Biochemical controls: molecular movements (Introduction)

by David Turell , Thursday, August 10, 2023, 18:52 (261 days ago) @ David Turell

The latest technique:

https://phys.org/news/2023-08-ultrafast-physics-biology-reveals-molecular.html

"Crystallography is a powerful technique in structural biology for taking 'snapshots' of how molecules are arranged. Over several large-scale experiments and years of theory work, the team behind the new study integrated this with another technique that maps vibrations in the electronic and nuclear configuration of molecules, called spectroscopy.

"Demonstrating the new technique at powerful X-ray laser facilities around the world, the team showed that when molecules within the protein that they studied are optically excited, their very first movements are the result of 'coherence.' This shows a vibrational effect, rather than motion for the functional part of the biological reaction that follows.

"This is important distinction, shown experimentally for the first time, highlights how the physics of spectroscopy can bring new insights to the classical crystallography methods of structural biology.

"Professor van Thor said, "Every process that sustains life is carried out by proteins, but understanding how these complex molecules do their jobs depends on learning the arrangement of their atoms—and how this structure changes—as they react.

***

"Members of the team have been working since 2009 at XFELs to use and understand the motions of reacting proteins on the femtosecond (one millionth of one billionth of a second) timescale, known as femtochemistry. Following excitation by a laser pulse, 'snapshots' of the structure are taken using X-rays. (my bold)

"Early success with this technique in 2016 resulted in a detailed picture of the light-induced change in a biological protein. However, researchers still needed to address a key question: what is the origin of the tiny molecular 'motions' on the femtosecond time scale directly after the first laser light pulse?

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"The conclusion was that the ultrafast motions measured with exquisite accuracy on the picometer scale and femtosecond time scale do not belong to the biological reaction, but instead to vibrational coherence in the remaining ground state.

"This means that the molecules that are 'left behind' after the femtosecond laser pulse has passed dominate the motions that are subsequently measured, but only within the so-called vibrational coherence time.

'Professor van Thor said, "We concluded that for our experiment, also if coherent control was not included, the conventional time resolved measurement was in fact dominated by motions from the dark 'reactant' ground state, which are unrelated to the biological reactions that are triggered by the light. Instead, the motions correspond to what is traditionally measured by vibrational spectroscopy and have a very different, but equally important, significance." (my bold)

Comment: note my bolds. The movement of free-floating molecules is affected by the liquid environment in which they exist. dhw wants them completely controlled, but by 'what' or 'how' is totally unclear. Another answer to the theodicy problem.