July 29, 2015 § Leave a comment
Frustration has its perks. In a paper just out in Nature, researchers describe making an artificial ribosome because they couldn’t get normal ribosomes to do what they wanted. In creating this artificial ribosome, called Ribo-T, the investigators unwittingly turned conventional molecular biology wisdom on its head: Unlike regular ribosomes, Ribo-T doesn’t need to fall apart and come together again to support protein synthesis.
Alexander Mankin from the University of Illinois at Chicago says his group and that of Michael Jewett at the Northwestern University were trying to teach normal ribosomes new tricks, like getting it to translate “difficult-to-make” proteins or to take in unnatural amino acids to make special polymers. “We were frustrated with our inability to test or alter the functions of the ribosome,” says Mankin.
Trying to tweak the existing ribosomal RNA, which does much of the work of protein synthesis in the ribosome, didn’t go anywhere. Changes to it killed the cell.
So Mankin, Jewett and their teams considered making a portion of the ribosome that would be able to guide the ribosome into making the special polymers. But the problem is that the ribosome, made up of two subunits, falls apart and comes together in every cycle of protein synthesis. How would they stop the re-engineered portion of the ribosome from being swapped out by the normal subunit?
That’s when the idea of a tether came in. But “dissociation of ribosomal subunits was believed to be a prerequisite for efficient translation, and it was unclear whether ribosome with the tethered subunits would be functional,” says Mankin. Still, the investigators decided to give it a shot.
After many tries, one design worked: the Ribo-T. Mankin, Jewett and colleagues engineered a ribosomal RNA that combined sequences from the two subunits of the ribosome into a single unit. Short RNA linkers separated the two subunit RNAs in the contiguous stretch of nucleic acid.
And Ribo-T worked even better than anticipated. Not only did Ribo-T make proteins in a test tube, it also made proteins in bacterial cells that lacked naturally occurring ribosomes and keep the cells alive. Mankin still sounds surprised: “We have created probably the first-ever-on-Earth organism which lived with the ribosome where two subunits are combined into a single entity.”
He adds that Ribo-T could pave the way to exploring properties of the ribosome and to make a independent protein-synthesis system in cells that does not interfere with the ribosomes that take care of expression the rest of the cellular proteins. But, for now, the investigators are focusing on what sparked off the whole project in the first place: Getting Ribo-T to carry out the tasks that are difficult for normal ribosomes to do.
June 19, 2015 § Leave a comment
Sometimes the end doesn’t justify the means. In a recent paper in the Journal of Lipid Research, investigators describe how spinning high-density lipoproteins fast, a typical way to isolate them quickly, damages them. The finding suggests that the current understanding of the hydrodynamic properties and composition of HDL “is incorrect,” states William Munroe at the University of California, Los Angeles.
HDL, known as the “good cholesterol,” is an important lipoprotein in diagnosing cardiovascular disease. Its abundance in the bloodstream is considered to be a sign of good cardiovascular health because HDL carries away cholesterol.
Ever since the discovery in 1949 that lipoproteins can be separated and isolated in an ultracentrifuge, spinning lipoproteins like HDL at speeds 40,000 rpm or greater has been the norm. Samples often get spun at speeds of 65,000 to 120,000 rpm within 48 hours to hasten the isolation process.
But there have been whispers in the lipid community that the high speeds damage the molecules. So a trio of researchers at UCLA, led by Verne Schumaker, decided to see how speed affects HDL. “The phenomenon of HDL potentially exhibiting sensitivity to the ultracentrifuge speed is sometimes mentioned between lipoprotein researchers,” says Munroe, who is the first author on the paper. “However, there was little in the literature describing this phenomenon.”
In their JLR paper, Munroe, Schumaker and Martin Phillips showed that damage to HDL began as soon as the ultracentrifuge speed hit 30,000 rpm. Using mouse plasma samples, the investigators demonstrated that the damage got worse as the rotor went faster. Proteins, which are integral to the lipoproteins, got ripped out of the protein-lipid complexes, leaving few intact particles. “With enough gravitational force or time, this protein-deficient HDL undergoes further damage to lose lipid,” notes Munroe.
