Biological systems are extraordinarily complex, and yet the most subtle changes at the molecular level can have dramatic consequences for human health. One such change, known as a mutation, occurs when there is an alteration in the genetic code, which can be caused by a variety of factors such as environmental influences, replication errors, or hereditary transmission. Among these mutations, missense mutations, which involve the substitution of one amino acid for another within a protein’s structure, have been recognized as significant contributors to a wide range of diseases. A monumental study, published in Nature, has shed new light on how these minimal genetic alterations affect human health on a molecular level, highlighting the destabilizing effects they have on proteins, which often leads to disease.
Researchers at the Center for Genomic Regulation (CRG) in Barcelona and BGI in Shenzhen took on an ambitious task of investigating how mutations causing diseases contribute to the destabilization of human proteins. The team focused on 621 missense mutations that have been well documented to be associated with different human diseases. They uncovered a profound insight: a vast majority of these mutations—around 61%—led to a detectable decrease in protein stability. The destabilized proteins were found to be more susceptible to misfolding, clumping together, and accumulating inside cells in damaging ways, all of which impede the proper function of the organism.
This critical finding speaks to an important question about the genetic underpinnings of human diseases. If these mutations are as seemingly small as a single amino acid change, how do they lead to such serious consequences? The answer lies in the structural integrity of the proteins involved. Proteins are highly specialized molecules that execute a wide array of essential functions in the body, from providing structural support to catalyzing biochemical reactions. The shape or structure of a protein determines its function, and even slight distortions in its structure can render it nonfunctional, cause it to aggregate, or trigger a cascade of harmful events within the cell.
One of the areas where protein instability plays a significant role is in the formation of cataracts. The study investigated missense mutations related to cataract formation and found that in 72% of the cases, mutations in beta-gamma crystallins destabilized the protein. Crystallin proteins are crucial for maintaining the clarity of the lens in the human eye. When these proteins become unstable due to mutations, they are more likely to aggregate into clumps, forming opaque regions in the lens and leading to cataracts. This finding highlights how even minor genetic alterations can result in visually significant and debilitating outcomes.
The research doesn’t just address disorders of the eye. The instability of proteins was found to contribute to other devastating diseases, including reducing body myopathy and ankyloblepharon-ectodermal defects-clefting (AEC) syndrome. Reducing body myopathy is a rare muscle-wasting disorder characterized by weakness and the atrophy of muscle tissue. In AEC syndrome, the effects of the mutation disrupt development, manifesting as a cleft palate along with other developmental defects. Both these conditions are linked to the destabilization of crucial proteins, showcasing the widespread impact of protein instability across different organ systems.
While protein destabilization is a dominant theme, some disease-causing mutations do not involve this mechanism at all. The study also delved into Rett Syndrome, a severe neurological disorder that primarily affects females and leads to cognitive and physical impairments. Rett syndrome is caused by mutations in the MECP2 gene, which encodes a protein that helps regulate gene expression in the brain. The intriguing finding here was that many of the mutations in MECP2 do not destabilize the protein, but instead alter how it interacts with DNA. This could impair its ability to regulate the expression of other genes, leading to the disruption of brain development and function, providing insights into the broader molecular mechanisms that underlie this devastating condition.
Dr. Antoni Beltran, a leading researcher in the study, emphasizes that understanding whether a mutation causes a protein to lose its stability or alters its function without affecting stability offers crucial guidance in the development of precise treatments. These insights will enable scientists and medical professionals to approach disease treatment in a more tailored manner. For instance, therapies could focus on stabilizing a protein in cases where misfolding and aggregation are the primary concern, or alternatively, on inhibiting a harmful protein function in diseases like Rett syndrome, where the problem stems from dysfunctional protein-DNA binding rather than misfolding.
The findings from this research also touch upon the genetic principles governing how mutations cause disease. It turns out that the type of genetic disorder—whether it is dominant or recessive—often correlates with the effect a mutation has on the protein. In dominant genetic disorders, the presence of a mutation in just one allele (copy of the gene) is sufficient to cause the disease. Recessive disorders, on the other hand, require mutations in both alleles for disease manifestation. The study showed that recessive mutations were more likely to destabilize proteins, whereas mutations linked to dominant conditions generally affected protein function in ways other than simply destabilizing the protein structure, such as interfering with protein interactions or regulatory activities.
For example, researchers observed that a recessive mutation in the CRX protein, which plays a key role in vision, destabilizes the protein so significantly that it impairs retinal function, leading to heritable retinal dystrophies and progressive loss of vision. In contrast, mutations associated with dominant retinal diseases preserved the stability of the CRX protein but altered its functionality in a way that still resulted in visual impairments. This distinction provides important insights into the molecular mechanisms that differentiate dominant and recessive diseases.
The revolutionary discovery that the vast majority of disease-causing missense mutations lead to protein instability would not have been possible without the creation of Human Domainome 1, an enormous catalog of protein variants. This database includes more than half a million mutations across 522 human protein domains, a domain being a region of the protein that folds into a stable shape and performs a specific task. The sheer scale of this effort, now four and a half times larger than previous efforts to catalog protein variants, allows researchers to study the effects of mutations not just within individual proteins but across entire families of related proteins.
This expansive database enabled the scientists to employ yeast cells as a model system to assess the stability of mutated protein domains. When they introduced mutated proteins into the yeast, the cells were able to grow well if the proteins were stable, while unstable proteins caused growth to be stunted or halted entirely. By analyzing which mutated proteins allowed the yeast cells to grow, they could determine which mutations led to stable proteins and which caused instability. Although this system has limitations (especially in not accounting for interactions with other molecules inside human cells), it provided a vital means to evaluate protein stability on a large scale.
The significance of the Human Domainome 1 catalog lies not just in the scope of its coverage, but in its predictive potential. Because related protein domains often respond to mutations in similar ways, the data gathered from these 522 domains can help scientists predict the effects of mutations in proteins beyond those included in the study. With further expansions to the catalog, researchers expect even greater accuracy in understanding the link between genetic mutations and protein destabilization, and subsequently, disease.
Despite the immense progress made by the study, the researchers acknowledge that there is still much work to be done. They plan to extend their study by exploring the effects of mutations on full-length proteins and their natural environments in human cells. The ultimate goal is to map the effects of every possible mutation in the human genome and better understand how these mutations contribute to a range of diseases at the molecular level. Such efforts represent a monumental shift toward precision medicine, allowing for personalized treatments that target the specific molecular mechanisms driving a patient’s disease.
Reference: Ben Lehner, Site saturation mutagenesis of 500 human protein domains, Nature (2025). DOI: 10.1038/s41586-024-08370-4. www.nature.com/articles/s41586-024-08370-4
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