Nabble - Bio.net - Proteins

Re: plant protein extraction

2009-11-05T12:57:17Z

In article <mailman.32.1254676405.1133.proteins@...>, elham
rastegari <elham.rastegar@...> wrote:

> Dear all,
>
> I did protein extraction from fruit (Curculigo latifolia) according to the
> attached protocol. I got the white pellet. but while i left it to air dry
> briefly, i saw the color of pellet got darker, in some parts, it changed to
> black. i think while i took the phenol phase, unwanted substances entered.Do
> you have any idea of the type of the substance that causes this,
>
> then the pellet was solubilised with urea, thiourea, chaps. agitated for
> two hours at 4 degree then no parts of pellet remained and all solubilised.
> then i centrifuge at 12000g for 10 min, in one tube a white substance and in
> another one an almost dark substance precipitated. i took the supernatant
> for bradford protein assay.
>
> i would be grateful if you could help me identify these unwanted substances.
>
> Regards,
> Eli

I am sure that what is causing your problem (darkening to black) is
residues of polyphenolics, biphenolics, etc. Most land plants have enzymes
called polyphenol/biphenol oxidases which cause huge problems when
attempting to purify RNA or DNA (and apparently protein). I have had a
moderate amount of experience in isolating (or trying to isolate) usable
nucleic acids from ferns, mosses, a liverwort as well as gymnosperms and
angiosperms. Generally, flowering plants that are food sources tend to be
low in polyphenols so they are usually easier to work with. Curculigo
latifolia (Molineria latifolia) is known for its protein curculin (a
potential artificial sweetener) but I would suspect the fruit does contain
lots of polysaccharides as well as apparently the phenolic compounds.
I think you have a challenging problem here. I know how nucleic acid
extraction could probably be accomplished but what you want (the protein)
is normally in the part you throw out in nucleic acid extractions, and
phenolic compounds are also normally in the organic phase except for those
permanently cross-linked to the RNA or DNA that you may be trying to
purify.
Certainly keeping a reducing agent like mercaptoethanol or DTT in the
solutions will inhibit the phenol oxidases, but I think the whole protocol
will have to be rethought to attempt to separate the protein fraction from
the phenolics as early as possible.
Your difficulties are certainly not unexpected or unique because they are
faced frequently by anyone trying to do much molecular biology on plants.

Cheers,

David
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Secondary Structure and Surface Accessibility predictions easily made

2009-10-07T12:51:08Z

Hi Everyone,
I have seen that many people are interested in Secondary Structure
predictions, and
also interested in the surface of proteins.

I therefore want to bring your attention to a paper I have recently
published, which has the title: A generic method for assignment of
reliability scores applied to solvent accessibility predictions.,

which is freely available here: http://www.biomedcentral.com/1472-6807/9/51

It describes a new method, which is implemented in our freely
available method: NetSurfP:
http://www.cbs.dtu.dk/services/NetSurfP/

Basically it predicts the secondary structure of a protein, its
surface accessibility and also the reliability of surface
accessibility prediction in form of a z-score :-)

I hope you will find it useful in your research :-)

Best Regards,

Bent Petersen, Ph.D Student, M.Sc.

Center for Biological Sequence Analysis - CBS
Department of Systems Biology,
Technical University of Denmark.
Bld. 208, DK-2800 Lyngby, Denmark
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Re: How to compare multiple pdb's according to secondary struc+torsion angles

2009-10-07T06:25:58Z

Am 05.10.2009, 06:13 Uhr, schrieb Afonso Duarte <afonsomduarte@...>:

> Dear All,
>
> I have approximately 40 to 50 pdb structures of homologous proteins
> that I want to compare.
> I am interested on plotting the sequence vs (secondary
> structure/torsion_angles/accessibility/hydrophobicity). I have tried
> software like VMD and WHATIF to do such plots (or part of them) but I
> am getting problems when the number of structures compared is getting
> close to 10...
> Does anybody knows a software/script/webpage that allows such
> comparison of such number of pdb ?

DeepView (formerly the Swiss PDB viewer, www.expasy.ch/spdbv/) can
superimpose structures for optical comparison. It can also save a list of
phi/psi values (Save - Ramachandran plot) for each protein as text file.
You could then enter these values into a spreadsheet for further analysis,
or write your own software to do further evaluation. It may be necessary
to align the proteins first with Clustal, so that you compare like with
like.
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How to compare multiple pdb's according to secondary struc+torsion angles

2009-10-05T03:13:13Z

Dear All,

I have approximately 40 to 50 pdb structures of homologous proteins
that I want to compare.
I am interested on plotting the sequence vs (secondary
structure/torsion_angles/accessibility/hydrophobicity). I have tried
software like VMD and WHATIF to do such plots (or part of them) but I
am getting problems when the number of structures compared is getting
close to 10...
Does anybody knows a software/script/webpage that allows such
comparison of such number of pdb ?

