ISMB News

The original article was published in the June 2nd, 2011 issue of Nature: Phan et al. (2011). Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate. Nature. 474, 49–53.n

Read the ISMB featured article and commentary by Michael Gross.

Since his appointment in 2006, Chris Kay (UCL SMB) has established an interdisciplinary Electron Paramagnetic Resonance (EPR) Facility at UCL that is bringing this methodology to research as diverse as oxidative stress and aging due to reactive oxygen species (known as ROS) in medicine, structural biology where EPR complements X-ray crystallography, and characterisation of novel materials including thin films for organic solar cells and quantum information processing. A CIF investment through the BEAMS School enabled outdated equipment from the Departments of Chemistry and Biology to be upgraded and a state of the art pulsed EPR spectrometer to be purchased from Bruker. The Faculty of Life Sciences provided a refurbished space to house all three instruments which is located on the main campus in the Darwin Building.

Recent publications include the first demonstration that EPR could be used to precisely measure distances between protein-bound copper ions (Kay et al (2007) J. Am. Chem. Soc. 129 4868), characterisation of radical activation of carbon nanotubes (Menzel et al. (2010), Chemical Science 1 603), a FRET and EPR strudy of RNA-Binding to Archaeal RNA Polymerase Subunits F/E (Grohmann et al. (2010) J. Am. Chem. Soc. 132 5954), and the observation of exceptionally long relaxation times of bismuth dopants in silicon (Morley et al. (2010) Nature Materials 9 725).

Chris holds his post jointly between the LCN and the Institute of Structural & Molecular Biology (UCL/Birkbeck) and has strong links with UCL Chemistry. He welcomes potential collaborations and can be contacted at: c.kay [at] ucl.ac.uk

Congratulations to Felix Schumacher (ISMB) and Lamya Al-Haj (ISMB), two PhD students at the ISMB who won Poster prizes at the Annual UCL poster competition that was open to all departments at UCL. ISMB Students presented 18 posters, which is the highest number in the Division of Biosciences at UCL.

Congratulations to the multidisciplinary BiCE team (Biocatalysis-Chemistry-Engineering interface programme) who won the Institution of Chemical Engineers (IChemE) Innovation and Excellence Award for Bioprocessing at the end of last year. The team, who focus on novel biocatalytic manufacturing routes to speciality chemicals and pharmaceuticals, also received the Royal Society of Chemistry’s 2010 Rita and John Cornforth Award in June for studies at the Chemistry-Biology interface. The principals of BiCE span three UCL Faculties and include Gary Lye, Paul Dalby, Frank Baganz (UCL Biochemical Engineering), Helen Hailes (UCL Chemistry) and John Ward (UCL Structural and Molecular Biology). Recent staff additions to the team bring in expertise in bioreactor engineering and automation (Martina Micheletti), microfluidics (Nicolas Szita) and synthetic biology (Darren Nesbeth).

Finn Werner and Dina Grohmann from the RNAP laboratory at UCL SMB have developed a novel theory on the evolution of transcription regulation – the ‘elongation first hypothesis’ 1. By studying the structure and function of the engine of transcription, RNA polymerase (RNAP), and the factors that orchestrate its activities they conclude that the ancestral RNAP of the last universal common ancestor (LUCA) of all extant life was regulated during the elongation phase of the transcription cycle. This theory represents a paradigm shift in the field since according to textbook dogma RNAP - and thereby gene expression - is principally controlled at the level of transcription initiation.

Read full article in the ISMB newsletter (Issue 7)

The Winter 2011 issue of the ISMB newsletter is now available.

ISMB NEWS is a short news bulletin published twice a year. The aim is to share information between the various departments involved in the Institute. This includes information such as events, research highlights, new staff appointments, awards and grants.

Contributions for next issue should be sent to ismb-admin@ismb.lon.ac.uk

Click here to download ISMB NEWS - Issue 7 or previous issues of the newsletter

Fourniol F, Sindelar CV, Amigues B, Clare DK, Thomas G, Perderiset M, Francis F, Houdusse A & Moores CA (2010). Template-free 13-protofilament microtubule-MAP assembly visualised at 8 Å resolution. J Cell Biol. 191:463-70. (DOI: 10.1083/jcb.201007081)

A new ISMB commentary by Dr Clare Sansom and Dr Carloyn Moores is available for this article. The original article was published in the November 1st 2010 issue of The Journal of Cell Biology.

