There are 11 messages totaling 3841 lines in this issue.
Topics of the day:
1. xdscc12 Expires (2)
2. 2 year BBSRC funded PDRA position at the University of Liverpool, UK
3. Vacancy: structural biologist with cryo-EM expertise at GSK closing date
24th March (2)
4. refinement / modeling of partly mobile domain
5. PDRA position available in Leeds
6. Cold Spring Harbor Asia conference on Membrane Proteins: Structure &
Function
7. Fwd: how to calculate a difference map between two heterodimers in
heterotetrameric protein (3)
------------------------------------------------------------ ----------
Date: Fri, 10 Mar 2017 08:27:54 +0000
From: Kay Diederichs <[log in to unmask]DE>
Subject: Re: xdscc12 Expires
Hi Carlos,
sorry - the problem should be fixed now.; pls download a fresh copy.
Since I didn't find bugs for quite some time, the new binaries have no expiration date.
best wishes,
Kay
On Thu, 9 Mar 2017 21:18:12 +0100, Carlos CONTRERAS-MARTEL <[log in to unmask]FR> wrote:
>Hi CCP4BB
>
>My XDSGUI is reporting :
>
>
>xdscc12 -cdef -nbin 3 -t 1 XDS_ASCII.HKL > XDSCC12.LP
>expired
>
>
>So, downloaded again from the XDSWiKi link, but :
>
>
>xdscc12/20170309> ./xdscc12.rhel6.64 -h
>xdscc12 KD 2017-01-12. Academic use only; no redistribution. Expires
>2016-12-31. -h option shows options.
>Please cite Assmann, G., Brehm, W., Diederichs, K. (2016) J.Appl.Cryst.
>49, 1021-1028
>usage: xdscc12 -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or
>2> -<abcdeftwz> FILE_NAME
>dmax (default 999A), dmin (default 1A) and nbin (default 10) have the
>usual meanings.
>mode can be 1 (equal volumes of resolution shells) or 2 (increasing
>volumes; default).
> -t: total oscillation (degree) to batch fine-sliced frames into
>other options can be combined (e.g. -def), and switch the following off:
> -a: individual isomorphous summary values
> -b: individual (Fisher-transformed) delta-CC1/2 values
> -c: individual delta-CC1/2 reflection numbers
> -d: individual anomalous summary values
> -e: individual (Fisher-transformed) delta-CC1/2ano values
> -f: individual delta-CC1/2ano reflection numbers
> -w: weighting of intensities with their sigmas
> -z: Fisher transformation of delta-CC1/2 values
>
>
>it seems to me also be a expired version ...
>
>Somebody know where I can find a newer-working version?
>
>
>All the best
>
>
>Carlos
>
>--
> Carlos CONTRERAS MARTEL, Ph.D.
> (CR1 CNRS)
>
> [log in to unmask]
>
> "Bacterial Pathogenesis Group"
> Institut de Biologie Structurale
> UMR5075 CEA-CNRS-UGA
>
> IBS
> Campus EPN
> 71, avenue des Martyrs
> CS 10090
> 38044 Grenoble CEDEX 9
> FRANCE
>
>
> tel : (+33) (0)4 57 42 86 41
>
>http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/ ?lang=fr
>http://www.ibs.fr/groups/bacterial-pathogenesis-group/? lang=en
------------------------------
Date: Fri, 10 Mar 2017 09:31:03 +0000
From: "Antonyuk, Svetlana" <[log in to unmask]>
Subject: 2 year BBSRC funded PDRA position at the University of Liverpool, UK
THE UNIVERSITY OF LIVERPOOL
FACULTY OF HEALTH AND LIFE SCIENCES
INSTITUTE OF INTEGRATIVE BIOLOGY
DEPARTMENT OF BIOCHEMISTRY
POSTDOCTORAL RESEARCH ASSOCIATE GRADE 7
£32,958 - £34,956 pa
An exciting opportunity has emerged in the Molecular Biophysics<http://www.biophysics.liv.ac.uk/ > group to work on a BBSRC-supported project on structure-function-mechanism studies of Cu-nitrite reductase and membrane bound nitric oxide (NO) reductase and the role of metabolon complex formation in controlling levels of cytotoxic NO. The project will link crystallographic studies with techniques to probe factors that control delivery of electrons and protons to the active site of these enzymes. You will be responsible for using established molecular biology procedures underpinning the overexpression and purification of a number of enzymes and their mutants including membrane proteins and undertake crystallographic, spectroscopic and mechanistic aspects of the programme. You will have the opportunity to spend up to 4 weeks in the RIKEN laboratories in Japan as part of a collaborative programme alongside two PhD students working on membrane-bound nitric oxide reductases. You should have a PhD in the area of physics, chemistry, biological sciences or biophysics, with experience in protein crystallography and practical knowledge of molecular biology preferably with experience in membrane proteins. Excellent verbal and written communication skills are essential. The post is available for 2 years and the ability to commence immediately would be advantageous.
