[ccp4bb] PhD position in time resolved crystallography

[Harmer, Nicholas]

Dear Colleagues,

I have a PhD position in time resolved crystallography open as part of the 
SWBio DTP programme. I'd appreciate this being passed on to any interested 
students.

This is a CASE collaborative studentship with Syngenta and Jim Spencer 
(Bristol). The project aims to develop a structural movie of the activity of 
herbicide targets so that we can generate better herbicides. It will be a great 
opportunity to learn some of the latest structural biology techniques and to 
experience working with industry.
Another advantage is that the stipend will have a £4,000pa supplement beyond 
the standard UK PhD stipend.

Full details of the project are at 
https://www.exeter.ac.uk/study/funding/award/?id=4940, which has a link to the 
application site, and I'm happy to answer any questions by email.

Kind regards,

Nic Harmer

Nicholas Harmer
Associate Professor in Biochemistry, Director of Business Engagement and 
Innovation
University of Exeter
Ext: 5179
www.exeter.ac.uk
Living Systems Institute, Stocker Road, Exeter, EX4 4QD
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[ccp4bb] Academic position openings in Exeter, UK

[Harmer, Nicholas]

Dear all,

The Living Systems Institute in Exeter, south-west England, is advertising 
eight new academic positions at all levels. The details are available at 
https://www.exeter.ac.uk/research/livingsystems/joinus/lsirecruitment2023/. 
Most of the positions can be in any topic relevant to the institute's mission 
to discover, understand and control the fundamental rules of life. We would be 
very interested in particular in an appointment in integrative structural 
biology. We have good resources for crystallography and cryo-EM, and are part 
of BAGs with regular access to Diamond, eBIC, and ESRF.

We're very happy to speak informally to anyone interested!

Kind regards,

Nic Harmer

Nicholas Harmer
Associate Professor in Biochemistry
University of Exeter
Ext: 5179
www.exeter.ac.uk
Living Systems Institute, Stocker Road, Exeter, EX4 4QD
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[ccp4bb] Postdoc and PDRA positions in enzyme cascades

[Harmer, Nicholas]

Dear all,

I have a 21 month postdoc position and a 3.5 year PhD position available in my 
lab at the Living Systems Institute in Exeter, UK. These would be suitable for 
someone looking for an exciting project building enzyme cascades to produce 
novel chemicals. The full adverts are linked to below. Unfortunately the PhD 
position only has funding for UK based applicants. Anyone interested in more 
information is very welcome to mail me. Please pass this on to anyone who might 
be interested!

Thanks,

Nic Harmer

Postdoc:  
https://jobs.exeter.ac.uk/hrpr_webrecruitment/wrd/run/ETREC107GF.open?VACANCY_ID=080252aNH2=3817591jNg=USA
PhD: A synthetic biology platform to develop novel tetrazoles, Biosciences - 
PhD (Funded) at University of Exeter on 
FindAPhD.com

Nicholas Harmer
Associate Professor in Biochemistry
Living Systems Institute, Stocker Road, Exeter, EX4 4QD




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Re: [ccp4bb] Unidentified electron density

[Harmer, Nicholas]

Dear Sayan,

It's a little hard to see from the images, but there seems to be continuous 
density to the aspartate indicating a covalent adduct. Perhaps it would be best 
to extract a crystal and run it through mass spec to get an exact mass on the 
adduct (and so its chemical formula)?
Others who have done this might comment on whether that is a good idea!
I dare say that we can speculate; but if it is important to the story of your 
paper, you will need additional evidence to support whatever you model into 
this density.

Kind regards,

Nic Harmer

Prof. Nicholas Harmer
Associate Professor in Structural Biochemistry
University of Exeter
Living Systems Institute
Stocker Road
Exeter EX4 4QD
UK


From: CCP4 bulletin board  On Behalf Of Sayan Saha
Sent: 30 June 2022 08:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified electron density

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

Dear All,

I am trying to refine a protein structure. I observed an additional electron 
density (Figures attached) connected to the aspartate residue.

Any suggestion in this regard would be appreciated.

