December 2013 – Chemical Science Blog

Archive for December, 2013

HOT Chemical Science articles for December

20 Dec 2013

The conformational behaviour of free D-glucose—at last
José L. Alonso, María A. Lozoya, Isabel Peña, Juan C. López, Carlos Cabezas, Santiago Mata and Susana Blanco
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52559G, Edge Article

GA?id=C3SC52559G

Free to access until 19th January 2014

Simultaneous detection and quantification of three bacterial meningitis pathogens by SERS
Kirsten Gracie, Elon Correa, Samuel Mabbott, Jennifer A. Dougan, Duncan Graham, Royston Goodacre and Karen Faulds
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52875H, Edge Article

C3SC52875H

Free to access until 19th January 2014

Constraint-induced structural deformation of planarized triphenylboranes in the excited state
Tomokatsu Kushida, Cristopher Camacho, Ayumi Shuto, Stephan Irle, Masayasu Muramatsu, Tetsuro Katayama, Syoji Ito, Yutaka Nagasawa, Hiroshi Miyasaka, Eri Sakuda, Noboru Kitamura, Zhiguo Zhou, Atsushi Wakamiya and Shigehiro Yamaguchi
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52751D, Edge Article

C3SC52751D

Free to access until 19th January 2014

Direct observation of a lithiated oxirane: a synergistic study using spectroscopic, crystallographic, and theoretical methods on the structure and stereodynamics of lithiated ortho-trifluoromethyl styrene oxide
Antonio Salomone, Filippo M. Perna, Aurelia Falcicchio, Sten O. Nilsson Lill, Anna Moliterni, Reent Michel, Saverio Florio, Dietmar Stalke and Vito Capriati
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52099D, Edge Article

C3SC52099D

Free to access until 19th January 2014

Sugar-coated sensor chip and nanoparticle surfaces for the in vitro enzymatic synthesis of starch-like materials
Ellis C. O’Neill, Abdul M. Rashid, Clare E. M. Stevenson, Anne-Claire Hetru, A. Patrick Gunning, Martin Rejzek, Sergey A. Nepogodiev, Stephen Bornemann, David M. Lawson and Robert A. Field
Chem. Sci., 2014,5, 341-350
DOI: 10.1039/C3SC51829A, Edge Article

C3SC51829A

Free to access until 19th January 2014

Electrochemistry in a drop: a study of the electrochemical behaviour of mechanically exfoliated graphene on photoresist coated silicon substrate
Peter S. Toth, Anna T. Valota, Matěj Velický, Ian A. Kinloch, Kostya S. Novoselov, Ernie W. Hill and Robert A. W. Dryfe
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52026A, Edge Article

C3SC52026A

Free to access until 19th January 2014

Core solution: a strategy towards gold core/non-gold shell nanoparticles bearing strict DNA-valences for programmable nanoassembly
Huiqiao Wang, Yulin Li, Ming Gong and Zhaoxiang Deng
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52445K, Edge Article

C3SC52445K

Free to access until 19th January 2014

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A cut above the rest: the evolution and application of inteins

19 Dec 2013

In this new Perspective, Chemical Science Associate Editor Tom Muir of Princeton University elucidates the biological role and evolutionary origin of inteins – a fascinating class of proteins which have the ability to “process”, or sever, their own peptide backbone. Usually, this type of post-translational modification is done enzymatically by proteases, but inteins contain a module which allows the spontaneous scission of peptide bonds with no external factor or energy source required. The only things needed are certain chemical functional groups in the neighbouring peptide residues, and the correct spatial folding of the domain.

