Protein structure solved by computer gamers (and phaser)!

From: Kevin Cowtan
Date: 19 September 2011 11:33

"Crystal structure of a monomeric retroviral protease solved by protein folding game players"

The paper (Nature SB):
http://www.cs.washington.edu/homes/zoran/NSMBfoldit-2011.pdf

The game:
http://fold.it/portal/

----------
From: Dirk Kostrewa
Great! Maybe, they should add an extra term for correlation of Fcalc to Fobs (or LLG or R) to their game. I wonder, if structures could be solved ab inition by players, then :-).

Best regards,

Dirk.

Am 19.09.11 12:33, schrieb Kevin Cowtan:

--

*******************************************************
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
*******************************************************

----------
From: Nat Echols

Actually, Kam Zhang's group did something exactly like that by calling Phaser from Rosetta:

http://www.ncbi.nlm.nih.gov/pubmed/21904033

-Nat

----------
From: H. Raaijmakers
That's progress! A century ago we'd need an infinite amount of monkeys
typing on an infinite amount of typewriters to produce a single paper. Now
we need just a finite amount of gamers to produce 70000+ models to get one
that looks quite like a folded protein. And it saved an heavy atom soak as
well.

cheers,

Hans

ref. Émile Borel (1913). "Mécanique Statistique et Irréversibilité". J.
Phys. 5e série 3: 189–196.




Kevin Cowtan schreef:

LIBCHECK download

From: Mecy Shi
Date: 19 September 2011 03:35



Dear members.

I want to download a LIBCHECK for Mac, but I couldn't find it in the internet! Does anybody know where to download it?

Thank you very much!



Mecy Shi
Institute of Biochemistry and Cell Biology,
Shanghai Institutes for Biological Sciences,
Chinese Academy of Sciences,
320 Yue-yang Road, Shanghai 200031, China.

density modification help

From: James Garnett
Date: 16 September 2011 18:27


Dear BB,

I hope you can help. I have been trying to density modify my potential SAD solutions but I think it would help if I could conceptualize the arrangement of molecules in my crystals and it is making my head hurt.

I have 2 crystal forms. I  only obtained a single crystal for the first form which I have never been able to reproduce. It processes well to ~3A in P6122/P6522 (a=52.3, b=52.3, c=216.9; 1 mol/AU) and C2221 (a=52.3, b=90.5, c=216.9; 3 mol/AU), systematic absences are convincing and there does not look like any twinning issues. MR has not worked but the closest model has less than 20% similarity. A self rotation function shows strong peaks along x, y and z (k=180) and weaker ones along z (k=60 and 120).

In a slightly altered condition I can obtain reproducible crystals although the space group has now changed. I have collected native and iodide-SAD data to ~3.2A on these crystals which now index in P222. Systematic absences suggest they are P212121 (a=52.61, b=88.261, c=212.072 in the SAD data), however, they contain pseudotranslational NCS (0.5,0.5,0.03) which is ~40% of the origin, so it may be another choice of P222. The self rotation function is similar to the previous data. As these cell dimensions and that of the C2221 data are almost identical it looks like there has been a slight shift in the lattice arrangement causing the pseudotranslational symmetry (therefore 6 mols/AU). The native and SAD data are isomorphous within 1% but I get much better statistics from phasing with SAD alone. The anomalous signal is reasonable to 4.5-5A but I do get some potential solutions using PHENIX (FOMs ~0.5, BAYES-CC ~40, scew 10-20). Whilst I can see solvent/protein boundaries, at this resolution it is hard to tell what is going on and I am finding it hard to trace any sheets (it is an Ig-like fold) and I think some NCS averaging may do a world of good.

The problem is how do I apply this with  improper NCS - i.e. how is the 6-fold NCS from the self rotation related to the translational NCS. Also am I missing something which is blatantly obvious which can help me improve these maps and hopefully push the resolution out to its full potential. I might be asking for a lot with this data but if you can help it would be much appreciated - and if I have left out any details please ask away.

Many thanks

James

Dr James Garnett
Division of Molecular Biosciences,
Imperial College London
Level 5, Biochemistry Building,
South Kensington,
LONDON,
SW7 2AZ,
UK.