A team of researchers from the ISMB and Melbourne, Australia have shown how a protein called perforin punches holes in, and kills, rogue cells in our bodies. Read the ISMB featured article and commentary by Michael Gross. This article is reproduced courtesy of Chemistry World.

Their discovery of the mechanism of this assassin has been published in the science journal Nature.

Find out more about:

• Professor Helen Saibil, FRS
• The EM and Image Processing group
• Research within the Department of Biological Sciences, Birkbeck
• The BBSRC news release
• The Wellcome Trust News release
• The Birkbeck news release

A paper published by Steve Perkins' group at UCL Research Department of Structural and Molecular Biology has been selected as a Journal of Biological Chemistry (JBC) Paper of the Week:

Complement Factor H Binds at Two Independent Sites to C-reactive Protein in Acute Phase Concentrations. Azubuike I. Okemefuna, Ruodan Nan, Ami Miller, Jayesh Gor and Stephen J. Perkins. J. Biol. Chem. 2010, 285, 1053–1065

The Papers of the Week is a feature of JBC Online. JBC Editorial Board members and Associate Editors select papers that rank in the top 1% of papers they review in a year in significance and overall importance.

This work was also awarded a poster prize at the 18th International Analytical Ultracentrifugation Conference, Uppsala University, Sweden (September 13–18, 2009).

A summary of the paper is available on the JBC website: please click here
The full article text and PDF is available here.

Chandran V, Fronzes R, Duquerroy S, Cronin N, Navaza J and Waksman, G. Structure of the outer membrane complex of a type IV secretion system. Nature, 2009, Epub ahead of print. Doi 10.1038/nature08588

The commentary for this article is available for reading here.

iGEM

This year a team of three students from UCL has won a Silver medal at the 2009 iGEM competition. The UCL iGEM team was composed of one of our final year biochemists, Xiang Chen, and two Biochemical Engineering students, Anike Akinrinlade and Axel Nystrom. They competed with 110 other teams from all over the world, see: http://ung.igem.org/Results?year=2009. Their success is even more stunning when one considers that the majority of teams often have 10 or more students. The UCL iGEM team are the ‘Stress Busters’ and they designed in vivo detectors of stress for E. coli that could monitor and report on shear stress and pH stress in real time for cells growing in fermenters.
They have submitted several new BioBricks to the BioBrick registry
http://partsregistry.org/Part:BBa_K239000
http://partsregistry.org/Part:BBa_K239001
http://partsregistry.org/Part:BBa_K239005
http://partsregistry.org/Part:BBa_K239006

They divided their time between John Wards lab on the ground floor in SMB for their molecular biology work and the Advanced Centre for Biochemical Engineering for their fermentations. Dr Darren Nesbeth helped them in the lab and Darren has recently given up his position as a postdoc supervised by John Ward and Eli Keshavarz-Moore (Biochemical Engineering) to become a Lecturer in Synthetic Biology in the Biochem. Eng. Department, UCL.

What is iGEM?

iGEM stands for International Genetically Engineered Machines and is an undergraduate Synthetic Biology competition that has now been running since 2003. Students have access to the toolkit of biological parts at the Registry of Standard Biological Parts and are encouraged to construct new parts, called BioBricks, to add to the repository. The iGEM teams have from January till September to plan, design and implement their project. The kinds of projects that have been done by this years iGEM teams can be seen at http://ung.igem.org/Results?year=2009

Well Done ‘Stress Busters’ and all who helped aided and assisted.