Job Ref: 006744 Closing Date: 11 April 2017
For full details and to apply online, please visit: https://recruit.liverpool.ac.uk
------------------------------
Date: Fri, 10 Mar 2017 10:34:01 +0100
From: Carlos CONTRERAS-MARTEL <[log in to unmask]FR>
Subject: Re: xdscc12 Expires
Hi Kay
Thank you very much ... xdscc12 is working now perfectly ... so xdsgui
Best
Carlos
On 03/10/17 09:27, Kay Diederichs wrote:
> Hi Carlos,
>
> sorry - the problem should be fixed now.; pls download a fresh copy.
> Since I didn't find bugs for quite some time, the new binaries have no expiration date.
>
> best wishes,
>
> Kay
>
> On Thu, 9 Mar 2017 21:18:12 +0100, Carlos CONTRERAS-MARTEL <[log in to unmask]FR> wrote:
>
>> Hi CCP4BB
>>
>> My XDSGUI is reporting :
>>
>>
>> xdscc12 -cdef -nbin 3 -t 1 XDS_ASCII.HKL > XDSCC12.LP
>> expired
>>
>>
>> So, downloaded again from the XDSWiKi link, but :
>>
>>
>> xdscc12/20170309> ./xdscc12.rhel6.64 -h
>> xdscc12 KD 2017-01-12. Academic use only; no redistribution. Expires
>> 2016-12-31. -h option shows options.
>> Please cite Assmann, G., Brehm, W., Diederichs, K. (2016) J.Appl.Cryst.
>> 49, 1021-1028
>> usage: xdscc12 -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or
>> 2> -<abcdeftwz> FILE_NAME
>> dmax (default 999A), dmin (default 1A) and nbin (default 10) have the
>> usual meanings.
>> mode can be 1 (equal volumes of resolution shells) or 2 (increasing
>> volumes; default).
>> -t: total oscillation (degree) to batch fine-sliced frames into
>> other options can be combined (e.g. -def), and switch the following off:
>> -a: individual isomorphous summary values
>> -b: individual (Fisher-transformed) delta-CC1/2 values
>> -c: individual delta-CC1/2 reflection numbers
>> -d: individual anomalous summary values
>> -e: individual (Fisher-transformed) delta-CC1/2ano values
>> -f: individual delta-CC1/2ano reflection numbers
>> -w: weighting of intensities with their sigmas
>> -z: Fisher transformation of delta-CC1/2 values
>>
>>
>> it seems to me also be a expired version ...
>>
>> Somebody know where I can find a newer-working version?
>>
>>
>> All the best
>>
>>
>> Carlos
>>
>> --
>> Carlos CONTRERAS MARTEL, Ph.D.
>> (CR1 CNRS)
>>
>> [log in to unmask]
>>
>> "Bacterial Pathogenesis Group"
>> Institut de Biologie Structurale
>> UMR5075 CEA-CNRS-UGA
>>
>> IBS
>> Campus EPN
>> 71, avenue des Martyrs
>> CS 10090
>> 38044 Grenoble CEDEX 9
>> FRANCE
>>
>>
>> tel : (+33) (0)4 57 42 86 41
>>
>> http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/ ?lang=fr
>> http://www.ibs.fr/groups/bacterial-pathogenesis-group/? lang=en
--
Carlos CONTRERAS MARTEL, Ph.D.
