Proteins are long chains of amino acids that must fold into precise three-dimensional structures before they can perform their functions. This folding process is governed by a complex balance of chemical forces, including hydrogen bonding, hydrophobic interactions, electrostatic attraction and the movement of water around the protein surface. A small change in temperature, pH, genetic sequence or chemical environment can destabilize that balance. When a protein fails to maintain its native structure, it may partially unfold and expose normally hidden regions. These exposed surfaces can interact with equivalent regions on other molecules, allowing the proteins to associate into oligomers, fibers and eventually amyloid deposits. Such assemblies are central features of several neurodegenerative and cardiovascular diseases, but their formation is not a simple chemical accident. It is a dynamic process that can potentially be redirected with carefully designed molecules.

Kelly’s research has focused on understanding that process at a level detailed enough to reveal where therapeutic intervention is possible. His laboratory has combined organic chemistry, biophysics, structural biology and cell-based approaches to examine how proteins move between folded, unfolded and aggregated states. Rather than viewing misfolding as a single catastrophic event, the work has treated it as an energy landscape containing multiple intermediate forms. Some intermediates may be short-lived and harmless, while others can act as especially efficient seeds for further aggregation. Identifying which molecular states initiate disease is essential because a treatment may need to stabilize the healthy protein before it begins to unravel, block the formation of toxic intermediates or prevent already formed assemblies from damaging cells. This framework has helped shift protein-misfolding research from observation toward rational therapeutic design.

One of Kelly’s most influential achievements involved transthyretin, or TTR, a protein produced primarily by the liver and responsible for transporting thyroxine and retinol-binding protein in the bloodstream. TTR normally circulates as a tetramer made of four identical subunits. In hereditary forms of transthyretin amyloidosis, mutations can weaken the interactions holding the tetramer together. The complex may then dissociate into individual subunits, which can partially unfold and assemble into amyloid fibrils. These fibrils accumulate in tissues, damaging peripheral nerves in transthyretin amyloid polyneuropathy and impairing the structure and function of the heart in transthyretin amyloid cardiomyopathy. Even the normal, nonmutated protein can become amyloidogenic with age, making the disease relevant beyond inherited mutations. Kelly’s studies clarified that tetramer destabilization is a critical early event and therefore a promising point for intervention.

That mechanistic insight contributed to the development of tafamidis, the active pharmaceutical ingredient in Vyndamax and Vyndaqel, medicines approved by the U.S. Food and Drug Administration for transthyretin-related disease. Tafamidis functions as a kinetic stabilizer: it binds to thyroxine-binding sites within the TTR tetramer and makes dissociation less likely. The distinction between thermodynamic and kinetic stabilization is important. A drug does not necessarily need to make the folded state the only energetically favorable state; it can instead slow the rate at which the protein reaches a disease-associated state, extending the lifetime of the functional tetramer. By reducing the supply of misfolded TTR subunits, the treatment can limit the production of new amyloid material. The approach demonstrates how defining the molecular sequence of disease can reveal a practical treatment strategy that operates before irreversible tissue damage becomes extensive.

The development of TTR stabilizers also illustrates why protein aggregation cannot be addressed solely by searching for compounds that dissolve visible deposits. Amyloid fibrils may represent the endpoint of a much longer process, and the most harmful species can arise earlier, when small assemblies interact with cell membranes or disrupt intracellular pathways. A drug that targets the earliest destabilizing transition may therefore have greater impact than one aimed at mature deposits. Kelly’s research helped establish this preventive logic by linking the behavior of individual protein molecules to disease progression in patients. It also provided a general model for studying other amyloid disorders, in which the identities of the proteins differ but the underlying challenges—conformational instability, intermolecular association and tissue-specific toxicity—are conceptually related. The work has made protein chemistry a direct engine of therapeutic discovery.

The European Academy of Engineering, founded in Sweden in 1992, brings together experts from a broad range of technical disciplines and advises on issues involving policy, public health and education. Its members are elected by peers across 13 engineering classes, each representing a specialized area. Kelly’s election recognizes a career in which discoveries traditionally associated with chemistry have produced consequences for biomedical engineering, drug development and clinical care. His honors include the Canada Gairdner International Award, election to the U.S. National Academy of Sciences, the Wolf Prize in Chemistry in 2023 and the Breakthrough Prize in Life Sciences in 2022, in addition to numerous other distinctions. Together, these awards reflect the unusual reach of research that began with questions about molecular structure and ultimately helped produce a medicine for a life-threatening protein-aggregation disorder.

Kelly’s election arrives as scientists increasingly seek therapies that modify the physical behavior of disease-linked proteins rather than merely treating symptoms after damage has occurred. Advances in cryo-electron microscopy, nuclear magnetic resonance, mass spectrometry and computational modeling are making it possible to observe unstable conformations and transient protein assemblies with growing precision. These tools may reveal additional opportunities to stabilize vulnerable proteins, remove harmful species or correct the cellular systems responsible for protein quality control. The broader lesson of Kelly’s work is that understanding how a protein fails can be as important as understanding how it functions when healthy. By tracing the molecular steps that connect folding errors to human disease, researchers can convert a seemingly microscopic chemical event into a clear therapeutic target—and, in some cases, into a treatment capable of changing the course of illness.

Subject of Research: Protein folding, protein misfolding and amyloid aggregation, with a focus on transthyretin amyloidosis and therapeutic protein stabilization.

