Tag: Biochemistry

The genome encodes the complete information needed by an organism, including that required for protein production. Viruses, which are up to a thousand times smaller than human cells, have considerably smaller genomes. Using a type of herpesvirus as a model system, the scientists of the Max Planck Institute (MPI) of Biochemistry in Martinsried near Munich and their collaboration partners at the University of California in San Francisco have shown that the genome of this virus contains much more information than previously assumed. The researchers identified several hundred novel proteins, many of which were surprisingly small. The results of the study have now been published in Science. More than 80 percent of the world’s population is infected with the herpesvirus, which can cause severe diseases in newborns and in persons with weakened immune system. Researchers had already sequenced the herpesvirus genome 20 years ago, thinking they could then predict all proteins that the virus produces (virus proteome). Now scientists from the research department of Matthias Mann, director at the MPI of Biochemistry, and their American colleagues have analyzed the information content of the genome more precisely.

To carry out their study, the scientists infected cells with herpesvirus and observed which proteins the virus produced inside the cell over a period of 72 hours. In order for proteins to be produced at all, the cell machinery must first make copies of the genetic material as intermediate products (RNA). While investigating the intermediate products of the herpesvirus, the American collaborators discovered many novel RNA molecules which were in large part surprisingly short. They also found that the organization of information required for protein production in the virus genome was far more complex than previously assumed. Annette Michalski, a scientist in the Department of Proteomics and Signal Transduction at the MPI of Biochemistry, was subsequently able to confirm directly the predicted viral proteins in the infected cell using mass spectrometry. This method enables an overview of the complete proteome of the virus-infected cell. The results of the American and German researchers provide detailed insight into the complex mechanisms used by the virus. “We showed that it’s not enough merely to know the virus genome to understand the biology of the herpesvirus,” Annette Michalski said. “What is important is to look at the products actually produced from the genome.” Even human genes may be much more complex than the genome sequence itself indicates, commented the researchers. Matthias Mann and his colleagues plan to investigate this question further in the coming years.

Science Daily
December 11, 2012

Original web page at Science Daily

Computer-designed proteins are under construction to fight the flu. Researchers are demonstrating that proteins found in nature, but that do not normally bind the flu, can be engineered to act as broad-spectrum antiviral agents against a variety of flu virus strains, including H1N1 pandemic influenza. “One of these engineered proteins has a flu-fighting potency that rivals that of several human monoclonal antibodies,” said Dr. David Baker, professor of biochemistry at the University of Washington, in a report in Nature Biotechnology. Baker’s research team is making major inroads in optimizing the function of computer-designed influenza inhibitors. These proteins are constructed via computer modeling to fit exquisitely into a specific nano-sized target on flu viruses. By binding the target region like a key into a lock, they keep the virus from changing shape, a tactic that the virus uses to infect living cells. The research efforts, akin to docking a space station but on a molecular level, are made possible by computers that can describe the landscapes of forces involved on the submicroscopic scale.

Baker heads the new Institute for Protein Design Center at the University of Washington. Biochemists, computer scientists, engineers and medical specialists at the center are engineering novel proteins with new functions for specific purposes in medicine, environmental protection and other fields. Proteins underlie all normal activities and structures of living cells, and also regulate disease actions of pathogens like viruses. Abnormal protein formation and interactions are also implicated in many inherited and later-life chronic disorders. Because influenza is a serious worldwide public health concern due to its genetic shifts and drifts that periodically become more virulent, the flu is one of the key interests of the Institutes for Protein Design and its collaborators in the United States and abroad. Researchers are trying to meet the urgent need for better therapeutics to protect against this very adaptable and extremely infective virus. Vaccines for new strains of influenza take months to develop, test and manufacture, and are not helpful for those already sick. The long response time for vaccine creation and distribution is unnerving when a more deadly strain suddenly emerges and spreads quickly. The speed of transmission is accelerated by the lack of widespread immunity in the general population to the latest form of the virus.