(CR1 CNRS)
[log in to unmask]
"Bacterial Pathogenesis Group"
Institut de Biologie Structurale
UMR5075 CEA-CNRS-UGA
IBS
Campus EPN
71, avenue des Martyrs
CS 10090
38044 Grenoble CEDEX 9
FRANCE
tel : (+33) (0)4 57 42 86 41
http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/ ?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/? lang=en
------------------------------
Date: Fri, 10 Mar 2017 20:53:12 +0900
From: Anindito Sen <[log in to unmask]>
Subject: Re: Vacancy: structural biologist with cryo-EM expertise at GSK closing date 24th March
Hello Dr. Chung,
It was nice talking to you. I have submitted the application online. However I have not received any email conformation. In any case, I am attaching the screenshot of my submission below.
Kindly acknowledge when you receive my application.
Best Regards
Andy
Anindito Sen. Ph.D
Scientist and Application Specialist in Biological Sciences
JEOL LTD.
13F, Ohtemachi Nomura Bldg.
2-1-1 Ohtemachi, Chiyoda-ku, Tokyo
100-0004
Tel: +81-3-62623563
Fax: +81-3-6262-3577
www.jeol.com
> On Mar 6, 2017, at 7:03 PM, Chun-wa Chung <[log in to unmask]> wrote:
>
> Job-posting - Seeking structural biologist with cryo-EM expertise at GSK
>
> A vacancy for a structural biologist with cryo-EM expertise has opened up within the UK structural and biophysical sciences group at GlaxoSmithKline R&D. Joining an experienced multi-disciplinary group, this is an exciting opportunity for a motivated individual to complement and help shape our current capabilities in the EM area.
> This is a permanent, full-time position suitable for a PhD degree holder (or equivalent).
>
> To apply for this role and for further details, please click on the link below (Vacancy no : WD106591) https://careers.peopleclick.com/careerscp/client_gsk/ <https://careers.peopleclick.external1931/gateway.do? functionName=viewFromLink& jobPostId=330903&localeCode= en-us com/careerscp/client_gsk/ >external1931/gateway.do? functionName=viewFromLink& jobPostId=330903&localeCode= en-us
> A full job description is also included at the end of this message.
>
> Applications for this vacancy are to be made online by 24th MARCH
> Informal inquiries can be sent to [log in to unmask] <mailto:[log in to unmask]com>
> Thank you for your interest,
>
> Chun-wa Chung
>
> UK Head Structural & Biophysics Sciences
> GlaxoSmithKline R&D
> Stevenage
> SG1 2NY
> Tel no: +44 1438 763342
> email : [log in to unmask] <mailto:[log in to unmask]com>
>
>
>
> Full Job Description (WD78277):
> GlaxoSmithKline is a world leading research-based pharmaceutical company. We are focused around three core businesses: Pharmaceuticals, Vaccines and GSK Consumer Healthcare. We have a significant global presence with commercial operations in more than 150 countries, a network of 84 manufacturing sites in 36 countries and large R&D centres in the UK, US, Belgium and China.
> The UK Structural and Biophysical Sciences group is a multi-disciplinary department within GSK R&D that provides molecular insights into drug discovery for both small molecule and biopharmaceutical programs.
>
> We currently have an exciting opportunity for a laboratory-based scientist with expertise in state-of-the-art electron microscopy techniques to play an influential and key role in the application and development of these methods across small molecule and therapeutic protein programs. This individual will have extensive experience in the sample preparation and optimisation processes necessary to produce high-quality molecular images of protein structure, including direct experience of Cryo-EM methodologies. Experience of data analysis and interpretation is also expected. Being responsible for delivering structural insights to support program teams and contributing to the wider protein structural and biophysical area by identifying and driving forward improvements and innovations that advance drug discovery projects, the individual must be a collaborative team player able to work successfully with other scientists within the department and within diverse teams.
>
> Key Responsibilities and Accountabilities:
> • Design and perform technical experiments in the EM area (sample preparation, optimisation and analysis).
> • Document and communicate scientific results clearly and promptly.
