[ccp4bb] software molecular replacement

[LISA]

Hi all,
There are so many software for MR, such as phaser, balbe,molrep, and amore.
What is difference between them? Which one is powerful?
Please give some comments for these software?Thank you.

Sincerely,
lisa

Re: [ccp4bb] software molecular replacement

[Mark J van Raaij]

Hi Lisa,

I would start with learning AMoRe. It is relatively simple, runs fast and uses 
little memory, so you can experiment easily with lots of parameters. It is also 
relatively easy to modify the parameters, radii etc. and get a feel for which 
ones to use. If after a few days or weeks you understand AMoRe, you will have a 
good basic understanding of the practical aspects of molecular replacement. 
Also, most molecular replacement problems can be solved with it.

Molrep is also relatively fast, but a bit black-box compared to Amore. You can 
modify the search model to be more like the sequence of your protein by 
incorporating Chainsaw. This could lead to success in some cases where Amore 
might fail.

For some difficult molecular replacement problems, the other programs will 
provide some benefits. Balbes basically tries to improve success by changing 
the search model, by trying lots of different ones automatically using the pdb 
as a source. I think it may also automatically incorporate Chainsaw?

Phaser is very sophisticated, and probably therefore takes more time to run. It 
is incorporated both in CCP4 and Phenix and easy to set up and run from either 
GUI. Because the longer runtime, it is not so easy to experimentally test 
different search parameters, so to use these optimally it is better have a good 
understanding of molecular replacement. It does appear to solve some molecular 
replacement problems where other programs might fail.

This is what I tell my students and is just my opinion and other, more expert 
crystallographers, might disagree on some of the points. (Of course, my 
students anyway just ignore me and always go for the GUI that looks hottest).

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 22 Apr 2013, at 09:05, LISA wrote:

> Hi all,
> There are so many software for MR, such as phaser, balbe,molrep, and amore. 
> What is difference between them? Which one is powerful?
> Please give some comments for these software?Thank you.
> 
> Sincerely,
> lisa

Re: [ccp4bb] xprep simulated powder diffraction

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear James,

my guess is that xprep removes ( 0 0 0) for a better contrast, but I
don't know for sure - George is going to tell you, I guess, because he
will know ;-)

The reason I answer is rather a comment: I would not call the tutorial
you refer to a 'manual' (I don't think a manual for xprep exists).
It's really a tutorial for students to learn small molecule (singe
crystal) crystallography and as far as I remember it was created by
Eftichia Alexopoulos & Fabio Dall'Antonia (main url is
http://shelx.uni-ac.gwdg.de/tutorial/english/) and further improved by
other PhD students of George's - they did a really good job worth
working through, but since it is a tutorial with a certain objective
rather than a manual there is no reference to ALL capabilities of xprep.

Best,
Tim

On 04/20/2013 03:42 AM, James Stroud wrote:
> Hello All,
> 
> I calculated structure factors from a pdb with sfall and then used
> those to generate a simulated powder diffraction pattern with
> xprep. To compare, I also plotted the intensities (F x F*) straight
> from the mtz file. Attached are the two patterns as png files
> (sfall only: "mtz.png"; sfall→xprep: "xprep.png").
> 
> Does anyone know what xprep is doing to the low resolution data (>
> ~20 Å)? It seems to be clipped. The xprep manual[1] says nothing
> about simulated powder diffraction. The patterns < ~20 Å are
> more-or-less comparable (although you can't tell from the
> pictures).
> 
> James
> 
> 
> [1] http://shelx.uni-ac.gwdg.de/tutorial/english/xprep.htm
> 
> 
> 
> 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
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K7iBOAs903lL32PfSzioWPI=
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Re: [ccp4bb] software molecular replacement

[Roger Rowlett]

There are three general approaches to molecular replacement:

1. rotation-translation algorithms: these divide the 6-dimensional
   problem of placing a replacement model in the ASU into two
   sequential 3-parameter searches, which, if it works, converges more
   quickly than a 6-dimensional search. Examples include Amore, MOLREP,
   Phaser, etc.
2. genetic algorithms: these use an evolutionary search model to more
   quickly converge a 6-dimensional search. Example: EPMR.
3. brute-force algorithms: these use brute-force stochastic methods to
   attempt to find the global best fit to a 6-dimensional search for
   the best placement of the model in the ASU. Example: Queen of Spades.