Flu trackers refer to strains by their H and N subtypes. H stands for hemagglutinins, which are the molecules on the flu virus that enable it to invade the cells of respiratory passages. The virus’s hemagglutinin molecules attach to the surface of cells lining the respiratory tract. When the cell tries to engulf the virus, it makes the mistake of drawing it into a more acidic location. The drop in pH changes the shape of the viral hemagglutinin, thereby allowing the virus to fuse to the cell and open an entry for the virus’ RNA to come in and start making fresh viruses. It is hypothesized that the Baker Lab protein inhibits this shape change by binding the hemagglutinin in a very specific orientation and thus keeps the virus from invading cells. Baker and his team wanted to create antivirals that could react against a wide variety of H subtypes, as this versatility could lead to a comprehensive therapy for influenza. Specifically, viruses that have hemagglutinins of the H2 subtype are responsible for the deadly pandemic of 1957 and continued to circulate until 1968. People born after that date haven’t been exposed to H2 viruses. The recent avian flu has a new version of H1 hemagglutinin. Data suggests that Baker’s proteins bind to all types of the Group I Hemagglutinin, a group that includes not just H1 but the pandemic H2 and avian H5 strains.

Recognizing the importance of new flu therapies to national and international security, the Defense Advanced Research Projects Agency and the Defense Threat Reduction Agency funded this work, along with the National Institutes of Health’s National Institute for Allergy and Infectious Diseases. The researchers also used the Advanced Photon Source at Argonne National Laboratories in Illinois, with support from the Department of Energy, Basic Energy Sciences. The methods developed for the influenza inhibitor protein design, Baker said, could be “a powerful route to inhibitors or binders for any surface patch on any desired target of interest.” For example, if a new disease pathogen arises, scientists could figure out how it interacts with human cells or other hosts on a molecular level. Scientists could then use protein interface design to generate a diversity of small proteins that they predict would block the pathogen’s interaction surface. Genes for large numbers of the most promising, computer-designed proteins could be tested using yeast cells. After further molecular chemistry studies to find the best binding among those proteins, those could be re-programmed in the lab to undergo mutations, and all the mutated forms could be stored in a “library” for an in-depth analysis of their amino acids, molecular architecture and energy bonds. Advanced technologies would allow the scientists to quickly thumb through the library to pick out those tiny proteins that clung to the pathogen surface target with pinpoint accuracy. The finalists would be selected from this pool for excelling at stopping the pathogen from attaching to, entering and infecting human or animal cells.

The use of deep sequencing, the same technology now used to sequence human genomes cheaply, was especially crucial in creating detailed maps relating sequencing to function. These maps were used to reprogram the design to achieve a more precise interaction between the inhibitor protein and the virus molecule. It also enabled the scientists, they said, “to leapfrog over bottlenecks” to improve the activity of the binder. They were able to see how small contributions from many tiny changes in the protein, too difficult to spot individually, could together create a binder with better attachment strength. “We anticipate that our approach combining computational design followed by comprehensive energy landscape mapping,” Baker said, “will be widely useful in generating high-affinity and high-specificity binders to a broad range of targets for use in therapeutics and diagnostics.”

eBioNews
June 26, 2012

Original web page at eBioNews

One of the big mysteries in biology is why cells age. Now scientists at the Salk Institute for Biological Studies report that they have discovered a weakness in a component of brain cells that may explain how the aging process occurs in the brain. The scientists discovered that certain proteins, called extremely long-lived proteins (ELLPs), which are found on the surface of the nucleus of neurons, have a remarkably long lifespan. While the lifespan of most proteins totals two days or less, the Salk Institute researchers identified ELLPs in the rat brain that were as old as the organism, a finding they reported February 3 in Science. The Salk scientists are the first to discover an essential intracellular machine whose components include proteins of this age. Their results suggest the proteins last an entire lifetime, without being replaced. ELLPs make up the transport channels on the surface of the nucleus; gates that control what materials enter and exit. Their long lifespan might be an advantage if not for the wear-and-tear that these proteins experience over time. Unlike other proteins in the body, ELLPs are not replaced when they incur aberrant chemical modifications and other damage.