> • Provide strong scientific lead to shape EM strategy within structural biology and across therapeutic discovery programs.
> • Build EM capabilities and infrastructure through interactions with the internal and external scientific community.
> • Maintain scientific excellence and lead in a rapidly evolving area e.g. through interactions such as the FEI/LMB/Pharm consortium.
> • Become an integral team member of multiple project teams.
>
> Key Capabilities and Proficiency:
> 1. Technical expertise leading to Impact
> Evidence of specific and in depth knowledge of transmission electron microscopy used as a structural technique, especially single particle cryo-EM. A track record of its application to address scientific problems relevant to pharmaceutical research.
> 2. Influence and Scientific awareness
> Evidence of engagement with external scientific environment including the ability to identify and pursue opportunities that advance capabilities within own research area.
> 3. Team work
> Demonstrable ability to both directly and indirectly influence and impact the progression of programs of research and to work in multi-disciplinary teams, displaying appropriate interpersonal skills and team work
>
>
>
>
>
> This e-mail was sent by GlaxoSmithKline Services Unlimited
> (registered in England and Wales No. 1047315), which is a
> member of the GlaxoSmithKline group of companies. The
> registered address of GlaxoSmithKline Services Unlimited
> is 980 Great West Road, Brentford, Middlesex TW8 9GS.
> GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.
------------------------------
Date: Fri, 10 Mar 2017 21:21:09 +0900
From: Anindito Sen <[log in to unmask]>
Subject: Re: Vacancy: structural biologist with cryo-EM expertise at GSK closing date 24th March
Apologies to you All.
The email got copied to every one. In any case its a junk for rest of you. Kindly delete it, if you can.
Best Regards
Andy
Anindito Sen. Ph.D
> On Mar 10, 2017, at 9:17 PM, Vellieux Frédéric <[log in to unmask]> wrote:
>
> Hello,
>
> I am not “Dr Chung” and I haven’t received anything from you. Sorry to disappoint you.
>
> Perhaps a “reply all” isn’t appropriate when replying to a ccp4bb message ? I let you be the judge on that…
>
> Fred.
>
> From: CCP4 bulletin board [mailto:[log in to unmask] <mailto:[log in to unmask]>] On Behalf Of Anindito Sen
> Sent: Friday, March 10, 2017 12:53 PM
> To: [log in to unmask] <mailto:[log in to unmask]>
> Subject: Re: [ccp4bb] Vacancy: structural biologist with cryo-EM expertise at GSK closing date 24th March
>
> Hello Dr. Chung,
>
> It was nice talking to you. I have submitted the application online. However I have not received any email conformation. In any case, I am attaching the screenshot of my submission below.
>
> Kindly acknowledge when you receive my application.
>
> Best Regards
>
> Andy
>
>
>
>
> <image001.png>
>
> Anindito Sen. Ph.D
> Scientist and Application Specialist in Biological Sciences
> JEOL LTD.
> 13F, Ohtemachi Nomura Bldg.
> 2-1-1 Ohtemachi, Chiyoda-ku, Tokyo
> 100-0004
> Tel: +81-3-62623563
> Fax: +81-3-6262-3577
>
> www.jeol.com <http://www.jeol.com/>
>
> On Mar 6, 2017, at 7:03 PM, Chun-wa Chung <[log in to unmask] <mailto:[log in to unmask]COM>> wrote:
>
> Job-posting - Seeking structural biologist with cryo-EM expertise at GSK
>
> A vacancy for a structural biologist with cryo-EM expertise has opened up within the UK structural and biophysical sciences group at GlaxoSmithKline R&D. Joining an experienced multi-disciplinary group, this is an exciting opportunity for a motivated individual to complement and help shape our current capabilities in the EM area.
> This is a permanent, full-time position suitable for a PhD degree holder (or equivalent).
>
> To apply for this role and for further details, please click on the link below (Vacancy no : WD106591) https://careers.peopleclick.com/careerscp/client_gsk/ <https://careers.peopleclick.external1931/gateway.do? functionName=viewFromLink& jobPostId=330903&localeCode= en-us com/careerscp/client_gsk/ >external1931/gateway.do? functionName=viewFromLink& jobPostId=330903&localeCode= en-us
> A full job description is also included at the end of this message.