----------
From: Eleanor Dodson


First the C2221 cell is a version of the hexagonal with the 2-fold axes now aligned along the a=b 2-fold in the hexagonal.
But I dont think you can define NCS properly without some knowledge of coordinates.

If you have enough anomalous scatterers that might allow you to get a start.

Does trhe self rotation for the P222 form suggest a 3-fold or 6-fold axis along c?

Eleanor

Insoluble ligand?

From: Chaudhary, Ritcha
Date: 16 September 2011 17:04
Hi All

I have a ligand that is dissolved in 100% DMSO. The ligand crashes out even when diluted to 20% final DMSO concentration in the protein buffer. I have heard of people using detergents such as n octyl Beta D glucoside to keep the ligand solubilized at lower DMSO concentrations. Can someone give me pointers in this direction? Any suggestions, references etc.....

Thanks much
Ritcha
----------
From: Smita Mohanty
Hi Ritcha,

Did you try Methanol or Ethanol to see if your ligand dissolve in these
solvents? You should try these solvents first before adding any
detergents.

Good luck.

Smita Mohanty

----------
From: Roger Rowlett

Keep in mind it may also be possible to soak in ligand from the solid if the binding constant is tight enough. Le Chatelier's principle will drag it from the undissolved solid into the complex. This process will be improved if you can increase solubility in solution, e.g. by incuding 20% DMSO or some other cosolvent in your drop. If you crystals will tolerate some cosolvent without cracking or dissolving, the equilibrium concentration of ligand in solution may still be high enough to populate your protein. This won't work for a loose-binding ligand.

Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 1334
6

----------
From: <Herman.Schreuder
Dear Ritcha,

You could also try low molecular weight PEG's, e.g. PEG400 in fairly
high concentrations. They often do a good job in solubilizing ligands
and are usually much more crystal-friendly than e.g. DMSO.

Best,
Herman

Stereo

From: Hena Dutta
Date: 14 September 2011 15:48
Dear Members,

Is any one using NVidia NVision 3D Setup with active stereo in linux distribution for crystallographic work? Which one would be the best choice to set up, an active stereo or a passive stereo for crystallographic work? Can anyone shade some details on this? I am planning to buy or build a new workstation with stereo set up. It would be great if someone can give some estimate on this.
Many thanks,

Hena
----------
From: Jim Fairman

I run the Alienware OptX AW2310 on two of our 3D Linux workstations and it looks spectacular. Make sure that you have a Quadro FX Nvidia video card that is on the approved list (http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html) with 3-pin stereo (3-pin stereo connector required for Linux, it will work without one in Windows through USB) output and not just a normal GeForce Nvidia card or you won't be able to run stereoscopic 3D in Linux.

One option that supports both Mac and Linux are the "Zalman" brand 3D monitors.  Some people like them, some people don't.  Unless Zalman significantly improved the technology on their monitors (ie: the right eye can see odd numbered rows of pixels and the left eye can see even numbered rows of pixels) you lose a significant amount of resolution from displaying 3D on these.  Due to half the pixels being drawn to each eye, the display on the 3D Vision system using a 120 Hz monitor will look crisper and higher quality than the equivalent Zalman monitor when displaying stereoscopic 3D.  That being said, this solution is significantly cheaper than the Nvidia system.

I've used and seen both and prefer the quality of the Nvidia 3D Vision, but some people are happy with the Zalman setup.  It's really up to personal preference as to which you will choose.

Cheers, Jim

--
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK

The Buchanan Lab

----------
From: Sabuj Pattanayek
Hi,
Yes
Active has better quality, greater 3D viewing area for people not
sitting right in front of the monitor, but is more expensive if you
have to purchase additional goggles ($70 non-nvidia online retailers -
$120 currently from nvidia)
Going with the lowest prices:

$300 Quadro 3700 :
http://www.google.com/products/catalog?q=quadro+3700&cid=5758926893192813358&ei=i8FwTpqJGpGkwgXtw9H4CQ&ved=0CAkQgggwAA#scoring=tp
$320 Acer GD235HZ :
http://www.google.com/products/catalog?q=acer+gd235hz&hl=en&um=1&ie=UTF-8&tbm=shop&cid=114906938122589343&sa=X&ei=d8JwTr7TM8WgtwfFuZWJCg&ved=0CHsQgggwAA#scoring=tp
$150 3D Vision kit with the 3 pin mini din "VESA" to 2.5mm stereo
cable : http://www.nvidia.com/object/product_geforce_3D_VisionKit_us.html

Total = $770

Passive stereo :

$490 (open box) - $550 : Zalman ZM-M240W :
http://www.compuvest.com/Search.jsp?Search=ZM-M240W&advsite=froogle&sku=756009288-08&dp=3:CVS:51392:0:21

You can use the black RealD 3D movie theater goggles with the Zalman
if you need extras. People also sell these online for a $1 + shipping.

HTH,
Sabuj

> Many thanks,
>
> Hena
>

----------
From: Sabuj Pattanayek
Hi,

On Wed, Sep 14, 2011 at 10:52 AM, Hena Dutta  wrote:
> Hi Sabuj,
>
> Can I use LED monitor instead LCD? I heard the color contrast is better. If

We haven't tried any, but here's an interesting 120 HZ LED monitor
(Acer HS244HQ):

http://www.newegg.com/Product/Product.aspx?Item=N82E16824009301&nm_mc=OTC-Froogle&cm_mmc=OTC-Froogle-_-Monitors+-+LCD+Flat+Panel-_-Acer+America-_-24009301

It comes with active 3D goggles, but it's noted that these only work
with the 3D sync signal built into Bluray movies which I think is
transmitted off the monitor. Now if this works like 3D DLP link stereo
then you don't necessarily need the 3D vision stereo kit/emitter at
all. In fact, we have an Infocus IN3116 projector that does 120Hz at
720p and a bunch of $50 DLP link goggles, a quadro 3700 video card in
the box, and can do stereo in Windows 7 and Linux using Option
"Stereo" "3" (standard quad buffered stereo). We use a cheap $2 DVI to
HDMI converter to connect a long HDMI cable into the projector from
the Quadro 3700 and that's it, no super long 3 pin mini din cable is
needed. The only downside is that sometimes the left and right eye
images are on the wrong sides when stereo is enabled, but most apps
(e.g. pymol, chimera, and coot too probably) have an option to swap
the eyes when in stereo so that's easily fixed.

> I buy higher level quadro graphics card (say FX 5600), will it improve the
> stereo quality? How big difference the prices are? Thanks for your

A better card won't improve the stereo quality itself, but will
improve surface, vdw, etc renderings with high polygon counts. For
building models, most people are looking at wireframes/lines which you
can still do for huge macromolecules on an SGI Octane. So yes, the
5600 will work with nvidia 3d vision, it has at least a G8x core
(http://en.wikipedia.org/wiki/Nvidia_Quadro) and the stereo connector
in the back. If you decide to go with something like that Acer HS244HQ
it would be interesting to see if it can be made to work without the
nvidia 3d vision kit at all.

HTH,
Sabuj

> information.
>
> Hena

----------
From: David Schuller

Hi,

What is being marketed as "LED" monitors recently are actually LCD monitors which use LEDs rather than fluorescent lamps for backlighting. So long as your monitor is compatible with the stereo technology you are using, LED backlighting is fine (and more efficient).

--
=======================================================================
All Things Serve the Beam
=======================================================================
                              David J. Schuller
                              modern man in a post-modern world
                              MacCHESS, Cornell University
                           

----------
From: Sabuj Pattanayek
On Wed, Sep 14, 2011 at 3:23 PM, Hena Dutta  wrote:
> Hi,
>
> Isn't that an LCD monitor (Acer HS244HQ)?

It's edge LED backlit. I don't know if there are any direct LED
backlit 120Hz monitors. Couldn't find much information on those types.

