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[thread]
[date]
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From: Allen P. Minton <minton@helix.nih.gov>
To : rasmb@bbri.eri.harvard.edu
Date: Fri, 24 Jun 1994 10:29:16 +0059 (EDT)
Re: simultaneous determination of M and vbar
Mystery solved (I think). Geoff Howlett kindly pointed out to us that
one had to correct both the molar mass and vbar to take into account
exchange of protons and deuterons between protein and solvent, as first
pointed out by Edelstein & Schachman. So the revised model goes as
follows. M = Mo * [ 1 + del*(rho - rhoo) ], vbar = vbaro * Mo/M, where
Mo and vbaro are the respective values in pure H2O buffer, and it is
assumed that the amount of proton-deuteron exchange is linear in the
composition of mixed buffers and hence linear in density. From Edelstein
& Schachman's value for the average ratio of protein molecular weight in
pure D2O and pure H2O, 1.0155, we calculated a corresponding value of
del, 0.162. When we fixed this value and floated Mo and vbaro to fit
this model to our ovalbumin data, we got Mo = 45.4 K and vbaro = .746.
This is uncannily close to literature values and makes a believer of me
(for the time being, at any rate).
Thank you Geoff, and thank you Howard and Stu. Allen Minton
"JOHN PHILO" <JOHN_PHILO@amgengate.amgen.com>
"rasmb" <rasmb@bbri.eri.harvard.edu>
new software
I have deposited two new programs for the Beckman XL-A in
the RASMB software depot, developed in-house at Amgen:
"XLAGraph", a graphing/data transformation utility, and
"Svedberg", a sed velocity analysis program. Both require
Microsoft Windows 3.1.
XLAGraph provides an interim solution to the problem of not
being able to see your data during XL-A Auto Scans. If you
run your XL-A data acquisition as a background task under
Windows, then XLAGraph allows you to display, print, or
process scans on disk while data acquisition continues. If
you wish, it can automatically find the new files for all cells
and graph them. In this respect it is similar to Allen Minton's
TRACKER, but requires Windows rather than DESQVIEW, and
can track 3 cells on one overlaid graph rather than running 3
copies of TRACKER.
XLAGraph is also useful for general graphing of XL-A data
and data transformations. It can read and overlay up to nine
data files, with or without baselines subtracted. You can
zoom in on any region of a graph by dragging the mouse, or
manually set axes as you wish. XLAGraph can generate
publication quality graphs on any Windows-supported printer,
freeing you from the dreaded dot-matrix printouts. It can also
export publication quality graphs to other Windows programs.
The usual data transformations to ln(c) vs. r^2 / 2 plots and of
the x axis to Svedbergs are supported, again for up to 9
overlaid files. It can also write out new XL-A data files which
have had baselines subtracted and/or which are averages of
other data files. XLAGraph is entirely menu and point-and-click
driven.
Svedberg is a data analysis program for velocity data. It
simultaneously fits up to 9 absorbance scans to an
approximate solution of the Lamm equation, to derive BOTH
sedimentation and diffusion coefficients from the data.
This means that you can also determine MW from a velocity
experiment, and our experience is that this can be accurate
within a few percent for proteins of 15-60 kDa.
Svedberg is primarily intended for situations where diffusion
makes the boundaries quite broad. It can also fit up to 3
species, under the assumption that they are entirely
non-interacting, and has functions for both conventional and
synthetic-boundary cells. A rigorous error analysis to find
confidence intervals for the fitted parameters can be performed.
The data sets may have a baseline data set subtracted, and/or
an overall zero offset may be included in the fit.
Svedberg is entirely menu and point-and-click driven.
It uses the same graphics engine as XLAGraph to display
high quality graphs of the data, overlaid data and fits,
residual plots, etc., and all may be printed at
publication quality or exported to word processors.
Both programs are distributed together as a self-extracting
archive, with an installation program. It may be down
loaded by anonymous ftp at BBRI.ERI.HARVARD.EDU from
the RASMB/SPIN/MS_DOS/SVEDBERG-PHILO directory.
See the files README.TXT and INSTALL.TXT for more
information.
John Philo, Protein Chemistry, Amgen
From: "O. Byron" <ob1@leicester.ac.uk>
Date: Fri, 5 Aug 94 15:30:38 +0100
Message-Id: <882.9408051430@hawk.le.ac.uk>
To: rasmb@bbri.eri.harvard.edu
*******************************************************************************
3RD UK ANALYTICAL ULTRACENTRIFUGE USERS' GROUP MEETING
22nd September 1994
UK National Centre for Macromolecular Hydrodynamics,
University of Leicester, Leicester, UK
*******************************************************************************
This is a one-day intensive Meeting which will focus on advances in
instrumentation and applications of the analytical ultracentrifuge.
It is the aim of the organisers to establish the UK Meeting as a biennial
event which alternates with the biennial German Symposia.
TALKS WILL INCLUDE:
Emory Braswell (University of Connecticut, USA)
The study of associating systems at the National Analytical
Ultracentrifugation Facility at the University of Connecticut
Malcolm Jones & Jason Birkett (Manchester University, UK)
The application of analytical ultracentrifugation techniques & digital
densimetry to the partial specific volumes of humic substances in
relation to their structure
Don McRorie (Beckman Instruments, USA)
An interference optics system for the XL-A (provisional title)
Peter Morgan (University of Leicester, UK)
Modelling the bacterial protein toxin, pneumolysin, in its monomeric
and oligomeric form
Steve Perkins (Royal Free Hospital School of Medicine, UK)
The hydrodynamic modelling of IgE and its interaction with its
high-affinity cell receptor
Hans-Joachim Schoenfeld (F Hoffman-La Roche, Switzerland)
Quaternary structures of molecular chaperones give insight into the
mechanisms of chaperone mediated protein folding
Walter Stafford (Boston Biomedical Research Institute, USA)
An alternative Rayleigh interference optics system for the XL-A
(provisional title)
REGISTRATION:
The registration fee is 25 pounds sterling (which includes tea, coffee
and lunch). Accommodation at nearby hotels is available (at a typical
cost of 25-30 pounds sterling).
Further details are included in the registration form which can be
obtained from:
Dr Olwyn Byron, NCMH, Department of Biochemistry,
University of Leicester, University Road, Leicester, LE1 7RH, UK.
tel: (44) (0)522 523452/523447
fax: (44) (0)522 523369
email: ob1@le.ac.uk
The closing date for registration is 9th September.
Please register soon so that we can get on with the admin!
*******************************************************************************
Date: Thu, 11 Aug 1994 9:27:58 -0400 (EDT)
From: Walt Stafford <STAFFORD@BBRI.ERI.HARVARD.EDU>
To: RASMB@BBRI.ERI.HARVARD.EDU
CC: STAFFORD@BBRI.ERI.HARVARD.EDU
Message-Id: <940811092758.19c7@BBRI.ERI.HARVARD.EDU>
Subject: error in equilibrium constants response...
This corrects a typo as indicated below
-------
Consider the following chemical reaction:
A + B + C = D + E + F
The general form for conversion between equilibrium constants expressed on
either the c-scale (g/L) or the molar scale (moles/L) is just
Km = [D][E][F]/[A][B][C]
={(d)(e)(f)/(a)(b)(c)}{MaMbMc/MdMeMf}
= Kc{MaMbMc/MdMeMf}
or, in general,
(product of mol masses of the reactants)
Km=Kc * --------------------------------------- <----- error was here
(product of mol masses of the products)
where [X] is the molar concentration of X (moles/L)
(x) is the mass concentration of X (g/L)
Mx is the molar mass of x
and Km is the equilbrium constant on the molar concentration scale
Kc is the equilbrium constant on the mass concentration scale
So, for a monomer dimer reaction:
Km = Kc Ma/2
and for monomer, n-mer
Km = Kc {Ma^(n-1)}/n (as I think Tom Laue already said...)
etc... after conversion from measured units to c-scale.
