Protein research: The computer as microscope

January 16, 2017

Using a combination of infrared spectroscopy and computer simulation, researchers at Ruhr-Universität Bochum (RUB) have gained new insights into the workings of protein switches. With high temporal and spatial resolution, they verified that a magnesium atom contributes significantly to switching the so-called G-proteins on and off.

G-proteins affect, for example, seeing, smelling, tasting and the regulation of blood pressure. They constitute the point of application for many drugs. "Consequently, understanding their workings in detail is not just a matter of academic interest," says Prof Dr Klaus Gerwert, Head of the Department of Biophysics. Together with his colleagues, namely Bochum-based private lecturer Dr Carsten Kötting and Daniel Mann, he published his findings in the Biophysical Journal. The journal features the subject matter as its cover story in the edition published on January 10, 2017.

G-proteins as source of disease

GTP can bind to all G-proteins. If an enzyme cleaves a phosphate group from the bound GTP, the G-protein is switched off. This so-called GTP hydrolysis takes place in the active centre of enzymes within seconds. If the process fails, severe diseases may be triggered, such as cancer, cholera or the rare McCune-Albright syndrome, which is characterised by, for example, abnormal bone metabolism.

Magnesium important for switch mechanism

In order for GTP hydrolysis to take place, a magnesium atom has to be present in the enzyme's active centre. The research team observed for the first time directly in what way the magnesium affects the geometry and charge distribution in its environment. After being switched off, the atom remains in the enzyme's binding pocket. To date, researchers had assumed that the magnesium leaves the pocket after the switching off process is completed.

The new findings have been gathered thanks to a method developed at the RUB Department of Biophysics. It allows to monitor enzymatic processes at a high temporal and spatial resolution in their natural state. The method in question is a special type of spectroscopy, namely the time-resolved Fourier Transform Infrared Spectroscopy. However, the data measured with its aid do not provide any information about the precise location in the enzyme where a process is taking place. The researchers gather this information through quantum-mechanical computer simulations of structural models. "Computer simulations are crucial for decoding the information hidden in the infrared spectra," explains Carsten Kötting. The computer, so to speak, becomes a microscope.

How proteins accelerate the switching off process

In the current study, the RUB biophysicists also demonstrated in what way the specialised protein environment affects the acceleration of GTP hydrolysis. They analysed the role of a lysine amino acid, which is located in the same spot in many G-proteins. It binds precisely that phosphate group of the GTP molecule from which a phosphate is separated when the G-protein is switched off.

"The function of lysine is to accelerate GTP hydrolysis by transferring negative charges from the third phosphate group to the second phosphate group," elaborates Daniel Mann. "This is a crucial starting point for the development of drugs for the treatment of cancer and other severe diseases in the long term."
-end-


Ruhr-University Bochum

Related Protein Articles from Brightsurf:

The protein dress of a neuron
New method marks proteins and reveals the receptors in which neurons are dressed

Memory protein
When UC Santa Barbara materials scientist Omar Saleh and graduate student Ian Morgan sought to understand the mechanical behaviors of disordered proteins in the lab, they expected that after being stretched, one particular model protein would snap back instantaneously, like a rubber band.

Diets high in protein, particularly plant protein, linked to lower risk of death
Diets high in protein, particularly plant protein, are associated with a lower risk of death from any cause, finds an analysis of the latest evidence published by The BMJ today.

A new understanding of protein movement
A team of UD engineers has uncovered the role of surface diffusion in protein transport, which could aid biopharmaceutical processing.

A new biotinylation enzyme for analyzing protein-protein interactions
Proteins play roles by interacting with various other proteins. Therefore, interaction analysis is an indispensable technique for studying the function of proteins.

Substituting the next-best protein
Children born with Duchenne muscular dystrophy have a mutation in the X-chromosome gene that would normally code for dystrophin, a protein that provides structural integrity to skeletal muscles.

A direct protein-to-protein binding couples cell survival to cell proliferation
The regulators of apoptosis watch over cell replication and the decision to enter the cell cycle.

A protein that controls inflammation
A study by the research team of Prof. Geert van Loo (VIB-UGent Center for Inflammation Research) has unraveled a critical molecular mechanism behind autoimmune and inflammatory diseases such as rheumatoid arthritis, Crohn's disease, and psoriasis.

Resurrecting ancient protein partners reveals origin of protein regulation
After reconstructing the ancient forms of two cellular proteins, scientists discovered the earliest known instance of a complex form of protein regulation.

Sensing protein wellbeing
The folding state of the proteins in live cells often reflect the cell's general health.

Read More: Protein News and Protein Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.