Damage to the ELLPs weakens the ability of the three-dimensional transport channels that are composed of these proteins to safeguard the cell’s nucleus from toxins, says Martin Hetzer, a professor in Salk’s Molecular and Cell Biology Laboratory, who headed the research. These toxins may alter the cell’s DNA and thereby the activity of genes, resulting in cellular aging. Funded by the Ellison Medical Foundation and the Glenn Foundation for Medical Research, Hetzer’s research group is the only lab in the world that is investigating the role of these transport channels, called the nuclear pore complex (NPC), in the aging process. Previous studies have revealed that alterations in gene expression underlie the aging process. But, until the Hetzer lab’s discovery that mammals’ NPCs possess an Achilles’ heel that allows DNA-damaging toxins to enter the nucleus, the scientific community has had few solid clues about how these gene alterations occur. “The fundamental defining feature of aging is an overall decline in the functional capacity of various organs such as the heart and the brain,” says Hetzer. “This decline results from deterioration of the homeostasis, or internal stability, within the constituent cells of those organs. Recent research in several laboratories has linked breakdown of protein homeostasis to declining cell function.”

The results that Hetzer and his team just report suggest that declining neuron function may originate in ELLPs that deteriorate as a result of damage over time. “Most cells, but not neurons, combat functional deterioration of their protein components through the process of protein turnover, in which the potentially impaired parts of the proteins are replaced with new functional copies,” says Hetzer. “Our results also suggest that nuclear pore deterioration might be a general aging mechanism leading to age-related defects in nuclear function, such as the loss of youthful gene expression programs,” he adds. The findings may prove relevant to understanding the molecular origins of aging and such neurodegenerative disorders as Alzheimer’s disease and Parkinson’s disease.

Science Daily
February 21, 2012

Original web page at Science Daily

A team of scientists from The Scripps Research Institute has successfully reengineered an important antibiotic to kill the deadliest antibiotic-resistant bacteria. The compound could one day be used clinically to treat patients with life-threatening and highly resistant bacterial infections. The results were published in an advanced online issue of the Journal of the American Chemical Society. “These results have true clinical significance and chart a path forward for the development of next generation antibiotics for the treatment of the most serious resistant bacterial infections,” said Dale L. Boger, who is Richard and Alice Cramer Professor of Chemistry at The Scripps Research Institute and senior author of the new study. “The result could not be predicted. It really required the preparation of the molecule and the establishment of its properties.” The compound synthesized is an analogue of the well-known commercial antibiotic vancomycin. The new analogue was prepared in an elegant total synthesis, a momentous achievement from a synthetic chemistry point of view. “In addition to the elegantly designed synthesis,” said Jian Xie, postdoctoral fellow in Boger’s group and first author on the publication, “I am exceedingly gratified that our results could have the potential to be a great service to mankind.”

Vancomycin is an antibiotic of last resort, which is used only after treatment with other antibiotics has failed. Clinically, it is used to treat patients that are either infected with the virulent methicillin-resistant Staphylococcus aureus (MRSA), individuals on dialysis, or those allergic to beta-lactam antibiotics (penicillin, cephalosporins). The drug was first used clinically in the 1950s, and the first vancomycin-resistant bacterial strains were isolated in the 1980s. Vancomycin normally works by grabbing hold of and sequestering the bacterial cell-wall making machinery, a peptidoglycan (carbohydrate and peptide containing molecule). Only Gram-positive bacteria have a cell wall, which is a membrane on the cell’s outer surface. The antibiotic binds so tightly to the peptidoglycan that the bacteria can no longer use the machinery to make their cell wall and thus die. Unfortunately, bacteria have found a way to alter the peptidoglycan in such a way that the antibiotic can no longer grab hold. Think of it as trying to hold a ball without any fingers. Biochemically the bacteria express a mutant form of the peptidoglycan in which properties of a key atom used in the recognition process are changed. This simply means where there once was something attractive there is now something repulsive. Chemically, the bacteria replace an amide (carbonyl, RC=O linked to an amine) with an ester (a carbonyl, RC=O linked to an oxygen, O).

