New Method For Improving The Functional Characteristics Of Enzymes.

SOURCE

ScienceDaily (Sep. 28, 2009) — An international team of scientists from the Czech Republic, Germany and Japan have developed a new method for improving the properties of enzymes. The method has potential for wide application in the chemical, medicinal and food industries. The research has been published in Nature Chemical Biology.

The modified enzymes can be used, for example, for disposal of highly harmful chemical substances which enter into the environment as a result of human activity and can have a very negative influence on human and animal health. Nature cannot degrade many of these chemicals but, in this work, the scientists have developed an approach that can be applied to remove them efficiently from the environment.
The principle of the discovery is based on genetic manipulation of the enzyme which is starting and accelerating the chemical reaction. „Now we can use genetic modifications for changing the properties of the enzymes so they can faster and more easily dispose of harmful substances in the environment,” says Jiri Damborsky, leader of the Protein Engineering Group at the Institute of Experimental Biology, Faculty of Science, Masaryk University.
Up to now, the scientists had focused during the modification of an enzyme’s properties on the site in its structure where the chemical reaction happens, the active site. The new method is based on the modification of so-called access tunnels that connect the active site with the surface of the enzyme. “Specialized computational techniques guided the experimental work to engineer these tunnels to alter their accessibility to the degraded substances,” notes Rebecca Wade, leader of the Molecular and Cellular Modeling Group at EML Research in Heidelberg.
The scientists applied the approach by modifying an enzyme to degrade the highly toxic substance, trichloropropane (TCP). This colourless liquid is a secondary product of chemical production. It can reside in the soil and groundwater for over 100 years, can contaminate drinking water and is a carcinogen. Using the new approach, the protein engineers developed a modified enzyme capable of degrading this substance 32 times faster than the original enzyme.
But the method has much wider scope for application than just in the fight against harmful substances and in environmental protection. The targeted modification of the tunnels in enzymes can be utilized in different application areas, including biomedicine, and the chemical and food industries.
Journal reference:
Martina Pavlova et al. Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nature Chemical Biology, 5, 727 - 733 (2009); Published online 23 August 2009 DOI: 10.1038/nchembio.205
Adapted from materials provided by European Media Laboratory (EML), via AlphaGalileo.

Yale engineers have for the first time observed and tracked E. coli bacteria moving in a liquid medium with a particular motion.

SOURCE

ScienceDaily (Sep. 26, 2009) — Yale engineers have for the first time observed and tracked E. coli bacteria moving in a liquid medium with a motion similar to that of a kayak paddle.

Their findings, which appear online September 29 in the journal Physical Review Letters, will help lead to a better understanding of how bacteria move from place to place and, potentially, how to keep them from spreading.
Scientists have long theorized that the cigar-shaped cell bodies of E. coli and other microorganisms would follow periodic orbits that resemble the motion of a kayak paddle as they drift downstream in a current. Until now, no one had managed to directly observe or track those movements.
Hur Koser, associate professor at Yale's School of Engineering & Applied Science, previously discovered that hydrodynamic interactions between the bacteria and the current align the bacteria in a way that allows them to swim upstream. "They find the most efficient route to migrate upstream, and we ultimately want to understand the mechanism that allows them to do that," Koser said.
In the new study, Koser, along with postdoctoral associate and lead author of the paper, Tolga Kaya, devised a method to see this motion in progress. They used advanced computer and imaging technology, along with sophisticated new algorithms, that allowed them to take millions of high-resolution images of tens of thousands of individual, non-flagellated E. coli drifting in a water and glycerin solution, which amplified the bacteria's paddle-like movements.
The team characterized the bacteria's motion as a function of both their length and distance from the surface. The team found that the longer and closer to the surface they were, the slower the E. coli "paddled."
It took the engineers months to perfect the intricate camera and computer system that allowed them to take 60 to 100 sequential images per second, then automatically and efficiently analyze the huge amount of resulting data.
E. coli and other bacteria can colonize wherever there is water and sufficient nutrients, including the human digestive tract. They encounter currents in many settings, from riverbeds to home plumbing to irrigation systems for large-scale agriculture.
"Understanding the physics of bacterial movement could potentially lead to breakthroughs in the prevention of bacterial migration and sickness," Koser said. "This might be possible through mechanical means that make it more difficult for bacteria to swim upstream and contaminate water supplies, without resorting to antibiotics or other chemicals."
Adapted from materials provided by Yale University, via EurekAlert!, a service of AAAS.