With best regards,
Sayan Saha.



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Re: [ccp4bb] open review?

[Harmer, Nicholas]

Dear all,

I'd agree with Frank's sentiment. There is a strong risk that it would put 
reviewers in a conflicted position. You only have to look at say the world of 
literature to see that authors very rarely say anything that isn't positive 
about another author's work publicly. As a grant panellist I've already seen 
plenty of reviews that are little more than hagiographies of the great 
professor!

That doesn't mean that James's suggestion is a bad one; it just means that it 
would need a change in the whole ecosystem. Perhaps it is time that funding 
agencies considered hiring professional reviewers, rather than expecting 
academics to do it for free. Professional reviewers would likely gain from 
open, appropriately critical reviews as their reputation would depend on 
delivering reviews that are valid, selective, and high quality. This could 
offer an attractive alternative career for postdocs who have decided not to go 
for academic positions or academics looking for a part-time role as they move 
into retirement.
I would argue that one of the consequences of the pandemic is that academic 
workloads have changed from "unsustainably high" to "completely unsustainable". 
Academia is becoming increasingly non-inclusive as those with caring 
responsibilities, disabilities, and other issues that constrict their time 
cannot keep up with all the "extras" that are expected. Removing the burden of 
reviews from our backs would help bringing back balance.

I suspect that what is needed is proper trials of different approaches, with 
pre-defined criteria for success. Winston Churchill described democracy as "the 
worst form of government - except for all the others that have been tried." I'd 
feel that same about our current peer review system until we have clear 
evidence that there is something better!

Nic

From: CCP4 bulletin board  On Behalf Of Frank von Delft
Sent: 23 June 2022 07:09
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] open review?

I suspect funders will worry about it becoming even harder to find reviewers - 
they're already hard to flush out, if I'm not mistaken, and might become even 
more reclusive if they run the risk of being pilloried in public.

If that sounds theoretical:  even in this community, for all its collegiality 
and friendliness, we pillory one another in public and print just about our 
data.

Frank

On 23/06/2022 02:08, James Holton wrote:
Greetings all,

I'd like to ask a question that I expect might generate some spirited 
discussion.

We have seen recently a groundswell of support for openness and transparency in 
peer review. Not only are pre-prints popular, but we are also seeing reviewer 
comments getting published along with the papers themselves. Sometimes even 
signed by the reviewers, who would have traditionally remained anonymous.

My question is: why don't we also do this for grant proposals?

I know this is not the norm. However, after thinking about it, why wouldn't we 
want the process of how funding is awarded in science to be at least as 
transparent as the process of publishing the results? Not that the current 
process isn't transparent, but it could be more so. What if applications, and 
their reviewer comments, were made public? Perhaps after an embargo period?  
There could be great benefits here. New investigators especially, would have a 
much clearer picture of format, audience, context and convention. I expect 
unsuccessful applications might be even more valuable than successful ones. And 
yet, in reality, those old proposals and especially the comments almost never 
see the light of day. Monumental amounts of work goes into them, on both sides, 
but then get tucked away into the darkest corners of our hard drives.

So, 2nd question is: would you do it? Would you upload your application into 
the public domain for all to see? What about the reviewer comments? If not, why 
not?  Afraid people will steal your ideas? Well, once something is public, its 
pretty clear who got the idea first.

3rd question: what if the service were semi-private? and you got to get 
comments on your proposal before submitting it to your funding agency? Would 
that be helpful? What if in exchange for that service you had to review 2-3 
other applications?  Would that be worth it?

Or, perhaps, I'm being far too naiive about all this. For all I know there are 
some rules against doing this I'm not aware of.  Either way, I'm interested in 
what this community thinks. Please share your views!  On- or off-list is fine.