Obviously, this is a truly interesting process, as the functions and actions of a protein are determined by its amino acid sequence and structure. By breaking peptide bonds and creating new ones, inteins essentially act as an on/off switch for the protein, the potential application for which is staggering. The intein is flanked on either side by two exteins; during the “processing” reaction, the bonds between intein and exteins are broken, and a new bond between the exteins is created. Inteins share a common biochemical mechanism for this process, which is illustrated below. Crucially, all inteins must contain a cysteine or serine at their N-terminus which provides the nucleophile for the initial acyl shift. A subsequent trans(thio)esterification and an additional acyl shift forms the spliced product and the excised intein.: Mechanism of protein splicing

Muir and co-author Neel Shah investigate the evolutionary origin of inteins, which can be found in all domains of life – eukaryotes, bacteria, archaea and viruses. Although they are often found in proteins involved in genetic “housekeeping” – DNA replication, transcription, and maintenance – inteins have no obvious biological role, and do not provide any benefit to the host organism. As such, they are known as “selfish” genes. Despite the mystery of their purpose and origin, what is clear is that the future is bright for inteins.

The authors discuss a number of applications of inteins, the most exciting of which is conditional protein splicing (CPS) where inteins can be used as an on/off switch for the proteins they are splicing, even in vivo. CPS is currently achieved in a number of ways, shown below, in which the intein is kept in an inactive state – via (a) conformational distortion, (b) caging of the active site, or (c) the physical separation of a split intein – until activation is desired. Ligand binding, deprotection or dimerisation, respectively, then releases the active intein and triggers the peptide splicing. CPS is a promising tool for cell biology and should facilitate the development of “smart” protein therapeutics that are activated only at the target site. All in all, this Perspective makes for an interesting read on a class of proteins with impressive potential. I think it’s a safe bet to predict that when it comes to future smart therapeutics, inteins will definitely make the cut.: Conditional protein splicing (CPS): a) Allosteric intein activation by ligand binding; b) Intein activation via deprotection of a photo-caged active site residue; c) Activation via chemically-induced dimerisation

For more, you can read Muir and Shah’s Chemical Science Perspective here:

Inteins: nature’s gift to protein chemists

Neel H. Shah and Tom W. Muir

Chem. Sci., 2014, Advance Article

DOI: 10.1039/C3SC52951G

Professor Muir serves as one of Chemical Science‘s Associate Editors, handling submission in chemical biology – read more about him and what useful advice he wishes someone had told him as an undergraduate.

Our Associate Editors Tom Muir and Ben Davis have highlighted their recommended chemical biology papers on Chemical Science – read their Editor’s Choice selection for FREE today!

Find many more excellent articles on chemical biology here: Online collection: Chemical biology

Ruth E. Gilligan is a guest web-writer for Chemical Science. She recently completed her PhD in the group of Prof. Matthew J. Gaunt at the University of Cambridge, and is currently pursuing an internship at Science Foundation Ireland.

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ISACS14 call for abstracts – Organic Chemistry

17 Dec 2013

Abstract submission now open – submit today

We are delighted to announce that abstract submission for Challenges in Organic Chemistry (ISACS14), the 14th conference in the highly successful International Symposia on Advancing the Chemical Sciences (ISACS) series, is now open.

Take advantage of this excellent opportunity to showcase your latest research alongside the following leading scientists from across the globe.

Confirmed speakers

Varinder Aggarwal	David W. C. MacMillan	Yong Tang
Vy M. Dong	Ruben Marten	F. Dean Toste
Greg C. Fu	Keiji Maruoka	M. Christina White
Matthew Gaunt	Cristina Nevado	Qi-Lin Zhou

Tristan H. Lambert

Melanie Sanford

Dawei Ma

Erik J. Sorensen

Don’t miss your chance to be a part of this significant event – submit today

We look forward to welcoming you to Shanghai in August 2014.

Professor Kuiling Ding
Conference Chair

Dr Robert D. Eagling
Editor, Chemical Science

RSClogo

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Disarming bacteria to beat infection

16 Dec 2013

Researchers in Germany looking to find unprecedented ways of combating bacterial infection have demonstrated that certain small molecules can reduce the ability of Staphylococcus aureus to cause disease. ‘The classic antibiotic approach puts bacteria in a life or death situation, meaning that they need to become resistant in order to survive. We aimed to find a way of reducing the ability of bacteria to make the toxins that harm eukaryote cells during infection, without putting them under selective pressure,’ explains Stephan Sieber of the University of Technology in Munich who led the study.

