s item but they used to sell this as well
When you get an answer can everyone know here as well
best
*Pius Padayatti*
On Tue, Jan 2, 2024 at 9:54 AM Firdous Tarique
wrote:
> Hi
>
> I would appreciate it if someone could share with me a step by step
> protocol for making a stable
https://pymolwiki.org/index.php/APBS
*Pius Padayatti*
On Tue, Aug 15, 2023 at 5:20 PM khaja faisal tarique <
khajafaisaltari...@gmail.com> wrote:
> Hi everyone
>
> Is there any way to make surface representation of a protein structure
> similar to the 'Illustrate:
a passion
and never had a second thought about looking at this abstract art science.
With respect to a scientist who want to contribute to India's science and
inspired
a generation of structural biologists in India RIP.
respectfully
Padayatti PS.
*Pius Padayatti*
On Sun, Apr 24, 2022 at 1:08 AM ASHI
Hi Bulletin members
My question is relatively general regarding some protein engineering
The aim is to design a peptide of approx length 25 nm mostly
helical in nature that can conduct current.
The ends of the peptide have to have some properties that it can
bind to metal electrodes
Heart felt condolences to the loss of a legend
padayatti
On Tue, May 14, 2019 at 6:12 PM Hasan, Syed Saif
wrote:
> Dear Colleagues,
>
>
> It is with profound sadness that I must announce the passing away of Prof.
> Michael Rossmann earlier today on May 14th 2019 in West Lafayette IN.
> Michael
Forwarding a job advertisement
Please contact the person here copied
Lorin
-- Forwarded message -
From: Lorin Raats
Date: Tue, Feb 12, 2019 at 6:53 AM
Subject: Head of Membrane Protein Science opportunity available at
fast-growing biotech company
It would be great to get in
googled it
and there is many more of them in Pubmed
by the way if you googles it as UPS and inhibitor you will not find any
also who knows what is USP? i hope this is what you looking for
Cancer Cell. 2012 Sep 11;22(3):345-58. doi: 10.1016/j.ccr.2012.08.007.
A small molecule inhibitor of
26 and 33 tells me you are over fitting your structure
the spread is more than 5%
If there is a ligand added and it really doesn't look like a good fit i
would try work on it
(remove it and look at alternatives)
When you refine you may use NCS if you have (NCS in your structure)
If there is a
Hi forum
Please send suggestions on your favorite fermentor
We are looking at New Brunswick BioFlow 415
I know there are many, and that is why wanted to hear the communities picks
Thanks in advance
Padayatti
--
P
pramod
Do a spin after bacterial cell breaking at 8K to get rid of a nuclear pellet
Also there is a nuclease preparation available called benzonase
it is most effective when you also add magnesium in your buffer
so in your homogenization buffer add magnesium and should avoid any EDTA
Pius
On Thu,
These are the usual culprits
My buffers for cleavage and an on-column digestion
worked good. (see below)
Also most likely your TEV source (do not go cheap) enzyme is inactive
(gone bad). Get a clone for TEV and make your own TEV in the lab. It save
you a ton of money
.
10 mM Tris-HCl (pH 8.0)
The SDS PAGE estimation can be done
plus there are some nice glycoportein stains (periodic acid schiffs
staining)
could be used (if Coomasie staining is a problem)
I do not know if the PAS staining is linear to standard staining.
but regular staining should work like a charm
use bovine rhodopsin
Sudipta,
the link for the cyanin dyes are at the following link
http://www.lifetechnologies.com/us/en/home/references/molecular-probes-the-handbook/nucleic-acid-detection-and-genomics-technology/nucleic-acid-stains.html
Sorry for the wrong link
P
On Fri, Feb 13, 2015 at 1:50 PM, Sudipta
an effective modification to your protein preparations would be to add
phosphatase inhibitor tablets during all
stages of purification. Pierce sell a combination protease and PI tablet
that is effective and economical to be added during protein preps. Also you
invitro buffers should have
https://hamptonresearch.com/product_detail.aspx?cid=10sid=65pid=109
Granada box will work for you
Thaumatin can be grown to large single crystals suitable size
On Mon, Jan 5, 2015 at 9:25 AM, Georg Mlynek georg.mly...@univie.ac.at
wrote:
Dear Colleagues,
After reading a few papers about
you may buy them from BASF
Even sometime back they gave some free samples for experimentation
Call them directly
Padayatti
On Mon, Dec 29, 2014 at 2:59 PM, Srinivasan Rengachari
02062d79acb8-dmarc-requ...@jiscmail.ac.uk wrote:
Dear all,
I recently had a few initial hits for my
Hi friends
Does anybody have Monodihydrosterculin that can be shared?
or anybody can direct to a source to buy
Thanks
Pius
--
P
levodopa solutions are stable in refrigerator conditions for a day.
