Tag: biomolecules

Quantum Physics in Proteins

Quantum Physics in Proteins

Artificial intelligence affords unprecedented insights into how biomolecules work

A new analytical technique is able to provide hitherto unattainable insights into the extremely rapid dynamics of biomolecules. The team of developers, led by Abbas Ourmazd from the University of Wisconsin–Milwaukee and Robin Santra from DESY, is presenting its clever combination of quantum physics and molecular biology in the scientific journal Nature. The scientists used the technique to track the way in which the photoactive yellow protein (PYP) undergoes changes in its structure in less than a trillionth of a second after being excited by light.

“In order to precisely understand biochemical processes in nature, such as photosynthesis in certain bacteria, it is important to know the detailed sequence of events,” Santra explains their underlying motivation. “When light strikes photoactive proteins, their spatial structure is altered, and this structural change determines what role a protein takes on in nature.” Until now, however, it has been almost impossible to track the exact sequence in which structural changes occur. Only the initial and final states of a molecule before and after a reaction can be determined and interpreted in theoretical terms. “But we don’t know exactly how the energy and shape changes in between the two,” says Santra. “It’s like seeing that someone has folded their hands, but you can’t see them interlacing their fingers to do so.”

Read more on the PETRAIII website

Image: Illustration of a quantum wave packet in close vicinity of a conical intersection between two potential energy surfaces. The wave packet represents the collective motion of multiple atoms in the photoactive yellow protein. A part of the wave packet moves through the intersection from one potential energy surface to the other, while the another part remains on the top surface, leading to a superposition of quantum states

Credit: DESY, Niels Breckwoldt

A clear path to better insights into biomolecules

A clear path to better insights into biomolecules

An international team of scientists, led by Kartik Ayyer from the Max Planck Institute for the Structure and Dynamics of Matter, Germany, has obtained some of the sharpest possible 3D images of gold nanoparticles, and the results lay the foundation for getting high resolution images of macromolecules. The study was carried out at European XFEL’s Single Particles, Clusters, and Biomolecules & Serial Femtosecond Crystallography (SPB/SFX) instrument and the results have been published in Optica.

Carbohydrates, lipids, proteins, and nucleic acids, all of which populate our cells and are vital for life, are macromolecules. A key to understanding how these macromolecules work lies in learning the details about their structure. The team used gold nanoparticles, which acted as a substitute for biomolecules, measured 10 million diffraction patterns and used them to generate 3D images with record-breaking resolution. Gold particles scatter much more X-rays than bio-samples and so make good test specimens. They are able to provide lot more data and this is good for fine-tuning methods that can then be used on biomolecules.

Read more on the European XFEL website

Image: Illustration of 3D diffraction pattern of octahedral nanoparticles obtained by combining many snapshots after structural selection.

Credit: Kartik Ayyer and Joerg Harms, Max Planck Institute for the Structure and Dynamics of Matter

Quantum X-ray Microscope underway to enable “ghost image” biomolecules

Quantum X-ray Microscope underway to enable “ghost image” biomolecules

Scientists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory have begun building a quantum-enhanced x-ray microscope at the National Synchrotron Light Source II (NSLS-II). This groundbreaking microscope, supported by the Biological and Environmental Research progam at DOE’s Office of Science, will enable researchers to image biomolecules like never before.

NSLS-II is a DOE Office of Science User Facility where researchers use powerful x-rays to “see” the structural, chemical, and electronic makeup of materials down to the atomic scale. The facility’s ultrabright light already enables discoveries in biology, helping researchers uncover the structures of proteins to inform drug design for a variety of diseases—to name just one example.

NSLS-II is a DOE Office of Science User Facility where researchers use powerful x-rays to “see” the structural, chemical, and electronic makeup of materials down to the atomic scale. The facility’s ultrabright light already enables discoveries in biology, helping researchers uncover the structures of proteins to inform drug design for a variety of diseases—to name just one example.

Read more on the Brookhaven National Laboratory website

Image: An artist’s interpretation of ghost imaging. In this research technique, scientists split an x-ray beam (represented by the thick pink line) into two streams of entangled photons (thinner pink lines). Only one of these streams of photons passes through the scientific sample (represented by the clear circle), but both gather information. By splitting the beam, the sample being studied is only exposed to a fraction of the x-ray dose.