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.
Deep in the ocean, where sunlight barely penetrates, life thrives. This article explores how organisms in these light-starved environments survive. It focuses on rhodopsins, light-sensitive proteins used by microbes for energy production and signaling. Scientists have discovered rhodopsins remarkably tuned to the faint blue light that reaches these depths, maximizing energy capture. Further research has revealed the surprising diversity and adaptability of rhodopsins, showing they can even utilize thermal energy when light is completely absent. This challenges our understanding of life's limits and suggests that rhodopsin-based life could exist in even more extreme environments, including other planets.
Hacker News users discussed the surprising adaptability of life to extremely low-light environments, as described in the Quanta article. Several commenters highlighted the efficiency of biological systems in capturing and utilizing even the smallest amounts of available photons. Some discussed the implications for finding life in other environments, like the subsurface oceans of icy moons, and the possibility of life using alternative energy sources besides light. Others delved into the specific biochemical mechanisms mentioned in the article, like the role of rhodopsins and the challenges of studying these organisms. A few questioned the "barely any light" framing, pointing out that even seemingly dark environments like the deep ocean still have some bioluminescence and faint light penetration. One commenter also mentioned the possibility of life existing solely on chemical energy, independent of light altogether.
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.