Each of these methods will have their strengths and weaknesses. The 
brute-force algorithms nearly always work but may take a very, very long 
time. For routine problems the rotation-translation or genetic 
algorithms are quite efficient. (Some are faster than others.) When 
searching for multiple models in the ASU, some algorithms may work 
better than others for a particular case. In my experience EPMR and 
Phaser seem to be very good at accurately placing multiple models within 
an ASU in a reasonable amount of time, but all these programs have their 
quirks when trying to solve specific problems, or when working with 
low-homology search models. So it's good to have a variety of approaches 
to choose from.


Cheers,

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu

On 4/22/2013 3:05 AM, LISA wrote:

Hi all,
There are so many software for MR, such as phaser, balbe,molrep, and 
amore. What is difference between them? Which one is powerful?

Please give some comments for these software?Thank you.

Sincerely,
lisa

[ccp4bb] Struther Arnott

[James Naismith]

Older members of the bulletin board will be sad to learn that Struther Arnott 
FRS, fibre diffractionist and biophysicist (as well as former St Andrews 
Principal) died on Saturday.

Jim Naismith


James H. Naismith FRSE FMedSci| naism...@st-andrews.ac.uk
Professor of Chemical Biology   | j...@st-andrews.ac.uk (teaching)
BSRC  |
The North Haugh   |+44(0)1334463792
The University, St Andrews|Secretary: +44(0)1334463401
Fife KY16 9ST U.K.   |Fax: (44) or (0) 1334467229

Google scholar is free and tracks your outputs, mine are
http://scholar.google.co.uk/citations?hl=en&user=fLmKKQMJ

The University of St Andrews is a charity registered in Scotland : No SC013532

Re: [ccp4bb] Struther Arnott

[Peter Moody]

Sad news indeed, he mentored my mentors,   His influence on crystallography
(rather than fibre diffraction) in not always as well appreciated as it
might be.

Peter


On 22 April 2013 14:44, James Naismith  wrote:

> Older members of the bulletin board will be sad to learn that Struther
> Arnott FRS, fibre diffractionist and biophysicist (as well as former St
> Andrews Principal) died on Saturday.
>
> Jim Naismith
>
>
> James H. Naismith FRSE FMedSci| naism...@st-andrews.ac.uk
> Professor of Chemical Biology   | j...@st-andrews.ac.uk (teaching)
> BSRC  |
> The North Haugh   |+44(0)1334463792
> The University, St Andrews|Secretary: +44(0)1334463401
> Fife KY16 9ST U.K.   |Fax: (44) or (0) 1334467229
>
> Google scholar is free and tracks your outputs, mine are
> http://scholar.google.co.uk/citations?hl=en&user=fLmKKQMJ
>
> The University of St Andrews is a charity registered in Scotland : No
> SC013532
>

[ccp4bb] Off topic: type X collagen

[Rex Palmer]

Does anyone have a nice graphic of type X collagen?
Thanks in advance.

 
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com

[ccp4bb] cyclising proteins

[Dean Derbyshire]

Hi all, perhaps not the right forum but...
...is there a way in coot to make a lysine side-chain // carboxy-terminal 
iso-peptide bond?

Cheers in advance
Dean

[ccp4bb] gelification of a pure protein

[Pascal Egea]

Dear All,

I am presently faced with a peculiar case in the lab. We are expressing a
protein in E. coli and we are able to express it as a fusion
protein without problems . Fusion cleavage goes well and the final product
looks homogenous by size-exclusion chromatography with the expected
molecular weight. There are no signs of aggregation. However when we lower
the salt concentration by dialysis then the protein forms a gel.
transparent , optically clear, with no fluffy material (in the cold room).

Gelification seems to occur when we lower the concentration below 100 mM
NaCl. This protein has a fairly high pI (~9.0). Attempts to reverse the
process by gentle heating or salt addition have been so far unsuccessful.
It is not a thermophilic protein. We have not been able to obtain crystals
so far.

Has anyone already observed this kind of behavior and/or have any
suggestions?

Many thanks in advance .