Thanks in advance

Afonso

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plant protein extraction

2009-10-04T08:44:10Z

Dear all,

I did protein extraction from fruit (Curculigo latifolia) according to the
attached protocol. I got the white pellet. but while i left it to air dry
briefly, i saw the color of pellet got darker, in some parts, it changed to
black. i think while i took the phenol phase, unwanted substances entered.Do
you have any idea of the type of the substance that causes this,

then the pellet was solubilised with urea, thiourea, chaps. agitated for
two hours at 4 degree then no parts of pellet remained and all solubilised.
then i centrifuge at 12000g for 10 min, in one tube a white substance and in
another one an almost dark substance precipitated. i took the supernatant
for bradford protein assay.

i would be grateful if you could help me identify these unwanted substances.

Regards,
Eli
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Practical Course in Biomolecular Modelling

2009-09-25T05:50:33Z

Dear colleagues,

please be informed that online applications are still accepted for the
following course until October 16, 2009:

8TH NCCR PRACTICAL COURSE IN BIOMOLECULAR MODELLING

January 10 - 15, 2010
Kandersteg, Switzerland
http://www.structuralbiology.uzh.ch/course2010.asp

Course topics include
Simulation techniques, force-field development, conformational search,
computation of free energy and entropy, treatment of electrostatic
forces, simulation of folding, comparison of simulation with experiment

This course is primarily directed to PhD students and postdocs from
experimental structural biology groups wishing to learn more on
biomolecular modelling. The course format will include morning lectures
and late-afternoon/early evening tutorials, and provide ample
opportunities for discussions with experts and fellow participants.
Participants will be invited to bring own problems for tutorials and/or
discussion. The course will be organized as a winter retreat in the
Swiss Alps offering a stimulating learning atmosphere with the
afternoons available for informal participation in discussions, reading
and self-study or recreational activities in the area.

Interested candidates are encouraged to apply online on
http://www.structuralbiology.uzh.ch/course2010_application.asp.
Application deadline will be October 16, 2010. We will be able to accept
20 participants to this course.

Best regards,
Patrick Sticher

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www.structuralbiology.uzh.ch

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University of Zürich
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Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08
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SDS-PAGE

2009-09-23T07:10:06Z

Dear all,

I perform *TCA-acetone, methanol washes and phenol precipitation* to extract
protein from fruit sample. To see clear bands in SDS-PAGE, I need to remove
polysaccharide. Does anybody know how to remove extracellular
polysaccharide?

Thanks in advance
Eli
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Hettich centrifuge schematics

2009-09-21T05:42:13Z

Does anybody have a Hettich centrifuge schematics. The Hettich 30RF Universal
centrifuge repair manual would be best but any Hettich should do as we just
want to limit a broken centrifuge to a set speed.
The expense to buy the circuit diagram is too much. So if anyone could help it
would be greatly appreciated.

Thanks James.

James Herbert

Lab Manager
School of Biological Sciences
Flinders University
Adelaide
South Australia

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Re: Proteins Digest, Vol 52, Issue 3

2009-09-13T18:22:25Z

Are you sure the aggregation is not caused by dna interweaving between protein molecules? If that's the cause, Benzonase will be a good choice for DNA clearance.

> -----Original E-mail-----
> From: proteins-request@...
> Sent Time: 2009-9-10 1:04:09
> To: proteins@...
> Cc:
> Subject: Proteins Digest, Vol 52, Issue 3
>
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> Today's Topics:
>
> 1. Re: QUERY (Dr Engelbert Buxbaum)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 08 Sep 2009 09:58:37 -0400
> From: "Dr Engelbert Buxbaum" <engelbert_buxbaum@...>
> Subject: [Protein-analysis] Re: QUERY
> To: proteins@...
> Message-ID: <op.uzxyfzdu66vu6s@...>
> Content-Type: text/plain; format=flowed; delsp=yes;
> charset=iso-8859-15
>
> Am 04.09.2009, 10:59 Uhr, schrieb Monica Mittal <monicamittal41@...>:
>
> > HI
> > I'M FACING PROBLEM IN PURIFYING A protein which is a dna binding protein
> > but its showing a kind of hydrophobic behaviour as its max part is going
> > into pellet after lysis.
> > moreover its not responding to ni2+ nta column also and the lysis sol.
> > is not so clear that i go for gel filteration as it may probably clog it
> > so can u suggest any solution?
>
> Does that mean you are expressing a poly-His tagged protein in bacteria?
> If so, have you checked that your protein is not in inclusion bodies? How
> did you lyse? How long and at what g did you try to clarify your lysate (1
> h at 100000 g should do the trick)? Have you fragmented the bacterial DNA,
> and are you sure that your protein is not binding to the fragments? Are
> you protecting against oxidation and proteolysis?
>
>
> ------------------------------
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Re: QUERY