Professor Bonnie Ann Wallace of the School of Crystallography, Birkbeck, and the ISMB, has recently published a book about using circular dichroism spectroscopy as a technique for the biological sciences. She is senior editor and principal author. The book is entitled “Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy” and is the first in a series of monographs on “Advances in Biomedical Spectroscopy” published by IOS press (Amsterdam). It was co-edited by Dr. Robert Janes, of the School of Biological and Chemical Sciences, Queen Mary, University of London. This is the first monograph published which focuses on the emerging technique of synchrotron radiation circular dichroism (SRCD), a technique in which the editors are recognised world experts. It includes contributions co-authored by Dr. Lee Whitmore and Dr. Andy Miles, both of the School of Crystallography.

More information:
http://people.cryst.bbk.ac.uk/~ubcg25a/

Prof Helen Saibil has been elected a fellow of the Academy of Medical Sciences. The Academy’s Fellows are the United Kingdom’s leading medical scientists from hospitals, academia, industry and the public service. http://www.acmedsci.ac.uk/

Professor Bonnie Ann Wallace from the School of Crystallography at Birkbeck and the Institute of Structural and Molecular Biology has been awarded the AstraZeneca Award for 2010 for her pioneering work on new methods of Circular Dichroism (CD) and Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy for biological studies. This major prize is awarded triennially by The Biochemical Society.

She was honoured for her work on the development of new CD techniques for studying membrane proteins, for the creation of new methodologies for analyses of protein structures, and for the demonstration of new applications of SRCD in Structural Molecular Biology. These developments have lead to significant new advances in our understanding of the structure and function of proteins. Professor Wallace has recently co-edited (with Dr. Robert Janes, Queen Mary University of London) the monograph Modern Techinques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy, which will be published in the summer of 2009 by IOS press. Professor Wallace will be the Plenary Speaker at the SRCD2009 international meeting in Beijing in April 2009. She has organised the Annual EU Circular Dichroism Meeting for the past six years, and has been co-organiser and lecturer on both the UK and USA Summer School Courses in Circular Dichroism for the past five years. She sits on (or chairs) international advisory/review boards for synchrotron radiation beamlines in the UK, USA, Japan, Taiwan, Denmark, Germany and Australia.

Bonnie Wallace will give a lecture on Tuesday 12 January 2010 at the University of Sheffield as part of the "Experimental approaches to protein:protein interactions" conference.
For more information, click here.

Wendler P, Shorter J, Snead D, Plisson C, Clare DK, Lindquist S, Saibil HR. Motor mechanism for protein threading through Hsp104. Mol Cell. 2009 Apr 10;34(1):81-92.

The commentary for this article is available for reading here.

The 2008 Newcomb Cleveland Prize of the American Association for the Advancement of Science (AAAS) has been awarded to the 5 authors of the paper “Molecular Basis for the Nerve Dependence of Limb Regeneration in an Adult Vertebrate” published in Science 318, 772-777 (2007) by Anoop Kumar, James W. Godwin, Phillip B. Gates, A.Acely Garza-Garcia & Jeremy P. Brockes.
Dr Garza-Garcia is located at NIMR (MRC, Mill Hill) and the other authors are in the Department of Structural and Molecular Biology at UCL, where Dr Brockes is an MRC Non-clinical Research Professor.
The prize is the oldest award of the AAAS, and is given each year for the outstanding paper published in Science for the year between June 1 and May 31. This paper is the first from Biology to win the prize in the last four years. The prize is 25,000 dollars (to be shared equally between the five authors) along with a medal, and is to be presented at the AAAS Annual Meeting at Chicago in February 2009.

More information:
www.smb.ucl.ac.uk/additional-staff-pages/professor-jeremy-brockes-frs.html

Clare DK, Bakkes P, van Heerikhuizen H, van der Vies SM and Saibil HR (2009).
A chaperonin complex with a newly folded protein encapsulated in the folding chamber. Nature, 457, 107-111

The commentary for this article is available for reading here.

Two Lectureships in Microbial Macromolecular Systems
The Institute of Structural and Molecular Biology (ISMB) is seeking applications to fill two lectureships in Microbial Macromolecular Systems that the ISMB wishes to fill by September 2009.

Deadline for applications: 15 February 2009

Lectureship in Biomolecular NMR Spectroscopy
The Institute of Structural and Molecular Biology (ISMB) is seeking applications for a Lectureship in the field of Biomolecular NMR Spectroscopy.

