[ccp4bb] Fully funded MSD (Masters by Research) studentships at the University of Essex

[Hough, Mike]

Dear CCP4bbers,

I would be grateful if you could pass details of the below studentships to any 
interested final year undergraduates.

Many thanks,

Mike




Fully Funded Christine Desty MSD positions

These scholarships are for a one year research-based Master’s degree (MSD) that 
have all fees paid and a stipend of ~£15,000. The full list of projects and 
information on how to apply is available here:
https://www.essex.ac.uk/departments/biological-sciences/scholarships-and-funding

https://www.findaphd.com/phds/project/mining-for-novel-cu-proteins-in-ammonia-oxidising-archaea-a-missing-link-in-the-nitrogen-cycle-to-start-october-2019-for-an-msc-by-dissertation-msd/?p107794
This project aims to characterise novel copper enzymes from archaea that may 
represent a missing link in the global nitrogen cycle. The project will 
encompass biochemistry, structural biology and microbiology. Supervised by Dr 
Mike Hough, Dr Corinne Whitby, Dr Richard Strange and Dr Jonathan Worrall.

https://www.findaphd.com/phds/project/creating-the-next-generation-lpmos-for-biofuel-production-to-start-october-2019-for-an-msc-by-dissertation-msd/?p107760
This project will involve the optimisation of an enzyme for the production of 
biofuels - and is directly relevant to industrial biotechnology. Supervised by 
Dr Jonathan Worrall and Dr Mike Hough.

https://www.findaphd.com/phds/project/effect-of-oxidative-stress-on-the-biochemistry-of-dimethylsulfoniopropionate-dmsp-lyase-enzymes-in-tropical-reef-organisms-to-start-october-2019-for-an-msc-by-dissertation-msd/?p107911
In this project you will characterise the role of DMSP lyase enzymes in 
organisms from tropical reefs. Supervised by Dr Michael Steinke, Dr Jonathan 
Worrall and Dr Mike Hough.

https://www.findaphd.com/phds/project/high-throughput-drug-screening-of-a-cancer-target-using-room-temperature-serial-crystallography-to-start-october-2019-for-an-msc-by-dissertation-msd/?p107795
This project will use novel X-ray crystallography methods to screen for the 
binding of drug-like molecules to a cancer target protein. This will involve 
molecular biology, biochemistry and structural biology and is supervised by Dr 
Mike Hough and Dr Filippo Prischi.

The application deadline is Wednesday, April 24.



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] PhD studentship at Diamond Light Source and University of Essex: Time-resolved crystallography

[Hough, Mike]

Dear CCP4bbers,

I’d be grateful if you could bring this studentship opportunity to the 
attention of any suitable candidates.


Fully-funded 4 year PhD Studentship: Diamond Light Source and University of 
Essex

Time-resolved synchrotron and XFEL crystallography of metalloenzymes using 
anaerobic photocages


Project outline
X-ray crystallography has been the leading method to understand the structure 
and function of proteins and enzymes for decades. Despite this, it has a key 
limitation in that structures are not time-resolved and so do not represent the 
dynamic and changing nature of a protein’s structure as it carries out its 
function or enzymatic reaction. Time-resolved crystallography is one approach 
for capturing structures of reaction intermediates, though for probing fast 
changes approaches are typically limited to light activated processes.

Metalloproteins are vital to a wide range of biological functions and are 
particularly susceptible to site-specific radiation damage, a problem that is 
considerably worse when working at room temperature. Serial sample delivery and 
the use of photocages to trap and trigger reactions offer a means of resolving 
both of the above challenges, making fast time-resolved experiments applicable 
to a wide range of targets.

In this joint studentship between the University of Essex and Diamond Light 
Source you will perform cutting-edge research in the areas of metalloprotein 
structure determination, serial synchrotron crystallography (SSX), and X-ray 
free electron laser (XFEL) data collection to develop approaches for 
time-resolved SSX at Diamond. To this end you will exploit state-of-the-art 
fixed target instrumentation at Diamond and characterise photocages and their 
activation in crystals. Experiments and developments will be carried out using 
metalloproteins prepared by you at the University of Essex. There will also be
the opportunity to carry out experimental work at the SACLA XFEL in Japan.

You will spend approximately half of the studentship based at the University of 
Essex and half based at Diamond.

We are looking for an exceptional and highly motivated candidate with a good 
Undergraduate or Masters degree in a relevant subject including Life Sciences, 
Physics or Chemistry. A willingness to travel to carry out experimental work at 
international facilities is essential. Start date October 2019.