α-methylene-γ-butyrolactones can inhibit virulence factors like α-haemolysin (hla) to render pathogenic bacteria harmless

Transcriptional regulators control the virulence factors in bacteria, that enable a microorganism to establish itself within a host or enhance its potential to cause disease, by directly binding to DNA promoter regions of toxin-encoding genes. In the study, the researchers identified a series of α-methylene-γ-butyrolactones that covalently modify cysteine residues on three transcriptional regulators in S. aureus, markedly decreasing the expression of α-haemolysin, one of the most prominent virulence factors.

Read the full article in Chemistry World»

Read the original journal article in Chemical Science:
α-Methylene-γ-butyrolactones attenuate Staphylococcus aureus virulence by inhibition of transcriptional regulation
Martin H Kunzmann, Nina C. Bach, Bianca Bauer and Stephan Axel Sieber
Chem. Sci., 2013, Accepted Manuscript, DOI: 10.1039/C3SC52228H

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Compressing/decompressing data with DNAzymes

16 Dec 2013

When most people read a book they don’t remember every word. They compress the story down to the main points and remember those. The reverse is also true – given a few facts most people can embellish a story to a suitably lengthy tale of adventure and mystery.

These data compression/decompression processes are called logic operations and are a central theme in information theory. They are also replicated in biological systems where scaffolding proteins within the regulatory cellular networks carry out the operations. However, there has been no synthetic DNA-based system that can carry out this data compression/decompression process, until now.

Logic circuit showing how 4 inputs (I) can be compressed to one output (S)

Itamar Willner from the Hebrew University of Jerusalem and colleagues have developed such a system based on Mg²⁺-dependent DNAzyme subunits. Unlike previous approaches where the demonstration is done using two inputs and one output the team have investigated enhanced multiplexing in the compression process with four inputs producing one output.

Additionally they have also demonstrated the expansion of a single input to produce two outputs. Having such systems based on nucleic acids also raises the possibility of resetting the computational module. This means you could reconfigure and change its operation in situ by the addition of suitable complementary nucleic acid strands.

This article details important advances in DNA based logic networking and raises the potential to compress information held within genes into a single output. It also raises challenges for the future that must be overcome before these synthetic biomolecular computational systems can control natural intracellular processes.

For more, read the Chemical Science Edge article in full:

DNAzyme-Based 2:1 and 4:1 Multiplexers and 1:2 Demultiplexer
Ron Orbach, Francoise Remacle, R. D. Levine and Itamar Willner*
Chem. Sci., 2013, Accepted Article
DOI: 10.1039/C3SC52752B

Iain Larmour is a guest web writer for Chemical Science. He has researched a wide variety of topics during his years in the lab including nanostructured surfaces for water repellency and developing nanoparticle systems for bioanalysis by surface enhanced optical spectroscopies. He currently works in science management with a focus on responses to climate change. In his spare time he enjoys reading, photography, art and inventing.

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5 minutes with Haw Yang, Chemical Science Associate Editor

03 Dec 2013

Haw Yang is Associate Professor of Chemistry and Director of Graduate Studies at Princeton University, USA. Haw and his experimental physical chemistry group work on single-molecule chemical dynamics and develop new single-molecule- and single-nanoparticle-based methods for the study of complex systems. His team’s ultimate goal is to arrive at a level of understanding that affords a quantitative prediction of the dynamics and how they contribute to systems behaviour.

Haw serves as one of Chemical Science’s Associate Editors, handling submissions in physical chemistry.

Who or what inspired you to study physical chemistry?

Madame Curie. I really didn’t know who she was until, as a kid, I watched a movie about her, based on her daughter’s autobiography. That movie left a very strong impression on me because I saw her dedication and her passion for science. And she did it, not for personal gain, but for humankind – for years, she used her discovery to cure cancer. She went from doing fundamental research to helping humanity, and that left an enduring mark on me.

