Joined: Dec. 2005
I am a member of the American Chemical Society and get the weekly magazine Chemical & Engineering News. The latest issue has a lot of articles that would be interesting to anyone in the evolution/creation debate. The articles had no intention of applying to the debate, but it was just coincidental that they all were in the same issue. Oh, and one was a letter.
I just wanted to post them because they have certain buzzwords or "buzzconcepts."
|I am a chemist working in an engineering environment. I recently saw something through an optical microscope that I did not expect to see. In fact, it sent my heart racing. Molecules of hyaluronan, a biomacromolecule, appeared to self-assemble before my very eyes. I repeated the experiment several times and found that the results were reproducible. The highly ordered and crystalline structures showed a periodicity and a long-range order that I never thought was possible.|
As a good scientist, I captured all these images and searched for a scientific answer. It appears that the light source from the optical microscope causes mixed oligomers of hyaluronan to self-assemble spontaneously. Perhaps the light sources removed water from the hydrated oligomers and caused them to crystallize into incredible structures that already existed in solution. I am not sure about all the details, but I thought I would let the readers get a peek at the diversity of the spontaneous structures I found.
The crystalline matrices seen in these images certainty open the mind to a number of possibilities. Hyaluronan, a versatile biopolymer and chief architect of the extracellular matrix and the human eye vitreous, never ceases to amaze me. Its properties outside of human tissue have far-reaching implications for biomaterials research. I envision the first biocompatible integrated programmable device. I suspect this technology will blossom, and I recommend that such devices resulting from this technology be called Nano-BITS, for Nanoscale Biocompatible Information Transfer Systems.
I can't wait to tell more.
Raymond E. Turner
Buzzwords: self-assembly, information storage
|Mammalian Amyloid Has Useful Role|
Fibers that have amyloid structure serve as templates for melanin biosynthesis
Amyloid, an insoluble and fibrous protein aggregate, is usually thought of as a bad actor. It's associated with disorders like Alzheimer's disease and type 2 diabetes, so preventing its formation is considered highly desirable. Now, however, researchers at Scripps Research Institute find for the first time that amyloid also plays a useful or even essential role in mammals (PLoS Biol. 2006, 4, e6).
In mammalian cell experiments, chemistry professor Jeffery W. Kelly, cell biology professor William E. Balch, and coworkers have found that the protein Pmel17 adopts an amyloid fold in cell organelles called melanosomes and provides a template that approximately doubles the rate of polymerization of melanin, a biopolymer that protects cells against UV and oxidative damage. The amyloid also binds and possibly mitigates the toxicity of reactive compounds in melanosomes. The Scripps work elucidates the mechanism of melanin biosynthesis and could also lead to a better understanding of amyloid pathology and to the discovery of other functional, nonpathologic amyloid.
Amyloid with normal function has been found in bacteria and yeast and in spider silk but never in mammals. Amyloid generally forms insoluble “plaques” that can be highly toxic to mammalian cells. “So the finding that amyloid can be beneficial in higher organisms is a significant step forward in understanding the nature of this alternative form of protein structure,” comments Christopher M. Dobson, professor of chemical and structural biology at Cambridge University, in England.
Kelly, Balch, and coworkers propose the name “amyloidin” for functional amyloid, “with the expectation that the number and diversity of structures of this type will continue to grow,” they write.
“This paper adds a new dimension to the increasing evidence that the amyloid structure is a generic form of protein structure,” says Dobson, whose group has demonstrated that many ordinary proteins, not just those present in disease states, are capable of forming amyloid fibrils. The new study “should fuel still further the search for more examples of the functional use of the amyloid structure.”
Robert Tycko of the National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, Md., a specialist in amyloid structure, says the work is “quite interesting” and comments that it “will undoubtedly stimulate future efforts to find additional functional amyloids, elucidate their mechanisms, and possibly develop new uses for amyloid fibrils based on their biological roles.”
There are caveats, however. A researcher in the field who requests anonymity comments that the paper's experimental evidence for amyloid-templated biosynthesis “is weak. The rate acceleration provided by the fibrils is only 2.2-fold, and if the mechanism invoked by the authors was operating, I would expect at least an order of magnitude greater acceleration.”
Buzzconcept: Usefullness from a normally deleterious biostructure
|Tracking Cellular Machine Assembly|
Technique observes how parts of a macromolecular complex bind in real time
By combining isotopic labeling and mass spectrometry, researchers have devised a way to study how huge cellular macromolecular complexes assemble in real time (Nature 2005, 438, 628).
