Nilesh Ramchandra Dhumal, Johannes Kiefer, David Andrew Turton, Klaas Wynne, and Hyung J Kim

http://cdn-pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b00160?journalCode=jpcbfk

Dielectric relaxation of the ionic liquid, 1-ethyl-3-methylimidazolium ethylsulfate (EMI+ETS–), is studied using molecular dynamics (MD) simulations. The collective dynamics of polarization arising from cations and anions are examined. Character- istics of the rovibrational and translational components of polarization dynamics are analyzed to understand their respective roles in the microwave and terahertz regions of dielectric relaxation. The MD results are compared with the experimental low- frequency spectrum of EMI+ETS–, obtained via ultrafast optical Kerr effect (OKE) measurements.

Abstract-Terahertz underdamped vibrational motion governs protein-ligand binding in solution

• 
  

• David A. Turton,
• Hans Martin Senn,
• Thomas Harwood,
• Adrian J. Lapthorn,
• Elizabeth M. Ellis
• &Klaas Wynne

Nature Communications

 

5,

 

Article number:

 

3999

 

doi:10.1038/ncomms4999

Received

 

07 October 2013 

Accepted

 

29 April 2014 

Published

 

03 June 2014

Low-frequency collective vibrational modes in proteins have been proposed as being responsible for efficiently directing biochemical reactions and biological energy transport. However, evidence of the existence of delocalized vibrational modes is scarce and proof of their involvement in biological function absent. Here we apply extremely sensitive femtosecond optical Kerr-effect spectroscopy to study the depolarized Raman spectra of lysozyme and its complex with the inhibitor triacetylchitotriose in solution. Underdamped delocalized vibrational modes in the terahertz frequency domain are identified and shown to blue-shift and strengthen upon inhibitor binding. This demonstrates that the ligand-binding coordinate in proteins is underdamped and not simply solvent-controlled as previously assumed. The presence of such underdamped delocalized modes in proteins may have significant implications for the understanding of the efficiency of ligand binding and protein–molecule interactions, and has wider implications for biochemical reactivity and biological function.

Semi-OT Proteins 'ring like bells'

http://phys.org/news/2014-06-proteins-bells.html
As far back as 1948, Erwin Schrödinger—the inventor of modern quantum mechanics—published the book "What is life?" In it, he suggested that quantum mechanics and coherent ringing might be at the basis of all biochemical reactions. At the time, this idea never found wide acceptance because it was generally assumed that vibrations in protein molecules would be too rapidly damped.
Now, scientists at the University of Glasgow have proven he was on the right track after all.

Using modern laser spectroscopy, the scientists have been able to measure the vibrational spectrum of the enzyme lysozyme, a protein that fights off bacteria. They discovered that this enzyme rings like a bell with a frequency of a few terahertz or a million-million hertz. Most remarkably, the ringing involves the entire protein, meaning the ringing motion could be responsible for the transfer of energy across proteins.

The experiments show that the ringing motion lasts for only a picosecond or one millionth of a millionth of a second. Biochemical reactions take place on a picosecond timescale and the scientists believe that evolution has optimised enzymes to ring for just the right amount of time. Any shorter, andbiochemical reactions would become inefficient as energy is drained from the system too quickly. Any longer and the enzyme would simple oscillate forever: react, unreact, react, unreact, etc. The picosecond ringing time is just perfect for the most efficient reaction.

These tiny motions enable proteins to morph quickly so they can readily bind with other molecules, a process that is necessary for life to perform critical biological functions like absorbing oxygen and repairing cells.

The findings have been published in Nature Communications.

Klaas Wynne, Chair in Chemical Physics at the University of Glasgow said: "This research shows us that proteins have mechanical properties that are highly unexpected and geared towards maximising efficiency. Future work will show whether these mechanical properties can be used to understand the function of complex living systems."

 Explore further: The symphony of life, revealed: New imaging technique captures vibrations of proteins