Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


"Funnel" attracts bonding partners to biomolecule


Water movement as detection aid for molecules

RESOLV combines terahertz spectroscopy and simulation

Water is a ubiquitous solvent in all life sciences – sometimes referred to as the "matrix of life". Contrary to earlier assumptions, it is not a passive witness of biochemical processes; rather, it participates in them actively.

By influencing the movement of water molecules surrounding their binding pockets, proteins can create a type of “funnel” in the surrounding water, which assists the bonding of certain binding partners that are solvated in water.

Valeria Conti Nibali and Prof Dr Martina Havenith-Newen (Cluster of Excellence RESOLV – Ruhr explores Solvation) made this discovery by using a combination of terahertz absorption spectroscopy and molecular dynamics simulations. The researchers report their findings in the Journal of the American Chemical Society (JACS).

Schematic diagram of the hydration funnel in an enzyme-substrate complex (the protein is depicted in grey, its binding partner in green, and the funnel in yellow).

© Havenith/Conti Nibali

Choreography of water movements

New experimental technologies, such as terahertz absorption spectroscopy, pave the way for studies of the dynamics of water molecules surrounding biomolecules. Using this method, the researchers proved some time ago that proteins influence water molecules in their surroundings: they determine the choreography of their movements. This effect occurs not only in the immediate vicinity of the protein, but can also be detected in the remote layers of the surrounding water molecules.

Collective interaction helps choose binding partner

But what purpose would such an interaction have? The researchers have come closer to finding an answer to this question by employing molecular dynamics simulations. It was demonstrated that the movement of water molecules in the vicinity of the protein’s active centre, the so-called binding pocket, is connected to potential binding partners in the water solvent.

"This movement causes the water molecules to form a hydration funnel of sorts, making up part of the molecular recognition mechanism in both partners," explains Prof Dr Martina Havenith-Newen. Moreover, the movements of the water molecules have proved to be specific for certain binding partners.

Thus, if there are different potential binding candidates in the solvent, all competing to bind to the protein, these collective water movements are thought to assist binding.To conclude, such correlated water movements could support the interaction of biomolecules like enzymes and proteins with their binding partners and play a significant role in their mutual recognition, allowing the biomolecule to select or reject certain binding partners.

Cluster of Excellence RESOLV

The project was carried out under the auspices of the Cluster of Excellence RESOLV – Ruhr explores Solvation (ECX 1069), supported by the German Research Foundation.

Title catalogue

V. Conti Nibali, M. Havenith (2014): New Insights into the Role of Water in Biological Function: Studying Solvated Biomolecules Using Terahertz Absorption Spectroscopy in Conjunction with Molecular Dynamics Simulations, JACS, 10.1021/ja504441h

Meike Drießen | Eurek Alert!

More articles from Life Sciences:

nachricht ‘Farming’ bacteria to boost growth in the oceans
24.10.2016 | Max-Planck-Institut für marine Mikrobiologie

nachricht Calcium Induces Chronic Lung Infections
24.10.2016 | Universität Basel

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Light-driven atomic rotations excite magnetic waves

Terahertz excitation of selected crystal vibrations leads to an effective magnetic field that drives coherent spin motion

Controlling functional properties by light is one of the grand goals in modern condensed matter physics and materials science. A new study now demonstrates how...

Im Focus: New 3-D wiring technique brings scalable quantum computers closer to reality

Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.

"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...

Im Focus: Scientists develop a semiconductor nanocomposite material that moves in response to light

In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.

A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...

Im Focus: Diamonds aren't forever: Sandia, Harvard team create first quantum computer bridge

By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.

"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...

Im Focus: New Products - Highlights of COMPAMED 2016

COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.

In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...

All Focus news of the innovation-report >>>



Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

Agricultural Trade Developments and Potentials in Central Asia and the South Caucasus

14.10.2016 | Event News

World Health Summit – Day Three: A Call to Action

12.10.2016 | Event News

Latest News

Oasis of life in the ice-covered central Arctic

24.10.2016 | Earth Sciences

‘Farming’ bacteria to boost growth in the oceans

24.10.2016 | Life Sciences

Light-driven atomic rotations excite magnetic waves

24.10.2016 | Physics and Astronomy

More VideoLinks >>>