This one atom change changes the entire game and renders vancomycin ineffective. Until now. Like magnets, molecular interactions can be attractive (oppositely charged) or repulsive (identically charged). What chemists in the Boger lab have done is made this key interaction no longer repulsive, but attractive. So now the new vancomycin analogue can grab hold of the mutant peptidoglycan, and again prevent the bacteria from making the cell wall and killing the resistant bacteria. But what is so remarkable about the design is that the redesigned antibiotic maintains its ability to bind the wild type peptidoglycan as well. Changing the properties of a key amide at the core of the natural products structure required a new synthetic strategy that only the most talented chemists could achieve in the lab. The preparation of the entire structure took a great deal of time and a fresh approach. The new compound has an amidine (an iminium, RC=NH+ linked to a nitrogen, N) instead of an amide at a key position buried in the interior of the natural product. However, to install such a functional group, the chemical properties of the amide carbonyl were not useful, as the natural product has seven of them. Instead, the group relied on the chemical properties of sulfur (S), oxygen’s downstairs neighbor in the periodic table, to install the desired nitrogen. To do this, a second analogue was prepared in which the key amide was chemically altered to a thioamide. “The thioamide allowed us to make any modification at the residue 4 amide that we would like to make, such as the amidine, but we could also make the methylene analogue,” said Boger citing work published in another paper (B. Crowley and D. L. Boger, J. Am. Chem. Soc. 128: 2885-2892). “And there are other modifications that we are making at the present time that we haven’t disclosed. We are just getting to that work.”

The most fundamental finding in the synthesis was that the installation of the amidine could be done in the last step, as a single-step conversion, on the fully unprotected thioamide analogue. Providing an elegant and novel approach to the analogue, which contrasts other published multistep procedures. This chemical behavior was, as Boger said, “an astonishing result as there are no protecting groups and it is a single step reaction… in the end it was the simplest and most straightforward way to prepare the amidine.” Although it is still at its early stages and there is much work ahead. Currently, the only route known to make the new antibiotic is the one published by Boger and his co-workers, which presently provides laboratory amounts of the compound. So Professor Boger now looks forward and will continue to investigate the “host of alternative approaches” for the preparation of the molecule “such as reengineered organisms to produce the material or semi-synthetic approaches to the analogue. That is going to be part of the next stage of the work.”

Science Daily
September 6, 2011

Original web page at Science Daily

A new research paper sheds light on the way antibodies distinguish between different but closely related ‘biomarkers’ — proteins which reveal information about the condition of the human body. This new understanding could enable pharmaceutical companies to develop new technologies for quickly diagnosing and treating fatal diseases. All diseases have proteins, or concentrations of proteins, specifically linked to them called biomarkers. Identifying these can prove a powerful diagnostic tool. These biomarkers are detected by immunoassays — a test which mixes a substance (e.g. blood, urine) with antibodies, which bind to the protein if it is present. The antibodies can then be measured to identify the level of the biomarker, which in turn indicates the presence and extent of an illness. Antibodies bind with high specificity to one protein molecule or a limited group of molecules (e.g. hormones), which is why we can use antibodies to test for specific biomarkers. Problems arise when they bind to groups of similar hormones that are associated with normal bodily changes. This leads to false positives and therefore unreliable information. New research, carried out by the National Physical Laboratory (NPL), the University of Edinburgh and industrial partners from the UK (Mologic ltd), US (IBM’s Watson Research Center) and the Netherlands (Pepscan Presto BV), changes this. The research shows how different proteins are made up, and therefore how they can be identified reliably.

The highly sought solution is ‘intelligent selection’ of antibody-specific interaction sites on hormones that can differ from similar sites of other hormones by just one molecule. The research focused on hCG (human chorionic gonadotropin), a hormone produced during pregnancy. A subunit of hCG — hCGβ — is secreted by some cancers, meaning detection can give early warning of tumors. hCG is very similar to other reproductive hormones, known as LH and FSH, which are always present in the body. Detecting hCG can be confused with these other hormones, leading to unreliable results. The immunoassay antibodies bind to a tiny part of the hormone called an epitope. Hormones are made up of thousands of ‘building blocks’, with epitopes making up less than 10 of these blocks. The difference between hormones can be as little as one of these epitope blocks. The research team took a variety of precise measurements of the hCG hormone. The team showed how very subtle, atomic level characteristics define the antibody selectivity in closely related epitopes of different proteins. They identified that specific antibodies are highly selective in immunoassays and can distinguish between hCGβ and closely related LH fragments. Understanding these structural differences explains the observed selectivity in the full hormones. Armed with this knowledge, scientists can develop intelligent epitope selection to achieve the required assay performance. This means reliable tests can be developed to identify the presence of different hormones — in this case the presence of hCGβ which indicates cancer, as opposed to LH, which is always present.