James R. Williamson, Megan W. T. Talkington, and Gary Siuzdak of Scripps Research Institute demonstrate the power of their technique on the bacterial 30S ribosome. The 30S ribosome is part of the bacterial protein-making machinery and contains a large RNA molecule and 20 different proteins. Using their technique, the team measured the rates at which 17 of the 20 proteins bind to the RNA during 30S ribosome assembly.
“The elegance of their experimental design should allow it to be adapted to a wide range of such complexes,” comments Sarah A. Woodson of Johns Hopkins University in an accompanying Nature commentary. A clearer picture of how large cellular complexes assemble should improve our understanding of how such complexes evolved and may guide the development of materials that mimic their properties, she adds.
To track assembly, the Scripps team introduced isotopically labeled components during a certain time window during complex assembly. They then measured the isotopic ratios of the resulting complexes and their individual protein components by matrix-assisted laser desorption ionization mass spectrometry. By varying the length of the isotopic “pulse,” the researchers were able to calculate the rates at which each protein binds to the complex.
By repeating the experiment at different temperatures, Williamson and coworkers obtained results allowing them to conclude that, contrary to previous observations, assembly of the 30S ribosome doesn't irreversibly stall under less-than-perfect conditions. “This suggests that the assembly of key macromolecular complexes such as the ribosome might proceed via an energetic landscape of multiple pathways,” a situation that might have evolutionary advantages, Talkington says.
Buzzconcept: Things don't have to be perfect for life to work
|Protein's Lipid Coat Revealed|
High-resolution structure of membrane protein captures its lipid environment
Relatively little is known about how membrane proteins interact with the lipids that surround them because structural studies typically fail to capture these proteins' lipid environment. Now, a high-resolution structure of a membrane-embedded water channel protein has opened a window to how lipids pack around membrane proteins (Nature 2005, 438, 633).
“The key to an effective membrane is to get the packing of the lipids and proteins right,” explains Anthony G. Lee of the University of Southampton, England, in an accompanying Nature commentary. The new structural data “clearly illustrate how this packing is achieved.”
Thomas Walz of Harvard Medical School and coworkers captured the 1.9-Å structure of aquaporin-0 (AQP0) immersed in an artificial lipid bilayer. AQP0 is a water channel that is the most abundant membrane protein in the lens of the eye. They used electron crystallography, a well-established technique that employs the beam of an electron microscope to produce diffraction patterns from frozen two-dimensional crystalline arrays. It's particularly powerful for imaging membrane proteins, Walz says, because “it allows them to be imaged in their native environment, the lipid bilayer.”
Previously, crystal structures of a number of membrane proteins have revealed a small number of specifically bound lipids. But the AQP0 structure, which Walz solved with the help of Tamir Gonen, Yifan Cheng, and Stephen C. Harrison of Harvard and Yoshinori Fujiyoshi of Kyoto University in Japan, provides a very different picture.
In the structure, a thin shell of lipid bilayer surrounds the hydrophobic midsection of the protein. The lipid is dimyristoylphosphatidylcholine, a non-endogenous lipid with a zwitterionic “head” and two 14-carbon fatty acid “tails.” The lipid molecules stack tail-to-tail, with their fatty acyl chains packed tightly around the protein's bumpy midsection. The resulting shell provides a uniform surface against which the rest of the lipids in the membrane can pack. Their heads interact with charged side chains on the hydrophilic portions of the protein that would typically be at the membrane-water interface.
Walz suggests that the lipid-protein interactions observed in the structure may be representative of the “nonspecific interactions that occur between any membrane protein and the natural lipids in cell membranes.” The lipid used in this study, however, is not found in natural membranes, so it remains to be tested whether endogenous lipids make similar interactions with AQP0, he admits.
Eventually, structural biologists hope “to determine at a molecular level the arrangement of proteins in cell membranes,” notes James Allen of Arizona State University. He calls the new study “an exciting advance toward that goal.”
Mark S. P. Sansom of the University of Oxford adds that “from a chemical perspective, this detailed picture of lipid-protein interactions should help us sort out the design rules of how to lock a macromolecule into a membrane.”
Buzzconcept: gaps in knowlege being filled
("It is useless to attempt to reason a man out of a thing he was never reasoned into."--Jonathan Swift)