This interdisciplinary project offers exceptional training opportunities in the 
rapidly developing field of serial and time-resolved structural biology. Full 
training in all required methodology will be provided. The University of Essex 
Proficio scheme offers an extensive range of training courses in transferable 
skills.

Applications should be submitted electronically by the 8th April 2019 see here 
for details 
https://www.essex.ac.uk/pgapply/enter.aspx
 and should state the project title and supervisors. Potential applicants are 
strongly encouraged to informally contact the supervisors in advance: Dr Mike 
Hough (maho...@essex.ac.uk; 
https://www.essex.ac.uk/people/hough20300/mike-hough)
 or Dr Robin Owen (robin.o...@diamond.ac.uk; 
https://www.diamond.ac.uk/Instruments/Mx/I24/Staff/Owen.html)

For general information about the School of Biological Sciences at the 
University of Essex please visit our webpages 
http://www.essex.ac.uk/bs/.
 For information regarding macromolecular crystallography beamlines at Diamond 
please visit 
https://www.diamond.ac.uk/Instruments/Mx
Funding Notes

This is a fully-funded 4-year PhD Studentship covering Home/EU fees and with an 
enhanced stipend.
Please note: International students need to have additional funding to cover 
the difference in tuition fees which is currently £12,410 per year, evidence 
will be requested that you have these additional funds.

Further details are here:
https://www.findaphd.com/phds/project/time-resolved-synchrotron-and-xfel-crystallography-of-metalloenzymes-using-anaerobic-photocages/?p106337\

Many thanks!

Mike




Dr Michael Hough
Senior Lecturer in Structural Biology
School of Biological Sciences
University of Essex
Wivenhoe Park, Colchester
CO4 3SQ
United Kingdom
Phone number: +44 1206 87 3317

Re: [ccp4bb] normal-coordinate structural decomposition (NSD) server?

[Hough, Mike]

Hi Sarah,

Fantastic, thank you!

Best wishes,

Mike


On 2 May 2018, at 16:20, Sarah Bowman 
<sbow...@hwi.buffalo.edu<mailto:sbow...@hwi.buffalo.edu>> wrote:

Hi Mike,

Here is a link to a current NSD calculator for heme distortions from planarity 
available online from the Liptak Group in Vermont:

http://mliptak.w3.uvm.edu/nsd.html

This uses the method originally developed by Shelnutt.

Hope that helps!
Sarah


Sarah EJ Bowman, PhD

High-Throughput Crystallization Screening Center
Hauptman-Woodward Medical Research Institute
www.getacrystal.com<http://www.getacrystal.com/>

sbow...@hwi.buffalo.edu<mailto:sbow...@hwi.buffalo.edu>
716-898-8623

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of "Hough, Mike" <maho...@essex.ac.uk<mailto:maho...@essex.ac.uk>>
Reply-To: "Hough, Mike" <maho...@essex.ac.uk<mailto:maho...@essex.ac.uk>>
Date: Wednesday, May 2, 2018 at 11:14 AM
To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" 
<CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: normal-coordinate structural decomposition (NSD) server?

Dear CCP4bbers,

I would like to analyse the out of plane distortions in a heme protein 
structure using the normal-coordinate structural decomposition (NSD) method. 
This would be a way to assess e.g. ruffling and saddling distortions. At one 
point this was available via a
web server at: http://jasheln.unm.edu/jasheln/content/nsd/nsd__welcome.htm


but this no longer seems to be active.

Is anyone aware if there is a new home for the server or alternatively a source 
of the program used?

Many thanks,

Mike

[ccp4bb] normal-coordinate structural decomposition (NSD) server?

[Hough, Mike]

Dear CCP4bbers,

I would like to analyse the out of plane distortions in a heme protein 
structure using the normal-coordinate structural decomposition (NSD) method. 
This would be a way to assess e.g. ruffling and saddling distortions. At one 
point this was available via a
web server at: http://jasheln.unm.edu/jasheln/content/nsd/nsd__welcome.htm

but this no longer seems to be active.

Is anyone aware if there is a new home for the server or alternatively a source 
of the program used?

Many thanks,

Mike

[ccp4bb] PhD Studentship opportunity at University of Essex

[Hough, Mike]

Dear CCP4bb,

I would like to bring to your attention a PhD studentship opportunity in my 
group, which I would be grateful if you would advertise to potential candidates.

The details are available here:

https://www.findaphd.com/search/ProjectDetails.aspx?PJID=94398

and

https://www1.essex.ac.uk/bs/documents/research_documents/MH-JW-RS-DS-advert.pdf


The project will involve the study of two biotechnological important enzymes 
and will offer the opportunity to conduct synchrotron and XFEL crystallography, 
fast kinetics and EPR.

