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News Article | May 24, 2017
Site: www.cemag.us

Proteins digest food, and fight infections and cancer, and serve other metabolic functions. They are basically nano-machines, each one designed to perform a specific task. But how did they evolve to match those needs, and how did genes encode the structure and function of proteins? Researchers from the University of Geneva (UNIGE) in Switzerland, the Institute for Basic Science in Korea, and Rockefeller University in the U.S. have conducted a study that tackles this question and explains the basic geometry of the gene-to-protein code by connecting proteins to properties of amorphous physical matter. A protein is a chain made of 20 different kinds of amino acid with elaborate interactions, and unlike standard physical matter, proteins are selected by evolution. "The blueprint for protein synthesis is written in long DNA genes, but we show that only a small fraction of this huge information space is used to make the functional protein," explains Jean-Pierre Eckmann, Professor at the Department of Theoretical Physics from the Faculty of Science of UNIGE. Together with Professor Tsvi Tlusty from the Center for Soft and Living Matter, Institute for Basic Science (IBS) in Korea, and Professor Albert Libchaber from the Rockefeller University in New York, Eckmann shows that the only changes in the code that matter are those occurring in the segment of the gene coding the mechanically relevant hinges of the nano-machine. The changes in other regions of this highly redundant code have no impact. "We are now using this new approach to understand the relation between the function and dynamics of several important proteins."


News Article | May 24, 2017
Site: www.cemag.us

Proteins digest food, and fight infections and cancer, and serve other metabolic functions. They are basically nano-machines, each one designed to perform a specific task. But how did they evolve to match those needs, and how did genes encode the structure and function of proteins? Researchers from the University of Geneva (UNIGE) in Switzerland, the Institute for Basic Science in Korea, and Rockefeller University in the U.S. have conducted a study that tackles this question and explains the basic geometry of the gene-to-protein code by connecting proteins to properties of amorphous physical matter. A protein is a chain made of 20 different kinds of amino acid with elaborate interactions, and unlike standard physical matter, proteins are selected by evolution. "The blueprint for protein synthesis is written in long DNA genes, but we show that only a small fraction of this huge information space is used to make the functional protein," explains Jean-Pierre Eckmann, Professor at the Department of Theoretical Physics from the Faculty of Science of UNIGE. Together with Professor Tsvi Tlusty from the Center for Soft and Living Matter, Institute for Basic Science (IBS) in Korea, and Professor Albert Libchaber from the Rockefeller University in New York, Eckmann shows that the only changes in the code that matter are those occurring in the segment of the gene coding the mechanically relevant hinges of the nano-machine. The changes in other regions of this highly redundant code have no impact. "We are now using this new approach to understand the relation between the function and dynamics of several important proteins."


News Article | May 25, 2017
Site: www.sciencedaily.com

Proteins perform vital functions of life, they digest food and fight infections and cancer. They are in fact nano-machines, each one of them designed to perform a specific task. But how did they evolve to match those needs, how did the genes encode the structure and function of proteins? Researchers from the University of Geneva (UNIGE), Switzerland, the Institute for Basic Science, Korea, and the Rockefeller University, United States, have conducted a study that tackles this yet unanswered question, and explains the basic geometry of the gene-to-protein code, by connecting proteins to properties of amorphous physical matter. The full article appears in Physical Review X. A protein is a chain made of twenty different kinds of amino acids with elaborate interactions, and, unlike standard physical matter, it is selected by evolution. "The blueprint for protein synthesis is written in long DNA genes, but we show that only a small fraction of this huge information space is used to make the functional protein," explains Jean-Pierre Eckmann, Professor at the Department of Theoretical Physics from the Faculty of Science of UNIGE. Together with Prof. Tsvi Tlusty from the Center for Soft and Living Matter, Institute for Basic Science (IBS) in Korea and Prof. Albert Libchaber from the Rockefeller University in New York, Prof. Eckmann shows that the only changes in the code that matter are those occurring in the segment of the gene coding the mechanically relevant hinges of the nano-machine. The changes in other regions of this highly redundant code have no impact. "We are now using this new approach to understand the relation between the function and dynamics of several important proteins."