The advances described in this research will enable development of further immunoassays to identify other biomarkers from similar groups. Pharmaceutical companies could use this to develop new technologies for diagnostics and clinical disease treatments, for example tests for tumour as part of routine screenings. Max Ryadnov, Principal Research Scientist at the National Physical Laboratory, says “This work answers one of the big questions in distinguishing biomarkers which are critical for identifying and treating serious diseases. We hope this breakthrough will underpin the development of a range of new diagnostic techniques and treatment.” Prof Paul Davis, Chief Scientific Officer of Mologic ltd — a UK diagnostic company that initiated the study, said: “It was a great collaborative effort, and it stands as a fine example of what can be achieved when motivated scientists work together openly across boundaries.”

Science Daily
August 9, 2011

Original web page at Science Daily

Mitochondria, those battery-pack organelles that fuel the energy of almost every living cell, have an insatiable appetite for calcium. Whether in a dish or a living organism, the mitochondria of most organisms eagerly absorb this chemical compound. Because calcium levels link to many essential biological processes — not to mention conditions such as neurological disease and diabetes — scientists have been working for half a century to identify the molecular pathway that enables these processes. After decades of failed effort that relied on classic biochemistry and membrane protein purification, Vamsi Mootha, HMS associate professor of systems biology, and colleagues have discovered, through a combination of digital database mining and laboratory assays, the linchpin protein that drives mitochondria’s calcium machinery. “This channel has been studied extensively using physiology and biophysics, yet its molecular identity has remained elusive,” said Mootha, who also has appointments at Massachusetts General Hospital and at Broad Institute. “But thanks to the Human Genome Project, freely downloadable genomic databases, and a few tricks — we were able to get to the bottom of it.” These findings appeared online June 19 in Nature.

The results build on work from Vamsi and his group over the past decade. In 2008, he and his team published a near-comprehensive protein inventory, or proteome, of human and mouse mitochondria. This inventory, called MitoCarta, consisted of just over 1,000 proteins, most of which had no known function. In a September 2010 paper, Mootha’s group described using the MitoCarta inventory to identify the first protein specifically required for mitochondrial calcium uptake. Their strategy was simple. They knew that mitochondria from humans and Trypanosomes (a parasitical organism), but not baker’s yeast, are capable of absorbing large amounts of calcium. By simply overlapping the mitochondrial protein profiles of these three organisms, the group could spotlight roughly 50 proteins out of the 1,000 that might be involved with calcium channeling. They found that one protein, which they dubbed MICU1, is essential for calcium uptake. “That was an significant advance for the field,” says Mootha. “We showed that MICU1 was required for calcium uptake, but because it did not span the membrane, we doubted it was the central component of the channel. But what it provided us with was live bait to then go and find the bigger fish.”

Traditionally, researchers used standard laboratory methods for such a fishing exhibition, such as attaching biochemical hooks to the protein, casting it into the cell’s cytoplasm, then reeling it back in the hope that another, related protein will have bitten. But MICU1’s function as a regulator of a membrane channel made this technically prohibitive. Instead, graduate student Joshua Baughman and postdoctoral researcher Fabiana Perocchi went fishing in publicly available genomic databases. With MICU1 as their point of reference, they scoured those databases that measure whole genome RNA and protein expression, as well as an additional database containing genomic information for 500 species, and looked for proteins whose activity profile mirrored MICU1’s. A single anonymous protein with no known function stood out. The researchers named it MCU, short for “mitochondrial calcium uniporter.” To confirm that MCU is central to mitochondria’s calcium absorption, the team collaborated with Alnylam Pharmaceuticals, a company that leverages a laboratory tool called RNAi in order to selectively knock out genes in both cells and live animals. Using one of the company’s platforms, the researchers deactivated MCU in the livers of mice. While the mice displayed no immediate reaction, the mitochondria in their liver tissue lost the capacity to absorb calcium.

