It takes a neutron beam to find a proton

April 27, 2020

Osaka - Understanding the behavior of proteins and enzymes is key to unlocking the secrets of biological processes. The atomic structures of proteins are generally investigated using X-ray crystallography; however, the precise information for hydrogen atoms and protons (hydrogen ions) is usually unattainable. Now a team including Osaka University, Osaka Medical College, National Institutes for Quantum and Radiological Science and Technology, Ibaraki University, and University of Tsukuba has used neutron crystallography to reveal high-resolution structural details of a very large oxidase protein. Their findings are published in PNAS.

The hydrogen atoms and protons that make up about half of the atoms in proteins and enzymes often play crucial roles in the jobs these biomolecules do; however, their exact positions are difficult to pinpoint because of their small size. The most common approach for working out the structure of a protein is to direct a beam of high-energy X-rays at a protein crystal and analyze the diffraction pattern that results from the interactions of the X-rays with the electrons of atoms in the structure. Unfortunately, X-rays do not interact strongly with hydrogen atoms or protons, which have low or no electron density, making them difficult to "see."

One solution is to apply a neutron beam to the crystal instead of X-rays. Neutrons interact with the nuclei of the atoms in their path, including those of hydrogen atoms and protons, despite them being small. The diffraction patterns resulting from these interactions are recorded after the neutron beam has passed through the crystal, and are decoded into the precise locations of the nuclei, including the hydrogen nuclei.

"Hydrogen atoms and protons are particularly interesting components of enzyme structures because they can exhibit quantum behaviors that have recently been found to be crucial to enzyme function. It is therefore important to accurately determine their locations in the protein structure in order to unravel what is happening," study corresponding author Toshihide Okajima explains. "Using neutron crystallography, we were able to determine the structure of a bacterial copper amine oxidase with a molecular weight of 70,600--which is extremely large for neutron crystallography and significantly exceeds previously recorded molecular masses--and still precisely locate the hydrogen atoms and protons in the structure. An unusual "levitated" proton was observed between a cofactor, topa quinone, and an amino acid residue strictly conserved in this class of enzymes."

The topa quinone cofactor covalently bound to the enzyme plays an essential role in the catalytic function. The researchers were finally able to establish a complete picture of topa quinone 30 years after its discovery as a protein-derived cofactor. They found that the cofactor actually exists in equilibrium between two different forms.

"Enzyme active sites--where the reactions take place--can provide us a great deal of information and inspiration if we are able to fully understand what is happening," Okajima explains. "Our demonstration of using neutron crystallography to uncover proton quantum effects promises to be very useful for many researchers studying enzymes and their mechanisms."
The article, "Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing" was published in PNAS at DOI:

About Osaka University

Osaka University was founded in 1931 as one of the seven imperial universities of Japan and now has expanded to one of Japan's leading comprehensive universities. The University has now embarked on open research revolution from a position as Japan's most innovative university and among the most innovative institutions in the world according to Reuters 2015 Top 100 Innovative Universities and the Nature Index Innovation 2017. The university's ability to innovate from the stage of fundamental research through the creation of useful technology with economic impact stems from its broad disciplinary spectrum.


Osaka University

Related Proteins Articles from Brightsurf:

New understanding of how proteins operate
A ground-breaking discovery by Centenary Institute scientists has provided new understanding as to the nature of proteins and how they exist and operate in the human body.

Finding a handle to bag the right proteins
A method that lights up tags attached to selected proteins can help to purify the proteins from a mixed protein pool.

Designing vaccines from artificial proteins
EPFL scientists have developed a new computational approach to create artificial proteins, which showed promising results in vivo as functional vaccines.

New method to monitor Alzheimer's proteins
IBS-CINAP research team has reported a new method to identify the aggregation state of amyloid beta (Aβ) proteins in solution.

Composing new proteins with artificial intelligence
Scientists have long studied how to improve proteins or design new ones.

Hero proteins are here to save other proteins
Researchers at the University of Tokyo have discovered a new group of proteins, remarkable for their unusual shape and abilities to protect against protein clumps associated with neurodegenerative diseases in lab experiments.

Designer proteins
David Baker, Professor of Biochemistry at the University of Washington to speak at the AAAS 2020 session, 'Synthetic Biology: Digital Design of Living Systems.' Prof.

Gone fishin' -- for proteins
Casting lines into human cells to snag proteins, a team of Montreal researchers has solved a 20-year-old mystery of cell biology.

Coupled proteins
Researchers from Heidelberg University and Sendai University in Japan used new biotechnological methods to study how human cells react to and further process external signals.

Understanding the power of honey through its proteins
Honey is a culinary staple that can be found in kitchens around the world.

Read More: Proteins News and Proteins Current Events 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