News Article | May 24, 2017
Site: phys.org

The essential nano-mechanic features of proteins can be conveniently studied by a simplified geometry. Taking, for example, a cylinder, and asking for «evolution» to find a fluid channel (shown in blue) a multitude of realistic properties of real proteins appear naturally, and exhibit the advantage of conceptual, rather than detailed models of proteins. Credit: © UNIGE - Jean-Pierre Eckmann Proteins digest food, and fight infections and cancer, and serve other metabolic functions. They are basically nano-machines, each one designed to perform a specific task. But how did they evolve to match those needs, and how did genes encode the structure and function of proteins? Researchers from the University of Geneva (UNIGE), Switzerland, the Institute for Basic Science, Korea, and the Rockefeller University, U.S., have conducted a study that tackles this question and explains the basic geometry of the gene-to-protein code by connecting proteins to properties of amorphous physical matter. A protein is a chain made of 20 different kinds of amino acid with elaborate interactions, and unlike standard physical matter, proteins are selected by evolution. "The blueprint for protein synthesis is written in long DNA genes, but we show that only a small fraction of this huge information space is used to make the functional protein," explains Jean-Pierre Eckmann, Professor at the Department of Theoretical Physics from the Faculty of Science of UNIGE. Together with Prof. Tsvi Tlusty from the Center for Soft and Living Matter, Institute for Basic Science (IBS) in Korea and Prof. Albert Libchaber from the Rockefeller University in New York, Prof. Eckmann shows that the only changes in the code that matter are those occurring in the segment of the gene coding the mechanically relevant hinges of the nano-machine. The changes in other regions of this highly redundant code have no impact. "We are now using this new approach to understand the relation between the function and dynamics of several important proteins."


News Article | May 24, 2017
Site: www.eurekalert.org

Proteins perform vital functions of life, they digest food and fight infections and cancer. They are in fact nano-machines, each one of them designed to perform a specific task. But how did they evolve to match those needs, how did the genes encode the structure and function of proteins? Researchers from the University of Geneva (UNIGE), Switzerland, the Institute for Basic Science, Korea, and the Rockefeller University, United States, have conducted a study that tackles this yet unanswered question, and explains the basic geometry of the gene-to-protein code, by connecting proteins to properties of amorphous physical matter. The full article appears in Physical Review X. A protein is a chain made of twenty different kinds of amino acids with elaborate interactions, and, unlike standard physical matter, it is selected by evolution. "The blueprint for protein synthesis is written in long DNA genes, but we show that only a small fraction of this huge information space is used to make the functional protein", explains Jean-Pierre Eckmann, Professor at the Department of Theoretical Physics from the Faculty of Science of UNIGE. Together with Prof. Tsvi Tlusty from the Center for Soft and Living Matter, Institute for Basic Science (IBS) in Korea and Prof. Albert Libchaber from the Rockefeller University in New York, Prof. Eckmann shows that the only changes in the code that matter are those occurring in the segment of the gene coding the mechanically relevant hinges of the nano-machine. The changes in other regions of this highly redundant code have no impact. "We are now using this new approach to understand the relation between the function and dynamics of several important proteins."


Luijten E.,Northwestern University | Granick S.,Stanford University | Granick S.,Urbana University | Granick S.,Center for Soft and Living Matter
Annual Review of Physical Chemistry | Year: 2015

Burgeoning interest in supracolloidal assembly has reached the point at which the field can seek so-called intelligent design rather than solely rely on evolution. Emphasizing Janus and triblock particles, this review presents a progress report on formulating design rules for the assembly of interesting structures. We discuss how to design building blocks, bearing in mind that patchy particles embody not just geometric shape but also chemical shape, that chemical shape determines particle-particle interactions, and that the assembly process can be designed to proceed in hierarchical stages. Remarks are included about the potential of kinetic and nonequilibrium control, as well as the potential for the augmented use of soft building blocks. Whereas the reverse design problem, in which arbitrarily selected structures can be designed from the bottom up, still stands as a grand challenge, the field has reached the point of understanding necessary, although not always sufficient, conditions. © 2015 by Annual Reviews. All rights reserved.


