Integrating Physics Into Structural Biology

Structural Biology is one of the most prominent branches of biology. Groundbreaking works which were highlighted in #LINO24 sessions can be achieved by focusing on the molecular structures of various organelles within cells and giving insights into their dynamics. The crucial step of integrating physics into biology means delving into the cells and discover the secrets of life. This unseen world aroused the curiosity of scientists, also at the recent Lindau Meeting.

Navigation Through Time

For his Lindau premiere, Nobel Laureate Richard Henderson entered the stage at the main hall to deliver a lecture entitled “The Impact of Physics in Structural Biology”, navigating through the history of interdisciplinarity that unraveled the structure of biology.

Henderson is a key pioneer of electron microscopy who succeeded in producing three-dimensional images of small biological molecules, and shared the 2017 Nobel Prize in Chemistry with Joachim Frank and Jacques Dubochet for “Developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution”. His work undoubtedly contributed to advancing drug and medication development.

Flash Back

Henderson traveled back to around 100 years ago when some scientists made groundbreaking discoveries of X-rays by Wilhelm Röntgen in 1895, electrons by J.J. Thomson in 1897, and neutrons by Chadwick in 1932. In addition, nuclear magnetic resonance (NMR) spectroscopy, which produces great details, was developed by Nobel Laureate Kurt Wüthrich. All of these techniques were utilized to analyze macromolecules.

“A hundred years is nothing in terms of the revolution of humanity and the problems we have in the world. This is a very recent development,” said Henderson

During his journey through time, Henderson mentioned Rosalind Franklin, as one of the high-impact scientists in structure biology. She could record an image of DNA fibers. However, she was not appreciated enough, she is known as “The Dark Lady of DNA”.

Then, the biologist James Watson and the physicist Francis Crick delved into the structure of DNA and shared the Nobel Prize in Physiology/Medicine in 1962. They played instrumental roles in pioneering the molecular biology revolution and contributed significant insights. It is manifested that the cooperative work of Watson and Crick highlights the fruitful outcomes of the synergy of diverse disciplines when working together.

High Precision

Following that, Henderson began explaining the operational mechanisms of the Cryo-EM apparatus and enhancing the precision of the detailed images, thereby facilitating the observation of the micro-structures, ultimately leading to the advancement of effective treatments. Sharing his perspectives, Henderson supposed that the Cryo-EM would offer faster freezing and lower cost.

From Oxygen to Water

On the same day, an Agora Talk was held by Hartmut Michel and Johann Deisenhofer, recipients of the 1988 Nobel Prize in Chemistry for their work on “determining the three-dimensional structure of a photosynthetic reaction centre”.

The Agora Talk is entitled “The Future of Structural Biology: Artificial Intelligence and In Situ Structures”. Michel began his presentation by discussing the enzyme “cytochrome c oxidase”, a membrane protein and essential enzyme in the respiratory process responsible for converting the oxygen we inhale into water within the mitochondria.

Proteins play a vital role in essential processes. Michel’s research focused on investigating photosynthesis, a process that uses solar energy to produce nutrients and oxygen. Hartmut Michel utilized photosynthetic bacteria to observe the electron transfer process through proteins in cell membranes. And he mainly discussed the “Cytochrome c oxidase” reaction cycle.

During his discussion, Michel delved into the challenges and potential contradictions when tracking enzymes, highlighting the limitations of cryo-EM’s high resolution, as well as the challenges associated with X-ray crystallography, both of which are susceptible to radiation damage.

Hartmut Michel shared insights on in situ structural biology, discussing both its limitations at the atomic level and proposing a vision for conceptualizing a 4D visual representation of organelles and cells in the future.

Solving the Puzzle

Michel then passed the microphone to his Co-Laureate, Johann Deisenhofer, who retired a decade ago, a step that provided him with the opportunity to observe the advancements in structural biology from a comfortable distance.

Deisenhofer recalled discussions in Lindau back in the 1960s following the determination of the protein structure. At that time, the central question was: “What lies behind these three-dimensional structures? What determines them?” The answer, as it turned out, was the amino acid. However, a significant challenge arose known as “the protein folding problem”. Scientists lacked sufficient knowledge about how amino acids govern the intricate three-dimensional atomic structure of proteins, resembling a complex puzzle. This was particularly challenging given the swift changes observed in many proteins within a narrow timeframe ranging from tens of microseconds to milliseconds.