2009-09-08T06:58:37Z

Am 04.09.2009, 10:59 Uhr, schrieb Monica Mittal <monicamittal41@...>:

> HI
> I'M FACING PROBLEM IN PURIFYING A protein which is a dna binding protein
> but its showing a kind of hydrophobic behaviour as its max part is going
> into pellet after lysis.
> moreover its not responding to ni2+ nta column also and the lysis sol.
> is not so clear that i go for gel filteration as it may probably clog it
> so can u suggest any solution?

Does that mean you are expressing a poly-His tagged protein in bacteria?
If so, have you checked that your protein is not in inclusion bodies? How
did you lyse? How long and at what g did you try to clarify your lysate (1
h at 100000 g should do the trick)? Have you fragmented the bacterial DNA,
and are you sure that your protein is not binding to the fragments? Are
you protecting against oxidation and proteolysis?
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Re: QUERY

2009-09-04T21:01:06Z

its not going into pellet due to hydrophobicity. It is forming inclusion bodies during overexpression.
You are required to dissolve the protein and refold it.
Please fiollow the procedure "how to refold protein from inclusion bodies"
Good luck with your work
Yogendra
-- Original Message --
From: Monica Mittal <monicamittal41@...>
To: proteins@...
Date: Fri, 4 Sep 2009 20:29:26 +0530 (IST)
Subject: [Protein-analysis] QUERY
HI
I'M FACING PROBLEM IN PURIFYING A protein which is a dna binding protein but its showing a kind of hydrophobic behaviour as its max part is going into pellet after lysis.
moreover its not responding to ni2+ nta column also and the lysis sol. is not so clear that i go for gel filteration as it may probably clog it
so can u suggest any solution?
monica
Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com
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RE: QUERY

2009-09-04T20:25:02Z

Hi Monica,

If your protein is in the pellets I hope you are using denaturing conditions to solubilize it before purification over Ni-NTA.

solubilize the protein in urea or guanidine for one hour and spin down to get a clear lysis solution before you proceed to further purification steps Ni-NTa or gel.

cheers

wajahat

> Date: Fri, 4 Sep 2009 20:29:26 +0530
> From: monicamittal41@...
> To: proteins@...
> CC:
> Subject: [Protein-analysis] QUERY
>
> HI
> I'M FACING PROBLEM IN PURIFYING A protein which is a dna binding protein but its showing a kind of hydrophobic behaviour as its max part is going into pellet after lysis.
> moreover its not responding to ni2+ nta column also and the lysis sol. is not so clear that i go for gel filteration as it may probably clog it
> so can u suggest any solution?
>
> monica
>
>
>
> Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com
> _______________________________________________
> Proteins mailing list
> Proteins@...
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QUERY

2009-09-04T07:59:26Z

HI
I'M FACING PROBLEM IN PURIFYING A protein which is a dna binding protein but its showing a kind of hydrophobic behaviour as its max part is going into pellet after lysis.
moreover its not responding to ni2+ nta column also and the lysis sol. is not so clear that i go for gel filteration as it may probably clog it
so can u suggest any solution?

monica

Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com
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Re: plant proteomics

2009-08-27T23:53:27Z

On Aug 26, 6:44 pm, elham rastegari <elham.raste...@...> wrote:

> Dear all,
>
> My project is protein extraction and identification of Curculigo latifolia
> fruit(somehow protein profiling). i already extracted all the proteins
> through TCA-aceton methanol washes phenol precipitation. and i plan to do
> two dimensional gel electrophoresis to get spots and then send the spots to
> Ms/MS to sequence, but it would be very expensive to apply for all spots.So
> would you tell me if you were me, which kind of spots you would choose?
> please help me narrow my identification.
>
> cheers Eli

Hi,

there are just few proteins or cDNA sequences for Curculigo
latifolia / C. capitulata and Hypoxidaceae in general. So you will be
going for de novo protein sequencing. This will make sense if you want
to spot a difference, say between ripe / non-ripe fruit .
As a method for characterising proteome, de novo protein sequencing is
to costly/to low throughput.
IMHO it is way easier to go for EST sequencing first, as a stepping
stone for proteome characterisation.

