News Article | February 15, 2017
The new method offers unprecedented detail in measuring molecular motion and energy – enabling better control and understanding of chemical reactions in the field of biotechnology research. The technique, which was recently published in Nature Communications, uses X-ray scattering to measure the specific movements of atoms in a molecule with extreme energy resolution. "The idea is based on exciting a molecule to a high-energy, localized state," says Victor Kimberg, a researcher in the department of Theoretical Chemistry and Biology, at KTH Royal Institute of Technology in Stockholm. The X-ray radiation that it emits then scans the energy landscape of the molecule with a level of precision that Kimberg compares to observing the movements of individual insects from on top of a mountain. Every molecule has its own energy "landscape", or the full multidimensional spectrum of motion that atoms undergo when the molecule is energized. These motions include bending and stretching of bonds. Expressed in geometric terms, the relationships of atoms to one another in a single molecule are among the key things scientists need to know in order to determine a molecule's potential energy surface (PES) – an important value in the study of molecular structures, properties and reactivity. "The PES is useful for processes such as catalysis and photochemistry," Kimberg says. For the first time, the technique enables scientists to break down the collective atomic motion in a molecule into elementary components, he says. "We can now go further than examining the collective multidimensional atomic motion in a molecule, and look at specific vibrations along selected reaction coordinates," he says. "We are not aware of any other way to do this, so it looks like our idea is new." Typically when a molecule is excited, the only measurements available show all atomic motion simultaneously. The full PES landscape is complex with all types of vibrations. Kimberg says that with the method they propose, x-ray photon energy can be tuned to excite vibrations of a singled-out type of nuclear motion – which he says can serve as a basis for developing methods of reaction control. "We show clearly that tuning the x-ray photon energy in resonance with one core-excited state induces only symmetric stretching motion; while tuning to another core-excited state excites exclusively the bending motion," he says. The measurements were conducted at the Swiss Light Source (SLS) synchrotron laboratory in Zurich, in collaboration with the KTH group, comprised of Kimberg, Faris Gel'mukhanov and Hans Ågren, who were responsible for the underlying theory and simulations. Explore further: High-energy electrons synced to ultrafast laser pulse to probe how vibrational states of atoms change in time More information: Rafael C. Couto et al. Selective gating to vibrational modes through resonant X-ray scattering, Nature Communications (2017). DOI: 10.1038/ncomms14165
News Article | September 6, 2016
Using a unique computational approach to rapidly sample, in millisecond time intervals, proteins in their natural state of gyrating, bobbing, and weaving, a research team from UC San Diego and Monash University in Australia has identified promising drug leads that may selectively combat heart disease, from arrhythmias to cardiac failure. Reported in the September 5, 2016 Proceedings of the National Academy of Sciences (PNAS) Early Edition, the researchers used the computing power of Gordon and Comet, based at the San Diego Supercomputer Center (SDSC) at UC San Diego; and Stampede, at the Texas Advanced Computing Center at the University of Texas at Austin, to perform an unprecedented survey of protein structures using accelerated molecular dynamics or aMD - a method that performs a more complete sampling of the myriad shapes and conformations that a target protein molecule may go through. The computing resources were provided by the National Science Foundation-funded Extreme Science and Engineering Discovery Environment (XSEDE) program, one of the most advanced collections of integrated digital resources and services in the world. "The supercomputing power of Gordon, Comet, and Stampede allows us to run hundreds-of-nanosecond aMD simulations, which are able to capture millisecond timescale events in complex biomolecules," said the study's first author Yinglong Miao, a research specialist with the Howard Hughes Medical Institute at UC San Diego and research scientist with the UC San Diego Department of Pharmacology. Though effective in most cases, today's heart medications - many of which act on M2 muscarinic acetylcholine receptors or M2 mAChRs that decrease heart rate and reduce heart contractions - may carry side effects, sometimes serious. That's because the genetic sequence of M2 mAChR's primary 'orthosteric' binding site is "highly conserved," and found in at least four other receptor types that are widely spread in the body, yielding unwanted results. For this reason, drug designers are seeking a different approach, homing in on molecular targets or so-called "allosteric binding sites" that reside away from the receptor's primary binding site and are built around a more diverse genetic sequence and structure than their counterpart 'orthosteric' binding sites. Essentially, allosteric modulators act as a kind of cellular dimmer-switch that, once turned on, 'fine