News Article | March 18, 2016
Site: phys.org

Prof. Oh-Hoon Kwon (School of Natural Science) is posing for a portrait with the ultrafast laser spectroscopy in the background. Credit: UNIST A new research, affiliated with UNIST has been featured as a 'Hot Article' on the front cover of the March issue of Chemistry: A European Journal. This study has been regarded as "very important" because it offers a new framework for understanding reactions in organic chemistry. The team, made up of five Korean scientists and experts from the IBS Center for Soft and Living Matter, the Korea Advanced Institute of Science and Technology (KAIST), and Ulsan National Institute of Science and Technology (UNIST), reported the basicity enhancement of an alcohol by hydrogen-bonded clustering. In their study, the team addressed the cooperative role of alcohols, the simplest organic protic compounds, in one of elementary reactions in chemistry, the acid-base reaction, in a quantitative manner. According to Prof. Oh-Hoon Kwon (Department of Chemistry, UNIST), the corresponding author of this study, "The motivation of this work, in particular, was the observation that the photoinduced proton transfer can also occur in alcohol with a properly chosen photoacid." The formation of an alkyl oxonium ion has long been proposed as a key reaction intermediate in alcohol dehydration. This was examined by time-resolved fluorescence quenching of a strong photoacid in their study. Through their analysis, the research team revealed, for the first time, that the collaboration of two alcohol molecules through hydrogen bonding is critical to enhancing their reactivity and promotes the resulting alcohol cluster to form an effective Brønsted base when reacting with an acid as strong as sulfuric acid. Prof. Kwon states, "This finding addresses, as in water, the cooperative role of protic solvent molecules to facilitate nonaqueous acid-base reactions." He continues, "However, further systematic investigation on the size variation of clusters formed from diverse alcohols of different basicity and photoacids of different acidity is currently underway." Explore further: Researchers move one step closer to sustainable hydrogen production More information: Sun-Young Park, Young Min Lee, Kijeong Kwac, Yousung Jung, Oh-Hoon Kwon. "Alcohol Dimer is Requisite to Form an Alkyl Oxonium Ion in the Proton Transfer of a Strong (Photo) Acid to Alcohol". Chemistry: A European Journal. (2016)


Grzybowski B.A.,Center for Soft and Living Matter | Huck W.T.S.,Radboud University Nijmegen
Nature Nanotechnology | Year: 2016

For some decades now, nanotechnology has been touted as the 'next big thing' with potential impact comparable to the steam, electricity or Internet revolutions-but has it lived up to these expectations? While advances in top-down nanolithography, now reaching 10-nm resolution, have resulted in devices that are rapidly approaching mass production, attempts to produce nanoscale devices using bottom-up approaches have met with only limited success. We have been inundated with nanoparticles of almost any shape, material and composition, but their societal impact has been far from revolutionary, with growing concerns over their toxicity. Despite nebulous hopes that making hierarchical nanomaterials will lead to new, emergent properties, no breakthrough applications seem imminent. In this Perspective, we argue that the time is ripe to look beyond individual nano-objects and their static assemblies, and instead focus on systems comprising different types of 'nanoparts' interacting and/or communicating with one another to perform desired functions. Such systems are interesting for a variety of reasons: they can act autonomously without external electrical or optical connections, can be dynamic and reconfigurable, and can act as 'nanomachines' by directing the flow of mass, energy or information. In thinking how this systems nanoscience approach could be implemented to design useful-as opposed to toy-model-nanosystems, our choice of applications and our nanoengineering should be inspired by living matter.


Lach Sl.,Center for Soft and Living Matter | Yoon S.M.,Center for Soft and Living Matter | Grzybowski B.A.,Center for Soft and Living Matter
Chemical Society Reviews | Year: 2016

Under non-equilibrium conditions, liquid droplets coupled to their environment by sustained flows of matter and/or energy can become active systems capable of various life-like functions. When fueled by even simple chemical reactions, such droplets can become tactic and can perform "intelligent" tasks such as maze solving. With more complex chemistries, droplets can support basic forms of metabolism, grow, self-replicate, and exhibit evolutionary changes akin to biological cells. There are also first exciting examples of active droplets connected into larger, tissue-like systems supporting droplet-to-droplet communication, and giving rise to collective material properties. As practical applications of droplets also begin to appear (e.g., in single-cell diagnostics, new methods of electricity generation, optofluidics, or sensors), it appears timely to review and systematize progress in this highly interdisciplinary area of chemical research, and also think about the avenues (and the roadblocks) for future work. © 2016 The Royal Society of Chemistry.


Chen K.,Urbana University | Wang B.,Urbana University | Wang B.,Stanford University | Granick S.,Urbana University | Granick S.,Center for Soft and Living Matter
Nature Materials | Year: 2015

In contrast to Brownian transport, the active motility of microbes, cells, animals and even humans often follows another random process known as truncated Lévy walk. These stochastic motions are characterized by clustered small steps and intermittent longer jumps that often extend towards the size of the entire system. As there are repeated suggestions, although disagreement, that Lévy walks have functional advantages over Brownian motion in random searching and transport kinetics, their intentional engineering into active materials could be useful. Here, we show experimentally in the classic active matter system of intracellular trafficking that Brownian-like steps self-organize into truncated Lévy walks through an apparent time-independent positive feedback such that directional persistence increases with the distance travelled persistently. A molecular model that allows the maximum output of the active propelling forces to fluctuate slowly fits the experiments quantitatively. Our findings offer design principles for programming efficient transport in active materials. © 2015 Macmillan Publishers Limited. All rights reserved.

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