I seems that any other conversion would not be correct and probably should
be avoided. I agree with Greg Ralston to "avoid using 'the value in the
molar scale expressed in the g/L scale' altogether, and only use either the
g/L value or the molar value."
Walter Stafford
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Date: Thu, 11 Aug 94 14:57:48 EST
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: "Greg Ralston" <gregr@atp.biochem.su.oz.au>
: "Greg Ralston" <gregr@biochem.su.oz.au>
To: RASMB@BBRI.ERI.harvard.edu
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We have been playing with some of the many methods for analysing sedimentation
equilibrium data,and it has come to our attention that there exists the
potential for serious confusion and ambiguity in the future, unless users are
aware of the concentration scales in use.
There are several scales in use for expression of equilibrium constants. The
most fundamental, and the least likely to cause confusion, is the molar scale,
which pertains to the case when all concentrations are expressed in moles per
litre. Values like 1,000-10,000,000 are fairly common here. Use of these values
of K leads to free energy changes involved when 1 mole of A reacts with 1 mole
of B to make 1 mole of AB etc....
Because absorbance and fringe displacement give a measure proportional to the
g/L concentration, there has been a tendency to use in fitting equations a value
of the equilibrium constant(s) that is the molar value divided by the monomer
molar mass:
i.e., k2 = K2/M1
This quantity will have dimensions of L/g. This is also particularly useful for
characterising "isodesmic" reactions, in which the MOLAR change in free energy
at each step is assumed to be constant. This is the convention that has been
used in the Omega programs (SEDPROG.EXE on the RASMB server), and it appears to
be the convention used by Beckman in the ORIGIN programs.
An alternative formulation is the equilibrium constant in the g/L scale:
k2(g/L) = c(A2)/c(A)^2
where the c(i) represent g/L concentrations. This seems to be the convention
used in NONLIN (and possibly in EQASSOC).
k2(g/L) = 2 * K2/M1 = 2 * k2
The conversion is trivial. But you have to be aware that it needs to be made
(and whether to multiply by i or divide!). It gets more tricky for higher-order
oligomers.
I am not sure what is the best way to avoid confusion. It may be to avoid using
"the value in the molar scale expressed in the g/L scale" altogether, and only
use either the g/L value or the molar value.
Are there any strong opinions out there?
Greg Ralston
Phone 692 3906
Department of Biochemistry
University of Sydney
Sydney, NSW, 2006
Australia
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Date: Thu, 11 Aug 1994 04:42:10 -0400 (EDT)
: Thomas M Laue <tml@christa.unh.edu>
To: Greg Ralston <gregr@biochem.su.oz.au>
Cc: RASMB@BBRI.ERI.harvard.edu
In-Reply-To: <9408110457.AA16472@atp.biochem.su.oz.au>
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Hi Greg! I agree that you must be aware of the concentration scale in use,
and be ready to convert to another scale. Just to clarify the situation
with NONLIN, all association constants are written in terms of the
assembly of monomer to higher oligomer (e.g. a 4A<->A4 association
constant is written as you indicated K=[A4]/[A]^4). This has been done, in
part, to simplify the meaning of the association constant in cases where
there is nonideality. The association is actually written in terms of the
chemical activity of the monomer, with the monomer activity being one of
the usual fitting parameters. The "units" are reciprocal Y-axis (i.e.
absorbance or fringe displacement) to the i-1 power, where i is the
association stoichiometry. Conversion of the association constants from
NONLIN to a molar scale go like this:
K(i,M) = K(i,Y)(Ma^(i-1))/i (Yt/Ct)^(i-1)
where K(i,M) is the association constant in molar scale, K(i,Y) is the
value calculated from that returned by NONLIN (note that it is K and that
NONLIN returns ln K), Ma is the monomer molecular weight (i.e. the
molecular weight of the smallest species being fit), i is the
stoichiometry of the reaction, and Yt/Ct is the conversion from the
experimental Y axis (absorbance or fringe displacement) to the weight
concentration scale. For the absorbance system, this is the extinction
coefficient, for the Rayleigh system, this is the number of fringes per
mg/ml. Note that both the monomer molecular weight and the scale
conversion factor are raised to the i-1 power. For the monomer tetramer
case:
K(i,M) = K(i,Y)(Ma^3)/4 (Yt/Ct)^3
If the association under study is a 1<->2<->4, NONLIN will return the
monomer-dimer association and monomer-tetramer association constants. If
it is of interest to determine the dimer-tetramer association constant,
the dimer to tetramer association constant is K(2<->4) = K(1<->4)/K(1<->2)^2.
If a heterogeneous assembly is under examination, a slightly different
form results. For an A+B <-> AB:
K(M)= K(Y)(MaMb/Mab)(Yt/Ct)
These conversions assume that Yt/Ct is the same for all species (i.e. all
components have the same extinction coefficient on the weight scale). If
this is not true, then the equations become more complicated looking, but
only because the Yt/Ct term must be included for each component.
The "meaning" of the association constant for more complicated cases (e.g.
2A + B <-> A2B) can be derived from the definition of the association
constant and the understanding of how the data are being fit.
Best-
Tom
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Date: Thu, 11 Aug 1994 9:18:46 -0400 (EDT)
: Walt Stafford <STAFFORD@BBRI.ERI.HARVARD.EDU>
To: rasmb@BBRI.ERI.HARVARD.EDU
CC: STAFFORD@BBRI.ERI.HARVARD.EDU
Message-Id: <940811091846.19c7@BBRI.ERI.HARVARD.EDU>
Consider the following chemical reaction:
A + B + C = D + E + F
The general form for conversion between equilibrium constants expressed on
either the c-scale (g/L) or the molar scale (moles/L) is just
Km = [D][E][F]/[A][B][C]
={(d)(e)(f)/(a)(b)(c)}{MaMbMc/MdMeMf}
= Kc{MaMbMc/MdMeMf}
or, in general,
(product of mol masses of the products)
Km=Kc * --------------------------------------
(product of mol masses of the reactants)
where [X] is the molar concentration of X (moles/L)
(x) is the mass concentration of X (g/L)
Mx is the molar mass of x
and Km is the equilbrium constant on the molar concentration scale
Kc is the equilbrium constant on the mass concentration scale
So, for a monomer dimer reaction:
Km = Kc Ma/2
and for monomer, n-mer
Km = Kc {Ma^(n-1)}/n (as I think Tom Laue already said...)
etc... after conversion from measured units to c-scale.
I seems that any other conversion would not be correct and probably should
be avoided. I agree with Greg Ralston to "avoid using 'the value in the
molar scale expressed in the g/L scale' altogether, and only use either the
g/L value or the molar value."
Walter Stafford
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Date: Tue, 6 Sep 1994 09:59:44 -0400 (EDT)
From: Thomas M Laue <tml@christa.unh.edu>
Subject: Job Opening
To: RASMB group <rasmb@bbri.eri.harvard.edu>
Message-Id: <Pine.3.89.9409060904.A16246-0100000@christa.unh.edu>
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Please pass this along to any interested colleagues.