You make as much you want and prepare fresh everyday.
there is no easy ways
On Thu, Jul 3, 2014 at 10:34 AM, Keller, Jacob kell...@janelia.hhmi.org
wrote:
Dear Crystallographers,
Does anyone have experience with
I worked for several years on mammalian cell expression of extra-cellular
domains of single spanning membrane proteins
and other membrane proteins.
Just like you did when we switched stable lines from serum containing to
serum free medium the expression drastically
reduced.
So after switching to
It looks like a Hepes?
Padayatti
On Mon, Feb 3, 2014 at 8:37 AM, Annemarie Weber
annemarie.we...@uni-konstanz.de wrote:
Dear all,
I am refining a 1.4 A resolution structure and found some well-defined but
unfortunately unexplained density. The protein was purified in HEPES buffer
with PMSF
Hi Venkat,
For any protease digestion my best liked method is to
try digest while the protein is bound to the column.
make sure you know your resin dead volume
and incubate in the protease buffer overnight.
Just after adding enough volume try to rotate (gently, ideally on a roller
bottle) for an
Hi Brett,
Like everyone said best way is to find the crystal is worth pursuing
is to find its diffraction. On regular basis observing things in the
crystallization
drops and wondering what it might mean is a regular exercise during
crystallization.
And such observations are very valuable to go
The polybasic head indicative of your protein to have some possible
membrane association? Try a detergent in your buffers might help. Also some
of the polybasic head for protein need lipid association to be happy (PI
and PCh)?
Padayatti
On Fri, Aug 23, 2013 at 6:27 PM, Jahan Alikhajeh
Imolview and ndkmol are excellent apps on android to show structures.
Padayatti
On May 1, 2013 3:56 PM, David Roberts drobe...@depauw.edu wrote:
Hello all,
So, I find an ipad is a wonderful device for teaching (any tablet really -
but I'm partial to the ipad). I can project it in a
This is not a reply to the post by some one called Sham or the original
post calling for a faculty position.
Everyone here who ever had an experience to be an IIScian and especially
any one who been
fortunate to experience Molecualr Biophysics Unit
will disagree with what was writen about the
ad do not forget to recalibrate
On Thu, Jul 12, 2012 at 10:53 PM, Zhijie Li zhijie...@utoronto.ca wrote:
Hi,
Yes, it can be done by yourself. I repacked our 26/60 column a few years
ago with homemade apparatus. The column has been working for us since then.
Basically the loading apparatus
beta lactamase
cymal 6
and see this reference
Guan, R.-J., Wang, M., Liu, X.-Q, Wang, D.-C.
Optimization of soluble protein crystallization with
pH is the culprit here
Like some already mentioned
change your pH to 6.4 and use a different buffer like cacodylate
or you can use Zinc acetate in water pH still would be 6.4
from your last mail
why would you add Zn to your initial hit condition
is there any rationale?
Padayatti
On Fri, May 11,
In US Fisher Scientific sells CBS scientific , California different
ranges of gradient maker. I especially found them useful for my use
for density gradient centrifugation. the material
used in the manufacture is clear and easy to clean each time.
It is kind of not very controlled automatically
Hi Rajesh,
First of all you did the right thing to ask people here about our doubts.
There is nothing wrong in asking questions.
The board is for asking questions realted to crystallography
(all aspects).
Padayatti
On Tue, Apr 3, 2012 at 11:07 AM, Rajesh kumar ccp4...@hotmail.com wrote:
Dear
http://www.lablife.org/p?a=vdb_viewid=g2.XyCli.11qhPxFTK4WFNANgFD.Xc-
Is this that you were looking for?(all thanks to google)
lablife gives you the whole sequence. make it if you really need it.
All the best.
Padayatti PS
On Thu, Mar 22, 2012 at 8:39 PM, Nian Huang huangn...@gmail.com wrote:
This is in response to a comment to this thread
Kevin,
Could you explain how that worked?
How do you know your method worked?
Did you estimate the lipopolysaccharide before and after the method?
The method already mentioned here to wash using TritonX100 makes sense.
by washing bound protein
this will work for protein in all of case, but you try in
an eppendorf tube like amini-prep.
I guess this method may have been patented.