Deadline for applications: 15 March 2009

Chair of Single Molecule Biophysics
The post of Chair of Single Molecule Biophysics is available in the Institute of Structural and Molecular Biology (ISMB) and London Centre for Nanotechnology (LCN) at UCL and Birkbeck, University of London.

Deadline for applications: 31 March 2009


Further details are available here

The School of Crystallography has hosted seven budding scientists in its new Summer Internship Programme. Undergraduate students from universities across the UK, including UCL and Cambridge, and beyond, were given a taste of life as a researcher as they joined research teams in the School to begin to make scientific discoveries of their own.

Click here for the full article

Seven centres across the UK have just been awarded Network grants in Synthetic Biology. The ISMB is now host to one of these Networks that will be run by John Ward (ISMB, Division of Biosciences, UCL) and Irilenia Nobeli (School of Crystallography, Birkbeck). We have named our Network Synbion and it comprises researchers across 6 departments at UCL and Birkbeck and also includes 5 other universities in the UK. The Networks are jointly funded by the BBSRC and EPSRC with additional funds the Economic and Social Research Council (ESRC) and the Arts and Humanities Research Council (AHRC).

Click here for the full article

Click here to visit the Synbion website

Gabriel Waksman; Head of the Research Department of Structural & Molecular Biology; Director of the Institute of Structural & Molecular Biology and Head of the School of Crystallography, Birkbeck College has been elected a fellow of the Academy of Medical Sciences. The Academy’s Fellows are the United Kingdom’s leading medical scientists from hospitals, academia, industry and the public service.

Click here to read the report from the Academy and see the full list of new fellows.

Scientists have found a key protein that helps newts regrow severed limbs and which may guide future research into human regenerative medicine.

Biologists have long been intrigued by the ability of newts and salamanders to renew damaged body parts. But how they do it has been unclear. Now new research by a UK team publishing in the journal Science shows the role of a key protein nAG that's secreted by nerve and skin cells.

Click here to read the news item published by Reuters.

The Wellcome Trust will invest £4 million over three years from its Seeding Drug Discovery Initiative into a programme to develop UCL’s patented series of selective DDAH inhibitors for use in treating sepsis.

DDAH1 Dimethylarginine dimethylaminohydrolase1 (DDAH1) is an enzyme involved in the regulation of nitric oxide (NO) signalling. Researchers at UCL have developed small molecule inhibitors of DDAH1, which may provide novel therapeutics for the treatment of diseases involving excess NO synthesis, including sepsis.

Click here to read the full article.

A team led Dr Andrea Townsend-Nicholson at University College London is working towards developing a weight loss pill that makes people feel they are full after eating a small amount of food. The pill has been likened to chemical gastric banding. The potential new drug is described in the Journal of Pharmacology and Experimental Therapeutics by Dr Brian King and Dr Andrea Townsend-Nicholson. It made the front page of the 4 March edition of the Daily Telegraph.

Click here to read the Daily Telegraph article.

Wendler P, Shorter J, Plisson C, Cashikar AG, Lindquist SL, & Saibil HR (2007).
Atypical AAA+ Subunit Packing Creates an Expanded Cavity for Disaggregation by theProtein-Remodeling Factor Hsp104. Cell, 131(7), 1366-77.

The commentary for this article is available for reading here.

ISMB NEWS is a short news bulletin that will be published twice a year. The aim is to share information between the various departments involved in the Institute. This includes information such as events, research highlights, new staff appointments, awards and grants.

Contributions for next issue should be sent to ismb-admin@ismb.lon.ac.uk

Click here to download ISMB NEWS - Issue 1

We are glad to announce Gabriel Waksman’s election as a member of the European Molecular Biology Organization (EMBO). The organization announced today the election of 50 leading scientists to its membership. These new EMBO Members join a community of over 1,300 members in Europe and more than 80 associate members worldwide.
Election as an EMBO Member is a tribute to the significant contribution to the advancement of science made by each of these researchers. EMBO elects new members annually on the basis of scientific excellence.

Click here to view the new elected members' list.