-- 
Pascal F. Egea, PhD
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
Boyer Hall room 356
611 Charles E Young Drive East
Los Angeles CA 90095
office (310)-983-3515
lab  (310)-983-3516
email pe...@mednet.ucla.edu

Re: [ccp4bb] gelification of a pure protein

[Mark van Raaij]

reminds me of structure 1NEU, although here the gelation was reversible, see 
ref and abstract below - the paper has a photo of a tube of soluble protein and 
gelled protein

we have also had a couple of cold-sensitive proteins in our hands, that 
precipitated at 4 degrees when concentrated, but were soluble at room temp to 
quite high concentrations (and we got structures for both)


Neuron. 1996 Sep;17(3):435-49.
Crystal structure of the extracellular domain from P0, the major structural 
protein of peripheralnerve myelin.
Shapiro L, Doyle JP, Hensley P, Colman DR, Hendrickson WA.
P0, the major protein of peripheral nerve myelin, mediates membrane adhesion in 
the spiral wraps of the myelin sheath. We have determined the crystal structure 
of the extracellular domain from P0 (P0ex) at 1.9 A resolution. P0ex is folded 
like a typical immunoglobulin variable-like domain; five residues at the 
C-terminus are disordered, suggesting a flexible linkage to the membrane. The 
requirements for crystallization of P0ex are similar to those for maintaining 
the native extracellular spacing of adjacent myelin lamellae; thus, given the 
self-adhesive character of P0ex, the crystal itself may reveal some of the 
natural interactions that occur between P0 molecules in myelin. The structure 
leads to the suggestion that P0 extracellular domains may emanate from the 
membrane surface as tetramers that link to tetramers on the opposing membrane 
surface, to result in the formation of networks of molecules. We report 
analytical ultracentrifugation data for P0ex that support this idea.
PMID: 8816707


On 23 Apr 2013, at 00:36, Pascal Egea wrote:

> Dear All,
> 
> I am presently faced with a peculiar case in the lab. We are expressing a 
> protein in E. coli and we are able to express it as a fusion protein without 
> problems . Fusion cleavage goes well and the final product looks homogenous 
> by size-exclusion chromatography with the expected molecular weight. There 
> are no signs of aggregation. However when we lower the salt concentration by 
> dialysis then the protein forms a gel. transparent , optically clear, with no 
> fluffy material (in the cold room).
> 
> Gelification seems to occur when we lower the concentration below 100 mM 
> NaCl. This protein has a fairly high pI (~9.0). Attempts to reverse the 
> process by gentle heating or salt addition have been so far unsuccessful. It 
> is not a thermophilic protein. We have not been able to obtain crystals so 
> far.
> 
> Has anyone already observed this kind of behavior and/or have any suggestions?
> 
> Many thanks in advance .
> 
> -- 
> Pascal F. Egea, PhD
> Assistant Professor
> UCLA, David Geffen School of Medicine
> Department of Biological Chemistry
> Boyer Hall room 356
> 611 Charles E Young Drive East
> Los Angeles CA 90095
> office (310)-983-3515
> lab  (310)-983-3516
> email pe...@mednet.ucla.edu

[ccp4bb] Modelling Software for beta turn design

[Wenzong Li]

Dear All,

I want to use modelling software to design a tight beta turn replacing a loop 
between two beta strands. Can anyone suggest a program to do this sort of 
modelling?

Thank you
Wenzong

Re: [ccp4bb] Modelling Software for beta turn design

[Joel Tyndall]

Dear Wenzong,

Could you provide a bit more details please? Do you simply require some 
visualisation tool e.g. pymol to superimpose your turn mimic on your 
protein/peptide structure or are you looking for more indepth modelling to say 
identify new scaffolds to build amino acid sidechains onto based on an insilico 
screen against your peptide? The latter requires more high end software

Cheers

Joel 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenzong Li
Sent: Monday, 22 April 2013 3:48 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Modelling Software for beta turn design

Dear All,

I want to use modelling software to design a tight beta turn replacing a loop 
between two beta strands. Can anyone suggest a program to do this sort of 
modelling?

Thank you
Wenzong

Re: [ccp4bb] Modelling Software for beta turn design

[Wenzong Li]

I want to build the loop based on a computer screen against my peptide. 