To try to circumvent the damage, the investigators tested out an alternative method for isolating HDL. They poured a potassium bromide density gradient over their sample. Next, they spun the gradient with the sample at a low speed of 15,000 rpm. Admittedly, the isolation took longer at 96 hours, but at least the amount of HDL that rose to the top of gradient was significantly higher than when using the conventional method.
Based on their findings, the investigators now want “to identify HDL-associated proteins that previous identification studies may have missed because certain proteins may have been completely lost from the recovered HDL particle during its isolation by ultracentrifugation,” says Munroe. “This may give insight into additional roles the HDL may participate in besides reverse cholesterol transport.”
June 18, 2015 § Leave a comment
Some scientists credit schoolteachers or graduate-school and postdoctoral advisers as their career role models. Henrik Dohlman at the University of North Carolina stays within his family. He credits his father.
“I really look up to him,” he says of Claes Dohlman. “He’s not only done great things professionally, he’s a very kind man.”
“Great things professionally” is a fair description. Claes Dohlman is a well-known figure in vision research. Inducted into the American Society of Cataract and Refractive Surgery’s Hall of Fame in 2004 and the recipient in 2007 of the American Academy of Ophthalmology’s highest honor, the Laureate’s Award, the elder Dohlman who is an emeritus professor at Harvard University, is considered the founder of modern corneal science. His research into corneal physiology established the basis for current clinical practice with dry eye disease, corneal burns, wound healing and corneal transplantation.
Although he retired from university administration in 1989, Claes Dohlman has stayed on as a scientist. At 92, he is the director of Boston Keratoprosthesis Research and Development, which is part of Massachusetts Eye and Ear, where he created and works to perfect a device he is now famous for: an artificial cornea known as the “Boston keratoprosthesis.” The artificial cornea can be used on patients who can’t rely on standard human corneal transplants, such as chemical-burn victims. A prosthetic that resembles a collar button, it is made of medical-grade plastic and titanium. Since cleared by the FDA in 1992, over 10,000 patients have had the device inserted in their eyes.
The older Dohlman turned his full attention to the device in the 1990s, once he retired from being the chair of Harvard’s ophthalmology department, director of his ophthalmology laboratory, and a chief at Massachusetts Eye and Ear.
With a hint of understatement, the younger Dohlman says of his father, “He has a lot of energy.”
From Sweden to the U.S.
Science and medicine surrounded Claes Dohlman as he grew up in Sweden. His father was the chairman of the ear, nose, and throat department at the University of Lund. “It was hinted that there was only one worthwhile profession to consider and that was academic medicine,” remembers Dohlman. “All my friends were heading for medicine so I followed the path of least resistance.”
Dohlman got an M.D. and finished a residency in ophthalmology at the University of Lund’s Eye Clinic. Drawn by the work of Jonas Friedenwald at Johns Hopkins University on the histochemistry and biochemistry of corneal wound healing, Dohlman did a fellowship with him in the early 1950s in Baltimore, Md. He returned to Sweden to get a Ph.D. in biochemistry from the Karolinska Institute.
A famous retina surgeon in Boston, Charles Schepens, noticed Dohlman’s work. He offered Dohlman a fellowship at Harvard. Having been in the U.S. for the Hopkins fellowship, Dohlman says, he knew that “the possibilities, professionally, were so much greater.”
So in 1958, Dohlman and his wife, Carin, moved to the U.S. with three children. Two years later, Henrik became their fourth child and the first to be born in the U.S. Two more children followed.
The little professor
Henrik Dohlman displayed traits of an academic at a young age. “He was a little professor from the start,” says his father. “He was always very curious, always eager to lecture people on how things really are and copiously read all kinds of literature.”