We are pleased to announce the creation of an interdisciplinary 4-year PhD programme, which has its primary objective the training of the next generation of young scientists at the interface of computational biology, structural biology and chemical biology.

This programme is the result of collaboration between the Institute of Structural Molecular biology at UCL/Birkbeck, the Bloomsbury Centre for Bioinformatics (BCB) and the Structural Biology group of the national Institute for Medical Research (NIMR).

The general organisation of the PhD programme is based on a first year rotation system, in which students will be expected to undertake projects in all three core areas of the programme, followed by a research intensive 3-year period in the laboratory of choice.

Applications are invited for entry in September 2008. Deadline for applications: 8 January 2008.

Click here for details of this unique programme.

Following the success of the first Institute of Structural Molecular Biology retreat, held in Hinxton in June 2005, a Joint Departmental / ISMB Retreat was held almost exactly two years later. It took place at the Wellcome Trust Conference Centre in Hinxton, Cambridgeshire, on June 19 and 20, 2007. The packed, two-day-long programme included keynote lectures from three distinguished scientists, posters and oral presentations from students and postdoctoral researchers at Birkbeck College and University College, London, and an interesting session on careers in science.

The full article is available for reading here.

Domainex, a spin-out company from Birkbeck, UCL and the Institute of Cancer Research, has been recognised by UK Trade and Investment for the important contribution that the company has made to the biotechnology industry. On 4 July 2007, Domainex was announced as the winner of the Award for Innovation in Enabling Biotechnology in the 2007 UK BioEntrepreneurial Awards.

Click here for the full article on Birkeck website

Click here to read the UKTI article

Elad N, Farr GW, Clare DK, Orlova EV, Horwich AL & Saibil HR (2007).
Topologies of a Substrate Protein Bound to the Chaperonin GroEL. Molecular Cell, 26, 415-426.

The commentary for this article is available for reading here.

Leiper J, Nandi M, Torondel B, Murray-Rust J, Malaki M, O’Hara B, Rossiter S, Anthony S, Madhani M, Selwood D, Smith C, Wojciak-Stothard B, Rudiger A, McDonald NQ & Vallance P. (2007)
Disruption of methylarginine metabolism impairs vascular homeostasis. Nature Medicine, 13(2), 198 - 203.

The commentary for this article is available for reading here.

A new blood based breast cancer detection test is reported in the Journal of Proteome Research by Prof Jasminka Godovac-Zimmermann, of University College London, who collaborated with international group, which included scientists from the universities of Pennsylvania and Pittsburgh and the company BioTraces, Inc in Herndon, Virginia. The group has developed novel biomarker panels which include tissue-specific cancer biomarkers as well as cytokines and angiogenic factors. The new test based on ultra-sensitive method of immunoassay using multi-photon-detection increases sensitivity by 200- to 1000-fold (1 femtogram/ml). This has allowed the measurement of cancer biomarkers with very low concentrations in blood that could not be measured for full patient cohorts with conventional immunoassays. The new method revealed that patient to patient variations in the concentrations of individual biomarkers in blood can extend over many orders of magnitude (up to six) and that the distributions of biomarker concentrations over patient cohorts are non-Gaussian. A new method of data analysis which correlate abundances of multiple, different biomarkers have also been developed to deal with such data sets. Among 345 women the blood test picked up 95% of cancers, making it much more sensitive than existing tests. The developed blood test can reveal if a woman has breast cancer and at an earlier stage than is possible with currently available tests.

Click here for the BBC coverage.

Click here for the Telegraph coverage.

Click here to read the publication.

The Inauguration of the ISMB Biophysics Centre took place on Tuesday 28 November 2006 . Further details are available on the Biophysics section of the ISMB website.

It is a great pleasure to announce that Helen Saibil has been elected a Fellow of the Royal Society. The Fellowship of the Royal Society is composed of 1284 of the most distinguished scientists from the United Kingdom, other Commonwealth countries and the Republic of Ireland. Fellows of the Royal Society are elected for life and designate themselves through the use of the letters FRS after their names.

Fellows are elected through a peer review process that culminates in a vote by existing Fellows. The main criterion for election as a Fellow is scientific excellence.