----------
From: Sabuj Pattanayek
Hi,

On Thu, Sep 15, 2011 at 1:55 PM, Hena Dutta  wrote:
> Hi Sabuj,
>
> Thanks for all your answers. I finally came to this plan. Please tell me if
> I am doing anything wrong.
>
> Option 1.
>
> HP Workstation Z400 FL998U8#ABA Desktop PC - Intel Xeon W3550 3.06GHz, 8GB
> DDR3, 160GB 10k RPM HDD, DVDRW, NVIDIA Quadro FX3800, Windows 7 Professional
> 32-bit ----$1000

> Acer HN274H bmiiid 27" Class Widescreen 3D LED HD Monitor - 1920 x 1080,
> 16:9, 100000000:1 Dynamic, 1000:1 Native, 120Hz, 2ms, HDMI, DVI-D, VGA,
> NVIDIA 3D Glasses, Energy Star ----$670

I highly doubt this monitor will work in Linux unless you buy the 3d
vision kit which comes with the emitter that you can hook into the 3
pin mini din port of your quadro (btw your quadro 3800 requires an
extra 3 pin mini din bracket, more on that below).

This monitor has a built in emitter that works with the pair of nvidia
(these are not generic active shutter goggles) 3d vision goggles it
comes bundled with :

http://3dvision-blog.com/review-of-the-27-acer-hn274h-3d-vision-ready-lcd-monitor/

...but does not have an input for the 3 pin mini din coming off a
proper quadro. The latest nvidia driver for linux still mentions that
you need the 3 pin mini din for nvidia 3d vision stereo in linux:

http://us.download.nvidia.com/XFree86/Linux-x86_64/280.13/README/xconfigoptions.html

####
Option "Stereo" "integer"

   10  NVIDIA 3D Vision mode for use with NVIDIA 3D Vision glasses.
The NVIDIA 3D Vision infrared emitter must be connected to a USB port
of your computer, and to the 3-pin DIN connector of a Quadro graphics
board (based on G8xGL or higher GPU) before starting the X server.
Hot-plugging the USB infrared stereo emitter is not yet supported.
Also, 3D Vision Stereo Linux support requires a Linux kernel built
with USB device filesystem (usbfs) and USB 2.0 support. Not presently
supported on FreeBSD or Solaris.
####

Having just the USB connected to the emitter still only works in
windows with the standard emitter. I also know that the windows nvidia
driver explicitly checks to see what sort of monitor you have before
enabling 3d vision (see the nvidia 3d vision wizard in the nvidia
control panel), i.e. that's probably why you don't need a USB cable
connected from your computer to this particular monitor where the
emitter is housed in the bezel.

So, basically if you decide to go with this monitor you'll still
probably need to get the 3D vision kit with the proper emitter and
you'll also need to get the 3 pin mini din bracket for your Quadro
3800 since it doesn't have the 3 pin mini din output:

There's a forum about it here :

http://forums.nvidia.com/index.php?showtopic=96163

which leads to this PNY part # 900-50762-0000-000 :

http://www.google.com/products/catalog?q=900-50762-0000-000&cid=17694678402912029306&ei=OoVzTvKqH6mExgXwi5HRAQ&ved=0CAkQgggwAA#scoring=tp

> Ofcourse I have to install linux. Do I need to buy anything else(say emiter
> or connector) for 3D stereo set up in linux distribution. What linux you
> like to suggest? I am familiar with open suse or ubuntu.

Either would be fine.

> Lenovo IdeaCentre K330B 7747-1GU Desktop PC - Intel Core i7-2600 3.40GHz,
> 8GB DDR3, 1.5TB HDD, DVDRW, ATI Radeon HD 6450, Windows 7 Home Premium
> 64-bit ----$750
>
> But, then I have to buy the right graphics card.

Yes.

> I think buying the NVIDIA Quadro FX 3800 graphics card will be much costly
> than to increase the hard drive.
>
> Which one is better processor?
>
> Intel Xeon W3550 3.06GHz or  Intel Core i7-2600 3.40GHz

i'd say the i7 2600 @ 3.4GHz, uses less power too.

> If they are not big difference, I will go with the first one and increase
> the hard drive. What do you think?

Buy the 2nd one, get a quadro 3700, get the 3d vision kit, and if you
want a 120Hz 27" "LED" monitor, here's one :

http://www.buy.com/prod/samsung-syncmaster-s27a750d-27-3d-led-lcd-monitor-16-9-2-ms-adjustable/223430191.html

that doesn't have a built in emitter which as mentioned above probably
isn't going to work in linux.