Best,

darked
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7th Georgia Tech - ORNL Conference on Bioinformatics

2009-08-26T12:13:06Z

--------------------------------------------
CALL FOR PAPERS

Dear Colleagues

The 7th Georgia Tech - ORNL Conference on Bioinformatics -
In silico Biology: Genome Biology and Bioinformatics
will be held in
Atlanta, Georgia, November 12-14, 2009
http://www2.isye.gatech.edu/binf2009/

Georgia Tech continues the tradition of organizing bi-annual
International Conference on Bioinformatics, bringing together leading
researchers in genomics, bioinformatics and genome biology to present recent
advances in the field and to discuss open problems.

Important Dates
Deadline for early registration: October 15, 2009
Deadline for poster abstract subsmission: October 1, 2009
Notification of acceptance of abstracts: October 11, 2009

We invite papers submissions in the following areas
* genomics;
* transcriptomics;
* proteomics;
* reconstruction and modeling of gene networks;
* evolutionary biology;

SPEAKERS

Margaret O. Dayhoff lecture
David Lipman , NCBI/NIH, Bethesda, MD, USA

Plenary Speakers:
Vineet Bafna, University of California at San Diego, USA
Gill Bejerano, Stanford University, Stanford, CA, USA
Jeffrey Bennetzen, University of Georgia, Athens, GA, USA
Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA
Nick Grishin, University of Texas, Dallas, TX, USA
Curtis Huttenhower, Harvard University, Boston, MA, USA
King Jordan, Georgia Tech, Atlanta, GA, USA
Igor Jouline (Zhulin), University of Tennessee - ORNL, Oak Ridge, TN, USA
Eugene Koonin, NCBI/NIH, Bethesda, MD, USA
Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA
Boris Lenhard, University of Bergen, Norway
Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA
Yael Mandel-Gutfreund, Technion, Israel Insitute of Technology, Haifa, Israel
Joanna Masel, University of Arizona, Tucson, AZ, USA
Andrey Mironov, Moscow State University, Russia
Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA
Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA
Natasa Przulj, University of California at Irvine, CA, USA
John Reinitz, State Uiversity of New York at Stony Brook, NY, USA
Pierre Rouze, Gent University, Gent, Belgium

CONFERENCE CHAIRS
Mark Borodovsky, Georgia Tech and Emory University
Eva K. Lee, Georgia Tech and Emory University

PROGRAM COMMITTEE
Nicholas Bergman, Georgia Tech
Dmitrij Frishman, Munich Polytechnic University, Germany
Andrey Gorin, Oak Ridge National Laboratory
Andrzej M. Kierzek, University of Surrey, UK.
Eileen Kraemer, University of Georgia
Jun Liu, Harvard University
Andrey Rzhetsky, University of Chicago
Andre Rogatko, Samuel Oschin Comprehensive Cancer Institute
Gary Stormo, Washington University
Ying Xu, University of Georgia and Oak Ridge National Laboratory
Soojin Yi, Georgia Tech
Igor Zhulin, Oak Ridge National Laboratory and University of Tennessee

ADMINISTRATION
Harry Sharp, Georgia Tech

CONFERENCE LOCATION
The Georgia Tech Ferst Center for the Arts. The Georgia Tech campus is located in Midtown Atlanta near the center of the 1996 Olympic development, close to the Fox Theatre and Margaret
Mitchell house.

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plant proteomics

2009-08-26T09:44:41Z

Dear all,

My project is protein extraction and identification of Curculigo latifolia
fruit(somehow protein profiling). i already extracted all the proteins
through TCA-aceton methanol washes phenol precipitation. and i plan to do
two dimensional gel electrophoresis to get spots and then send the spots to
Ms/MS to sequence, but it would be very expensive to apply for all spots.So
would you tell me if you were me, which kind of spots you would choose?
please help me narrow my identification.

cheers Eli
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Seeking collaboration

2009-08-25T18:27:50Z

Seeking collaboration for studying interaction between proteins and different inorganic surfaces. For details: http://tinyurl.com/m2bjof
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Re: Protein biosynthesis

2009-08-25T07:27:19Z

Am 25.08.2009, 03:48 Uhr, schrieb <kaj.stenberg@...>:

> David Bienvenue <DBienvenue@...> wrote:
>
>> Protein biosynthesis starts at the N-terminus.
>
> However, this means that each new amino acid is attached to the
> C-terminus of the growing peptide.