On Thu, Mar 8, 2012 at 7:16 AM, Pius Padayatti ppadaya...@gmail.com wrote:
This is in response to a comment to this thread
Kevin
Hi,
Please see a similar thread at ccp4bb earlier at the following link
http://www.proteincrystallography.org/ccp4bb/message16011.html
Padayatti
2012/3/5 anna anna marmottalb...@gmail.com:
Dear all, I hope you can help me!
I solved a structure at 3.0 A res and everything is quite
Rashmi,
Has anyone
seen this kind of behaviour?
Yes, have seen differentially Glycosylated protein samples elute off
affinity resins as separate peaks.
but not that they behave different on gelfiltration like you described
in your case.
possible the samples interact with resin
Will there be
Hi
i do not want to get into trouble by going against any products
The plates what you are talking about as soon it came out we tested.
I did not look back to see if there was a monoolein:cholestrol coated plate.
The ones i used were for sure monoolein coated ones.
That tells it all.The rest of
QuoteParticulalrly the monoolein and monoolein/cholesterol coated plates
( I am not sure I can mention the vendor here but it should not matter)
Since the person who asked this question here
forget about it alltogether to write something back
here is what he was asking about (i think)
Anybody
as well as glass or plastic bases
and glass, plastic or film covers.
If you have not tested Laminex I would be pleased to send you a sample trial
pack.
Tony Savill
Molecular Dimensions Inc.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pius
Hi Yuri,
i strongly suggest these plates sold through Hampton research
Paul Marienfeld GmbH plates for your use.
here is a link , best plates in the market.
link: http://hamptonresearch.com/product_detail.aspx?cid=10sid=182pid=611
Plates comes with extra cover slips in addition to single glass
some more thoughts,
Do a cryo-EM imaging, it will be ideal than DLS.
if the particle sizes are uniform i would think your protein in that state
might be useful.
cheers
Padayatti
On Tue, Feb 21, 2012 at 6:21 PM, Raji Edayathumangalam
r...@brandeis.edu wrote:
Hi Folks,
As crazy as it sounds, if
This was meant to Raji,
So here it goes to all.
-- Forwarded message --
From: Zhang, Zhen zhen_zh...@dfci.harvard.edu
Date: Wed, Feb 22, 2012 at 12:15 PM
Subject: RE: [ccp4bb] Aggregated protein for crystallization
To: Pius Padayatti ppadaya...@gmail.com
Hi Pius,
I have done
there is one nice JOVE video and article from Jeff Abramson lab
which was neat showing using mosquito to set up bicelle.
No offense to Art people
J Vis Exp. 2012 Jan 9;(59). pii: 3383. doi: 10.3791/3383.
High-throughput Crystallization of Membrane Proteins Using the Lipidic
Bicelle Method.
Hi Enricho,
The scenario of streak seeding follows Ostwald ripening but will
this happen in other situations as follows
But in a special case where you have some crystals that appear as large
rods which dissolved when taken out of the incubator (or) during the
observation( these were
a comment to add about phosphatase (PP2A, C class serine theronine)
buying phosphatase for crystallization trials was kind of not
practical( very high prices )
so we tried expressing and purify it from overexpressed in bacterium
with yields very low.
Also the purified phosphtase co-purify some
my comment on expression of protein being low
and nonspecific binding.
Amount of protein of expressed protein less = less resin = less
nonspecific binding?
(one have to do experiments to
find right amount of resin to get least non-specific binding
still pull out most of your protein of interest
Rajesh,
The fonts error please follow the guidelines from following link
http://www.scripps.edu/~arvai/adxv.html
see relevant parts under the heading questions
it did solve issues for me
cheers
psp
On Tue, Nov 22, 2011 at 10:37 AM, Rajesh kumar ccp4...@hotmail.com wrote:
Dear All,
All the
I have few personal remarks about revere matrix seeding protocol suggested here
just an addition to Artems suggested protocol
harvesting the whole drop of interest invite guaranteed
salt crystals in the second round especially if one is
using the same screen back.
If one found crystals all over
jobey,
the last two are kind of phase separation. In some cases the oil like
droplets are
more in number througout the drop.
First two are microcrystalline but the second one is
more looks like made from protein precipitate.
hope this helps
if needed please refer to Terese Bergfors website at
Sorry Jay,
They are for sure phosphate crystals.
They always looked like that.
psp
On Sun, May 29, 2011 at 5:18 PM, Jayashankar s.jayashan...@gmail.com wrote:
Dear Friends ,
I need to know whether phosphate can form hexagon shaped crystals.
In one particular condition i have 4 different
by adding new external keywords as described as in the PDF described by
Garib N Murshudov
www.ccp4.ac.uk/schools/China-2011/talks/refmac_Shanghai.pdf
Padayatti PS
On Mon, Apr 25, 2011 at 5:19 AM, Zhipu Luo zhipu...@yahoo.com wrote:
I know that refmac5 can run Jelly-body refinement for low
To all Laue experts up here
How does a Laue data is collected?