Mechanism Related To Onset Of Various Genetic Diseases Revealed

SOURCE

ScienceDaily (Sep. 17, 2009) — Researchers at the Department of Biochemistry and Molecular Biology of Universitat Autònoma de Barcelona (UAB) have revealed the process by which proteins with a tendency to cause conformational diseases such as amyotrophic lateral sclerosis, familial amyloidotic polyneuropathy, familial amyloidotic cardiomyopathy, etc. finally end up causing them.

Researchers have carried out an analysis of their 3D structure and studied why these proteins finally become toxic although they are correctly folded, an indicator that they are functioning correctly. The answer can be found in the separation of the proteins, which under normal conditions are found in groups of two or more, caused by a genetic mutation in their composition. Researchers believe this discovery, published recently in the journal PLoS Computational Biology, could also be the cause of other diseases of unknown origins.
Every day cells produce thousands of new proteins which renew themselves every second and which, by obeying the orders prescribed in our genetic code, work towards the proper functioning of our body. However, these proteins occasionally suffer genetic mutations which can cause changes in their composition, thus preventing them from carrying out their functions and the activities they are assigned. In many cases this gives way to the formation of toxic macromolecular aggregates - amyloid fibrils - which block our body's protein quality control system and finally provoke cell death.
Protein aggregation and the misfolding of proteins can be linked to the origin of many conformational diseases which can be either genetic or spontaneous. The proteins involved can either have an unstructured or lineal unfolded form such as in Alzheimer's and Parkinson's disease or Type II Diabetes, or can be globular, showing a folded 3D-structure. The former have been widely characterised by scientists and the process by which they unfold is known. The process leaves regions uncovered which are in the risk of becoming aggregated and these eventually form toxic assemblies. Globular proteins are known to be linked to hepatic, cardiac, renal and neurological disorders. However scientists do not know exactly how they manage to aggregate despite the fact that they are correctly folded within the body.
Through computational analysis, researchers Salvador Ventura and Virgínia Castillo, from the UAB Department of Biochemistry and Molecular Biology, have discovered that, in non-disease conditions, globular proteins related to conformational diseases are found associated in pairs to other proteins or in complex subunits, in a way that one protein covers the aggregation-prone region of the other and thus prevents the onset of this process. Therefore these regions remain obscured in the interior of the structure and are inoffensive to the organism as long as the two proteins are joined together. Researchers have found that genetic mutations produced in the interaction sites of the protein pair prevents their association, leaving aggregation-prone regions uncovered and favouring the formation of toxic aggregates. According to researchers, this would explain why out of two people with the same globular proteins and the same risk regions, only the one who suffers a genetic mutation would finally develop a disease.
The conclusions obtained have led researchers to contemplate the possibility that dissociation is a general mechanism, which not only affects globular proteins with a clearly defined structure, but also others which have not yet been characterised and which could be the cause of diseases of unknown origin.
As possible strategies to prevent the dissociation of proteins, the authors propose introducing genetic mutations into the proteins to strengthen their association and developing specific molecules to block the risk regions of already dissociated proteins.
The results of the study carried out by UAB researchers coincides with those obtained by researchers at Cambridge University, who also published similar data in the journal Proceedings of the National Academic of Sciences.
In the future UAB researchers are planning to expand their computational analysis to cover the whole set of human proteins with a defined 3D-structure. With this objective they seek to discover the proteins responsible for different genetic diseases of unknown origins and offer a series of new therapeutic targets for these disorders.
Journal reference:
Castillo V, Ventura S. Amyloidogenic Regions and Interaction Surfaces Overlap in Globular Proteins Related to Conformational Diseases. PLoS Computational Biology, 2009; 5 (8): e1000476 DOI: 10.1371/journal.pcbi.1000476
Adapted from materials provided by Universitat Autonoma de Barcelona, via EurekAlert!, a service of AAAS.

Frontiers of Biomedical Engineering with Prof. Mark Saltzman (Yale University)