And note that above is true only for biological protein synthesis,
chemists do it the other way round (Merrifield peptide synthesis). In case
of daubt, it is worthwhile to write peptides like NH2-XXXXX-COOH (I have
been burned!)
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RE: Proteins Digest, Vol 51, Issue 3

2009-08-25T06:49:11Z

For ribosomal protein synthesis: The aminogroup of the next amino acid is linked to the carboxyl group of the previous amino acid.
Victor

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Today's Topics:

1. protein biosynthesis (gord)

----------------------------------------------------------------------

Message: 1
Date: Sun, 23 Aug 2009 18:27:49 -0400
From: "gord" <gayers07@...>
Subject: [Protein-analysis] protein biosynthesis
To: proteins@...
Message-ID: <Gnjkm.114076$rg4.44728@...>

Hello All

I would like to know to which end of the elongating protein chain, during biosysnthesis, is the next amino acid attached. Amino or carboxyl.

Thank you.

Gord

------------------------------

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Re: Protein biosynthesis

2009-08-25T00:48:55Z

David Bienvenue <DBienvenue@...> wrote:

> Protein biosynthesis starts at the N-terminus.

However, this means that each new amino acid is attached to the
C-terminus of the growing peptide.

--
Kaj
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Re: Protein biosynthesis

2009-08-24T15:14:56Z

Thank you very much for your reply

Gord

"David Bienvenue" <DBienvenue@...> wrote in message
news:mailman.836.1251144189.21502.proteins@......

>
> Protein biosynthesis starts at the N-terminus.
>
>
>
> David Bienvenue, Ph.D.
> Senior Principal Scientist
> VLST Corporation
> Seattle, WA 98109
>
>
> -----Original Message-----
> From: proteins-bounces@...
> [mailto:proteins-bounces@...] On Behalf Of
> proteins-request@...
> Sent: Monday, August 24, 2009 10:04 AM
> To: proteins@...
> Subject: Proteins Digest, Vol 51, Issue 3
>
> Send Proteins mailing list submissions to
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>
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>
>
> Today's Topics:
>
> 1. protein biosynthesis (gord)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 23 Aug 2009 18:27:49 -0400
> From: "gord" <gayers07@...>
> Subject: [Protein-analysis] protein biosynthesis
> To: proteins@...
> Message-ID: <Gnjkm.114076$rg4.44728@...>
>
> Hello All
>
> I would like to know to which end of the elongating protein chain,
> during biosysnthesis, is the next amino acid attached. Amino or carboxyl.
>
> Thank you.
>
> Gord
>
>
>
>
> ------------------------------
>
> _______________________________________________
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>
> End of Proteins Digest, Vol 51, Issue 3
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RE: Protein biosynthesis

2009-08-24T10:36:04Z

Protein biosynthesis starts at the N-terminus.

David Bienvenue, Ph.D.
Senior Principal Scientist
VLST Corporation
Seattle, WA 98109

-----Original Message-----
From: proteins-bounces@... [mailto:proteins-bounces@...] On Behalf Of proteins-request@...
Sent: Monday, August 24, 2009 10:04 AM
To: proteins@...
Subject: Proteins Digest, Vol 51, Issue 3

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Today's Topics:

1. protein biosynthesis (gord)

----------------------------------------------------------------------

Message: 1
Date: Sun, 23 Aug 2009 18:27:49 -0400
From: "gord" <gayers07@...>
Subject: [Protein-analysis] protein biosynthesis
To: proteins@...
Message-ID: <Gnjkm.114076$rg4.44728@...>

Hello All

I would like to know to which end of the elongating protein chain,
during biosysnthesis, is the next amino acid attached. Amino or carboxyl.

Thank you.

Gord

------------------------------

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End of Proteins Digest, Vol 51, Issue 3
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protein biosynthesis

2009-08-23T15:27:49Z

Hello All

I would like to know to which end of the elongating protein chain,
during biosysnthesis, is the next amino acid attached. Amino or carboxyl.

Thank you.