Web References: Jeffery Kelly — Scripps Research

Image Credits: Scripps Research

Keywords

Protein folding; neurodegenerative diseases; cardiomyopathy; transthyretin amyloidosis; amyloid aggregation; protein misfolding; biomedical engineering; tafamidis; Scripps Research; Jeffery Kelly

Oxidative stress, resulting from an imbalance between reactive oxygen molecules and antioxidant defenses, is known to alter the structure and function of biomolecules. Proteins, being central to cell machinery, are particularly susceptible to oxidative modifications, which can lead to changes in their stability and activity. Until now, the intricate details of how proteins chemically adapt or respond to such stress remained only partially understood. The discovery of novel nitrogen-oxygen-sulphur (NOS) based covalent linkages ushers in a new paradigm for protein biochemistry, highlighting molecular switches invisible to traditional analytical techniques.

The researchers embarked on an ambitious computational re-evaluation of over 86,000 high-resolution protein structures archived within the Protein Data Bank (PDB), the foremost global repository for protein data. Utilizing a cutting-edge algorithm developed in-house, termed SimplifiedBondfinder, the team employed a fusion of machine learning methodologies, quantum mechanical modeling, and rigorous structural refinement algorithms. This innovative pipeline allowed the detection of subtle bond formations—specifically NOS linkages—previously evading conventional structural analyses and experimental validation.

Traditionally, the existence of NOS bonds was recognized between cysteine and serine amino acid residues, with their role briefly characterized within redox biology. However, the Göttingen team’s computational deep dive uncovered NOS linkages in previously uncharted amino acid pairs, including arginine-cysteine and glycine-cysteine combinations. This discovery is particularly notable because it expands the chemical repertoire of post-translational modifications, thereby revealing hitherto unknown molecular mechanisms that proteins can harness under oxidative conditions.

The formation of NOS bonds involves a tri-atomic bridge containing nitrogen, oxygen, and sulfur atoms linking specific amino acid side chains. The chemical implications are profound. These bonds act as reversible molecular switches that confer structural stability and modulate protein function in response to fluctuating oxidative environments. Such mechanisms may fine-tune enzymatic activities, regulate protein-protein interactions, or even protect critical proteins from irreversible oxidative damage.

Dr. Sophia Bazzi, who spearheaded the study at the University of Göttingen’s Institute of Physical Chemistry, emphasized the importance of revisiting established datasets with modern computational tools. “Our findings demonstrate that the Protein Data Bank is not just a static archive but a reservoir teeming with hidden chemistry waiting to be uncovered,” Bazzi remarked. “By coupling machine learning with quantum chemistry, we have charted new chemical territory within proteins that had previously been invisible.”

The implications of this research ripple beyond basic science. Enhanced protein models that incorporate these newly recognized NOS linkages could revolutionize protein engineering efforts. For example, designing enzymes with built-in oxidative stress resilience becomes more feasible when these chemical switches are understood and manipulated. Similarly, drug discovery and synthetic biology stand to benefit from this enriched chemical understanding, potentially accelerating the creation of therapeutics and synthetic biomolecules with superior stability and functionality.

Methodologically, the combination of large-scale computational screening and quantum mechanical validation represents an emerging frontier in structural biology. The SimplifiedBondfinder pipeline was rigorously tested against benchmark data and demonstrated exceptional sensitivity and specificity in detecting otherwise overlooked covalent bonds. This comprehensive re-evaluation not only functions as an analytical breakthrough but also sets a precedent for future explorations into protein structural data, moving the field toward an era of enhanced protein characterization accuracy.

The discovery further underscores the latent value embedded within existing scientific databases. While experimental methodologies continue to advance, computational reinterpretations of archived data can yield transformative insights without the exhaustive need for new laboratory experiments. This synergy between data science and molecular biology maximizes resource utilization, fostering scientific breakthroughs that are both cost-effective and rapid.

Moreover, the chemical novelty of arginine-cysteine and glycine-cysteine NOS bonds hints at diverse biological roles across different protein families. Arginine and glycine are among the most abundant amino acids across proteomes, and their newfound ability to engage in these redox-sensitive linkages broadens the scope of oxidative signaling and regulation. Investigating the functional consequences of these bonds in vivo remains a crucial next step for deciphering their physiological relevance.

In essence, this study heralds a new frontier in our comprehension of protein chemistry, emphasizing that even extensively studied molecules like proteins harbor undiscovered secrets with far-reaching biological consequences. As researchers worldwide begin to incorporate these novel findings into experimental designs and theoretical frameworks, the molecular dance governing life’s vital processes will be better illuminated in its full chemical complexity.

Looking ahead, the development and refinement of similar computational pipelines will be pivotal in uncovering additional atypical bonds and post-translational modifications. This progression promises a more nuanced understanding of proteomic landscapes, potentially unveiling new targets for therapeutic intervention and innovative biomolecular design principles. The work from the University of Göttingen stands as a testament to the profound insights achievable when advanced computational methods meet exhaustive data scrutiny, reshaping the boundaries of molecular biology.

Subject of Research:
Not applicable

Article Title:
Revealing arginine–cysteine and glycine–cysteine NOS linkages by a systematic re-evaluation of protein structures

News Publication Date:
13-May-2025

Web References:
https://doi.org/10.1038/s42004-025-01535-w

References:
Bazzi et al., Communications Chemistry, 2025

Image Credits:
Sophia Bazzi (structural data from the Protein Data Bank, visualization using Coot software)

Keywords:
Protein analysis, Protein interactions, Proteins, Protein activity, Biochemical processes, Enzymology, Life sciences, Cell biology, Chemistry, Physics, Algorithms