Assistant Professor
Department of Biochemistry and Molecular Biology
The Biochemistry and Molecular Biology Department of the University of
New Hampshire seeks candidates for a tenure track, academic year position
at the assistant professor level. Candidates must have a Ph.D. and
postdoctoral experience. We are particularly interested in candidates
with research experience using molecular, biochemical, or genetic
techniques to address problems of protein structure and function. The
appointee will be expected to participate in undergraduate and graduate
teaching and to establish an extramurally funded research program. The
person would teach a one semester undergraduate general biochemistry
course and another course in their specialty compatible with the graduate
and undergraduate and graduate curriculum. The successful candidate will
have a joint appointment in the New Hampshire Agricultural Experiment
Station. The starting date will be August 1995, although an earlier date
is possible. Applicants should send a curriculum vitae, names of three
references, and a statement of teaching and research interests by October
21, 1994, to:
Dr. James A. Stewart
Department of Biochemistry and Molecular Biology
Spaulding Life Sciences Building
University of New Hampshire
Durham, NH 03824
UNH is an AA/EEO Employer
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To: rasmb@bbri.eri.harvard.edu
Date: Thu, 8 Sep 1994 09:32:36 -0600 (MDT)
From: "Borries Demeler/Biophysics" <demeler@selway.umt.edu>
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To all RASMB subscribers:
I have created a gopher archive at the University of Texas in San Antonio
that mirrors the rasmb software archive and offers the files contained
in this archive in the more user-friendly gopher format for downloading.
To access the gopher server, connect with your gopher
client to bioc02.uthscsa.edu (129.111.1.229). On most Unix and DEC systems
with gopher clients, this is accomplished by issueing following command at
the system prompt ($>):
$> gopher bioc02.uthscsa.edu
or for systems without proper routing tables:
$> gopher 129.111.1.229
The software archive can be found under:
/Department of Biochemistry/Analytical Ultracentrifugation/Software/
At this time the archive contains only the software available in the rasmb
archive. With your cooperation, I would like to create, manage and update
a "Submissions" archive, that contains all past and future discussion
mailings sent to rasmb for reference (as diskspace permits). For this purpose
I need access to all old articles, since I did not save them on disk.
If someone (Walter?) has archived all submissions, could you be so kind
to let me know where I can obtain a copy for the benfit of all, and I will
put them on the gopher server for easy browsing, as well as all future
submissions as well. In addition, I am working on getting WAIS (Wide Area
Information Server) installed on my machine which would allow you to browse
all previous submissions by keyword/date etc. I will send a separate message
when WAIS is up and running.
If you have any ideas, suggestions etc. on what else you would like to see
on the gopher server, let me know and I'll see if I can do it.
That's all for now, folks. Regards, -Borries Demeler
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Date: Thu, 15 Sep 94 11:50:27 +1000
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From: "Geoff Howlett" <geoff_howlett.biochem@muwaye.unimelb.EDU.AU>
To: rasmb@bbri.eri.harvard.edu
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Hi RASMBers
Thanks to Borries Demeler for the RASMB gopher site. I am pleased to report
this site takes 10 seconds to access from Australia (the speed of light?).
The home page in Mosaic has a great feel to it. Its certainly a lot easier
not having to download text files in order to read them.
To be able to "surf" through RASMB correspondence with keywords (eg sloping
baselines, temperature effects etc) will be a great addition if a WAIS server
can be installed as suggested by Borries.
The ability to search archival material suggests it may be worth raising more
issues via the network so that the collected wisdom can be used as a
resource. Would it make sense to encourage contributions in the way of
abstracts for upcoming conferences so that topics of interest can be pursued
at an individual level?
Thanks Borries
Geoff Howlett
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Date: 15 Sep 1994 08:51:19 U
From: "JOHN PHILO" <JOHN_PHILO@amgengate.amgen.com>
To: "rasmb" <rasmb@bbri.eri.harvard.edu>
Status: OR
RE> gophers; Mosaic
In answer to Jack Correia's question about the
advantages of gophers and Mosaic over FTP, and
sources of information:
In my view, the principle advantage of gophers over
FTP is that gophers can organize lists (menus) of
information that :
(1) may reside on multiple computers, but the user
need not know anything about the actual physical
location; and
(2) may contain multiple data types (text files,
program executables, image files, etc.) without the
user having to be directly aware of the file type,
directory structure, or file naming conventions of the
machine on which the information resides.
Also, not everyone has a 'point and click' FTP
program like Jack's, so this aspect of gophers
can also be a big advantage. Also, another nice
feature of gophers is that you can mark useful
items and menus (using "bookmarks") so you
can get back to them easily.
Mosaic has all the advantages and capabilities of
gophers, with an even slicker user interface. Rather
than presenting choices only as menus, information
in Mosaic is generally organized as hypertext. That
is, certain key words are highlighted, and when you
click on them it retrieves further information on that
subject (or a file by FTP). Mosaic can also integrate
images into the hypertext, and these images can
also be used to select information. For example, the
Natural History Museum at Berkeley has a Mosaic
application on dinosaurs that initially displays a
phylogenetic tree for dinosaur evolution. When
you click on a branch of the tree, you get a page
with images of that group of dinosaurs, text
information, and links to other information.
Mosaic also has the capability of using forms where
you fill in the blank or select from a drop-down list
of available items. Generally this is used for things
like searching for a particular phrase.
Jack also asked about sources of information about
these programs. I have not seen any articles about
gophers. A recent issue of SCIENCE (? 3 weeks ago)
highlighting computer applications had screens from
Mosaic on its cover, and more info inside. I believe
there was also an article about Mosaic in Trends in
Biochemical Sciences within the last 6-8 months.
There was also something about Mosaic in The
Scientist fairly recently, and in Newsweek (!) within
the last month or so.
John
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To: rasmb@bbri.eri.harvard.edu
From: jcorreia@fiona.umsmed.edu (Jack Correia)
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Status: OR
>Gopher users,
Being unfamiliar with gophers - would this be accessible through
something like mosaic? Why is this easier that ftp? My ftp software allows
me to edit text files, download with a click and a drag, etc. Searching by
key words sounds nice! Sources for reading about this option?
Jack
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Date: Fri, 16 Sep 94 9:38:04 +1000
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From: "Geoff Howlett" <geoff_howlett.biochem@muwaye.unimelb.EDU.AU>
To: rasmb@bbri.eri.harvard.edu
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Hi
Really respectable E-mail networks seem to have a FAQ which gets sent out
every now and again. As far as I can make out a FAQ (frequently asked
questions) consists of a series of seldomly asked questions which provide an
opportunity to explain the network. FAQs usually start with a table of such
questions:
1. What is RASMB and what are its goals?
2 How can I subscribe/unsubscribe?
3 How does one deposit and retrieve stored information related to the
network?
4. How are messages sent to the network?
5. Is there a gopher site for the network
6. Should I send this FAQ to anyone?
Now the answers:
1. What is RASMB and what are its goals?
The abbreviation stands for Reversible Associations in Structural and
Molecular Biology. The original idea was to orient the network around those
interested in the reversible interactions of macromolecules. The initiative
arose during discussions at the RASMB meeting in February 1994 at the
University of Melbourne, Melbourne Australia. Since reversible interactions
are are the basis of most of the interesting things which happen in biology
and at the heart of most regulatory phenomenon it seemed like a good idea to
keep a broad focus. The analytical ultracentrifuge is one of the most recent
developments in the field and the network currently play a significant role
in the exchange of information in this area. Contributions and subscribers
in other areas related to reversible interactions are especially welcome.
2. How can I subscribe/unsubscribe?
To subscribe or unsubscribe to the network send a message with the relevant
request to
RASMB-MANAGER@BBRI.ERI.HARVARD.EDU
3. How does one deposit and retrieve stored information related to the
network?
Information related to the network is stored on an anonymous FTP site at
Harvard where it is under the supervision of Walter Stafford (Boston
Biomedical Research Institute). To deposit a file, please put it in the
[.drop-off] directory. The email address list for the RASMB email server can
be found in the /rasmb directory.
A list of current information available on the FTP site is as follows:
Software for time derivative analysis of sedimentation velocity
data (g(s*) analysis) written by Walter Stafford can be found in the
/rasmb/spin/mac and /ms-dos directories.