Gord

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Help: Manual for Speed Vac Concentrator SVC-100H

2009-08-17T13:58:58Z

Dear Jim,
I realize your posting was over 3 years ago, but... for others with
this need too.
I just talked to John Olson at GMI (763-712-8717 USA), a distributer
for Savant items (mostly used), and he had an in-house version of of the
manual he could send you via an e-mail attachment. His e-mail is
jolson@....
The biggest reason speed vacs stop working, in terms of evaporative
power, is due to dirty pump oil. Get a gauge and check the amount of
vacuum it really provides. Or, more pragmatically, just change your vac
pump oil. Yah, it's a pain. If you have something more volatile than
water to evaporate, get dry ice onto your cold trap to get the vapor
coming off of your sample into liquid phase so you can drive more vapor
off of you sample.
Good Luck,

Laura
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Practical Course in Biomolecular Modelling

2009-08-14T07:33:37Z

Dear colleagues,

please be informed that online applications are accepted for the
following course:

8TH NCCR PRACTICAL COURSE IN BIOMOLECULAR MODELLING

January 10 - 15, 2010
Kandersteg, Switzerland
http://www.structuralbiology.uzh.ch/course2010.asp

Course topics include
Simulation techniques, force-field development, conformational search,
computation of free energy and entropy, treatment of electrostatic
forces, simulation of folding, comparison of simulation with experiment

This course is primarily directed to PhD students and postdocs from
experimental structural biology groups wishing to learn more on
biomolecular modelling. The course format will include morning lectures
and late-afternoon/early evening tutorials, and provide ample
opportunities for discussions with experts and fellow participants.
Participants will be invited to bring own problems for tutorials and/or
discussion. The course will be organized as a winter retreat in the
Swiss Alps offering a stimulating learning atmosphere with the
afternoons available for informal participation in discussions, reading
and self-study or recreational activities in the area.

Interested candidates are encouraged to apply online on
http://www.structuralbiology.uzh.ch/course2010_application.asp.
Application deadline will be October 16, 2010. We will be able to accept
20 participants to this course.

Best regards,
Patrick Sticher

--
_________________________________
Visit the NCCR on the Internet
www.structuralbiology.uzh.ch

Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08
Mail sticher@...

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NCCR Symposium on New Trends in Structural Biology / NCCR Practical Course on Biomolecular Modelling

2009-07-17T06:51:30Z

Dear colleagues,

we have two announcements to make:
_____________________________________________________________

7th International NCCR Symposium on New Trends in Structural Biology
7 + 8 September 2009, ETH Zürich, Lecture Hall HG E7, Zürich, Switzerland
www.structuralbiology.uzh.ch/symposium2009

The lecture program is available online at:
http://www.structuralbiology.uzh.ch/symposium2009/program.asp

Plenary lecturers:
Frédéric Allain, Pietro de Camilli, Raimund Dutzler, Arthur L. Horwich,
Brian Kobilka, Harry Noller,
Anna Marie Pyle, Ben Schuler, David Wemmer, Masasuke Yoshida

Online registration to this event is still possible through the
symposium homepage or directly at:
http://www.structuralbiology.uzh.ch/symposium2009/registration09.asp
_____________________________________________________________

8th NCCR Practical Course and 2nd Winter School
Biomolecular Modelling

The 8th NCCR Practical Course will cover key topics in the area of
computational structural biology. The course format includes morning
lectures by experts in the field that alternate with later afternoon to
evening tutorials and discussions. The course will be organized as a
winter retreat in the Swiss alps offering participants the opportunity
to learn in a stimulating atmosphere, enjoy winter activities in the
swiss alps during course breaks, and network and exchange ideas on an
informal basis with fellow participants, tutors, and lecturers.

More information at http://www.structuralbiology.uzh.ch/course2010.asp
Online Application will be possible as of July 31, 2009
_____________________________________________________________

Please do not hesitate to contact me anytime if you need further
information (sticher@...).

With best regards,
Patrick Sticher

The NCCR Structural Biology is a research initiative of the Swiss
Science Foundation. Its research encompasses the fields of recombinant
protein technologies, macromolecular structure determination and
computational biomolecular sciences with a special focus on membrane
proteins and supramolecular assemblies/interactions. 13 research groups
from Swiss Universities and Research Institutions participate in this
network. www.structuralbiology.uzh.ch/

--
_________________________________
Visit the NCCR on the Internet
www.structuralbiology.uzh.ch

Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08
Mail sticher@...