-James Holton
MAD Scientist



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[ccp4bb] Reminder - PhD position in structural biology - closing 6th December

[Harmer, Nicholas]

Dear Colleagues,

Just a reminder that I am advertising a PhD position in structural studies of 
microbial enzymes in my laboratory for autumn 2022 start. The project is 
partnering with Syngenta, focusing on potential herbicide targets. Students 
will benefit from the opportunity of a placement with Syngenta, and from 
Syngenta providing a £4,000 pa uplift to the student stipend. If you know a 
student who might be interested, please point them to the advert!

https://www.exeter.ac.uk/postgraduate/fees/award/?id=4288

Thanks,

Nic Harmer
Prof. Nicholas Harmer
Associate Professor in Biochemistry
University of Exeter
Ext: 5179
http://biosciences.exeter.ac.uk/staff/profile/index.php?web_id=nic_harmer
Living Systems Institute, Stocker Road, Exeter, EX4 4QD
Biocatalyic Cascade Reactions - Submit a paper into the Special Issue of 
Catalysts: 
https://www.mdpi.com/journal/catalysts/special_issues/biocata_cascade_reac

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[ccp4bb] 4-year PhD position in Exeter, UK, in partnership with Syngenta

[Harmer, Nicholas]

Dear all,

We have a fully funded 4-year PhD position available in my group in Exeter, UK. 
The position will be using structural and enzymology techniques to study 
thiamine diphosphate-dependent enzymes. The project is a collaborative project 
with Syngenta in the UK. The position is open to international applicants, and 
will benefit from an uplift in the stipend from Syngenta.

Details of the project and the application site are available at 
https://www.swbio.ac.uk/bioscience-for-sustainable-agriculture-and-food-2/.
 I am very happy to answer informal inquiries!

Thanks,

Nic Harmer
Prof. Nicholas Harmer
Associate Professor in Biochemistry
University of Exeter
Ext: 5179
www.exeter.ac.uk
Living Systems Institute, Stocker Road, Exeter, EX4 4QD
Biocatalyic Cascade Reactions - Submit a paper into the Special Issue of 
Catalysts: 
https://www.mdpi.com/journal/catalysts/special_issues/biocata_cascade_reac

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Re: [ccp4bb] Enzyme Vmax and Km

[Harmer, Nicholas]

Dear Prem,

I agree entirely with Tristan's conclusion that the processed substrate is also 
acting as an inhibitor at higher concentrations. You would need to run an 
experiment with a wider range of concentrations used (especially lower 
concentrations) to get a better feel for the range of the reaction. There is a 
well described substrate inhibition equation (see e.g. 
https://www.graphpad.com/guides/prism/latest/curve-fitting/reg_substrate_inhibition.htm)
 that you can try. I have a recent chapter on experiment design covering such 
cases 
(https://www.researchgate.net/publication/331806855_Reaction_Chemical_Kinetics_in_Biology)
 that I can share with you if you need.

I would strongly recommend to avoid the Lineweaver-Burk plot to calculate your 
Km and kcat. There are known issues with this (especially, as in your image, 
overweighting the lowest rate and usually least accurate point). Better is to 
fit directly to the equation with non-linear fitting, for example in R. This 
will also give you a better estimate of the error and confidence intervals.

Hope this helps,

Nic

From: CCP4 bulletin board  On Behalf Of Tristan Croll
Sent: 18 June 2021 08:19
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Enzyme Vmax and Km

Hi Prem,

The immediate problem here is that the curve for the processed substrate simply 
cannot be described by simple Michaelis-Menten kinetics. Assuming the assay has 
worked as expected, the declining rate with increasing substrate concentration 
suggests to me that this substrate also acts as an allosteric inhibitor, so 
assays at high [substrate] will make it *look* like the unprocessed substrate 
is preferred even though the processed one is cleaved faster by the uninhibited 
enzyme.