Thanks in advance to all
PSP
On Fri, Jan 28, 2011 at 3:43 AM, REX PALMER rex.pal...@btinternet.comwrote:
What programs are available for processing Laue data to produce an
intensity data set?
Are explanatory notes or
ealrier on this forum Artem have posted about PTM
in bacteria.
this answer your question on PTM in bacteria.
QUOTE
Yes, this does happen.
Spontaneous α-N-6-Phosphogluconoylation of a His Tag inEscherichia
coli:The Cause of Extra Mass of 258 or 178 Da in Fusion Proteins
a most approapriate paper for the method that i described earlier is
in the following
paper. Follow the link
Optimum solubility (OS) screening: an efficient
method to optimize buffer conditions for
homogeneity and crystallization of proteins
if you are crystallizing membrane protein
here is a useful protocol from JCIPMT website
follow the link
http://jcimpt.scripps.edu/protocols/JCIMPT_PreparationofCHSStock.pdf
in my experience even after extensive sonication i filter the buffers
otherwise we found that cholestrol comes out of
could try reverse matrix seed
On Sun, Apr 18, 2010 at 10:46 PM, tat cheung cheng
theif...@yahoo.com.hk wrote:
Hi all,
I have got some crystals, the purified protein was in Tris buffer with 300mM
NaCl for crystallization. they grew in light weight PEG, PEG400 or monomethyl
ethyl PEG500,
may be diafiltration devices might work for you. the membranes are
kind of expensive but we had used this effectively to reduce the volume
of cell culture media where we had secreted proteins in large volumes
of culture media.
here is a link
http://www.spectrapor.com/lit/hfdial.pdf
padayatti
On
may be diafiltration devices might work for you. the membranes are
kind of expensive but we had used this effectively to reduce the volume
of cell culture media where we had secreted proteins in large volumes
of culture media.
here is a link
http://www.spectrapor.com/lit/hfdial.pdf
padayatti
On
will work fine but leave overnight.
psp
On Tue, Jun 2, 2009 at 5:36 PM, Jerry McCully
for-crystallizai...@hotmail.com wrote:
Dear All:
Recent we expressed one protein using mammalian cells but this
protein was highly glycosylated (30% of the total molecular weight).
We want to
ping,
we had great success as far as price and level of synthesis
with a company called Synbiosci, Livermore, CA.
I am no way connected to this company but just a suggestion.
hope it helps
psp
On Mon, Jun 1, 2009 at 10:31 AM, ping sun ccp4@gmail.com wrote:
Dear All,
I would appreciate if
Hello fellow members of the forum,
Protein expression related question.
We need some recomendations for a reliable and quality
service for production of bacculovirus pellet in bulk.
people can send private email me.
Thanks for the attention.
Padayatti PS
--
Pius S Padayatti
Phone: 216-658-4528
Here is the original article.
Distinction between the weak hydrogen bond and the van der Waals
interaction
Thomas Steiner*a and Gautam R. Desiraju*
Chem. Commun., 1998 891-892
On Thu, Feb 19, 2009 at 11:27 PM, Pius Padayatti ppadaya...@gmail.com wrote:
Table 1 Numerical data for X–H···Y contacts
Table 1 Numerical data for X–H···Y contacts with H···Y 3.0 Å (2.7 Å for
H···H contacts). Data for normalised H-atom positions
MeanMeanMean
Contact typeNumber H···Y (Å) X···Y (Å) X–H···Y (°)
C(sp3)–O–H···ONC33301.974(6)
nanodrop system is wonderful. it helps very much in solutions with
high interference from detergents etc etc.
i highly receommend nanodrop specs
PSP
On Thu, Dec 4, 2008 at 10:16 AM, Tim Gruene [EMAIL PROTECTED] wrote:
Dear all,
we would like to purchase a UV spectrometer for measuring
Hi,
It is called Bacmam. Please see the following reference, it is not
the land mark reference, if you dig pubmed you should be able to find
the first description of the system.
BacMam recombinant baculovirus in transporter expression: a study of
BCRP and OATP1B1.
Protein Expr Purif. 2006
dollins,
I do have an excellent reference for you to read
J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Mar 25;769(1):133-44.
Strategies for the purification and on-column cleavage of
glutathione-S-transferase fusion target proteins.Dian C, Eshaghi S,
Urbig T, McSweeney S, Heijbel A, Salbert
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