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Concentration Protein after fluorescent labeling

2009-06-18T04:30:05Z

Does anyone knows how the concentration of labeled protein with Alexa 647 can be determined? Normal methods such as OD280, Bradford and coomassie stain have to much interference with the dye to give a good concentrations.

Peggy

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HPLC Troubleshooting question

2009-06-11T09:20:08Z

Hello;

I have a 486 Waters detector, and last day an erros message apears in were
the wavelnght should apear. We looked up what does the message means and was
related with change the battery. We open the instrumente, and change it and
the message disapears but now, there is no back comunication between the
detector and the computer, we can controll the flow and the parametres, but
we can´t see the chrommatogram.

I don´t know how can help me, thanks a lot. I would be pleasure if you could
help me or send me information about where I can look it up.

Elena Guinea
University of Guelph, On
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Invitation to Review: AJBR-08-041

2009-06-08T08:50:02Z

African Journal of Biochemistry Research

www.academicjournals.org/ajbr

Dear Collegue,

We received a manuscript titled: **

The contribution of Ser463 residue to the enzymatic and autoprocessing
activities of *Escherichia coli *��-glutamyltranspeptidase

Below you will find the abstract

A serine residue, Ser463, required for the proper function of *Escherichia
coli* g-glutamyltranspeptidase (*Ec*GGT) was identified by site-directed
mutagenesis on the basis of sequence alignment of human, pig, rat, and three
bacterial enzymes. Thr-, Asp-, and Lys-substituted variants were
overexpressed in *E. coli *M15 cells and the recombinant proteins were
purified to near homogeneity by nickel-chelate chromatography. With the
exception of S463T, the other two variants completely lost GGT activity,
implying the importance of this residue in *Ec*GGT. Moreover, substitution
of Ser463 with either Lys or Asp impaired the capability of autocatalytic
processing of the precursor into a- and b-subunit. Computer modeling showed
that the critical bonding distance of Gln390 C-Thr391 OG1 is significantly
increased in S463D and S463K, indicating that these distance changes might
be responsible for the lack of enzyme maturation. Measurements of intrinsic
tryptophan fluorescence revealed alteration of the microenvironment of
aromatic amino acid residues in S463D and S463K, while circular dichroism
spectra were nearly identical for wild-type and all mutant enzymes. The
temperature-dependent signal in the far-UV region for S463T was consistent
with that of wild-type enzyme but S463D and S463K showed a different
sensitivity towards temperature-induced denaturation. These results imply
that a significant conformational change occurred as a result of Asp- and
Lys-substitution.

Key words: *Escherichia coli*, g-glutamyltranspeptidase, site-specific
mutagenesis, autocatalytic processing, tryptophan emission fluorescence,
circular dichroism

i am looking forward to your response if you are interested in reviewing.

Best regards,

Prof. Johnson Lin

Editor, African Journal of Biochemistry Research

E-mail: * **ajbr.acadjourn@...* <ajbr@...>

http://www.academicjournals.org/AJBR
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Call for Papers: Computational Analysis of Biological Networks in Journal Advances in Bioinformatics

2009-06-05T07:59:26Z

Deadline: August 1, 2009

Computational Analysis of Biological Networks

Call for Papers

One of the fundamental goals of bioinformatics is to understand the
biological processes that are the driving forces behind organisms'
functions. Biological networks such as metabolic, gene regulatory, and
protein interaction networks show how various biochemical entities
interact with each other to perform vital functions that they cannot
perform alone. A critical common property of biological networks is that
although the individual entities of a pathway may have specific
functions, they play additional roles in the entire network by
communicating with other entities.

This Special Issue focuses on novel computational approaches and methods
for understanding biological networks. This issue will publish original,
high-quality research articles. High-risk/high-gain ideas for
understanding biological networks are welcome. Manuscripts should
include biological impact and validation as well as technical depth. The
topics that are included (but not limited to) in this issue are:

* Pathway reconstruction
* Comparison and querying of biological networks
* Annotation of functional subnetworks
* Motif discovery in networks
* Steady-state analysis of networks and the whole cell model
* Analysis of network-disease family relationships

Before submission, authors should carefully read over the journal's
Author Guidelines, which are located at
http://www.hindawi.com/journals/abi/guidelines.html. Prospective authors
should submit an electronic copy of their complete manuscripts through
the journal manuscript tracking system at http://mts.hindawi.com/,
according to the following timetable:

Manuscript Due August 1, 2009
First Round of Reviews November 1, 2009
Publication Date February 1, 2010