He also had a willingness to experiment. Claes Dohlman describes a moment in 1968 when he and Carin opened the front door of their home to a sales representative from a hearing-aid company. All of the adults were confused. The sales representative insisted that a Henrik Dohlman had contacted the company. The parents couldn’t figure out why a hearing-aid sales representative wanted to see an 8-year-old boy.
The confusion cleared when the child admitted to finding an advertisement that offered free testing of a hearing aid.
“I had this image that it would give me super powers, and I would hear what people were saying at great distances,” says Henrik Dohlman, still sounding sheepish almost five decades after the incident. “So I filled out the card, and then the salesman showed up. When he discovered that the person he was about to try to sell a hearing aid to was an 8-year-old boy with perfect hearing, he stomped off.”
The younger Dohlman recalls his childhood home in Arlington, Mass., as filled with joyful chaos of a large and close-knit family. “When my father came from work, we all swarmed to greet him and he would be tackled by his kids,” he says. “Dinnertime was masses of spaghetti and conversation.”
But Henrik Dohlman got hints from a young age that his father also was a well-known figure in the community. “Every time I would pass the principal of my elementary school, he’d tousle my hair and say, ‘How’s the son of the famous Dr. Dohlman?’ I figured if my principal knew who he was, then my father must be prominent.”
Education was critical in the Dohlman family. Among the six, two are M.D.s and the rest are Ph.D.s. Henrik Dohlman says his father is very proud of the fact that all his children hold advanced degrees. “If I can say one thing about my parents, it is that they were exceedingly generous financially,” says Dohlman. “They put six kids through college and then graduate or medical school. It’s something I took for granted when I was growing up. But once I got to college and grad school, I realized what a gift that was, to have no financial barriers to completing my education. That’s my inheritance.”
Henrik Dohlman was the only one to go into the life sciences. His other Ph.D.-toting siblings are economists. He credits his mother for turning him onto biology even though she holds a degree in political science. Carin Dohlman also grew up in Sweden, where, as her son notes, all schoolchildren are taught to appreciate the natural world and revere the 18th-century botanist and zoologist Carl Linnaeus who laid the foundations for modern species nomenclature and ecology. Carin Dohlman shared her love and wonder of nature with Henrik.
Identity of his own
Despite earning a Ph.D. in biochemistry like his dad, Henrik Dohlman, who is also an associate editor for the Journal of Biological Chemistry, is quick to point out that he was always intent on making his way through science as independently as possible. His research portfolio at UNC focuses on understanding the fundamental properties of yeast G protein-coupled receptors, a far cry from clinical corneal research.
Ironically, the first project Henrik Dohlman was involved in as a graduate student landed him in his father’s territory. The younger Dohlman was in the laboratory of Robert Lefkowitz at Duke University in the 1980s. At the time, the laboratory was focused on cloning the β-adrenergic receptor, the first hormone-based G protein-coupled receptor identified and cloned. The work later led to Lefkowitz’s Nobel Prize in chemistry in 2012, shared with Brian Kobilka at Stanford University.
“I thought I was working in an area that had nothing to do with vision research,” says Henrik Dohlman. “But the first thing we noticed about this receptor was it was clearly homologous to rhodopsin, the light receptor.”
Because of the striking similarities between the two systems, Henrik Dohlman’s first scientific conference was the annual meeting of the Association for Research in Vision and Ophthalmology. “It was not only one of my first public presentations, but it was a public presentation in front of about 500 of my father’s friends and colleagues, with my father in the front row,” recounts the younger Dohlman.
Perhaps realizing how unprepared his son was for his first presentation at a national scientific meeting, the older Dohlman pulled him aside and asked to see the slides and hear the talk before the event. “It was a very painful experience for both of us,” recalls his son. “The talk that came out in the end bore no resemblance to what I’d prepared. It was the first and last time I’ve given a scientific presentation with my father in the audience.”
But the younger Dohlman acknowledges that the pain of having his father redo his first public presentation for him was well worth it. “I’m a much better public speaker because of it!” he says with a laugh.