NONLIN.EXE (nonlinear fitting routine for anlysis of sedimentation
equilibriun data by Michael Johnson) for the VAX under VMS can be found in
directory /rasmb/spin/dec directory.
Software for simulation and analysis of equilibrium sedimentation
of interacting systems by Allen Minton can be found in the
/rasmb/spin/ms_dos directory as a self extracting archive called SEDEQ.EXE.
The following versions of Michael Johnson's NONLIN curve fitting
program for analysis of equilibrium data have been deposited in the /MS_DOS
and /DEC directories.
NONLIN for the PC.
NONLIN for the VAX Open VMS.
NONLIN for the DecAlpha
Several programs for the analysis of velocity data and equilibrium
data have deposited by Les Holladay; they can be found along with
appropriate readme and documentation files in /MS_DOS/SEDFIT-
HOLLADAY:
SEDFIT.EXE
EQFIT.EXE
APEQFIT.EXE
MWMZ.EXE
AXIAL.EXE
Allen Minton has contributed a program called TRACKER that will
allow the real time display of sedimentation profiles during a velocity run
on the XL-A. It can be found in /MS_DOS/TRACKER-MINTON
John Philo of Amgen Corp. has deposited a package of programs for
the analysis of sedimentation velocity data that can analyze mixtures by
fitting a series sedimentation profiles to the Faxen equation. A self-
extracting archive along with several text files can be found in
/MS_DOS/SVEDBERG-PHILO
INSTALL.TXT
README.TXT
SVEDBERG.DOC
SVEDBERG.WRI
SVXL9406.EXE
4. How are messages sent to the network?
If you would like to post a message to all participants send it to
RASMB@BBRI.ERI.HARVARD.EDU
Replies to a message from the network only go to the sender of the message.
5. Is there a gopher site for the network
Yes. Borries Demeler (University of Texas) has recently established a gopher
server which mirrors the rasmb software archive and allows convenient
browsing. To accesss the server:
$>gopher bioc02.uthscsa.edu
(or $>gopher 129.111.1.229). This site may ultimately allow WAIS searching
of keywords in the rasmb archives.
6. Should I send this FAQ to anyone?
Especially to those interested in the reversible associations of
macromolecules.
All suggestions for revision of this FAQ are welcome.
Best wishes and happy RASMBing
Geoff Howlett
Date: Thu, 15 Sep 1994 20:06:04 -0400 (EDT)
From: Walt Stafford <STAFFORD@BBRI.ERI.HARVARD.EDU>
To: rasmb@BBRI.ERI.HARVARD.EDU
Cc: STAFFORD@BBRI.ERI.HARVARD.EDU
Message-Id: <940915200604.4191@BBRI.ERI.HARVARD.EDU>
Status: OR
An RASMB FAQ (Frequently Asked Questions) authored by Geoff Howlett has
been posted at the anonymous FTP RASMB site at BBRI.ERI.HARVARD.EDU.
-Best regards to all,
Walter Stafford
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Date: 16 Sep 1994 10:37:54 U
From: "JOHN PHILO" <JOHN_PHILO@amgengate.amgen.com>
Subject: Re: XL-A stalling problems
To: "Borries Demeler/Biophysics" <demeler>
Status: OR
Reply to: RE>XL-A stalling problems
Borries,
Are you running the XL-A data acquisition as a task under Windows, as I
do? I have seen data acquisition fail if the computer is too busy doing
other things in Windows during the actual data transfer at the end of a scan
(any floppy access during this time is almost sure death). However, in my
experience, when this is a problem the acquisition does not stall completely
as you describe, but you just lose that data file. Anyway, if this may be a
Windows-related problem, I might have some suggestions of things to try.
'Best,
John
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Subject: Re: RASMB FAQ
To: rasmb@bbri.eri.harvard.edu
Date: Fri, 16 Sep 1994 07:17:28 -0600 (MDT)
From: "Borries Demeler/Biophysics" <demeler>
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Geoff,
thanks for creating the RASMB FAQ, very useful and I will place it on the
gopher server as well. Also, thanks for your excellent explanation of
gopher & mosaic. I am now working on a mosaic page for the RASMB group (as
time permits).
I am hoping to be able to deposit relevant publications including the figures
on the site, as well as documentary materials for the archived software.
Those documents may contain figures and graphs as well. As soon as a basic
Mosaic page is ready for networking I will announce it here on the RASMB
listserver.
I will accept contributions and suggestions for improvement for the
mosaic page - so get your docs ready. If you want to prepare your own HTML file,
format your document as 70 characters/line or less in ascii code. All graphics
should be in *.gif format (256 colors max, 1024*768 res max). Boldfaced
text should be enclosed in b-codes: <b>this is boldfaced</b>, Very large
text should be enclosed in h1-codes, medium sized in h2-codes:
<h1>this text appears very large</h1>, <h2> this text appears medium large</h2>
more info about mosaic and html formatting can be obtained from connecting
to <http://info.cern.ch/hypertext/WWW/TheProjetc.html>.
Regards, -Borries Demeler
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Subject: XL-A stalling problems
To: rasmb@bbri.eri.harvard.edu
Date: Fri, 16 Sep 1994 10:11:20 -0600 (MDT)
From: "Borries Demeler/Biophysics" <demeler>
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Status: O
Hi,
I am writing to see if others are seeing similar problems with the XL-A
as Jack Correia and we here at the UTHSCSA. The problem is that during
a run (usually velocity) data acquisition all of a sudden stalls out,
sometimes in the middle of a scan. The centrifuge keeps running, but
data acquisition stops (and I believe the lamp isn't flashing either).
The only way to get it to start again is to start over.
The Beckman people suggested to use a time value for "Time Between Scans"
that exceeds the time the scan actually needs to complete. For normal use
we usually set this to 1 minute, even though the scan took a little more than
2 minutes to complete - it used to work fine, but now it is a problem.
Sometimes you really want to acquire data as fast as possible without having
the XL-A wait for the next scan - especially in velocity runs.
Does anybody else experience similar problems, or can shed some light on
this situation?
thanks for any help, -Borries Demeler
UTHSCSA
Biochemistry
San Antonio, Texas
(demeler@selway.umt.edu)
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To: rasmb@bbri.eri.harvard.edu
From: jcorreia@fiona.umsmed.edu (Jack Correia)
Subject: Re: XL-A stalling problems
X-Mailer: <PC Eudora Version 1.4>
Status: OR
Time between scans:
Our experience is that the Beckman software ignores the time between
scans if the scan time is longer than the time set. It simply collects data
until it completes the # of scans requested. For velocity runs we always
leave it set to 1 and it just continuously collects the three sets of scans
requested. Recently we had a scan hang up - after 10 scans were collected
nothing happen for 30 minutes and we were not glued to the monitor checking
on. A restart of the scan with appropriate name change collected data at a
normal rate for the settings we use. It has not happen since, but we now
have an alert to watch the scans more closely for reoccurence of this
behavior. Bo & Jeff seem to have a continuous problem with the scan getting
hung up.
Jack
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Date: Fri, 16 Sep 1994 16:03:45 -0400 (EDT)
From: "E. Braswell" <BRASS@UConnVM.UConn.Edu>
Subject: Nonlin
To: RASMB@bbri.eri.harvard.edu
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Status: OR
Although Mike Johnson developed Nonlin and helped develop its use for the
Anal. UltraCent. I must point out that all the latest incarnations were
perfected by D. Yphantis and therefore I think that these should be referred
to as "Johnson-Yphantis" versions of Nonlin. I don't think Dave gives a damn
but in the interest of accuracy---
Date: Fri, 16 Sep 1994 02:06:31 -0600
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Resent-From: "Geoff Howlett" <geoff_howlett.biochem@muwaye.unimelb.EDU.AU>
From: geoff_howlett.biochem@muwaye.unimelb.EDU.AU
To: rasmb@bbri.eri.harvard.edu
Subject: ...no subject...
