 | University of Washington Health Sciences/UW Medicine

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Scientists decipher key principle behind reaction of metalloenzymes

So-called pre-distorted states accelerate photochemical reactions too

What enables electrons to be transferred swiftly, for example during photosynthesis? An interdisciplinary team of researchers has worked out the details of how...

Im Focus: The first precise measurement of a single molecule's effective charge

For the first time, scientists have precisely measured the effective electrical charge of a single molecule in solution. This fundamental insight of an SNSF Professor could also pave the way for future medical diagnostics.

Electrical charge is one of the key properties that allows molecules to interact. Life itself depends on this phenomenon: many biological processes involve...

Im Focus: Paradigm shift in Paris: Encouraging an holistic view of laser machining

At the JEC World Composite Show in Paris in March 2018, the Fraunhofer Institute for Laser Technology ILT will be focusing on the latest trends and innovations in laser machining of composites. Among other things, researchers at the booth shared with the Aachen Center for Integrative Lightweight Production (AZL) will demonstrate how lasers can be used for joining, structuring, cutting and drilling composite materials.

No other industry has attracted as much public attention to composite materials as the automotive industry, which along with the aerospace industry is a driver...

Im Focus: Room-temperature multiferroic thin films and their properties

Scientists at Tokyo Institute of Technology (Tokyo Tech) and Tohoku University have developed high-quality GFO epitaxial films and systematically investigated their ferroelectric and ferromagnetic properties. They also demonstrated the room-temperature magnetocapacitance effects of these GFO thin films.

Multiferroic materials show magnetically driven ferroelectricity. They are attracting increasing attention because of their fascinating properties such as...

Im Focus: A thermometer for the oceans

Measurement of noble gases in Antarctic ice cores

The oceans are the largest global heat reservoir. As a result of man-made global warming, the temperature in the global climate system increases; around 90% of...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

10th International Symposium: “Advanced Battery Power – Kraftwerk Batterie” Münster, 10-11 April 2018

08.01.2018 | Event News

See, understand and experience the work of the future

11.12.2017 | Event News

Innovative strategies to tackle parasitic worms

08.12.2017 | Event News

 
Latest News

Morbid Obesity: Gastric Bypass and Sleeve Gastrectomy Are Comparable

17.01.2018 | Health and Medicine

Researchers identify new way to unmask melanoma cells to the immune system

17.01.2018 | Health and Medicine

Genetic discovery may help better identify children at risk for type 1 diabetes

17.01.2018 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>