“Just shrug it off”
Besides teaching him the value of a good talk, Claes Dohlman has influenced Henrik in two other critical ways. “Probably the most important one was that I saw from an early age that he really loved his work,” says his son. “That’s not a bad way to go through life.”
Claes Dohlman also modeled what it is to be a good laboratory manager. “He’s always had a positive outlook. He rarely loses his temper. He tries to be generous in assigning credit. He does not get distracted by office politics or idle gossip,” says the younger Dohlman.
When it comes to research, Claes Dohlman knows how to roll with the punches. Something his son says he’s still working on. “There are many failures in this business. There are a lot of setbacks, and there’s no escaping that. You can drive yourself crazy if you let it get under your skin. The best that you can do is brush it off and move onto the next challenge,” says Henrik Dohlman. “I hear my father’s voice in my head saying, ‘Just shrug it off.’”
May 19, 2015 § Leave a comment
On October 14, 2010, construction workers excavating a site for a reservoir dam near Snowmass Village in Colorado, stumbled across bones. The bones belonged to a woolly mammoth. More careful digging revealed close to 5,000 bones from different Ice Age animals. Camels, mastodons, and bison were among them. In a recent paper from the journal Molecular & Cellular Proteomics, researchers reported the analysis of proteins found in the bones of an extinct species of giant bison from the site. From their analysis, they described an unexpected feature of ancient collagen.
The bones at the Snowmass Village fossil site (which is also known as the Ziegler reservoir site) were remarkably well-preserved. The high altitude of the site, which was a lake in the Ice Age, kept it at relatively cool temperatures over the past 130,000 to 150,000 years. The cooler temperatures probably contributed to the preservation the buried materials; even some of the ancient plant material buried at the site was still green at the time of the discovery.
Kirk Hansen at the University of Colorado, Denver, heard of the Snowmass Village discovery in 2010 “while listening to public radio on my way into work.” Hansen is a protein biochemist whose expertise is in the extracellular matrix. He called the Denver Museum of Nature & Science, which was directing the excavation of the bones, to see if he could help with analyzing samples.
Hansen’s laboratory carries out mass spectrometry analyses and he was aware of existing mass spectrometry work on fossilized proteins. Some studies have suggested that red blood cells can be preserved in ancient bones, but the validity of these interpretations have been questioned. Skeptics also have wondered about inadvertent contamination of ancient samples with modern proteins.
But, Hansen says, “I thought that the methods we were developing to improve characterization of proteins from the extracellular matrix could be used on these well-preserved samples.” Hansen knew he would get good quality samples from the Snowmass Village site when, he says, “one of the scientists described the smell of the bone fossils as ‘very organic. ’”
Mindful of the issue of contamination, Hansen and colleagues were careful with the samples given to them by the museum. The samples were skull bones from an extinct species of giant-horned bison from the Pleistocene era called Bison latifrons. “We took extra precautions by using new chromatography columns and ensuring the samples were placed in only new vials,” he says.
The investigators carried out mass spectrometry on the proteins left in the bison bones. The biggest challenge was in the data analysis. Some of the proteins had degraded, as expected of old proteins, giving a “laddering” effect in the peptides, and numerous peptides were changed by post-translational modifications.
But the investigators sorted through the data and identified extracellular matrix proteins and plasma proteins. Thirty-three of the ancient bison proteins mapped over to modern bovine proteins, showing the evolutionary kinship.
In particular, Hansen and colleagues sequenced in detail the collagen from the bison samples. The extracellular matrix protein, which forms a fibrous ropelike structure, bore modifications seen in other studies of ancient collagen, such as proline hydroxylation.
But one modification was new and unexpected—hydroxylysine glucosylgalactosylation. “This was the first discovery of a preserved glycan, to the best of my knowledge,” says Hansen. “Finding it in a sample that is over 100,000 years old was surprising.”