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Status: OR
Forwarded to: smtp@smtp@unimelb[rasmb@bbri.eri.harvard.edu]
cc:
Comments by: Geoff Howlett@BioChem@UNIMELB
Comments:
Just to add to the avalanche of RASMB mail I enclose the following abstract
for a poster to be presented at the Australian Society for Biochemistry and
Molecular Biology (ASBMB) to be held at the gold coast (Queensland) the week
after next.
Thanks to Walter Stafford and John Philo who helped during various stages of
this work.
Other abstracts?
Geoff Howlett
-------------------------- [Original Message] -------------------------
SEDIMENTATION ANALYSIS OF HOMOGENEOUS LIPID
EMULSIONS
C. E. MacPhee, W.H. Sawyer and G.J. Howlett.
Russell Grimwade School of Biochemistry, University of Melbourne, Parkville,
Victoria, 3052
This study describes a method for the synthesis and purification of
homogeneous populations of lipid emulsions of defined size and lipid
composition. Phospholipid/triacylglycerol emulsions were prepared by
sonication and pressure extrusion, resulting in a heterogeneous population of
particles ranging in diameter from 80 to 230 nm. Further purification, based
on computer simulation, involved flotation of emulsions at low speeds up
through a linear sucrose gradient. Fractionation of the gradient at the
conclusion of centrifigation yielded discrete fractions which were further
characterised using an XL-A analytical ultracentrifuge.
Flotation velocity studies of unfractionated emulsions yielded a diffuse
flotation boundary, whereas similar analyses of subfractions resulted in
sharper boundaries, indicating increased homogeneity. These subfractions were
relatively stable, as indicated by the reproducibility of their sedimentation
behaviour over a period of several days. The smallest and largest
populations so far analysed have flotation coefficients (Sf) of 180S and
1760S, respectively. The homogeneity of subfractions was further assessed by
the use of time-derivative G* analysis [1]. The particle density for each
subfraction was obtained in the XL-A analytical ultracentrifuge by alteration
of the solvent density using D20. This process allowed the determination of
the partial specific volume, molar mass, and particle radius for each
fraction. One such fraction had a calculated Sf of 180S, a molar mass of 2.24
x 108, a diameter of 90 nm, and a partial specific volume of 1.026 ml/g. The
experimentally determined value for the partial specific volume agreed to
within 2% with the value calculated on the assumption of a spherical particle
of triacylglycerol surrounded by a surface monolayer of phospholipid. Lipid
emulsions of defined composition and size will be useful in examining the
binding of proteins to the lipid surface, the affinity of binding as a
function of size, and the effect of lipid composition on emulsion-protein
interactions.
[1] Stafford, W. F., (1992) Analytical Biochemistry 203: 295-301.
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Date: Mon, 19 Sep 94 13:34:24 EST
Message-Id: <9409190334.AA22698@atp.biochem.usyd.edu.au>
From: "Greg Ralston" <gregr@atp.biochem.usyd.edu.au>
Reply-To: "Greg Ralston" <G.Ralston@biochem.usyd.edu.au>
To: RASMB@BBRI.ERI.harvard.edu
Subject: Re: XL-A stalling problems
Content-Length: 1485
Status: OR
In message <9409161611.AA03802@selway.umt.edu> "Borries Demeler/Biophysics"
writes:
> I am writing to see if others are seeing similar problems with the XL-A
> as Jack Correia and we here at the UTHSCSA. The problem is that during
> a run (usually velocity) data acquisition all of a sudden stalls out,
> sometimes in the middle of a scan. The centrifuge keeps running, but
> data acquisition stops (and I believe the lamp isn't flashing either).
> The only way to get it to start again is to start over.
Hi Borries,
We've had this happen a couple of times. We always use a very conservative time
intervals between scans, so as to try to avoid this type of problem, but it has
happened even when there was plenty of time between successive scans; i.e., it
wasn't that we simply tried to cut it too fine. In our case, we had to reboot
the computer, and we suspect that the RS-232 connection got screwed up somehow.
I would stress that it is not a common occurrence. (Not like the "R-Servo
Time-Out Error"! But that's a different story)
We have had Windows hang on us now and then, particularly if a number of
programs have been loaded and terminated over a period of time. We make a point
of shutting the computer down now and then and rebooting. Not elegant, but it
seems to keep this sort of problem at bay.
Greg Ralston
Phone 692 3906
e-mail: G.Ralston@biochem.usyd.edu.au
Department of Biochemistry
University of Sydney
Sydney, NSW, 2006
Australia
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Date: Tue, 20 Sep 94 08:20:10 EST
Message-Id: <9409192220.AA27097@atp.biochem.usyd.edu.au>
From: "Greg Ralston" <gregr@atp.biochem.usyd.edu.au>
Reply-To: "Greg Ralston" <G.Ralston@biochem.usyd.edu.au>
To: RASMB@BBRI.ERI.harvard.edu
Subject: Radial Rate errors in the XL-A
Content-Length: 1530
Status: OR
Greetings!
I would like to pass on our experience with the sudden appearance of a
Radial_Rate error in the XL-A. It may save somebody a lot of time in trying to
track down the cause of a similar problem.
Although we almost always get R_Servo_Timeout errors (usually at the END of a
scan, and it doesn't seem to cause a problem with the next scan, even if you're
not there to press 'ESC') the sudden appearance of a Radial_Rate error was much
more serious. When this happened, we got a flurry of R_Servo_timeout errors, as
well as R_Out_of_Range errors. The radial calibration got completely screwed up,
so that the whole cell image was scrunched into about 50% of the screen display,
and then rest was rubbish; i.e., even though the screen plot purported to go
from 5.8 to 7.2 cm, the top and bottom of the cell (the true 5.8 and 7.2 cm
positions) were each located well in from the frame of the plot. When we
checked, we also found that he CAL_PARM.CAL file was corrupted.
After a lot of false trails, the problem was tracked down to a loose grub screw
on the slit drive shaft. This was tightened, the radial scale was re-calibrated
and everything went back to normal. At least for a while. It has happened again
since. It didn't take quite so long to track down the second time, but for a
while we didn't believe that it could be the same fault again.
Greg Ralston
Phone 692 3906
e-mail: G.Ralston@biochem.usyd.edu.au
Department of Biochemistry
University of Sydney
Sydney, NSW, 2006
Australia
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From: "Geoff Howlett" <geoff_howlett.biochem@muwaye.unimelb.EDU.AU>
To: rasmb@bbri.eri.harvard.edu
Subject: ...no subject...
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Status: OR
Re: contract work with the XLA ultracentrifuge.
>From time to time one gets requests to do contract work with the XLA. Does
anyone have a policy for such work and is there a "going rate"?
For example if the request was for a simple 24 hour sedimentation equilibrium
run with analysis and consultancy how much would this cost in realistic terms?
I would be interested in responses which would be kept confidential. Perhaps
a general summary would then be of interest.
Cheers
Geoff Howlett
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From: "Geoff Howlett" <geoff_howlett.biochem@muwaye.unimelb.EDU.AU>
To: rasmb@bbri.eri.harvard.edu
Subject: contract work-summary
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Status: OR
Thank you to all who responded re. the XLA and contract work. At the moment
there is only a broad concensus since the process of breaking down the costs
depends on a number of local factors such as the facilities available,
expertise, wealth of local companies and of course the demand. A summary:
1. The idea of charging to a formula e.g.
rate/hr for advice and techician +rpm^2 x no of hours x factor + rate/hr for
analysis leads to estimates of $US3000-4000 for a complete set of 3
concentrations and 2 speeds for an equilibrium run or $US1000/day for a
sedimentation analysis on 3-4 samples.