Thanks

Wenzong

- Original Message -
From: "Joel Tyndall" 
To: "Wenzong Li" , CCP4BB@JISCMAIL.AC.UK
Sent: Monday, April 22, 2013 6:10:09 PM
Subject: RE: [ccp4bb] Modelling Software for beta turn design

Dear Wenzong,

Could you provide a bit more details please? Do you simply require some 
visualisation tool e.g. pymol to superimpose your turn mimic on your 
protein/peptide structure or are you looking for more indepth modelling to say 
identify new scaffolds to build amino acid sidechains onto based on an insilico 
screen against your peptide? The latter requires more high end software

Cheers

Joel 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenzong Li
Sent: Monday, 22 April 2013 3:48 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Modelling Software for beta turn design

Dear All,

I want to use modelling software to design a tight beta turn replacing a loop 
between two beta strands. Can anyone suggest a program to do this sort of 
modelling?

Thank you
Wenzong

Re: [ccp4bb] gelification of a pure protein

[Michael Thompson]

Does your protein have multiple exposed Cys residues? I have observed this 
before with a protein I worked with that had many exposed Cys residues. In my 
case I could add more DTT and minutes later the gel would be completely 
dissipated. My hand-wavy explanation was that the protein stays folded but 
becomes highly crosslinked when concentrated and exposed to air. I did have 
some small amount of DTT in my buffer to start with, but I assume it became 
oxidized relatively quickly (as DTT does), leaving my protein thiols to go wild 
and make S-S bonds between themselves. 

Good luck,

Mike






- Original Message -
From: "Pascal Egea" 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, April 22, 2013 3:36:24 PM GMT -08:00 US/Canada Pacific
Subject: [ccp4bb] gelification of a pure protein


Dear All, 


I am presently faced with a peculiar case in the lab. We are expressing a 
protein in E. coli and we are able to express it as a fusion protein without 
problems . Fusion cleavage goes well and the final product looks homogenous by 
size-exclusion chromatography with the expected molecular weight. There are no 
signs of aggregation. However when we lower the salt concentration by dialysis 
then the protein forms a gel. transparent , optically clear, with no fluffy 
material (in the cold room). 


Gelification seems to occur when we lower the concentration below 100 mM NaCl. 
This protein has a fairly high pI (~9.0). Attempts to reverse the process by 
gentle heating or salt addition have been so far unsuccessful. It is not a 
thermophilic protein. We have not been able to obtain crystals so far. 



Has anyone already observed this kind of behavior and/or have any suggestions? 


Many thanks in advance . 

-- 
Pascal F. Egea, PhD 
Assistant Professor 
UCLA, David Geffen School of Medicine 
Department of Biological Chemistry 
Boyer Hall room 356 

611 Charles E Young Drive East 
Los Angeles CA 90095 
office (310)-983-3515 
lab (310)-983-3516 
email pe...@mednet.ucla.edu 

-- 
Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

mi...@chem.ucla.edu

Re: [ccp4bb] gelification of a pure protein [SEC=UNCLASSIFIED]

[DUFF, Anthony]

I have experienced a similar thing with lysozyme immediately forming a clear 
gel when attempting to dissolve at high concentration in D2O.  The clear gel 
did not readily dissolve on dilution (in D2O) and I discarded it.  I later made 
the sample by dissolving in H2O and dialysing to D2O.

Another protein I have worked with, a multimeric ATPase, requiring ATP to 
assemble, forms a white gel when prepared in isolation from other proteins of 
its complex and ATP is added.  From memory, the gel formation is fast (minutes) 
at higher concentration (~20mg/ml), and slow (hours to days) at lower 
concentration 1-5mg/ml, but this formed a precipitate not a gel.  Presumably 
this was a polymerisation.   The white gel was resistant to dilution or 
addition of salts.

After baking, I find that meat juices cool to form a gel, transparent and 
optically clear.  Like gelatine.


Sincerely,
Anthony 

Anthony Duff    Telephone: 02 9717 3493  Mob: 0431891076 


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Michael 
Thompson
Sent: Tuesday, 23 April 2013 9:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] gelification of a pure protein

Does your protein have multiple exposed Cys residues? I have observed this 
before with a protein I worked with that had many exposed Cys residues. In my 
case I could add more DTT and minutes later the gel would be completely 
dissipated. My hand-wavy explanation was that the protein stays folded but 
becomes highly crosslinked when concentrated and exposed to air. I did have 
some small amount of DTT in my buffer to start with, but I assume it became 
oxidized relatively quickly (as DTT does), leaving my protein thiols to go wild 
and make S-S bonds between themselves. 