The closing date is at the end of February.

Many thanks,

Mike

Re: [ccp4bb] Iron Oxidising state

[Hough, Mike]

Dear Rohit,

If your protein has a spectroscopic signature corresponding to the different 
redox states, you could try using single crystal spectroscopy (e.g. UV-visible) 
to validate the redox state before and after data collection.

Best wishes,

Mike




On 5 Jan 2018, at 10:45, rohit kumar 
> wrote:

Dear All,

I am solving a structure (resolution 2 A) of an enzyme having Iron as a metal 
cofactor.

How could I know oxidising state of the bound Iron (Fe+2 or Fe+3)?


Thank you in advance


--
WITH REGARDS
Dr. Rohit Kumar Singh

[ccp4bb] PhD position in Structural Biology, University of Essex

[Hough, Mike]

Dear all,

We are looking for a highly motivated and talented PhD student for a project in 
the area of peroxidase biochemistry and crystallography, funded by the estate 
of the late Prof. Peter Nicholls. The student will be based at the University 
of Essex under the supervision of Mike Hough, Jonathan Worrall and Dimitri 
Svistunenko.

I would be very grateful if you could circulate this to any potential 
candidates that you are aware of.

Many thanks,

Mike





A FULLY-FUNDED 3 YEAR PHD SCHOLARSHIP IS AVAILABLE FROM OCTOBER 2017.



Illuminating the catalytic, structural and mechanistic features of a new class 
of haem peroxidases to dye for
Dye decolourising peroxidases (DyPs) are the most recent family of haem 
peroxidase to be discovered. The oxidizing potential of these enzymes is driven 
by the formation of ferryl intermediates, formed on H2O2 activation, that 
enable them to oxidize synthetic dye molecules widely used in the textile 
industry. Some DyPs have been implicated in biomass deconstruction through the 
oxidative breakdown of lignocellulose. Thus, DyPs have vast potential for use 
in biotechnology applications. At present, detailed catalytic and substrate 
reactivity information is sparse across the four sub-families (A to D) of DyPs 
and there is a strong need to address this to maximize future commercial 
applications.
At Essex we have identified an A-type DyP from Streptomyces lividans and have 
characterised its catalytic cycle and unusual dye decolourisation properties. 
Further to this, our X-ray structural work (including in-crystal generation of 
relevant intermediates) and EPR spectroscopy of transiently formed free 
radicals and high-valence haem states have informed on potential substrate 
binding sites and electron-transfer pathways. The overarching aim of this 
studentship is to extend these experimental approaches across several DyP 
sub-families incorporating new structural and fast reaction methodologies, such 
as state of the art synchrotron beamlines and time-resolved X-ray 
crystallography as well as rapid freeze-quench EPR for kinetics studies, to 
characterise the high-valence catalytic intermediates and tailor this knowledge 
to generate designer enzymes for commercial applications.

 The successful candidate will work under the supervision of Dr Jonathan 
Worrall, Dr Mike Hough and Dr Dimitri Svistunenko in the Protein Structure & 
Function Group in the School of Biological Sciences, University of Essex.


Entry requirements and application procedures

Informal queries may be addressed in the first instance to 
jworr...@essex.ac.uk or 
maho...@essex.ac.uk or 
sv...@essex.ac.uk. Applications should be submitted 
electronically by the 30th June 2017. See 
https://www.essex.ac.uk/pgapply/enter.aspx for details. The intended start date 
for this 3-year, fully-funded PhD studentship is 5th October 2017. This 
scholarship will be to the value of £12,500 per annum plus UK/EU tuition fees.

Applicants should write 500 words explaining why they are interested in this 
project and submit this with their CV.



This scholarship is generously supported by a bequest from the estate of 
Professor Peter Nicholls 
(https://www.theguardian.com/theguardian/2014/dec/30/peter-nicholls-obituary)

[ccp4bb] measurement of a dihedral angle in a heme protein

[Hough, Mike]

Dear CCP4 gurus…

I am looking at the structure of a heme protein that has a single axial 
histidine ligand. To compare to published data I would like to measure the 
'dihedral angle between the imidazole plane of the histidine and the nearest 
N(pyrrole)–Fe–N(pyrrole) axis'.

Could anyone advise me how to do this, either within Coot or another program?

Many thanks,

Mike

[ccp4bb] Post doctoral position in kinetic structural biology

[Hough, Mike]

Dear ccp4bb,

I have a post-doc position available in my lab (see below) and would be 
grateful if this advert could be passed on to suitable candidates.

Thanks,

Mike


SENIOR RESEARCH OFFICER (PDRA) - 18 months.