tunes' the activation and pharmacological profile of the target receptor. "Allosteric sites typically exhibit great sequence diversity and therefore present exciting new targets for designing selective therapeutics," said the study's co-investigator J. Andrew McCammon, the Joseph E. Mayer Chair of Theoretical Chemistry, a Howard Hughes Medical Institute investigator, and Distinguished Professor of Pharmacology, all at UC San Diego. In particular, drug designers have begun to aggressively search for allosteric modulators to fine-tune medications that bind to G protein-coupled receptors (GPCRs), the largest and most diverse group of membrane receptors in animals, plants, fungi and protozoa. These cell surface receptors act like an inbox for messages in the form of light energy, hormones and neurotransmitters, and perform an incredible array of functions in the human body. In fact, between one-third to one-half of all marketed drugs act by binding to GPCRs, treating diseases including cancer, asthma, schizophrenia, Alzheimer's and Parkinson's disease, and heart disease. Though many of the GPCR drugs have made their way to the medicine cabinet, most -- including M2 mAChR targeted drugs -- exhibit side effects owing to their lack of specificity. All these drugs target the orthosteric binding sites of receptors, thus creating the push to find more targeted therapies based on allosteric sites. "The problem here is that molecules that bind to these allosteric sites have proven extremely difficult to identify using conventional high-throughput screening techniques," said McCammon, also a chemistry and biochemistry professor in UC San Diego's Division of Physical Sciences. Enter accelerated molecular dynamics and supercomputing. As described in this latest study, called Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor, some 38 lead compounds were selected from a database of compounds from the National Cancer Institute, using computationally enhanced simulations to account for binding strength and receptor flexibility. About half of these compounds exhibited the hallmarks of an allosteric behavior in subsequent in vitro experiments, with about a dozen showing strong affinity to the M2 mAChR binding site. Of these, the researchers highlighted two showing both strong affinity and high selectivity in studies of cellular behavior. These cutting-edge experiments were performed by collaborators from the Monash Institute of Pharmaceutical Sciences. "To our knowledge, this study demonstrates for the first time an unprecedented successful structure-based approach to identify chemically diverse and selective GPCR allosteric modulators with outstanding potential for further structure-activity relationship studies," the researchers wrote. The next steps will involve an investigation of the chemical properties of these novel molecules by the molecular chemists from Monash, led by Celine Valant and her colleague Arthur Christopoulos. "This is just the beginning. We believe that it will be possible to apply our combined cutting-edge in silico and in vitro techniques to a wide array of receptor targets that are involved in some of the most devastating diseases," said Valant, the study's co-lead investigator from Monash.
Woodward C.E.,University of New South Wales |
Forsman J.,Theoretical Chemistry
Langmuir | Year: 2015
We developed an analytical theory for the manybody potential of mean force (POMF) between N spheres immersed in a continuum chain fluid. The theory is almost exact for a Θ polymer solution in the protein limit (small particles, long polymers), where N-body effects are important. Polydispersity in polymer length according to a Schulz-Flory distribution emerges naturally from our analysis, as does the transition to the monodisperse limit. The analytical expression for the POMF allows for computer simulations employing the complete N-body potential (i.e., without n-body truncation; n
Segad M.,Theoretical Chemistry |
Hanski S.,Aalto University |
Olsson U.,Lund University |
Ruokolainen J.,Aalto University |
And 2 more authors.
Journal of Physical Chemistry C | Year: 2012
Aqueous dispersions of pure sodium and calcium smectite clays with platelet sizes on the order of a few hundred nanometers were characterized using a combination of cryo-transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS). With monovalent sodium counterions the clay is dispersed as individual platelets, as seen by cryo-TEM, that order into a nematic phase. From SAXS a one-dimensional swelling of the clay in water is observed with the characteristic spacing h s = Î́/ Ï• c, where h s is the separation between the platelets, Î́ = 1 nm is the effective platelet thickness, and Ï• c is the clay volume fraction in the sample. In calcium montmorillonite, on the other hand, cryo-TEM images clearly show the presence of tactoids, where the platelets have aggregated into stacks with a periodic spacing of 2 nm. From imaging a large number of tactoids the distribution function f(N) for the number of platelets per tactoid was estimated, and the average number â'̈Nâ'© â‰̂ 10. The characteristic 2 nm spacing as well as the small number of platelets per tactoid was also confirmed by SAXS. The present study demonstrates that cryo-TEM, with carefully prepared specimen, is a very useful technique to characterize clay dispersions, particularly in aggregated systems. © 2012 American Chemical Society.