Good luck,

Mike






- Original Message -
From: "Pascal Egea" 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, April 22, 2013 3:36:24 PM GMT -08:00 US/Canada Pacific
Subject: [ccp4bb] gelification of a pure protein


Dear All, 


I am presently faced with a peculiar case in the lab. We are expressing a 
protein in E. coli and we are able to express it as a fusion protein without 
problems . Fusion cleavage goes well and the final product looks homogenous by 
size-exclusion chromatography with the expected molecular weight. There are no 
signs of aggregation. However when we lower the salt concentration by dialysis 
then the protein forms a gel. transparent , optically clear, with no fluffy 
material (in the cold room). 


Gelification seems to occur when we lower the concentration below 100 mM NaCl. 
This protein has a fairly high pI (~9.0). Attempts to reverse the process by 
gentle heating or salt addition have been so far unsuccessful. It is not a 
thermophilic protein. We have not been able to obtain crystals so far. 



Has anyone already observed this kind of behavior and/or have any suggestions? 


Many thanks in advance . 

-- 
Pascal F. Egea, PhD 
Assistant Professor 
UCLA, David Geffen School of Medicine 
Department of Biological Chemistry 
Boyer Hall room 356 

611 Charles E Young Drive East 
Los Angeles CA 90095 
office (310)-983-3515 
lab (310)-983-3516 
email pe...@mednet.ucla.edu 

-- 
Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

mi...@chem.ucla.edu

Re: [ccp4bb] gelification of a pure protein

[Pascal Egea]

Thanks to All for the diligent answers to my query,

The protein is not thermophilic and has only one cysteine. We are working
in presence of freshly added reducing agent and glycerol to promote
solubility (well kinda it seems).
This is not an RNA or DNA binding protein and it has no low-complexity
regions except at the N terminus, there maybe some left over from a cryptic
transit peptide (somehow basic) that supposedly targets the protein to a
specific organelle. We are probably going to truncate further to see if it
solves our problem

I appreciate all the comments and suggestions,
Cheers,

Pascal

-- 
Pascal F. Egea, PhD
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
Boyer Hall room 356
611 Charles E Young Drive East
Los Angeles CA 90095
office (310)-983-3515
lab  (310)-983-3516
email pe...@mednet.ucla.edu

Re: [ccp4bb] Modelling Software for beta turn design

[Pete Meyer]

Wenzong,

You may want to look at rosetta's design modules.

Pete

Wenzong Li wrote:
I want to build the loop based on a computer screen against my peptide. 


Thanks

Wenzong

- Original Message -
From: "Joel Tyndall" 
To: "Wenzong Li" , CCP4BB@JISCMAIL.AC.UK
Sent: Monday, April 22, 2013 6:10:09 PM
Subject: RE: [ccp4bb] Modelling Software for beta turn design

Dear Wenzong,

Could you provide a bit more details please? Do you simply require some 
visualisation tool e.g. pymol to superimpose your turn mimic on your 
protein/peptide structure or are you looking for more indepth modelling to say 
identify new scaffolds to build amino acid sidechains onto based on an insilico 
screen against your peptide? The latter requires more high end software

Cheers

Joel 


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenzong Li
Sent: Monday, 22 April 2013 3:48 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Modelling Software for beta turn design

Dear All,

I want to use modelling software to design a tight beta turn replacing a loop 
between two beta strands. Can anyone suggest a program to do this sort of 
modelling?

Thank you
Wenzong

Re: [ccp4bb] gelification of a pure protein

[Shane Caldwell]

Hi Pascal,

Your problem brings to mind this paper:

FG-Rich Repeats of Nuclear Pore Proteins Form a Three-Dimensional Meshwork
with Hydrogel-Like Properties Science 3 November 2006: 314 (5800), 815-817.[DOI:
10.1126/science.1132516]

Of course, in that case, the gellation was deliberate, but perhaps still
worth a look.