Bioarcheologist Matthew Collins at the University of York in the U.K., who specializes in studying ancient collagen, is most impressed with the finding of the hydroxylysine glucosylgalactosylated residue. Glycosylation is a key structural feature of collagen, crosslinking chains together to stablilize its ropelike structure. But it was assumed the seemingly labile glycosylated residues would not withstand the test of time.
“You’d imagine, over this period of time, you would have lost the sugars. That’s one of the reasons why we never bothered to look for them: We didn’t expect to find them. This work elegantly shows that I was wrong!” says Collins. “We’re now going back and looking at our samples for glycosylated residues.”
As Hansen and colleagues were working on the bison samples, data came from a young Siberian woolly mammoth called Lyuba. Her proteins bore similar modifications to those of the bison proteins. “Finding these modifications in modern tissue samples usually requires some form of enrichment,” says Hansen. But, with these two fossils, “the modifications were relatively easy to find.” He says the discoveries suggest that collagen with hydroxylysine glucosylgalactosylation might be enriched over time because it creates a stable complex.
Hansen and his team’s next aim is to study the relationships between collagen modifications and collagen fiber architecture. The ramifications of the work will go beyond the study of ancient proteins. As Hansen explains, “Once we make progress in this area, we will have a better understanding of the microenvironment’s role in tumor progression and the ability to rationally design biomaterials for tissue engineering applications.”
April 23, 2015 § 1 Comment
Universal blood is an appealing notion because it could be transfused into anyone regardless of blood type. Researchers have been kicking around the idea of using enzymes to create universal blood since the early 1980s, “but a major limitation has always been the efficiency of the enzymes,” says Stephen Withers at the University of British Columbia. “Impractically large amounts of enzyme were needed.”
Now in a paper just out in the Journal of the American Chemical Society, Withers, David Kwan, Jay Kizhakkedathu at the Centre for Blood Research and others describe the development of an improved enzyme that takes us a step closer to having universal and others describe the development of an improved enzyme that takes us a step closer to having universal blood.
Blood comes in four major types: A, B, AB and O. The difference between them lies in the sugar structures that festoon the surface of red blood cells. Both blood type A and B have the same core sugar structure as blood type O, but differ in an additional sugar at the tip of the sugar structure. Type A has an N-acetylgalactosamine residue. Type B has a galactose residue. Type AB has a mix of both residues. The moiety carrying the additional residue can be tacked onto the core structure in various ways, giving rise to subtypes of A and B blood.
The additional residue presents trouble during blood transfusions: It can trigger life-threatening immune responses. Type A people can’t take type B blood; type B people can’t take in type A blood. Type AB can take A or B. Only type O blood can be freely shared without the fear of immune responses.
The idea from the 1980s has been to use enzymes to remove the moieties with the terminal N-acetylgalactosamine or the galactose residues to leave the core sugar structure on red blood cells, just like in type O blood. But to date, sugar hydrolases have not been sufficiently efficient to make the idea practical.
So Withers’ group, which had some success in engineering different classes of sugar enzymes, tackled the creation of more efficient sugar hydrolases by directed evolution. In directed evolution, researchers carry out iterative rounds of mutations on a gene to ultimately produce a protein that performs better than the original gene product.
Kwan, Withers and the rest of the team carried out directed evolution on the family 98 glycoside hydrolase from a strain of Streptococcus pneumoniae. Kwan explains that the structure of the enzyme is known, which helped the investigators design their variants.
Kwan adds that the enzyme also is good at cleaving most A and B subtypes with the exception of a few A subtypes. The investigators decided to engineer the enzyme so it had better activity against those A subtypes. By directed evolution, the investigators got an engineered enzyme with a 170-fold greater efficiency than the original enzyme.
However, the engineered enzyme still doesn’t remove every single moiety with the N-acetylgalactosamine. Withers says that the immune system is sensitive enough to small amounts of the moiety to start an immune response. He says, “Before our enzyme can be used clinically, further improvements by directed evolution will be necessary to effect complete removal” of all moieties with the terminal N-acetylgalactosamine residues.