2. Another approach was to consider 10% depreciation, 10% maintenance and a
rate per cell based on a lifetime of about 100 runs (ie the cells being
considered consumables). Assuming the machine runs 24 hours of the day and
without considering the angular velocity used, this approach leads to
estimates of approx. $US 200/day with add-ons for technical work, analysis
and advice.
3. While not actually involved in contract work an estimate of $US 750-1000
per day was contributed based on labour costs, extent of machine time,
supplies, eventual replacement of cells, labour and service contracts. (Does
anyone know what the cost of a service contract is?).
4. Another estimate in the region of $US 3000 for a "standard" sedimentation
equilibrium run (3 concentrations, 2 speeds) was based on $20/hr machine
time, $100/run, $70 /hour technician and $105/hr for supervision and report
writing.
5. A common theme was that it was hard to factor in a cost for the amount of
fun obtained from using the machine and the "rub-off" experience gained.
Other messages received expressed interest on the basis of needing to develop
policies in the area. Collaborations were indicated as an alternate model in
selected cases.
Thanks again to all who responded. I am still to get some info. by regular
mail.
On the basis of the above, I am starting to think Australia may be a good
sunny place to get bargain ultracentrifuge runs.
Geoff Howlett
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Date: Fri, 14 Oct 1994 11:17:00 +0000
From: "Joachim Behlke" <behlke@orion.rz.mdc-berlin.de>
Sender: behlke@orion.rz.mdc-berlin.de
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To: rasmb@bbri.eri.harvard.edu
Subject: IX. Symposium on Analytical Ultracentrifugation 1995 in Berlin
Status: OR
Preliminary list of contributions: (October 14. 1994)
Emory H. Braswell, Univ. Conn. Storrs, USA
"Optimizing the Analysis of Simple Mixtures of Macromolecules"
Peter M. Budd, Univ. Manchester, UK
"Studies of Welan Gum using Analytical Ultracentrifuge"
Joachim Behlke, MDC Berlin, Germany
"The study of heterologous associating systems by sedimentation equilibrium"
Helmut C!lfen & Stephen E. Harding: Univ.Nottingham, UK
"Schlieren pattern with Optima XL-A absorption optics"
Helmut Durchschlag et al.: Univ. Regensburg, Germany
"Comparative Studies of Conformational Changes of Proteins by Analytical
Ultracentrifugation and other Techniques"
Christine Ebel: Inst. Biol. Struct. Grenoble, France
"Characterization of the solution structure of halophilic proteins"
Ariel Lustig, Harald Herrmann, Ueli Aebi: Biozentrum Basel, Switzerland
"Is the short-column sedimentation equilibrium (SE) centrifugation suitable
to characterize intermediate filement (IF) assembly intermediates?"
Stephen E.Harding: Univ. Nottingham, UK
"Sedimentation analysis of chitosan and its interaction with other molecules
analysis"
H. Hinsken, W. Borchard: Univ. Duisburg, Germany
"Characterization of thermoreversible gels in the AUC by means of the
gradient method"
E. Karpova et al.: Russ. Acad.Sci. St.Petersburg, Russia
"Hydrodynamic properties of nucleosomal fibers and chromatin higher-order
structure"
Tom Laue: Univ. New Hampshire, Durham NH. USA
"Interactions between components in Protein-DNA complexes"
M.D. Lechner, W. M!chtle, D. Steinmeier: Univ. Osnabr!ck, Germany
"Molar Mass Distribution from Absolute Sedimentation Fractiometry
(ASF)-Competion with size Exclusion chromatography"
Allen P. Minton: NIH Bethesda MD. USA
"Measurement and analysis of the concentration gradients of the individual
components in mixtures at sedimentation equilibrium"
G.M. Pavlov, S.Ya Frenkel: Univ.St.Petersburg, Russia
"Sedimentation Parameter of linear Polymers"
M.Ptschke,A.Fels,B.Schmidt,L.Heiliger,E.Kuchert,D.Riesner:Univ.D!sseldorf,
Germany
"Polymeric fluorescent dyes for labeling of proteins and nucleic acids"
K.Post,M.Pitschke,H.Serban,S.DPrusiner,D.Riesner: Univ. D!sseldorf,Germany
"Ultracentrifugation studies on prions and prion-proteins"
Dieter Schubert: Univ. Frankfurt/M. Germany
"Reversible heterologous associations between membrane proteins"
A.Seifert et al. Bergholz-Rehbr!cke, Germany
"Charakterization of Gliadin-Galactomannan Incubation Mixtures by analytical
ultracentrifugation"
Walter Stafford: BBRI Boston MA. USA
"The use of g(s*) for the analysis of interacting systems for the general
routine analysis of sedimentation velocity studies"
H.Triebel et al.: Univ. Jena Germany
"Sedimentation Analysis of the Effect of Netropsin and other Minor Groove
Binders on Structural Parameters of Supercoiled DNA"
Yujia Xu, David Yphantis: Univ. Conn. Storrs, Conn. USA
"Detection of Heterogeneity in Self-associating Systems by Equilibrium
Sedimentation technique"
Toni Aerts, J.Clauwaert: Univ. Antwerp Belgium
"Bovine Eyelens Polymeric alpha Crystallin: Size and Hydrodynamic Structure"
Helmut C!lfen, Peter Husbands, Stephen E. Harding: Univ. Nottingham UK
"Alternative light sources for the Schlieren optics of a Beckman Model E
analytical ultracentrifuge"
Hellmut Gerst, Joachim Behlke: MDC Berlin Germany
"Evaluation of ultracentrifugation experiment using interference optics"
G.M. Pavlov et al. Univ. St Petersburg, Russia
"Direct and Revers Polysterene Sedimentation in Benzene and CCl4"
G.M Pavlov et al.: Univ. St Petersburg, Russia
"Velocity Sedimentation of Water-soluble Methyl Cellulose"
A.Seifert et al.: Bergholz-Rehbr!cke Germany
"Characterization of the Coalescence stability of legumin stabilized o/w
emulsions by analytical ultracentrifugation"
Paul Voelker: Beckman Instr. Palo Alto, Calif. USA
"Measurements of the Extinction Coefficient of Prostate Specific Antigen
using Interference and Absorbance Optics in the XL-A Analytical
Ultracentrifuge"
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Date: Wed, 26 Oct 94 7:25:42 +1000
Message-Id: <zfH8+guLfia@muwaye.unimelb.EDU.AU>
From: "Geoff Howlett" <geoff_howlett.biochem@muwaye.unimelb.EDU.AU>
To: rasmb@bbri.eri.harvard.edu
Subject: vbar calculations
X-Incognito-Sn: 302
X-Incognito-Format: VERSION=1.72a ENCRYPTED=NO
Status: OR
re: calculation of vbar values from amino acid composition.
Zamyatnin (Prog in Biophys and Molecular Biology, vol 24,p 109 (1972)) has
tables based on the measured vbar for amino acids minus the volume of a H and
OH group whereas Cohn and Edsall (1943) have vbar values calculated from the
volumes from the component atoms.
Their are some significant discrepancies (eg ARG 0.666 vs. 0.70 ml/g).
I insert below some helpful comments from Tom Laue on this issue.
Insert starts here: Hi Geoff-
I have had poor luck using Zamyantin's values. There is a paper by Steve
Perkins (Eur. J. Biol., 157:169-180, 1986) in which he compared Cohn and
Edsall, Zamyantin and one other (I believe) set of vbars to neutron
scattering estimates of the amino acid volumes (as I recall). His
conclusion took two forms: 1) a "consensus" data base and 2) that the
consensus data base was nearly identical to Cohn and Edsall. The Cohn and
Edsall values seem to "work" better, but for the wrong reasons, and they
are even better yet when the McMeekin and Marshall corrections are applied
(M & M, 1952, Science 116:142-143).