Numerous efforts were made to address “the protein folding problem”, culminating in a breakthrough in 2010. A paper published in Science revealed that a team of scientists was able to induce folding using molecular dynamics simulations.

Protein Structure Prediction

The accumulation of experiments pertaining to 3D proteins in databases such as the Protein Data Bank and DNA sequences encoding proteins in various databases aids in comprehending and treating mutations. “A huge amount of experimental data has been accumulated,” said Deisenhofer.

Deisenhofer also referenced the Protein Structure Prediction Center (CASP), which utilizes amino acid sequences to identify structures based on the data accumulated in databases like the Protein Data Bank.

On the other hand, there is “AlphaFold”, an AI system developed by Google DeepMind (Alphabet/Google) that predicts the three-dimensional structure of proteins based on amino acid sequences. Deisenhofer elaborated that AI predicts protein structures by employing machine learning to train the system to recognize amino acid sequences using existing databases. This system can distinguish between blank, missing, and corrected sequences.

The Road to a Nobel Prize

Some time later during the Lindau Scientific Programme, the room was packed for a good reason. Kurt Wüthrich had committed to addressing the query: “How long does it take to receive the Nobel Prize?” This may seem like a simple question, but his response was anything but brief. He shared his intriguing journey in an Agora Talk entitled “My Way to NMR and to a Nobel Prize”.

In 2002, he was awarded the Nobel Prize in Chemistry for his groundbreaking work on the “development of nuclear magnetic resonance spectroscopy for determining the three-dimensional structure of biological macromolecules in solution”.

Wüthrich took the stage and began his presentation on the G Protein-Coupled Receptor (GPCR), which are protein receptors found in eukaryotes. A conformational change occurs in the GPCR in response to external signaling. One such protein is Rhodopsin, which originates from cow eyes. In 2000, a high-resolution structure of Rhodopsin was published. Wüthrich and his team in China are currently focused on studying GPCRs, particularly the Human GPCR.

“The human brain contains 826 different GPCRs, which play a crucial role in regulating various functions within our body,” Wüthrich stated.

“As a result, we are key targets for medical interventions, with approximately 40% of all approved prescription drugs targeting GPCRs. However, only about 40 GPCRs have been targeted so far, highlighting the vast unexplored potential in investigating the remaining 760 GPCRs as potential intervention targets for a variety of diseases,” Wüthrich added.

Wüthrich explained how the signals elicited by drugs are transmitted across the cell membrane, eventually triggering a cascade of reactions within the cell that deliver the drug’s impact. He then discussed the power of NMR in solving complex structures and emphasized their ongoing efforts to enhance its capabilities for more detailed insights. “We are not just interested in how proteins look; that is just the beginning. Our goal is to understand how they function,” Wüthrich said.

In comparison to NMR, Cryo-EM is more effective in determining the architecture of membrane proteins. It focuses on precise measurements that contribute valuable information to our understanding of molecular structures.

Approaching the significant question from his research group at ShanghaiTech University, “The Chinese students are very interested to know how one gets a Nobel Prize,” Wüthrich stated. (Actually, it is a common question among all researchers).

He presented his Co-Laureate Koichi Tanaka, who embarked on his engineering career at the age of 23, having to retake a year of college due to his grads in German – as indicated in his CV. Tanaka then explored various methods of utilizing laser light on compound vitality, ultimately demonstrating that laser pulses could disintegrate protein molecules. He authored one paper and holds one patent. Nearly 20 years later, he was awarded the Nobel Prize. “So you see he did all the work at the age of where most of you are,” Wüthrich quipped.

Moving to John Fenn, who had no publications until the age of 35 and worked in various industries. At 60, he joined Yale University as a professor of chemistry and in 1987, he discovered Electrospray evaporation, and patiently waited until 2002, at the age of 86, to receive the Nobel Prize.

When it comes to Wüthrich, his journey started in his boyhood days, growing up on a farm surrounded by animals and trees, sparking his keen interest in fishing and sports. These early experiences greatly shaped his future endeavors. He is best known for his groundbreaking work on cows, stemming from his farm upbringing. During the outbreak of mad cow disease, he successfully deciphered the protein structure linked to the illness. His passion for sports further fueled his exploration into myoglobin and hemoglobin, particularly intrigued by the process of oxygen debt during physical exertion, leading to insightful tests in his research efforts. His work extended into the development of NMR.

All of these scientists worked to apply physics and other disciplines to unveil the biological structure, leading to the advancement of treatments and the deepening of our knowledge of diseases, marking a significant breakthrough in the field of science.