HTH,
Sabuj


>
> Many thanks for your time.
>
> Hena

PhD positions in structural biology

I would like to point your attention to a number of PhD positions in structural biology that are available through the international PhD program at the Max Planck Institute for Developmental biology in Tuebingen, Germany.

For detailed information, please visit:

http://www.phd.eb.tuebingen.mpg.de/

or contact the PhD Program office:

Carolina Müller, PhD Program Coordinator
Max Planck Institute for Developmental Biology
Spemannstr. 35
72076 Tübingen, Germany


All the best,

Remco Sprangers

---------------------------------------------
Remco Sprangers
Max Planck Research Group Leader
NMR Spectroscopy
Max Planck Institute for Developmental Biology
Spemannstrasse 35
72076 Tübingen
Germany

Post-doctoral position in macromolecular crystallography at the Australian Synchrotron

Dear all,

A two year post-doctoral position associated with the macromolecular crystallography group at the Australian Synchrotron is currently open for applications.

To read the position description and application instructions please go to http://www.synchrotron.org.au/index.php/about-us/working-at-the-synchrotron/employment-opportunities

Regards

Christine

PhD studentship in Terahertz Spectroscopy

We are looking for an outstanding PhD student to apply Terahertz Spectroscopy to the study of protein librations and folding.

The studentship is funded at the standard research council rate for 3 years. A first class or upper second class degree (or equivalent) is essential. For further details contact Robert Donnan <robert.donnan@eecs.qmul.ac.uk> or myself. To apply, please email your cv to r.w.pickersgill@qmul.ac.uk (please put ?terahertz PhD? on the subject line); applications will be accepted until the 15th October and we should like to start this studentship January 2012 or earlier.

Richard W Pickersgill
Professor of Structural Biology
School of Biological and Chemical Sciences
Queen Mary University of London
London E1 4NS
England

Telephone 02078828444

Postdoctoral Fellowship in Membrane Protein Structural Biology at NIH

Structural studies on glutamate receptor ion channels:

A postdoctoral position in X-ray crystallography is available immediately in the group of Dr. Mark L. Mayer, in the Laboratory of Cellular and Molecular Neurophysiology at the NIH in Bethesda MD, USA. This opening is part of an established program with a long term focus on glutamate receptor ion channels: see http://snb.nichd.nih.gov/index.htm for recent publications and research interests. Substantial efforts have already been undertaken in construct design, protein expression and detergent screening, leading to very promising leads for crystallization.

The laboratory is located in the main NIH campus. We have shared state-of-the-art facilities large scale eukaryotic cell culture, and for crystallization, in-house X-ray data collection and other biophysical approaches. We also have regular synchrotron beamtime at the Advanced Photon Source (APS) through membership of SER-CAT.

Interested applicants must have a Ph.D. in biochemistry, molecular biology or structural biology, extensive experience in protein expression and purification, and X-ray crystallography. Experience working with insect cell culture and baculovirus expression systems would be an advantage is but not essential. The ideal candidate will be highly motivated, possess excellent communication skills and the ability to work in a collaborative and team-oriented environment.

To apply, please e-mail a CV including a list of publications, a brief statement of experience and scientific interests, and contact information for three references to mayerm@mail.nih.gov

Mark Mayer Ph.D.
LCMN NICHD NIH DHHS
Bldg 35, Room 3B 1002 MSC 3712
35 Lincoln Drive
Bethesda MD 20892 3712

--  

Postdoctoral position

We seek to recruit an outstanding postdoctoral scientist with strong interest in Structural Biology/Structural Enzymology.

The main goal of this project is to illuminate the chemistry of cobalamin biosynthesis in molecular and mechanistic detail exploiting our recent discovery that several of the biosynthetic enzymes trap their products. We want to understand how intermediates in the biosynthetic pathway are passed from one enzyme to the next. We shall do this using a combination of structural, biochemical, biophysical and genetic approaches.