>
> Applications for this vacancy are to be made online by 24th MARCH
> Informal inquiries can be sent to [log in to unmask] <mailto:[log in to unmask]com>
> Thank you for your interest,
>
> Chun-wa Chung
>
> UK Head Structural & Biophysics Sciences
> GlaxoSmithKline R&D
> Stevenage
> SG1 2NY
> Tel no: +44 1438 763342
> email : [log in to unmask] <mailto:[log in to unmask]com>
>
>
>
> Full Job Description (WD78277):
> GlaxoSmithKline is a world leading research-based pharmaceutical company. We are focused around three core businesses: Pharmaceuticals, Vaccines and GSK Consumer Healthcare. We have a significant global presence with commercial operations in more than 150 countries, a network of 84 manufacturing sites in 36 countries and large R&D centres in the UK, US, Belgium and China.
> The UK Structural and Biophysical Sciences group is a multi-disciplinary department within GSK R&D that provides molecular insights into drug discovery for both small molecule and biopharmaceutical programs.
>
> We currently have an exciting opportunity for a laboratory-based scientist with expertise in state-of-the-art electron microscopy techniques to play an influential and key role in the application and development of these methods across small molecule and therapeutic protein programs. This individual will have extensive experience in the sample preparation and optimisation processes necessary to produce high-quality molecular images of protein structure, including direct experience of Cryo-EM methodologies. Experience of data analysis and interpretation is also expected. Being responsible for delivering structural insights to support program teams and contributing to the wider protein structural and biophysical area by identifying and driving forward improvements and innovations that advance drug discovery projects, the individual must be a collaborative team player able to work successfully with other scientists within the department and within diverse teams.
>
> Key Responsibilities and Accountabilities:
> • Design and perform technical experiments in the EM area (sample preparation, optimisation and analysis).
> • Document and communicate scientific results clearly and promptly.
> • Provide strong scientific lead to shape EM strategy within structural biology and across therapeutic discovery programs.
> • Build EM capabilities and infrastructure through interactions with the internal and external scientific community.
> • Maintain scientific excellence and lead in a rapidly evolving area e.g. through interactions such as the FEI/LMB/Pharm consortium.
> • Become an integral team member of multiple project teams.
>
> Key Capabilities and Proficiency:
> 1. Technical expertise leading to Impact
> Evidence of specific and in depth knowledge of transmission electron microscopy used as a structural technique, especially single particle cryo-EM. A track record of its application to address scientific problems relevant to pharmaceutical research.
> 2. Influence and Scientific awareness
> Evidence of engagement with external scientific environment including the ability to identify and pursue opportunities that advance capabilities within own research area.
> 3. Team work
> Demonstrable ability to both directly and indirectly influence and impact the progression of programs of research and to work in multi-disciplinary teams, displaying appropriate interpersonal skills and team work
>
>
>
>
>
> This e-mail was sent by GlaxoSmithKline Services Unlimited
> (registered in England and Wales No. 1047315), which is a
> member of the GlaxoSmithKline group of companies. The
> registered address of GlaxoSmithKline Services Unlimited
> is 980 Great West Road, Brentford, Middlesex TW8 9GS.
>
> GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.
>
> -----
> Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato E-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i.
>
> Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology CAS. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract; nor does it create any pre-contractual liability on the part of Institute of Biotechnology CAS
>
------------------------------
Date: Fri, 10 Mar 2017 12:42:45 +0000
From: "Kajander, Tommi A" <[log in to unmask]>
Subject: refinement / modeling of partly mobile domain
Any hints on what might work for modeliing a domain that seems to be there visible in part and parly not?
(half ofan Ig-domain) - presumably the other end of the domain has larger ensemble of coordinate
postions (attached from one end to other part of the same molecule and neighbors in the crystal - and not at the other end,
causing maybe kind of swinging of it/positional disorder) - any good ideas how to model this welcome...
including the _whole domain model_ seems to drop R-factors but cant see much additional density - maybe we just model the
missing part then for this structure if nothing else..