Lead Guest Editor

* Tamer Kahveci <mailto:tamer@...>, Computer and
Information Sciences and Engineering Department, University of
Florida, FL 32610, USA

Guest Editors

* Tolga Can <mailto:tcan@...>, Department of Computer
Engineering, Middle East Technical University, 06531 Ankara, Turkey
* Limsoon Wong <mailto:wongls@...>, School of Computing,
National University of Singapore, Room 3-34, Building COM1, 13
Computing Drive, Singapore, Singapore 117417
* Zhongming Zhao <mailto:zzhao@...>, Virginia Commonwealth
University, VA 23284, USA

--
============================================
Zhongming Zhao, Ph.D.
Asst. Professor of Bioinformatics
Depts. Psychiatry and Human Genetics and Center for the Study of Biological Complexity
Virginia Commonwealth University
PO Box 980126, Richmond VA 23298-0126
Phone: (804) 828-8129 Fax: (804) 828-1471
http://bioinfo.vipbg.vcu.edu/

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Re: RNA LABELING

2009-05-22T11:11:21Z

Am 19.05.2009, 17:06 Uhr, schrieb nada mohamed <nadmsa1@...>:

> I am a PhD student and I am studying RNA-Protein interaction. I need a
> protocol to label my RNA at 5'end with biotin, I found some researches
> using megascript kit to incorporate biotin and others using Maxiscript I
> am confused which one is suitable ? and is there any alternative
> methods, also what is the criteria that must be taken in account for RNA
> biotin labeling (to be sure that my RNA is not affected by biotin
> incorporation), I mean the size of RNA the amount
> of labeled nucleotides. Any help will be appreciated.

Don't use any kit until you have fully understood the method and can
perform it with standard chemicals. Then kits can save you some time.
Doing kits blindly however is a recipe for disaster.
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RNA LABELING

2009-05-19T14:06:50Z

Dear all,

I am a PhD student and I am studying RNA-Protein interaction. I need a protocol to label my RNA at 5'end with biotin, I found some researches using megascript kit to incorporate biotin and others using Maxiscript I am confused which one is suitable ? and is there any alternative methods, also what is the criteria that must be taken in account for RNA biotin labeling (to be sure that my RNA is not affected by biotin incorporation), I mean the size of RNA the amount of labeled nucleotides. Any help will be appreciated.

Regards,

PhD student @IMPERIAL COLLEGE LONDON.

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Contaminating Proteins for Fluorescence Polarization Assay

2009-05-15T13:58:25Z

I am handing over some protein samples to a collaborator to do a fluorescence polarization assay to determine binding affinity as a check for activity of a protein that I'm modifying. Using quantitative Western or Coomassie Blue stain, I can determine the concentration of just the protein of interest in a mixture. My question is whether contaminating proteins (carrier protein, enzyme for modifications, etc) will affect the readout of the fluorescence polarization reading. I will lose a significant amount of modified protein if I purify it from the mixture, so I'm wondering if the "dirty" prep would work for fluorescence polarization if I know the concentration of the protein I'm interested in.

Thanks

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gene expression study

2009-05-15T04:04:09Z

Hi all,
I am interested to study the expression of a set of genes from rice
and arabidopsis.Can any one tell me the simplest server/site to
perform this analysis for me.
regards
chunnu
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EMBO Conference Series on Protein Synthesis and Translational Control

2009-05-05T19:07:19Z

Dear Colleagues,

EMBO Conference Series on Protein Synthesis and Translational Control
Partnered with the "CSHL Meeting on Translational Control"

EMBL Heidelberg, Germany, 9 - 13 September 2009
This is to alert you of the upcoming registration and abstract deadline 1 June 2009, which is less than 1 month away. There will be no deadline extension possible, because the organizers meet soon after the deadline to discuss the session allocations of the submitted abstracts. From the registrations that we have had already and based on the success of the 2005 and 2007 meetings here in Heidelberg, this will be a very popular meeting for which we will need to limit participation to a maximum of 300 attendees. The time of registration will be an admission criterium in case that the meeting is oversubscribed.

We invite you to register and submit your abstract as soon as possible via http://www.embl.de/conferences/TransControl/2009

Looking forward to welcoming you in September!
Anne, Marina, Nahum and Matt
For further inquiries, please contact:
EMBL Course and Conference Office
Bettina Schaefer
Meyerhofstr. 1
69117 Heidelberg
email: schaefer@...
phone: +49-6221-387-8836
If you do not wish to receive any further information about events taking place at EMBL, please reply with "unsubscribe" in the subject.
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