She was also very good at maths and physics and chemistry, and – because I’m a geek – this impressed me enormously, which is another reason why she became my heroine.

For you, what is the biggest and most important unanswered question in the chemical sciences?

The quantitative prediction of complex systems behaviour from first-principles understanding of atomistic and molecular actions.

Outside of science, what would your dream job be?

As I said, I’ve been a nerd, a geek, since I was a kid – I’ve never been any good at anything else. So, if I hadn’t been able to get a job in this profession, I would have been doomed! (Laughs)

So this – what I’m doing now – is my dream job. If I had to do it all again, I would do it exactly the same way – I would come to Princeton, and do what I’m doing right now. People pay me to do what I enjoy doing; not everyone can have this kind of career! I feel extremely lucky. This is the dream.

What do you consider the most fulfilling part of your job?

To see my students and post-docs do extremely well, do something really creative after they leave my group – and to have them still remember me! (Laughs) That’s really awesome. Sometimes I get emails or postcards from former students out of the blue, and I’d say, wow, I did not expect this.

“For me, the cello is a fitting instrument – it would let me be alone and be quiet, and at the same time, do something creative” – Haw Yang (Image © Shutterstock)

Making new discoveries in the lab – I don’t often get to do that anymore, but when I was still in the lab, I knew I was the first in the world to see those results and interpret them – that was extremely fulfilling. And these days, I take joy in doing experiments that people have been telling me are impossible to do. (Laughs) I love a challenge, I love to change the way people think.

Which musical instrument do you, or wish you could, play?

I wish that I could learn to play cello – it’s on my to-do list when I get the time. I guess I’m hitting that age when I’d like something more quiet, more introspective, and the cello has that quality, especially if one can play Bach’s unaccompanied cello concertos – those are my favourites. In this line of work, we’re alone most of the time, and we think a lot – that is, if we’re lucky, we get time to think. So for me, the cello is a fitting instrument – it would let me be alone and be quiet, and at the same time, do something creative.

Fire, earth, water, or air?

Water.

Describe Chemical Science in three words.

Breaking status quo

Your personal message to Chem Sci authors and readers?

What always gets me excited is original physical chemistry, broadly defined. It could be a new and relevant physical chemistry problem that’s well articulated, an ingenious approach that definitely answers an outstanding question, an innovative technique that enables new experiments to solve problems that matter, or a conceptual breakthrough that inspires new thinking.

We scientists are in the business of breaking the status quo, and we should do so with high scientific rigour. I strongly believe scientists must never do work which merely repeats what is already known, for the sake of hype, of joining the bandwagon, or aiming to please.

So, if you agree with me that ground-breaking substance and genuine originality are more important than hype, I invite you to submit your most creative papers to Chemical Science – your work could help define the future of physical chemistry!

Haw Yang and our dynamic international team of Associate Editors make direct decisions on the content of Chemical Science and actively drive its scientific development – submit your best and most innovative work to any of their Editorial Offices.

Read Haw Yang’s latest article in Chemical Science:

Harnessing thermal fluctuations for purposeful activities: the manipulation of single micro-swimmers by adaptive photon nudging
Bian Qian, Daniel Montiel, Andreas Bregulla, Frank Cichos and Haw Yang
Chem. Sci., 2013,4, 1420-1429
DOI: 10.1039/C2SC21263C, Edge Article

Our Associate Editors Haw Yang, Kopin Liu and Kazunari Domen have selected their recommended physical chemistry papers on Chemical Science – read their Editors’ Choice selection today and find out why they think these are must-reads!

Online collection: Physical chemistry

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Chemical Science Blog

Archive for December, 2013

HOT Chemical Science articles for December

A cut above the rest: the evolution and application of inteins

ISACS14 call for abstracts – Organic Chemistry

Disarming bacteria to beat infection

Compressing/decompressing data with DNAzymes

5 minutes with Haw Yang, Chemical Science Associate Editor

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