Insert ends here:
(reproduced with consent)
comments?
Geoff Howlett
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Date: Fri, 28 Oct 1994 09:48:03 -0500
To: rasmb@bbri.eri.harvard.edu
From: brooksis@sb.com (Ian Brooks)
Subject: Re: vbar calculations
Status: OR
Hi Geoff,
I have to agree with Tom's comments about the values of Cohn and
Edsall giving better results than Zamyatnin's. We have had a number of
systems, particularly IgGs which have given us consistently low molecular
weights with Zamyatnin's values, but which give much "better" answers with
Cohn and Edsall.
Although it is only a single data point we have also compared the
two computed vbars with the experimentally determined vbar values for
Phosphoglucose Isomerase. Experimentally the value determined was 0.740
by pycnometry and 0.743 by H20/D20 (Pon, Schnackerz, Blackburn, Chatterjee
and Noltmann: Biochemistry 9 1506 1970.) Computationally Cohn and Edsall
give 0.739 while Zamyatnin gives 0.729. Clearly in this case Cohn and
Edsall give a much better approximation.
I do have one concern with these comparisons from the practical
point of view. It is usally fairly clear when a sample is a monomer, even
if its molecular weight is slightly lower than expected. In this case
using Cohn and Edsall usually gives a value closer to the expected mass
than Zamyatnin and we are happy to use Cohn and Edsall. I wonder if there
are opposite cases where Zamyatnin is closer to the truth, but by using
Cohn and Edsall we get apparent association?
Comments?
Ian Brooks
Ian Brooks
brooksis@sb.com
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Date: Mon, 31 Oct 1994 18:33:52 +0000
From: "Joachim Behlke" <behlke@orion.rz.mdc-berlin.de>
Sender: behlke@orion.rz.mdc-berlin.de
Reply-To: behlke@orion.rz.mdc-berlin.de
Message-Id: <66834.behlke@orion.rz.mdc-berlin.de>
To: rasmb@bbri.eri.harvard.edu
Subject: Accommodation for the AUC-Meeting 1995 in Berlin
Status: O
Dear Colleagues,
As already mentioned we will have the IX. Symposium on Analytical
Ultracentrifugation in the Max-Delbrueck-Centre (MDC) in Berlin-Buch
from March 2. 9!! until March 3. about 17!!. Unfortunately in Berlin-Buch
is not an appropriate hotel for accommodation. The German travel agency
(Deutsches Reisebuero) has offered us the new Picco Hotel in Berlin,
Guertelstr 41 (3 min walk to the S-Bahn station "Frankfurter Allee" with
direct connection to Berlin-Buch) with reduction in prices: 115 Deutschmark
per night including breakfast and V.A.T. for a single room and 160 Deutsch-
mark per night for a double room. If you want to make use of this offer
please contact as participant of the AUC-meeting
Mrs. Diana Sigwanz
Deutsches Reisebuero
Augsburgerstr. 27
D-10789 Berlin
Tel. +49(30)21998-901
Fax +49(30)2118150
until December 15th 1994 with giving information about your arrival,
departure and the method of payment (who is to get the calculation).
You will get the hotel voucher from Mrs. Sigwanz. If you have other
wishes concerning the accommodation, perhaps Mrs. Sigwanz or we can
support you.
With best regards.
Joachim Behlke
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Date: Tue, 06 Dec 1994 08:51:34 -0500
From: SIEGELR@centocor.com
To: rasmb@bbri.eri.harvard.edu
Subject: RASMB
Status: OR
Dear Dr. Stafford,
Allow me to introduce myself. My name is Richard C. Siegel, Ph.D.
I am the Director of Pharmaceutical Development at Centocor, Inc.
I recently read about the RASMB in the Hansen et. al review
(Biochemistry 33,13155 (1994)) and am very interested in joining
with one of my colleagues, Richard Everett, Ph.D. We have a
Beckman XLA analytic ultracentrifuge and use it extensively to
characterize the therapeutic monoclonal antibodies we develop. I
would appreciate it if you could send me information about the
RASMB. My return address is SIEGELR@CENTOCOR.COM.
Sincerely,
Richard C. Siegel
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Date: Sun, 11 Dec 1994 16:57:08 +0000
From: "Joachim Behlke" <behlke@orion.rz.mdc-berlin.de>
Sender: behlke@orion.rz.mdc-berlin.de
Reply-To: behlke@orion.rz.mdc-berlin.de
Message-Id: <61030.behlke@orion.rz.mdc-berlin.de>
To: rasmb@bbri.eri.harvard.edu
Subject: IX. Symposium on Analytical Ultracentrifugation 1995 in Berlin
Status: OR
Dear Dr Garcia de la Torre,
Thank you for your e-mail and the information. I am very sorry that you
are not able to attend the Berlin meeting. At present I have to prepare
the program fro the 48 contributions. About the half of them will be
oral presentations, the other posters.
Thank you again and best wishes,
Joachim Behlke
Preliminary list of contributions: (December 7. 1994)
Emory H. Braswell, Univ. Conn. Storrs, USA
"Optimizing the Analysis of Simple Mixtures of Macromolecules"
Peter M. Budd, Univ. Manchester, UK
"Studies of Welan Gum using Analytical Ultracentrifuge"
Joachim Behlke, MDC Berlin, Germany
"The study of heterologous associating systems by sedimentation equilibrium"
Olwyn Byron: Univ. Leicester, UK
"Hydrodynamic Modelling of Macromolecular Structures"
John J Correia, Sharon Lobert, Anthony Frankfurter: Univ.Mississippi, Jackson
MS. USA
"Vinblastine-induced and divalent cation-induced selfassociation of tubulin
and tubulin isotypes"
David C Critchley, Alistair Macgregor, Geoffrey Flood, Arthur J Rowe:
Univ. Leicester, UK
"Characterisation of complex heterologous interactions in the cytoskeletal
protein alpha-actinin: the self and cross reactions between its repeat units
and its interactions with vinculin"
Helmut Coelfen & Stephen E. Harding: Univ.Nottingham, UK
"Schlieren pattern with Optima XL-A absorption optics"
Borries Demeler: Univ.Texas, San Antonio, TX, USA
"SEDVFIN: A new Program for XL-A Sedimentation Velocity Data Analysis"
Helmut Durchschlag et al.: Univ. Regensburg, Germany
"Comparative Studies of Conformational Changes of Proteins by Analytical
Ultracentrifugation and other Techniques"
Christine Ebel: Inst. Biol. Struct. Grenoble, France
"Characterization of the solution structure of halophilic proteins"
Ariel Lustig, Harald Herrmann, Ueli Aebi: Biozentrum Basel, Switzerland
"Is the short-column sedimentation equilibrium (SE) centrifugation suitable
to characterize intermediate filement (IF) assembly intermediates?"
