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SEDNTERP 3
Note: A new 'primary reference' paper detailing the methods and equations used
in SEDNTERP version 3 was recently (Feb. 2023) published in European Biophysics Journal (link).
This paper should now be cited when you publish results that use SEDNTERP.
What is the purpose of SEDNTERP?
The SEDNTERP program is a general purpose tool for the interpretation of
sedimentation equilibrium, sedimentation velocity, and diffusion experiments. It
collects many diverse functions into a single program. SEDNTERP is useful both
for computing molecular structural estimates from experimental data and for
calculation of physical parameters of common buffers used in sedimentation
experiments. It is also useful to create a database of:
 | The properties of samples (proteins) you work with (molar mass, partial specific volume, hydration, UV extinction coefficients,
dn/dc) |
| The properties of buffers that you use in your lab (density, viscosity,
refractive index, pH, composition) |
| Experimental results (sedimentation coefficients, diffusion coefficients,
sedimentation equilibrium results) |
| The derived hydrodynamic properties of your samples (maximum possible
sedimentation and diffusion coefficients, f/f0 ratio, Perrin P,
Stokes radius, computed shape
and dimensions from ellipsoidal or cylindrical models) |
Importantly, storing this information in the program database allows you to
document and reproduce any calculated values you will be using in reports or
publications.
What's new in version 3?
| A new user interface, drawing on some elements of the version 2
interface, but with better separation of sample and experimental properties
(and full separation of sedimentation equilibrium and sedimentation velocity
experiments) |
| Support for diffusion experiments (and diffusion coefficients determined
from sedimentation velocity) |
| Calculation of protein refractive increments and the refractive index of
your buffers (features which will be useful to the light scattering
community as well as in AUC) |
| Concentrations of buffer components can now optionally be entered in
molal, mg/mL, g/mL, or weight % units (or volume % for liquid solutes).
Different components also can use different concentration units |
| Values for sedimentation (or diffusion) coefficients at multiple
concentrations can be entered, fitted to evaluate ks and
s020,w (or kD and D020,w),
and stored in the database |
| Experimental molar masses can now be calculated by combining
sedimentation and diffusion experiments (which can be in different buffers) |
| Hydrodynamic results may now be based on either sedimentation or
diffusion data, and may now combine data from experiments run in different
buffers (e.g. equilibrium and velocity done in different buffers) |
| Partial specific volumes calculated from amino acid composition may now
optionally include corrections for the volume of the N- and C-terminal
residues and the Traube covolume term, which should give more accurate
results, particular for peptides. |
| Disk (short cylinder) shape models are now supported, and cylinder
models are now accurate for length/diameter ratios from 0.01 to 100 (vs.
only 2 to 20 for versions 1 and 2) |
| Hydration can now be calculated for rod and disk models when the
asymmetry (L/d or d/H ratio) is known |
| The displayed numeric values are now all color-coded to indicate whether
the value is a user input (black), calculated (blue), or a user "override"
input of a value that is normally calculated (green) |
| The graphs of hydrodynamic shape models and of sample properties
(titration curves and extinction spectra) are now generated automatically
and shown within the main program form |
| Both viscosity and refractive index can now be calculated for buffers
containing D2O |
| 53 tables of refractive index vs. concentration for existing solutes
were fitted to polynomials and the resulting polynomial coefficients added
to the database. Six new solutes of particular interest to the biotechnology
community were also added (L-arginine, L-alanine, L-histidine, L-glycine,
sorbitol, and Tween-80), all of which have both density and viscosity data
(and all but sorbitol and L-glycine have refractive index data also) |
| The equations for the density and viscosity of water have been updated
to reflect current "best" values and changes to the International Practical
Temperature Scale. The values of the fundamental constants have also been
updated to current recommended values. (Yes these things do change over the
~25 years since SEDNTERP was created!) |
| The Help file (manual) has been completely revised and re-formatted, and
28 additional references added. |
What's missing?
| "Loosely-bound" conjugates ("non-covalent" conjugates) are no longer
supported. All conjugates are assumed to be fully bound (either covalently
or non-covalently) and therefore are included when computing the total molar
mass, overall partial specific volume, etc. |
| Pasting or entering amino acid sequences in 3-letter AA codes is no
longer supported |
| Saving or reading sample composition or buffer composition files (.smp
and .buf files) is no longer supported. (Those features were a hold-over
from pre-release versions that did not use a database.) |
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