Thanks,
Tommi
------------------------------
Date: Fri, 10 Mar 2017 13:45:53 +0000
From: Glyn Hemsworth <[log in to unmask]>
Subject: PDRA position available in Leeds
Dear All,
Can I please bring the PDRA opportunity that is available here in Leeds once more to your attention as the deadline for applications - 21st March 2017 is approaching.
Funded by the BBSRC the position is available for an initial 2 year period, with the possibility of extending to 4 years. The position will suit someone interested in redox proteins, structural biology and biotechnology.
The full candidate brief can be downloaded from the following web address:
https://jobs.leeds.ac.uk/FBSMB1100
To apply for the position please register for an account on the Leeds website and submit a covering letter, together with a CV including details of at least two references.
Please feel free to get in touch with informal enquiries about the role. Thanks and best wishes,
Glyn
–––––––––––––––––––––––––––––––––
Glyn Hemsworth
Astbury Building, Room 10.107
Faculty of Biological Sciences,
University of Leeds, Leeds, LS2 9JT, UK
Tel: (+44) 0113 3434 349
Email: [log in to unmask]<mailto:[log in to unmask] uk>
Research Fellow
Are you an ambitious researcher looking for your next challenge? Do you have an established background in Structural Biology, Biochemistry or Chemistry? Do you want to further your career in one of the UKs leading research intensive Universities?
You will investigate the structure and function of a range of proteins, and their complexes, as potential activators of a class of enzymes known as lytic polysaccharide monooxygenases (LPMOs), (find out more in this recent review<http://www.cell.com/trends/biotechnology/abstract/ >). LPMOs have emerged as key enzymes in biomass conversion, both in nature and in the applied setting of a biorefinery. Using a combination of structural, biophysical, and biochemical methods we are seeking to characterise the molecular mechanisms used in nature to shuttle electrons to LPMOs. The knowledge gained from this research is of considerable interest from both a fundamental and applied standpoint and will ultimately be used in protein engineering approaches to produce more efficient enzyme systems to be used in the biorefinery.S0167-7799(15)00192-4?_ returnURL=http%3A%2F% 2Flinkinghub.elsevier.com% 2Fretrieve%2Fpii% 2FS0167779915001924%3Fshowall% 3Dtrue
Funded by the BBSRC, you will be based in the newly established laboratory of Dr Glyn Hemsworth in the Faculty of Biological Sciences and the Astbury Centre for Structural Molecular Biology. With the recent £17 million investment in the Astbury Biostructure lab to complement the already superb infrastructure for structural molecular biology, Leeds represents the perfect environment for you to learn new techniques whilst contributing vital knowledge towards realising the development of lignocellulosing biofuels as a more sustainable energy source for the future.
You should have, or be close to completing a PhD in Structural Biology, Biochemistry, Chemistry or a related discipline, where practical experience of cryo-electron microscopy or X-ray crystallography is essential. You will be expected to show enthusiasm for engaging in inter-disciplinary research and expanding your knowledge and expertise into new areas. Experience of studying protein-protein interactions would also be an advantage.
To explore the post further or for any queries you may have, please contact:
Glyn Hemsworth
Tel: 0113 343 4349, email: [log in to unmask]<mailto:[log in to unmask] uk>
Location: Leeds - Main Campus
Faculty/Service: Faculty of Biological Sciences
School/Institute: School of Molecular & Cellular Biology
Category: Research
Grade: Grade 7
Salary: £32,004 to £38,183 p.a.