Stephen E.Harding: Univ. Nottingham, UK
"Hydrodynamic Ellipsoid Modelling Revisited"
H. Hinsken, W. Borchard: Univ. Duisburg, Germany
"Characterization of thermoreversible gels in the AUC by means of the
gradient method"
E. Huber, P. Schuck, D. Schubert, Univ. Frankfurt/Main,Germany
"Stuying heterologous associations between membrane proteins by analytical
ultracentrifugation: Experience with erythrocyte band 3"
E. Karpova et al.: Russ. Acad.Sci. St.Petersburg, Russia
"Hydrodynamic properties of nucleosomal fibers and chromatin higher-order
structure"
Tom Laue: Univ. New Hampshire, Durham NH. USA
"Interactions between components in Protein-DNA complexes"
M.D. Lechner, W. Maechtle, D. Steinmeier: Univ. Osnabr!ck, Germany
"Molar Mass Distribution from Absolute Sedimentation Fractiometry
(ASF)-Competion with size Exclusion chromatography"
W.Maechtle, G.Ley, J.Streib: BASF, Ludwigshafen, Germany
"Studies of Microgel Formation in aqueous and organic Solvents by Light
Scattering and Ultracentrifuge"
Allen P. Minton: NIH Bethesda MD. USA
"Measurement and analysis of the concentration gradients of the individual
components in mixtures at sedimentation equilibrium"
G.M. Pavlov, S.Ya Frenkel: Univ.St.Petersburg, Russia
"Sedimentation Parameter of linear Polymers"
M.Pitschke,A.Fels,B.Schmidt,L.Heiliger,E.Kuchert,D.Riesner:Univ.D!sseldorf,
Germany
"Polymeric fluorescent dyes for labeling of proteins and nucleic acids"
K.Post,M.Pitschke,H.Serban,S.D Prusiner,D.Riesner: Univ. D!sseldorf,Germany
"Ultracentrifugation studies on prions and prion-proteins"
A.Seifert et al. Bergholz-Rehbr!cke, Germany
"Characterization of Gliadin-Galactomannan Incubation Mixtures by analytical
ultracentrifugation"
Walter Stafford: BBRI Boston MA. USA
"Analysis of interacting and non-interacting systems using of the apparent
sedimentation coefficient distribution function"
H.Triebel et al.: Univ. Jena Germany
"Sedimentation Analysis of the Effect of Netropsin and other Minor Groove
Binders on Structural Parameters of Supercoiled DNA"
Paul Voelker: Beckman Instr. Palo Alto, CA, USA
"Measurements of the Extinction Coefficient of Prostate Specific Antigen
using Interference and Absorbance Optics in the XL-A Analytical
Ultracentrifuge"
Yujia Xu, David Yphantis: Univ. Conn. Storrs, Conn. USA
"Detection of Heterogeneity in Self-associating Systems by Equilibrium
Sedimentation technique"
Toni Aerts, J.Clauwaert: Univ. Antwerp, Belgium
"Bovine Eyelens Polymeric alpha Crystallin: Size and Hydrodynamic Structure"
Joachim Behlke, Gudrun Lutsch, Martin Wieske, Rainer Benndorf: MDC
Berlin-Buch, Germany
"Supramolecular structure of the small heat shock protein Hsp25"
Joachim Behlke, Otto Ristau, Andreas Marg: MDC Berlin-Buch, Germany
"Complex formation and crystallization of adrenodoxin-reductase with
adrenodoxin"
P.Beyer, M.D. Lechner: Univ. Osnabrueck, Germany
"Molar Mass Characterisation of the Polycation
Poly[(dimethyleneimino)ethylene-(dimethyleneimino)-methylene-1,4-
phenylenemethylenedichloride] (Poly(XDC/TED))"
Helmut Coelfen, Peter Husbands, Stephen E. Harding: Univ. Nottingham, UK
"Alternative light sources for the Schlieren optics of a Beckman Model E
analytical ultracentrifuge"
Borries Demeler: Univ. Texas San Antonio, TX, USA
"Analysis of Complex Sedimentation Velocity Data: A Comparison between
methods"
Bruce H.Frank, Allen H. Pekar, Diane L. Bakaysa, Ronald F.Chance, Shun L.
Edwards, Henry A. Havel: Lilly Research Laboratories, Eli Lilly and Company,
Indianapolis, Indiana, USA
"Using analytical ultracentrifugation to define insulin analogs with
modified self-association behavior-the search for new therapeutic forms of
insulin"
Hellmut Gerst, Joachim Behlke: MDC Berlin, Germany
"Evaluation of ultracentrifugation experiment using interference optics"
E.Goernitz: Angew.Polymerforschung, Teltow-Seehof, Germany
"Molar Masses of Cationic Polyelectrolytes from Sedimentation Equilibrium and
Velocity Experiments"
Kornelia Jumel, Stuart Wilson, Maggie Smith, Stephen Harding: Univ.
Nottingham, UK.
"Molecular weight and subunit composition of a repressor isoform from the
Streptomyces temperate bacteriophage oC31"
E. Karpova, T.Osipova, V. Vorob'ev: Inst. Cytology, Russ. Acad. Science,
St.Petersburg, Russia
"Sedimentation Studies of Specific Association of Sea Urchin Sperm
Chromatin"
Moncef M. Ladjimi, Nadia Benaroudj, Gerard Batelier, Francoise Triniolles:
Laboratoire d'Enzymologie, CNRS, 91198 Gif-sur-Yvette, France
"Analysis of the self-Association Properties of the Molecular Chaperone HSC70
by Gel Permation Chromatography and Analytical Ultracentrifugation"
M.D.Lechner, W.Maechtle: Univ. Osnabrueck/BASF Ludwigshafen, Germany
"Molar Mass Distribution of Polymers from Sedimentation Velocity in an
Analytical Ultracentrifuge"
G.M. Pavlov et al. Univ. St Petersburg, Russia
"Direct and Revers Polysterene Sedimentation in Benzene and CCl4"
G.M Pavlov et al.: Univ. St Petersburg, Russia
"Velocity Sedimentation of Water-soluble Methyl Cellulose"
Hans-Joachim Schoenfeld, Dieter Schmidt:Hoffmann-La Roche, Basel Switzerland
"The DnaK chaperone system of E. coli:investigation of the molecular
chaperone DnaJ by analytical ultracentrifugation"
P.M.Schwarz, B.Demeler, J.C.Hansen: Univ. Texas, San Antonio, TX, USA
"Reversible Oligosome Self-Association studied by sedimentation velocity"
U. Sedlack, M.D. Lechner: Univ. Osnabrueck, Germany
"Direct digital data capture for sedimentation velocity experiments using
UV/VIS-optics"
A.Seifert et al.: Bergholz-Rehbruecke, Germany
"Characterization of the Coalescence stability of legumin stabilized o/w
emulsions by analytical ultracentrifugation"
Carsten Timmermann, Joachim Behlke, Otto Ristau, Hellmut Gerst, Udo
Heinemann: MDC Berlin-Buch, Germany
"Quaternary structure of HBsu and its interaction with DNA"
A. Zampieri, H. Wendt, R.M Thomas: ETH Zuerich, Switzerland
"Alpha-helical Coiled-Coils: Simple Models for Self-Associating Peptides and
Proteins"
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Tue, 20 Dec 94 10:36:06 PST
Date: Tue, 20 Dec 94 10:36:06 PST
From: alee%lcbvax.hepnet@Csa4.LBL.Gov
Message-Id: <941220103606.2f8006b7@Csa4.LBL.Gov>
Subject: sedimentation
To: rasmb@bbri.eri.harvard.edu
X-St-Vmsmail-To: LBL::"rasmb@bbri.eri.harvard.edu"
X-St-Vmsmail-Cc:
Status: OR
Hello,
I have been working with a piece of protein (14kD) which comes
from the activation domain of the eukaryotic transcription factor
c-jun. From CD and NMR data it appears that it has partial helical
structure which is induced by some organic solvents. We suspect
that this domain may be molten globule-like in its behavior. It
certainly has some random coil characteristics. We have attempted
to do velocity and equilibrium sedimentation and are having some
difficulty interpreting the results. The data suggests a molecular
weight much smaller that the actual weight. F/F0 is unusually high.
Has anyone had any experience performing ultracentrifugation
experiments on random coil/molten globule proteins? Is it possible
to do such studies on such a small (14kD) "partially unstructured"
polypeptide? Any comments would be greatly appreciated.
Andrew Lee alee@lcbvax.cchem.berkeley.edu
Larry Grace
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