This basic science finding may prove relevant in certain human diseases. “We’ve known for decades now that neurons in the brains of people suffering from neurodegenerative disease are often marked by mitochondrial calcium overload,” said Mootha, an expert on rare mitochondrial diseases who sees patients at Massachusetts General Hospital when he’s not in the lab. “We also know that the secretion of many hormones, like insulin, are triggered by calcium spikes in the cell’s cytoplasm. By clearing cytosolic calcium, mitochondria can shape these signals. Scientists studying the nexus of energy metabolism and cellular signaling will be particularly interested in MICU1 and MCU. It’s still very early, but they could prove to be valuable drug targets for a variety of diseases — ranging from ischemic injury and neurodegeneration to diabetes.”

Science Daily
July 26, 2011

Original web page at Science Daily

National Institutes of Health researchers have identified a new pathway that sets the clock for programmed aging in normal cells. The study provides insights about the interaction between a toxic protein called progerin and telomeres, which cap the ends of chromosomes like aglets, the plastic tips that bind the ends of shoelaces. The study by researchers from the National Human Genome Research Institute (NHGRI) appears online in the Journal of Clinical Investigation. Telomeres wear away during cell division. When they degrade sufficiently, the cell stops dividing and dies. The researchers have found that short or dysfunctional telomeres activate production of progerin, which is associated with age-related cell damage. As the telomeres shorten, the cell produces more progerin. Progerin is a mutated version of a normal cellular protein called lamin A, which is encoded by the normal LMNA gene. Lamin A helps to maintain the normal structure of a cell’s nucleus, the cellular repository of genetic information.

In 2003, NHGRI researchers discovered that a mutation in LMNA causes the rare premature aging condition, progeria, formally known as known as Hutchinson-Gilford progeria syndrome. Progeria is an extremely rare disease in which children experience symptoms normally associated with advanced age, including hair loss, diminished subcutaneous fat, premature atherosclerosis and skeletal abnormalities. These children typically die from cardiovascular complications in their teens. “Connecting this rare disease phenomenon and normal aging is bearing fruit in an important way,” said NIH Director Francis S. Collins, M.D., Ph.D., a senior author of the current paper. “This study highlights that valuable biological insights are gained by studying rare genetic disorders such as progeria. Our sense from the start was that progeria had a lot to teach us about the normal aging process and clues about more general biochemical and molecular mechanisms.” Collins led the earlier discovery of the gene mutation responsible for progeria and subsequent advances at NIH in understanding the biochemical and molecular underpinnings of the disease.

In a 2007 study, NIH researchers showed that normal cells of healthy people can produce a small amount of progerin, the toxic protein, even when they do not carry the mutation. The more cell divisions the cell underwent, the shorter the telomeres and the greater the production of progerin. But a mystery remained: What was triggering the production of the toxic progerin protein? The current study shows that the mutation that causes progeria strongly activates the splicing of lamin A to produce the toxic progerin protein, leading to all of the features of premature aging suffered by children with this disease. But modifications in the splicing of LMNA are also at play in the presence of the normal gene. The research suggests that the shortening of telomeres during normal cell division in individuals with normal LMNA genes somehow alters the way a normal cell processes genetic information when turning it into a protein, a process called RNA splicing. To build proteins, RNA is transcribed from genetic instructions embedded in DNA. RNA does not carry all of the linear information embedded in the ribbon of DNA; rather, the cell splices together segments of genetic information called exons that contain the code for building proteins, and removes the intervening letters of unused genetic information called introns. This mechanism appears to be altered by telomere shortening, and affects protein production for multiple proteins that are important for cytoskeleton integrity. Most importantly, this alteration in RNA splicing affects the processing of the LMNA messenger RNA, leading to an accumulation of the toxic progerin protein.

