UWM team the first to “see” atomic changes in proteins with record resolution
A research team led by physicists at the University of Wisconsin-Milwaukee (UWM) has proven a method that makes it possible to find the atomic structure of proteins in action by producing “snapshots” of them with unprecedented spatial and temporal resolution.
What made it possible were the ultra-short X-ray pulses of a Free Electron Laser (XFEL).
Physics professor Marius Schmidt and doctoral student Jason Tenboer recently completed the experiment with the XFEL at the Stanford Linear Accelerator Center (SLAC) in California.
It confirms that the XFEL imaging method, called time-resolved serial femtosecond crystallography (TR-SFX), can unmask protein structures that have never been seen before, determine what each protein does and reveal how they work together to carry out nearly every function in a living organism.
The experiment also involved researchers from Arizona State University, SUNY Buffalo, University of Chicago, Imperial College London, Lawrence Livermore National Laboratory, Stanford Linear Accelerator Center, and the Deutsches Elektronen-Synchrotron (DESY). Results are published today in the journal Science.
Structure equals function
The successful test of the method they used has opened the door to discovering what Schmidt calls “some of the grand challenges of biology.” Proteins are behind almost everything that happens in a living organism, and they play a pivotal role not only in human health, but also in issues as diverse as food, drug discovery and energy.
“We want to understand the molecular basis of life,” he says.
But advances are only possible if scientists know what each protein does. For that, they have to know the structure – the arrangements of the atoms in each and how they change when proteins work together.
“We could observe reactions in certain proteins before,” says Schmidt, “but our new results show that we can now investigate reactions in almost all proteins.”
X-ray crystallography is the method of choice to image proteins with near atomic resolution: X-rays are shot at a protein crystal and diffract off in many directions, creating a pattern of dots the way a single shake of a paintbrush will spray splotches of paint on a wall. The pattern is a kind of fingerprint for that protein.
The millions of data points can be mathematically reconstructed to form a three-dimensional image of the atomic structure at a single point in time.
Using the XFEL as the light source, this kind of imaging is improved from previous equipment.
Change in an instant
Schmidt and Tenboer employed a “pump and probe” experiment, first inducing a chemical reaction in a protein crystal the size of a bacterium using an optical laser to get the atoms moving. Immediately afterward, the X-rays bombarded the crystal, forming the diffraction patterns.
One experiment is over in less time than it takes to blink, but in that span, protein changes can be documented.
From this data, the researchers obtained high-resolution “maps” of time-resolved differences in the electron density, the cloud of electrons in molecules that shifts around during a reaction.
With the XFEL at their X-ray source, Schmidt and Tenboer have overcome limitations with previous methods to follow these shifts.
The XFEL’s ultra-quick X-ray pulses makes it possible to collect imaging data during a very short time span – nearly instantaneous – and record the change that occurred in the structure as proteins perform their function.
“Biology happens at inconceivably short time spans,” says Tenboer. “So the XFEL at Stanford allows us to do time-resolved studies of proteins in action down to the femtosecond time scale – that’s 10 -15 of a second. The blink of an eye probably happens on a millisecond time scale; so you’re still talking about twelve orders of magnitude faster.”
Also, because the XFEL is a billion times brighter than any existing equipment, scientists can use much smaller crystals, even those at nanoscale, which are easier to form. Laser light used to start a reaction in these very small crystals can penetrate fully through the entire crystal and uniformly initiate a reaction in them.
Both the incredible pulse speed of the XFEL and the strength of the reaction initiated by the optical laser boosted the signal, revealing finer detail.
“This is essential to show unambiguously the structural changes,” Schmidt says.
The next step for the research group is to perform a faster “pump and probe” experiment. With an X-ray pulse of 40 femtoseconds, they hope to see step-by-step changes in the resulting images and evidence of the very first elementary steps that lead to the function of these proteins.
UWM and the majority of the experimental team on this work is involved in a Science and Technology Center (STC) called “BioXFEL.” Its mission is to use the XFEL to watch biomolecular machines at work, understand how these molecular machines support life, and provide training and new tools to the scientific community. Funded by the National Science Foundation, the STC is led by SUNY Buffalo and includes Arizona State University, Cornell University, Rice University, Stanford University and the University of California at Davis and at San Francisco.
Laura Hunt | newswise
Basque researchers turn light upside down
23.02.2018 | Elhuyar Fundazioa
Attoseconds break into atomic interior
23.02.2018 | Max-Planck-Institut für Quantenoptik
A newly developed laser technology has enabled physicists in the Laboratory for Attosecond Physics (jointly run by LMU Munich and the Max Planck Institute of Quantum Optics) to generate attosecond bursts of high-energy photons of unprecedented intensity. This has made it possible to observe the interaction of multiple photons in a single such pulse with electrons in the inner orbital shell of an atom.
In order to observe the ultrafast electron motion in the inner shells of atoms with short light pulses, the pulses must not only be ultrashort, but very...
A group of researchers led by Andrea Cavalleri at the Max Planck Institute for Structure and Dynamics of Matter (MPSD) in Hamburg has demonstrated a new method enabling precise measurements of the interatomic forces that hold crystalline solids together. The paper Probing the Interatomic Potential of Solids by Strong-Field Nonlinear Phononics, published online in Nature, explains how a terahertz-frequency laser pulse can drive very large deformations of the crystal.
By measuring the highly unusual atomic trajectories under extreme electromagnetic transients, the MPSD group could reconstruct how rigid the atomic bonds are...
Quantum computers may one day solve algorithmic problems which even the biggest supercomputers today can’t manage. But how do you test a quantum computer to...
For the first time, a team of researchers at the Max-Planck Institute (MPI) for Polymer Research in Mainz, Germany, has succeeded in making an integrated circuit (IC) from just a monolayer of a semiconducting polymer via a bottom-up, self-assembly approach.
In the self-assembly process, the semiconducting polymer arranges itself into an ordered monolayer in a transistor. The transistors are binary switches used...
Breakthrough provides a new concept of the design of molecular motors, sensors and electricity generators at nanoscale
Researchers from the Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague), Institute of Physics of the CAS (IP CAS) and Palacký University...
15.02.2018 | Event News
13.02.2018 | Event News
12.02.2018 | Event News
23.02.2018 | Physics and Astronomy
23.02.2018 | Health and Medicine
23.02.2018 | Physics and Astronomy