Hope this helps,
Tristan

On 18 Jun 2021, at 05:05, Prem Prakash 
mailto:prem...@gmail.com>> wrote:
Dear all,
Sorry for this off topic. I am working on an enzyme that has an exonuclease 
activity. The enzyme preferentially cleaves an unprocessed substrate at a 
faster rate than the processed one (known by qualitative analysis). Recently, I 
calculated the Vmax, Km and kcat of the enzyme for unprocessed substrate which 
are 18.2 pmol/min, 182 nM and 7.1 sec-1 respectively. However, the Processed 
substrate has apparently a lower range of Km (not calculated) as reflected from 
the curve (because the same increasing concentration range which is used for 
unprocessed, shows a steep decline in the initial velocity of the enzyme with 
processed substrate.
The latter suggests that Km is way lower than expected. In this case, the 
question is, if the Km of processed substrate is way lower than the 
Unprocessed, how can we see a faster rate with the former substrate than later. 
i.e lower Km and slower rate of cleavage. If it's possible please give some 
insights. I have attached the plot comparison between two kinetic assays.

With kind regards,

Prem





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[ccp4bb] PhD position in Structural Biology, University of Exeter/Dstl

[Harmer, Nicholas]

Dear all,

My group at the Living Systems Institute in Exeter is seeking to appoint a PhD 
position on a four year studentship. This is an industrial partnership award 
with Dstl (UK). Unfortunately because of the conditions of the funding we can 
only consider UK nationals.

The position will be using structural and biochemical methods to characterise 
potential drug targets from the biosecurity pathogen Coxiella burnetii. We will 
use X-ray crystallography and single particle cryo-EM as necessary to solve the 
scientific challenges. The student appointed will have the opportunity to work 
with Dstl and experts in complementary techniques at the Living Systems 
Institute.

The deadline for applications is 15th June, and I am very happy to answer any 
queries from interested students. Full details and the applications portal are 
available at https://www.swbio.ac.uk/case-studentships-2/.

Thanks,

Nicholas Harmer



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Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

[Harmer, Nicholas]

I'm afraid that the "Kent" variant is also mutating and is likely to pick up 
some of the more challenging mutations. There is already a version circulating 
with the E484 mutation that has a clear impact on the vaccine ("Bristol" 
variant), and another picked up in Scotland that has several changes similar to 
the SA variant.

The UK is sequencing a _lot_ and picking up a lot of changes. Probably the 
message is that if a virus new to humans circulates enough, it's going to 
mutate to find its optimal niche.

Nic

-Original Message-
From: CCP4 bulletin board  On Behalf Of Ethan A Merritt
Sent: 17 February 2021 20:57
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

It may be here already.

For a value of B that includes "no worse than the starting point", the 
so-called "UK variant" currently spreading in the US meets your criteria.  Some 
projections show it displacing other potentially more dangerous variants while 
not not degrading the impact of vaccination and other public health measures.

Are you starting a conspiracy theory that it was the result of a clandestine 
good samaritan molecular biologist?

Ethan

On Wednesday, 17 February 2021 12:39:21 PST Jacob Keller wrote:
> I was under the impression that A,B,C are not strongly or 
> intrinsically coupled, for one, since there are so many varieties of 
> viruses with so much range of infectiousness and clinical severity. False 
> impression?
> 
> B + C = vaccine
> 
> A + B + C = immunosysadmin pandemic updater virus. Patient 0 honors 
> given for each (yearly?) edition to curry political favor.
> 
> JPK
> 
> 
> On Wed, Feb 17, 2021 at 3:03 PM Tim Gruene  wrote:
> 
> > Hi Jacob,
> >
> > how do you think this should be possible? In order to infect others, 
> > the virus particle needs to proliferate (that's the only thing it 
> > does). It profilerates by hijacking the machinery of one cell of 
> > your body and turn it into a virus factory. Your body does not like 
> > this abuse and kills the cell, and also tries to kill the virus particles.
> > The virus does not make you sick, it only captures one cell. The 
> > reaction of your body to kick out the virus, and the cell that does 
> > not do it's job anymore, make you sick. A and B are mutually 
> > exclusive. B + C is named vaccine.
> >
> > Best,
> > Tim
> >
> >
> > On Wed, 17 Feb 2021 12:33:09 -0500 Jacob Keller 
> >  wrote:
> >
> > > It would seem to me that it should be possible to generate 
> > > versions of the Covid virus that would:
> > >
> > > A. be extremely contagious and yet B. be clinically benign, and C. 
> > > confer immunity to the original covid virus.
> > >
> > > If, then, this virus could be released, with appropriate "kill switch"
> > > safeguards built in, would this not solve the world's pandemic 
> > > problems? Is there any reason, practically, why this approach 
> > > would not be feasible?
> > >
> > > Maybe we don't really know enough to manipulate A, B, C yet?
> > >
> > > Or maybe it's too scary for primetime...nightmare bio-warfare 
> > > apocalypse?
> > >
> > > Has this sort of thing been done, or does it have a name?
> > >
> > > Jacob
> >
> >
> >
> > --
> > --
> > Tim Gruene
> > Head of the Centre for X-ray Structure Analysis Faculty of Chemistry 
> > University of Vienna
> >
> > Phone: +43-1-4277-70202
> >
> > GPG Key ID = A46BEE1A
> >
> 
> 
> 