This is a four-year, full time position, funded by the BBSRC, starting in November 2011 or as soon as possible thereafter.  The salary is in the range of £30,350 - £33,794 per annum and is inclusive of London allowance. Benefits include 30 days annual leave, defined benefit pension scheme and an interest?free season ticket loan.

The successful candidates will hold a PhD in Structural Biology/Biochemistry or have equivalent experience and will have experience in producing and purifying proteins. A significant publication record would be an advantage.

Candidates must be able to demonstrate their eligibility to work in the UK in accordance with the Immigration, Asylum and Nationality Act 2006. Where required this may include entry clearance or continued leave to remain under the Points Based Immigration Scheme.

Informal enquiries can be made to Professor Richard W Pickersgill (r.w.pickersgill@qmul.ac.uk or 020-7882-8444).

Further details and an application form can be obtained from the Human Resources website on: http://www.hr.qmul.ac.uk/vacancies. For further information about the School, please see http://www.sbcs.qmul.ac.uk.

Complete application forms must not be sent directly to Prof Pickersgill but should be returned, together with a copy of your CV, to Ms Sunita Devi-Paul, School of Biological & Chemical Sciences, Queen Mary, University of London, Mile End Road, London, E1 4NS, or by e-mail: sbcs-vacancies@qmul.ac.uk. Please quote reference number 11226/NL.

The closing date for applications is 13 October 2011 at 4.00pm.


Richard W Pickersgill
Professor of Structural Biology
School of Biological and Chemical Sciences
Queen Mary University of London
London E1 4NS
England

Telephone 02078828444

Could you please place my open positions on your website?

Hi there,

 

I am a full professor at Harbin Institute of Technology, China. Could you please place my open positions on your website? Below is the details. Thanks in advance.

 

Zhiwei

 

Location: Harbin, China

Department: Harbin Institute of Technology BIO-X Center
Start Date: Negotiable
Duration: 2-3 Years, extendable
Description: Several postdoctoral positions are available in Dr. Zhiwei Huang's newly established laboratory at Harbin Institute of Technology (HIT), China. Our research interests focus on the understanding of structure-function relationships of macromolecules (soluble/membrane proteins, nucleic acids), and the mechanisms of cellular signaling transduction in immunology and neurobiology fields. We use multi-disciplinary approaches including X-ray crystallography, biochemistry, molecular biology, cell biology, and mouse genetics in our studies. We are equipped with a state-of-the-art facility to conduct soluble/membrane protein crystallography and functional studies including a recently established home X-ray source, an automated crystallization screening device, and other setups such as ITC.

A background in macromolecular X-ray crystallography, protein expression & purification or biochemistry is preferred, but enthusiastic individuals with a Ph.D degree in microbiology, molecular biology, cell biology, biophysics, physics or related fields and interested in utilizing both in vivo and in vitro techniques to study structure-function relationships of important soluble/membrane proteins and important signaling pathways in immunology and neurobiology fields are also encouraged to apply. We offer competitive salary and benefits, which will be commensurate with experiences. For more information, please check the university website (http://bio.hit.edu.cn/news/sub_szdw.asp?id=883) or contact me via email. Please send CV, a summary of research experience, and the contact information of three references to Zhiwei Huang at huangzhiwei2009@gmail.com

Please submit: CV, Brief description of research experience, contact information of three references
Person to contact: Zhiwei Huang
Email address: huangzhiwei2009@gmail.com

Postdoctoral position – University of British Columbia, Canada

Date: 30 September 2011 19:01

Postdoctoral position – University of British Columbia, Canada

We are seeking a self-motivated postdoctoral researcher with experience in protein crystallography to investigate the structural biology of natural product biosynthetic enzymes. The successful candidate will optimize expression and crystallization conditions for targeted proteins, solve structures in complex with purified substrates and products, and prepare manuscripts for publication. Previous experience in enzymology and synthetic chemistry would be an asset. Please send your CV (including contact information for three referees) and a statement of interest to ksryan@chem.ubc.ca.

UBC hires on the basis of merit and is committed to employment equity. All qualified persons are encouraged to apply. However, Canadians and permanent residents of Canada will be given priority.

________________________