Contract Type: Fixed Term (Fixed term for 2 years due to funding - optional 4 years)
Closing Date: Tuesday 21 March 2017
Reference: FBSMB1100
------------------------------
Date: Fri, 10 Mar 2017 14:00:45 +0000
From: Martin Caffrey <[log in to unmask]>
Subject: Cold Spring Harbor Asia conference on Membrane Proteins: Structure & Function
*Membrane Proteins: Structure & Function*
Suzhou, China. May 15-19, 2017
Organized by:
*Martin Caffrey,* Trinity College Dublin, Ireland
*Nancy Carrasco,* Yale University, USA
*Tian-Le Xu,* Shanghai Jiao Tong University, China
*Ming Zhou,* Baylor College of Medicine, USA
We are pleased to announce the *Cold Spring Harbor Asia conference on*
*Membrane
Proteins: Structure & Function* which will be held in Suzhou, China,
located approximately 60 miles west of Shanghai. The conference will begin
at *7:00 pm on the evening of Monday May 15, and will conclude after lunch
on May 19, 2017.*
The conference will include up to eight oral sessions and four poster
sessions covering the latest findings across a range membrane protein
related topics. Many talks will be selected from submitted abstracts on the
basis of scientific merit and relevance. Social events throughout the
conference provide ample opportunity for informal interactions.
*Major Topics*
*1. Channels*
*2. Cryo-EM 3. Dynamics*
*4. Emerging techniques*
*5. Enzymes*
*6. Functional characterization*
* 7. Transmembrane signalling*
*8. Transporters*
*Speakers*
*Martin Caffrey,* Trinity College Dublin, IRELAND
*Nancy Carrasco,* Yale Unviersity, USA
*Yifan Cheng,* University of California San Francisco, USA
*James Chou,* Harvard Medical School/National Center for Protein Science,
USA/CHINA
*Henry Colecraft,* Coumbia University, USA
*Raimund Dutzler,* University of Zurich, SWITZERLAND
*Karen Fleming,* Johns Hopkins University, USA
*Xin Huang,* Amgen Inc., USA
*Andy Kruse,* Harvard Medical School, USA
*Edmund Kunji,* Medical Research Council, UNITED KINGDOM
*Zhenfeng Liu,* Institute of Biophysics, CAS, CHINA
*Zhi-Jie Liu,* ShanghaiTech University, CHINA
*Kaspar Locher,* ETH Zurich, SWITZERLAND
*Aashish Manglik,* Stanford University School of Medicine, USA
*Yasushi Okamura,* Osaka University, JAPAN
*Eduardo Perozo,* The University of Chicago, USA
*Scott Prosser,* University of Toronto Mississauga, CANADA
*Daniel Rosenbaum,* UT Southwestern Medical Center, USA
*Irina Serysheva,* UTHealth Medical School, USA
*Yigong Shi,* Tsinghua University, CHINA
*Roger Sunahara,* University of California, San Diego, USA
*Chris Tate,* MRC Laboratory of Molecular Biology, UNITED KINGDOM
*Kutti Vinothkumar,* MRC Laboratory of Molecular Biology, UNITED KINGDOM
*Tian-Le Xu,* Shanghai Jiao Tong University, CHINA
*Bailong Xiao,* Tsinghua University, CHINA
*Nieng Yan,* Tsinghua University, CHINA
*Jian Yang,* Kunming Institute of Zoology, CHINA
*Maojun Yang,* Tsinghua Univeristy, CHINA
*Ming Zhou,* Baylor College of Medicine, USA
We encourage abstracts to contain new and unpublished materials. Abstracts
must be submitted electronically by the abstract deadline. Selection of
material for oral and poster presentation will be made by the organizers.
Status (talk/poster) of abstracts will be posted on this web site as soon
as decisions have been made by the organizers.
*Fellowships *
We are eager to have as many young people as possible attend since they are
likely to benefit most from this meeting. A certain number of presentations
by graduate students and postdocs attending the conference will be selected
for fellowship (US $100-$500) awards. For more details, please visit
http://www.csh-asia.org/stipends.html
We look forward to seeing you at Suzhou in May, 2017.
Early Registration: 17 April 2017
Website: https://www.csh-asia.org/2017meetings/membrane.html
--
Martin Caffrey [log in to unmask]
Schools of Medicine and Biochemistry & Immunology
Trinity Biomedical Sciences Institute, Trinity College Dublin
Room 5.62,152-160 Pearse St., Dublin 2, D02 R590, Ireland
http://www.tcd.ie/Biochemistry/research/m_ caffrey.php
phone: +353-(0)1-896-4253; mobile: +353-(0)86-818-7704
------------------------------
Date: Fri, 10 Mar 2017 14:24:30 -0800
From: Oleg Zadvornyy <[log in to unmask]>
Subject: Fwd: how to calculate a difference map between two heterodimers in heterotetrameric protein
Dear All,
We are working on a tetrameric protein containing 2 heterodimers which are
related to each other by 2 fold symmetry. There are difference at the
active site between the two heterodimers in the crystals, and we would like
to make a difference map to compare one heterodimer to the other. I would
really appreciate your advise and suggestions how to perform this
comparison.