--
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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[ccp4bb] PhD positions available

[Harmer, Nicholas]

Hi everyone,

I have three PhD opportunities available in my lab for students interested in 
structural biology. If you know anyone who might be interested please pass this 
message on to them!

The Living Systems Institute where I am based has funded positions available in 
our PhD programme 
(https://www.exeter.ac.uk/livingsystems/research/lsiphdprogramme/). These are 
open to anyone to apply. We have a thriving interdisciplinary structural 
biology team in the institute so as well as my group there are several other 
great teams as well.

Two positions in my lab are available through our local doctoral training 
programme. These are focused on structure-function of enzymes involved in 
polysaccharide biosynthesis from a human/animal pathogen. These will use a 
combination of X-ray crystallography, Cryo-EM, and (hopefully) MicroED as 
appropriate, and we hope to give a great interdisciplinary structural biology 
training. Unfortunately due to funder rules these are only open to UK residents.
http://www.exeter.ac.uk/studying/funding/award/?id=3974
http://www.exeter.ac.uk/studying/funding/award/?id=3991

Thanks!

Nicholas Harmer
Prof. Nicholas Harmer
Associate Professor in Biochemistry
University of Exeter
Ext: 5179
www.exeter.ac.uk
Living Systems Institute, Stocker Road, Exeter, EX4 4QD
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[ccp4bb] Postdoc and PhD positions available in Exeter UK

[Harmer, Nicholas]

Dear all,

We have a 6 month postdoc position (covering parental leave) and a PhD 
studentship available in my laboratory at the Living Systems Institute in 
Exeter to investigate the biosynthesis of the O-antigen of Coxiella burnetii. 
Both positions would suit people with an interest in enzyme structure-function 
relationships. The positions are part of a wider collaboration between research 
groups across the UK aiming to develop a vaccine against C. burnetii.

The postdoc position is advertised at: Click 
here'
 ; closing date 12th November

The PhD position is advertised at: 
https://www.findaphd.com/phds/project/structure-function-studies-of-coxiella-burnetii-o-antigen-biosynthesis-phd-in-biosciences-studentship-swbio-dtp/?p113957;
 closing date 2nd December

Questions about either position can be addressed to 
n.j.har...@exeter.ac.uk.

Kind regards,

Nic Harmer
Prof. Nicholas Harmer
Associate Professor in Biochemistry
University of Exeter
Ext: 5179
www.exeter.ac.uk
Living Systems Institute, Stocker Road, Exeter, EX4 4QD
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[ccp4bb] [off-topic] PhD position available

[Harmer, Nicholas]

Dear all,


A BBSRC funded PhD position is available in my laboratory in Exeter, focusing 
on enzymes for synthetic biology. The work is most likely going to be more 
enzymology than structural work, but please pass this on to any candidates who 
might be interested.


Full details are available at 
http://www.exeter.ac.uk/studying/funding/award/?id=2643


Kind regards,


Nic Harmer

University of Exeter

[ccp4bb] Structure-function PhD position (UK only)

[Harmer, Nicholas]

Dear all,

I have a PhD position in my laboratory, starting in September 2015. The 
position will be looking to elucidate the biosynthetic pathway for two unusual 
sugars from Coxiella, and will have good opportunities for interesting 
structural work. Unfortunately due to the funding it is only suitable for 
students in the UK. If anyone knows a good student who might be interested, the 
position is online at 
http://www.findaphd.com/search/ProjectDetails.aspx?PJID=60313LID=503, and I am 
very happy to take queries. Deadline is Friday 16th January.