Cheers,

Shane Caldwell
McGill University


On Mon, Apr 22, 2013 at 8:20 PM, Pascal Egea  wrote:

> Thanks to All for the diligent answers to my query,
>
> The protein is not thermophilic and has only one cysteine. We are working
> in presence of freshly added reducing agent and glycerol to promote
> solubility (well kinda it seems).
> This is not an RNA or DNA binding protein and it has no low-complexity
> regions except at the N terminus, there maybe some left over from a cryptic
> transit peptide (somehow basic) that supposedly targets the protein to a
> specific organelle. We are probably going to truncate further to see if it
> solves our problem
>
> I appreciate all the comments and suggestions,
> Cheers,
>
> Pascal
>
> --
> Pascal F. Egea, PhD
> Assistant Professor
> UCLA, David Geffen School of Medicine
> Department of Biological Chemistry
> Boyer Hall room 356
> 611 Charles E Young Drive East
> Los Angeles CA 90095
> office (310)-983-3515
> lab  (310)-983-3516
> email pe...@mednet.ucla.edu
>

Re: [ccp4bb] Modelling Software for beta turn design

[Joel Tyndall]

Ahh Ok, now I see. I guess you need a search engine that idenitifies an 
antiparallel beta sheet with a turn. Whilst I don't know how to do it, maybe 
the pdb or epdb may do this or even modeller loop via accelrys interface

Joel 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenzong Li
Sent: Monday, 22 April 2013 4:17 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Modelling Software for beta turn design

I want to build the loop based on a computer screen against my peptide. 

Thanks

Wenzong

- Original Message -
From: "Joel Tyndall" 
To: "Wenzong Li" , CCP4BB@JISCMAIL.AC.UK
Sent: Monday, April 22, 2013 6:10:09 PM
Subject: RE: [ccp4bb] Modelling Software for beta turn design

Dear Wenzong,

Could you provide a bit more details please? Do you simply require some 
visualisation tool e.g. pymol to superimpose your turn mimic on your 
protein/peptide structure or are you looking for more indepth modelling to say 
identify new scaffolds to build amino acid sidechains onto based on an insilico 
screen against your peptide? The latter requires more high end software

Cheers

Joel 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenzong Li
Sent: Monday, 22 April 2013 3:48 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Modelling Software for beta turn design

Dear All,

I want to use modelling software to design a tight beta turn replacing a loop 
between two beta strands. Can anyone suggest a program to do this sort of 
modelling?

Thank you
Wenzong

[ccp4bb] Mutated biological binding interactions as crystal contacts

[Owen Pornillos]

Hi all -

I am looking for examples of structures of protein-protein complexes  
(homo or hetero) wherein the crystallized proteins had mutations  
within their binding interfaces, and yet the same (weakened)  
interactions were still recapitulated in crystal contacts.


Any leads would be much appreciated.

Thanks,

Owen 

Re: [ccp4bb] gelification of a pure protein

[Antony Oliver]

To ask a potentially daft question - but why do you need to reduce the salt?   
You say you are able to purify it, and that it behaves on gel filtration - but 
only starts misbehaving when you dialyse, and the NaCl is below 100 mM.

We've crystallised many proteins, particularly DNA-binding proteins with high 
pI, in high salt concentrations - even up to 1M.

Tony.

Sent from my iPhone

On 22 Apr 2013, at 23:36, "Pascal Egea" 
mailto:pas...@msg.ucsf.edu>> wrote:

Dear All,

I am presently faced with a peculiar case in the lab. We are expressing a 
protein in E. coli and we are able to express it as a fusion protein without 
problems . Fusion cleavage goes well and the final product looks homogenous by 
size-exclusion chromatography with the expected molecular weight. There are no 
signs of aggregation. However when we lower the salt concentration by dialysis 
then the protein forms a gel. transparent , optically clear, with no fluffy 
material (in the cold room).

Gelification seems to occur when we lower the concentration below 100 mM NaCl. 
This protein has a fairly high pI (~9.0). Attempts to reverse the process by 
gentle heating or salt addition have been so far unsuccessful. It is not a 
thermophilic protein. We have not been able to obtain crystals so far.

Has anyone already observed this kind of behavior and/or have any suggestions?

Many thanks in advance .

--
Pascal F. Egea, PhD
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
Boyer Hall room 356
611 Charles E Young Drive East
Los Angeles CA 90095
office (310)-983-3515
lab  (310)-983-3516
email pe...@mednet.ucla.edu