Cells age as part of the normal cell cycle process called senescence, which progressively advances through a limited number of divisions in the cell lifetime. “Telomere shortening during cellular senescence plays a causative role in activating progerin production and leads to extensive change in alternative splicing in multiple other genes,” said lead author Kan Cao, Ph.D., an assistant professor of cell biology and molecular genetics at the University of Maryland, College Park. Telomerase is an enzyme that can extend the structure of telomeres so that cells continue to maintain the ability to divide. The study supplied support for the telomere-progerin link, showing that cells that have a perpetual supply of telomerase, known as immortalized cells, produce very little progerin RNA. Most cells of this kind are cancer cells, which do not reach a normal cell cycle end point, and instead replicate out of control.

The researchers also conducted laboratory tests on normal cells from healthy individuals using biochemical markers to indicate the occurrence of progerin-generating RNA splicing in cells. The cell donors ranged in age from 10 to 92 years. Regardless of age, cells that passed through many cell cycles had progressively higher progerin production. Normal cells that produce higher concentrations of progerin also displayed shortened and dysfunctional telomeres, the tell-tale indication of many cell divisions. In addition to their focus on progerin, the researchers conducted the first systematic analysis across the genome of alternative splicing during cellular aging, considering which other protein products are affected by jumbled instructions as RNA molecules assemble proteins through splicing. Using laboratory techniques that analyze the order of chemical units of RNA, called nucleotides, the researchers found that splicing is altered by short telomeres, affecting lamin A and a number of other genes, including those that encode proteins that play a role in the structure of the cell. The researchers suggest that the combination of telomere fraying and loss with progerin production together induces cell aging. This finding lends insights into how progerin may participate in the normal aging process.

Science Daily
June 28, 2011

Original web page at Science Daily

A large number of illnesses stem from misfolded proteins, molecules composed of amino acids. Researchers at the University of Zurich have now studied protein misfolding using a special spectroscopic technique. Misfolding, as they report in Nature, is more frequent if the sequence of the amino acids in the neighboring protein domains is very similar. Proteins are the main molecular machines in our bodies. They perform a wide range of functions, from digesting and processing nutrients, converting energy and aiding cell structure to transmitting signals in cells and the whole body. In order to perform these highly specific functions, proteins have to adopt a well-defined, three-dimensional structure. Remarkably, in most cases they find this structure unaided once they have been formed out of their individual building blocks, amino acids, as a long chain molecule in the cell.

However, the process of protein folding can also go wrong, which means the proteins affected are no longer able to perform their function. In some cases, this can even have much more serious consequences if these misfolded proteins clump and trigger neurodegenerative diseases such as Alzheimer’s or Parkinson’s disease. In the course of evolution, a crucial factor in the development of proteins has thus been to avoid such “misfolding processes.” However, this is no easy task since the same molecular interactions that stabilize the correct structure of the individual proteins can also bring about interactions between protein molecules, causing them to misfold. Using a special spectroscopic method called single-molecule fluorescence, researchers from the Universities of Zurich and Cambridge have now studied the circumstances under which misfolding occurs. The team headed by Prof. Benjamin Schuler from the University of Zurich studied sections, or “domains,” of the largest protein in our bodies, titin, which helps the stability and elasticity of the muscle fibers. It is assumed that individual titindomains can unfold while the muscle is heavily exerted to avoid damaging the muscle tissue. When the muscle relaxes again, however, there is a danger that these unfolded domains might fold incorrectly. There is also a similar risk for other multidomain proteins.

For their study, the researchers attached small dye molecules as probes in the protein. “Using our laser-spectroscopic method we were able to determine distances on a molecular scale, i.e. down to a few millionths of a millimeter, through the energy transfer between the probes,” explains Prof. Schuler. This enabled the structures of correctly and misfolded proteins to be distinguished and thus the proportion of misfolding determined. “The study of different titin domains in our experiments revealed that the probability of misfolding increases if neighboring domains are very similar in the sequence of their amino acids,” says Prof. Schuler. This is apparently the reason why neighboring domains in proteins have a limited degree of similarity. “This seems to be a key evolutionary strategy to avoid protein misfolding and thus guarantee their maximum functionality,” says Schuler.

Science Daily
June 15, 2011

Original web page at Science Daily