A new study has deciphered why the core of folded proteins exhibits a consistent packing density, regardless of protein size or family. Researchers found that the backbone of the protein chain itself, and not just the side chains, plays a crucial role in dictating this density. Specifically, the rigid geometry of peptide bonds, combined with the preference for certain dihedral angles, limits the possible arrangements and leads to a universally dense core. This discovery resolves a long-standing puzzle in protein folding and offers a deeper understanding of protein structure and stability.
A new study suggests calcium ions may have played a crucial role in establishing the "handedness" or chirality of life's molecules. Researchers found that calcium, abundant in early Earth environments, preferentially binds to and stabilizes one chiral form of RNA precursors, potentially explaining why life utilizes only right-handed sugars and left-handed amino acids. This selective stabilization could have amplified small initial imbalances in chirality, ultimately leading to the homochirality observed in all living organisms. This discovery offers a plausible explanation for a fundamental mystery surrounding the origins of life.
Hacker News users discussed the implications of the study, with some skeptical of the "handedness" explanation for life's origins. One commenter questioned if this finding truly addresses the origin of homochirality or simply shifts the question to why calcium phosphate favors one enantiomer. Others expressed excitement about the potential implications for understanding abiogenesis, even suggesting this could lead to creating life from scratch in the future. Some users also delved into more technical details, discussing the specific chirality observed in biological molecules and the role of minerals in catalyzing early biological processes. Several comments mentioned the frequency with which such origin-of-life discoveries are announced and subsequently challenged, suggesting a cautious optimism towards these findings. There was also a discussion about the distinction between this discovery showing a possible mechanism for homochirality versus proving it definitively.
Summary of Comments ( 18 )
https://news.ycombinator.com/item?id=43681132
HN users discuss the implications of the protein folding research, with some expressing skepticism about the "mystery solved" claim. Several commenters highlight that the study focuses on a simplified model and question its applicability to real-world protein folding complexity. There's debate about the significance of the findings, with some arguing it's an incremental step rather than a major breakthrough. A few users delve into the technical details of the research, discussing the role of hydrophobic interactions and the limitations of current computational models. Others question the practical applications of the research, wondering if it will lead to advancements in areas like drug discovery. Overall, the comments reflect a cautious optimism tempered by a recognition of the inherent complexity of protein folding.
The Hacker News thread discussing the protein folding research has a moderate number of comments, exploring various aspects of the findings and their implications.
Several commenters express enthusiasm for the research, viewing it as a significant step in understanding protein structure and function. They highlight the importance of packing density within protein cores and how this research sheds light on a previously unexplained phenomenon. The elegance and simplicity of the explanation are also praised, with some noting that it's a reminder that complex biological processes can sometimes have straightforward underlying principles.
A recurring theme is the potential impact of this discovery on protein engineering and drug design. Commenters speculate on how a deeper understanding of core packing could lead to more efficient methods for designing proteins with specific properties, including novel therapeutics and industrial enzymes.
Some commenters delve into the technical details of the research, discussing the methods used and the implications of the findings for related fields like computational biology and biophysics. There's a discussion about the role of hydrophobic interactions in protein folding and how this research contributes to that understanding.
A few commenters express a degree of caution, pointing out that while the research is promising, it's still early days. They emphasize the need for further research to validate the findings and explore their broader applicability. One commenter questions whether the model is truly universal or if it applies only to certain classes of proteins.
There's also a brief discussion about the accessibility of the original research paper. Some express disappointment that it's behind a paywall, limiting access for those outside of academic institutions.
Finally, a couple of commenters draw connections to other scientific fields, highlighting the interconnectedness of scientific disciplines and how discoveries in one area can inform and inspire research in others. They mention related work in materials science and nanotechnology. One comment humorously links the research to the efficient packing of groceries in a bag.