Thank you,
Oleg
--
Oleg A. Zadvornyy, PhD
Institute of Biological Chemistry,
Washington State University
237 Clark Hall
Pullman, WA 99163
Tel: (509)-335-9837
Lab: (509)-335-1958
------------------------------
Date: Fri, 10 Mar 2017 22:48:34 +0000
From: Eleanor Dodson <[log in to unmask]>
Subject: Re: Fwd: how to calculate a difference map between two heterodimers in heterotetrameric protein
This would be pretty difficult, but you know in COOT you can overlap the
maps for related chains / hetero dimers/ etc. ( Ask for NCS difference maps
in the DRAW menu ] The matrix which converts one set of coordinates to the
other is then applied to the electron density so you see the NCS relatd
maps together . I usually use the facility to get an averaged map of all
copies of a molecule to sped up rebuilding - fix a model with respect to
the average and do a fraction of the work - but you could also use it to
study the differences between the two active sites.
In fact it may be possible to use this to get a true difference map, but it
is complicated and I cannot remember how to do it off the top of my head -
you have to output the NCS generated maps then mask the maps then use these
maps to generate structure factors, then set up a diff map calculation..
Simpler to just inspect the differences by eye!
Eleanor
On 10 March 2017 at 22:24, Oleg Zadvornyy <[log in to unmask]>
wrote:
> Dear All,
>
>
> We are working on a tetrameric protein containing 2 heterodimers which are
> related to each other by 2 fold symmetry. There are difference at the
> active site between the two heterodimers in the crystals, and we would like
> to make a difference map to compare one heterodimer to the other. I would
> really appreciate your advise and suggestions how to perform this
> comparison.
> Thank you,
> Oleg
>
> --
> Oleg A. Zadvornyy, PhD
>
> Institute of Biological Chemistry,
> Washington State University
>
> 237 Clark Hall
> Pullman, WA 99163
>
> Tel: (509)-335-9837 <(509)%20335-9837>
> Lab: (509)-335-1958 <(509)%20335-1958>
>
------------------------------
Date: Fri, 10 Mar 2017 18:24:51 -0500
From: Phil Jeffrey <[log in to unmask]>
Subject: Re: Fwd: how to calculate a difference map between two heterodimers in heterotetrameric protein
Tricky - perhaps this could be viewed as "anti-averaging" methodologically.
Use USF programs MAMA, IMP to generate a mask and optimize the NCS
operator (or skip this step if you feel you know yours accurately)
Use CCP4's MAPROT to rotate the map of one monomer onto the other
Conceivably use USF program COMDEM to create the "difference map"
assuming it will tolerate a weighting of -1. Or perhaps MAPROT will
take a negative scale. Or MAPMASK, or.... there's a range of map
manipulation programs that can scale an input map, but I've never tried
to invert one. Unless you actually wanted Fourier coefficients it
shouldn't be impossible to create a masked volume of the difference
between two maps after rotating one of them.
Phil Jeffrey
Princeton
On 3/10/17 5:24 PM, Oleg Zadvornyy wrote:
> Dear All,
>
>
> We are working on a tetrameric protein containing 2 heterodimers which
> are related to each other by 2 fold symmetry. There are difference at
> the active site between the two heterodimers in the crystals, and we
> would like to make a difference map to compare one heterodimer to the
> other. I would really appreciate your advise and suggestions how to
> perform this comparison.
> Thank you,
> Oleg
>
> --
> Oleg A. Zadvornyy, PhD
>
> Institute of Biological Chemistry,
> Washington State University
>
> 237 Clark Hall
> Pullman, WA 99163
>
> Tel: (509)-335-9837
> Lab: (509)-335-1958
------------------------------