Ref   RE815
Location   School of Biological Sciences, University of Essex, Wivenhoe 
Park, Colchester, CO4 3SQ.
Salary  £31,342 per annum

Closing date30 June 2015
Post to start as soon as possible following interviews.



The School of Biological Sciences at the University of Essex is seeking to 
recruit a motivated and enthusiastic Senior Research Officer to work in the 
Structural Biology group under the supervision of Dr Michael Hough (Principal 
Investigator) on an 18 month project funded by the Biotechnology and Biological 
Sciences Research Council (BBSRC).

This project integrates rapid room temperature protein crystallography with 
large scale QM/MM simulations to elucidate a ‘minimum catalytic core’ model for 
the complex chemistry of key multi-copper and haem-cupredoxin containing 
nitrite reductase enzymes that are vital components of the global nitrogen 
cycle. Your role in this work as a structural biologist will be to develop and 
apply methodology to measure room-temperature diffraction data from protein 
crystals and to analyse sequences of many structures measured from the same 
crystals in rapid succession. You will produce a detailed structural 
understanding of catalytic processes allowing the dynamic processes of 
catalytic regulation and control to be understood.

The work will include elucidating the proton coupled electron transfer 
trigger-mechanisms that involves binding of nitrite and conversion to nitric 
oxide, the determination of efficient electron transfer pathways and the 
pathway(s) of solvent mediated electron transfer at the 
cytochrome(haem)-cupredoxin interface, and the critical ligand migration and 
escape pathways.

The successful candidate will hold, or be in the final stages of completion of, 
a PhD in a relevant area, have experience in structural biology and will work 
in close collaboration with a senior research officer in computational 
biological chemistry and scientists at Diamond Light Source and the Science and 
Technology Facilities Council (STFC) Hartree Centre.

Based at our Colchester Campus, appointment to this 18 month full-time, 
fixed-term post is immediately available.

Please use the link below for a full job description, person specification and 
further information relating to this post. Please read this information 
carefully before applying for this post as it contains details of documents 
that must be attached to your application. Applications should be made on-line, 
but if you would like advice or help in making an application, or need 
information in a different format, please telephone (01206 874588/873521).

http://jobs.essex.ac.uk/fe/tpl_essex01.asp?s=4A515F4E5A565B1Ajobid=84840,1258234865key=156435086c=51655614561223pagestamp=sevqpdcsinmurxbzje

Informal enquiries may be made to Dr Mike Hough 
maho...@essex.ac.ukmailto:maho...@essex.ac.uk or Dr Richard Strange 
stra...@essex.ac.ukmailto:stra...@essex.ac.uk

[ccp4bb] 3 PhD studentships available immediately

[Hough, Mike]

Dear CCP4bb,

The following three studentship positions are available immediately at the 
University of Liverpool. Could you please pass these details on to any students 
in your departments or elsewhere who may be interested? Replies to the email 
addresses listed below, rather than to me please.

Thanks,

Mike


School of Biological Sciences, University of Liverpool

4-year joint BBSRC PhD Studentships – applications invited immediately

Three PhD studentships are available in the Molecular Biophysics Group for 
research in the area of x-ray structural biology using the most advanced 
synchrotron radiation sources and the new light sources in the form of x-ray 
free electron lasers (XFELs). The studentships involve collaborations with 
scientists at the DIAMOND Light Source, UK and at the RIKEN Spring-8 Center, 
Japan. The successful candidates will have the exciting opportunity of spending 
up to 2 years at these premier science facilities working at the leading edge 
of structural biology. We are looking for applications now from highly 
committed and motivated graduates from any of the natural sciences who are 
ordinarily resident in the UK. Contact details and links to detailed project 
descriptions are given below: 

“Long wavelength X-ray diffraction experiments for structural studies from 
biological redox systems”
[Strange, UoL  Wagner, DIAMOND]
see: http://www.biophysics.liv.ac.uk/PhD_DLS.pdf
contact r.stra...@liv.ac.uk

“Metalloproteomics: Structure and function studies of metalloproteins of 
biomedical importance”
[Hasnain, UoL  Shiro, RIKEN]
see: http://www.biophysics.liv.ac.uk/PhD_RIKEN_Metalloprotein.pdf
contact: s.s.hasn...@liv.ac.uk

“New Science exploration from XFEL: A new paradigm for structural visualisation 
of macromolecules” 
[Grossmann, UoL  Ishikawa, RIKEN]
see: http://www.biophysics.liv.ac.uk/PhD_RIKEN_XFEL.pdf
contact: j.g.grossm...@liv.ac.uk