The investigators are now looking to tackle the remaining subtypes of type A blood that the S. pneumoniae hydrolase struggles to cut. Withers says, “Given our success so far, we are optimistic that this will work.”
April 10, 2015 § 2 Comments
What are the risks associated with mitochondrial replacement therapy which is a new technique to prevent mitochondrial diseases? This was a key scientific question asked last week at a meeting held by an Institute of Medicine committee focused on the ethics and social ramifications of MRT.
At the IOM meeting, held on March 31 and April 1 in Washington, D.C., experts presented on numerous ethical, scientific, and legal topics surrounding MRT in order to inform the committee made up of twelve doctors, lawyers, and scientists. The IOM committee was commissioned by the U.S. Food and Drug Administration to explore the ethical and scientific aspects of MRT. The committee will present its findings in a report in early 2016. The spring meeting was the second of five scheduled meetings.
Mitochondrial diseases are caused by mutations or deletions in the 37 genes encoded in the mitochondrial genome. The diseases have a variety of symptoms, including muscle weakness, blindness, dementia, and some cases, childhood death. There are no cures for mitochondrial diseases.
MRT, a process in which the nuclear DNA is transferred from an affected mother’s egg to a donor egg with healthy mitochondria, is intended to stop the transmission of mitochondrial diseases from a mother to her children. The procedure is controversial because it involves destroying fertilized human eggs. Also, critics say it could lead to the slippery slope of nuclear DNA germline modification. This technique has been approved in the U.K. but is still being considered by the FDA.
The scientific presentations at the latest IOM meeting included alternatives to MRT, as well as the possible risks to the children born by MRT, such as epigenetic modifications and haplotype incompatibility. Jacques Cohen, a founder of Reprogenetics, said that pre-implantation genetic diagnosis does not work for all women with mitochondrial diseases and should not be considered a viable alternative.
Carlos Moraes at the University of Miami explained a few alternatives to MRT that reduce the proportion of mutant mitochondrial genomes. In a single mitochondrion, the two to 10 copies of mitochondrial DNA can have different genotypes. Moraes has designed a way to get restriction endonucleases to cut a defective mitochondrial genome, shifting the proportion of healthy mitochondria in cell culture. He recognized that it is not always possible to find a unique recognition sequence in a mutant genome, which is why he also is investigating other targeting systems.
Howard Hughes Medical Institute investigator George Daley at Harvard Medical School talked about potential epigenetic effects of MRT in stem cells. He admitted that epigenetic differences between different stem cell types were considerable, and techniques for analyzing single cells at an epigenetic level are limited. In short, researchers don’t know what the right epigenetic patterns are for a developing embryo, and they don’t have reliable methods to analyze the patterns either.
The fact that different mitochondrial genomes could interact poorly with different nuclear genomes was rather contentious. Doug Wallace at The Children’s Hospital of Philadelphia talked about the evolution of different groups of normal mitochondrial genomes and possible interactions between mitochondrial and nuclear genotypes. Much of his data came from subtle behavioral tests performed on inbred mice strains with swapped mitochondria. He concluded that mitochondrial DNA does influence neural performance and behavior, and that one should ensure that the mitochondrial DNA in the donor and intending mother’s eggs were as similar as possible to reduce these risks.
Cohen rebutted Wallace’s presentation by pointing out the limitations of using subtle behavioral differences in inbred mouse models to conclude anything about the highly heterogeneous human population. Direct debate was not permitted—only the committee members could question each speaker.
It will be interesting to read the committee’s report in early 2016 and see their conclusions about the risks of MRT.
February 4, 2015 § Leave a comment
Samuel Sia at Columbia University, who spearheaded the work, says that the World Health Organization recommends that researchers develop new tests for HIV and syphilis because the two diseases carry the highest risks for mother-to-child transmission in pregnant women. “We have verified that with our field surveys of healthcare workers in developing countries,” notes Sia.