Best regards,

Nicholas Harmer
University of Exeter

[ccp4bb] Postdoctoral position available

[Harmer, Nicholas]

A postdoctoral position is available to join the lab of Dr. Nicholas Harmer, at 
the University of Exeter, UK, from 1st October 2010. The position is funded by 
the BBSRC to work on the structure and function of three novel proteins 
involved in the biosynthesis of the capsular polysaccharide of Burkholderia 
pseudomallei, an emerging pathogen and bioterror threat. Diffraction quality 
crystals are already available for one of these proteins. The position will 
involve protein purification, biochemistry and crystallography.

A full advertisement, containing further details of the position and how to 
apply, is available at 
http://admin.exeter.ac.uk/personnel/jobs.php?action=jobareaid=4jid=4847. For 
informal inquiries about the position, please e-mail me  
(n.j.har...@exeter.ac.uk).

Thanks,

Nic Harmer

[ccp4bb] Summary: Phasing statistics

[Harmer, Nicholas]

Dear Colleagues,

I am very grateful to everyone who contributed to the discussion regarding 
phasing statistics that I initiated. I certainly found it very informative. 
Below is a summary of the technical responses that I regarding this problem.

1) Use some of the statistics that SHELXD and SHELXE do provide (e.g. CC/CCfree 
for SHELXD, CCfree and connectivity for SHELXE). These could be compared to 
statistics produced for well determined structures (e.g. see Debreczeni et al. 
2003 Acta Cryst. D., D59, 688-696).

2) Take the results from SHELX and put them into SHARP to generate the 
statistics.

3) Take the results from SHELX and put them into phaser_er, CRANK, or MLPHARE 
(perhaps with more difficulty) to generate the statistics.

Thanks to Rick Lewis, Boaz Shaanan, Ed Lowe and Eleanor Dodson for suggestions.

Cheers,

Nic Harmer

[For anyone interested, I took approaches 1 and 2. I got a good figures for 
phasing power from SHARP (somehow I failed to find the Rcullis, never mind), 
quoted the FOM at the end of SHELX, and the values for CC/CCfree from SHELXD, 
and the map contrast in the original and inverted hands from SHELXE. These all 
looked quite convincing, so hopefully my referees will be happy.]

[ccp4bb] Phasing statistics

[Harmer, Nicholas]

Dear CCP4ers,

I've been asked by a referee to provide the phasing statistics for a SAD 
dataset that I used to solve a recent structure. Whilst I have been able to 
find a figure-of-merit for the data after phasing, I can't work out how to get 
any other statistics (e.g. phasing power or an equivalent or Rcullis). Does 
anyone know a good route to obtaining useful statistics to put in the paper for 
SAD data?

The structure solution was carried out using SHELX C/D/E and then ARP/wARP.

Thanks in advance,

Nic Harmer

=
Dr. Nic Harmer
School of Biosciences
University of Exeter
tel: +44 1392 725179

[ccp4bb] PhD studentship at the University of Exeter

[Harmer, Nicholas]

Dear CCP4-ers,

A PhD studentship in biochemistry and structural biology is available at the 
University of Exeter. The focus for this project will be toxin-antitoxin 
modules in the human pathogen Burkholderia pseudomallei, and their role in 
rendering bacteria resistant to antibiotics. The start date for the position is 
October 2009.

Further details of the position are available at: 
http://biosciences.exeter.ac.uk/postgraduate/newposts.php#disease

Please send informal enquiries to Professor Rick Titball 
(r.w.titb...@exeter.ac.ukmailto:r.w.titb...@exeter.ac.uk) or myself.

Best regards,

Nic Harmer

=
Dr. Nic Harmer
School of Biosciences
University of Exeter
tel: +44 1392 269179