Field tests used today to diagnose HIV and syphilis are not always accurate. The tests usually require an ELISA instrument that costs thousands of dollars, and it can take more than 2 hours to generate results (in developing countries, because of infrastructure issues, patients often wait at the healthcare center for the test results to come out).
The dongle developed by Sia and colleagues is estimated to cost $34 to make, and it spits out a result in 15 minutes. The microfluidic device plugs into the audio jack of a smartphone, such as an iPhone or an Android. Sia and colleagues showed that a fourth-generation iPod touch can power the dongle 41 times on a single charge.
The microfluidic device accommodates five different assays embedded in disposable plastic cassettes divided into zones. “Each zone has a different affinity-capture molecule,” says Sia. The molecules pick up antibodies against HIV and syphilis. The investigators also built in negative and positive controls.
When tested at healthcare centers in Kigali, the assays worked almost as well as the conventional ones. Most of the 96 patients on whom the device was tested said they preferred the dongle over the conventional ELISA tests because it was quicker. Some did say they liked the fact they could be tested for more than one disease in one shot.
Notably, “this trial was the first to have healthcare workers run the tests instead of our research team members,” says Sia. “We were all pleasantly surprised at how well the test performed the first time, but that is not to say there is no room for improvement.”
Besides improving the dongle, Sia says he and colleagues are exploring how make it into a commercial product.
December 18, 2014 § Leave a comment
Scientists have designed a stripped-down version of a protein that carries certain ions across a membrane. In doing so, the scientists have shown that the large, complex transporters found in all living things actually operate on simple principles. They’ve also demonstrated that we now know enough about these molecular machines to design them from scratch. The work is described in a paper just out in Science.
Natural transporters “are large and complex machines. And yet, transmembrane transport is an absolutely essential feature of cellular life so it must have evolved very early on,” says one of the scientists involved in the work, Gevorg Grigoryan at Dartmouth College. “How did such complex machines come into being?”
Grigoryan, William Degrado at the University of California, San Francisco, and others designed a bare-bones transporter, one that inserts into the lipid membrane to carry zinc or cobalt ions in one direction and protons in the opposite direction. They named their protein Rocker, after a feature engineered into the molecule that made it rock back and forth between different conformations to enable transport—similar to how natural transporters are thought to work. In Rocker’s case, it oscillated as it bound zinc ions at one end of the molecule and released them at the other
The researchers developed Rocker in two steps. First, they designed the minimalistic protein with the help of computer programs. “Because of the complicated design goals, having to balance membrane insertion, formation of the desired topology, ion binding in the membrane, and specific dynamic features of the molecule, we had to develop a novel computational design approach,” says Grigoryan, who led the computational work.
Next up was making the actual 25-amino acid protein in the lab and getting it to work as designed. The scientists showed that Rocker formed four-helix bundles in membranes, in agreement with the computational model. The amino acids within Rocker had to be precisely positioned so that the protein transported only zinc and cobalt, but not calcium, ions through it.
Every time Rocker transported a zinc or cobalt ion, it pushed three or four hydrogen ions in the opposite direction. The investigators used methods like X-ray crystallography, analytical ultracentrifugation, and nuclear magnetic resonance to study Rocker in action as it transported ions in and out of microscopic sacks made of lipids.
Although tiny in comparison to native transporters, “Rocker is essentially a reductive deconstruction of the transport process,” says Grigoryan. By designing a minimalistic transporter protein from scratch, Grigoryan says, he and his colleagues showed that “selective transport itself does not necessarily require complex structure and demonstrated a plausible evolutionary mechanism by which transport could have originated.”
Down the road, Rocker can be used as a model system to understand the structural and thermodynamic factors for ion transport. It also can be used as a mold to design other types of transporters.
Andrei Lupas at the Max Planck Institute for Developmental Biology, who wrote the Perspective article accompanying the paper by DeGrado’s and Grigoryan’s teams, used a quote of Richard Feynman to drive home the importance of the work: “What I cannot create, I do not understand.”