DASHA (Version 3.48c, May 2000)
DASHA (Version 3.48c, May 2000)
Model-Free Analysis of Protein Dynamics from Heteronuclear NMR
Relaxation Data.
Developed by
Vladislav Yu. Orekhov, Dmitry M. Korzhnev. Dmitry E.
Nolde, Alexander P. Golovanov
General advising
Prof. Alexander S. Arseniev.
DASHA is an interactive program designed to investigate dynamics of
biomolecules, for which data of 15N or 13C heteronuclear
relaxation are available from NMR measurements. A number of sets of
longitudinal and transverse relaxation rates of 15N or
13C nuclei and 1H-15N, 13C NOE's
obtained at various NMR spectrometer frequencies might be used as the input.
The measured longitudinal, transverse relaxation rates and NOE values are
interpreted using the model-free approach of Lipari and Szabo (1982, J. Am.
Chem. Soc., 104, 4546-4559). In addition to the overall rotational correlation
time of the molecule, the internal dynamics of backbone N-H or C-H vectors of
two types of internal motions - fast, on a time scale of <20 ps, and
intermediate, close to 1 ns could be evaluated by constructing correspondent
spectral density functions. Contribution of the conformational exchange to
transverse relaxation rates of individual nitrogens or carbons could be
elucidated using a set of different rates of the CPMG spin-lock pulse train in
measuring T2 relaxation times (Orekhov et al., 1994, Eur. J.
Biochem., 219, 887-896). Separate module DIFFC, included into the DASHA
software, performs hydrodynamic calculations for proteins with known spatial
structure. All input and output data could be easily presented in PostScript
format.
DIFFC: Hydrodynamic Properties of Macromolecules. Relaxation Times
and Coefficients of Spectral Density Function for Anisotropic Overall
Rotation
Dmitry M. Korzhnev, Vladislav Yu. Orekhov,
General advising
Prof. Alexander S. Arseniev.
The "model-free" approach (Lipari and Szabo, 1982) can be easily
generalized on the case of anisotropic overall rotation of the molecule. The
general approach of interpretation of nuclear spin relaxation in rigid
anisotropic molecules undergoing rotational brownian diffusion was developed by
Woessner (Woessner, D.,1962). This approach implies that the overall rotation
correlation times and spectral density function J([omega]) coefficients depend
on the rotational diffusion rates. This rates can be calculated using the
Brenner's theory of translation-rotation dynamics (Happel and Brenner 1973) and
the beads model approximation (Garsia de la Torre and Bloomfield, 1977a,b; 1981
with modifications of Lamm & Szabo, 1986). The beads model approximation
assumes the molecule as the rigid body, represented by a number of frictional
points with particular radii, otherwise called beads. The hydrodynamics
interactions between them are described by the Oseen tensor or its
modifications.
The DIFFC program was developed to characterize hydrodynamics
properties and calculate nuclear spin relaxation parameters (i.e. rotation
correlation times and spectral density function (J([omega])) coefficients) for
anisotropic molecules with known spatial structure. DIFFC provides flexible
tool for representation of structure by array of friction points, hydrodynamics
calculations, calculations of nuclear spin relaxation parameters and volume
calculations.
Orekhov, V.Yu., Nolde, D.E., Golovanov, A.P., Korzhnev, D.M. and Arseniev,
A.S., Processing of heteronuclear NMR relaxation data with the new
software DASHA, Appl. Magn. Reson., 9, 581-588, 1995
Addresses for correspondence
Any comments, suggestions, and bug reports can be sent to the authors:
Dr. V.Yu. Orekhov
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS
Ul. Miklukho-Maklaya 16/10
Moscow, 117871, Russia
Phone: +7 (095) 330 7483
Fax: +7 (095) 335 5033
E-Mail: orov@nmr.ru
D. M. Korzhnev
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS
Ul. Miklukho-Maklaya 16/10
Moscow, 117871, Russia
Phone: +7 (095) 330 7483
Fax: +7 (095) 335 5033
E-Mail: korzh@nmr.ru
Prof. A.S Arseniev
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS
Ul. Miklukho-Maklaya 16/10
Moscow, 117871, Russia
Phone: +7 (095) 330 5929
Fax: +7 (095) 335 5033
E-Mail: aars@nmr.ru
Maillist
Also, maillist is available. The aim of this maillist is to
inform DASHA users about new software releases, bugs,
hints, etc. To subscribe, send mail to Majordomo@mail.nmr.ru with the following
command in the body of your message:
subscribe dasha_users your_e-mail_address
When you have been added to the mailing list you will receive confirmation by electronic mail at
the subscribed address.
To unsubscribe from a list send an unsubscribe request like the above to the same
mail address; do not send administrative requests to the mailing list.
Academic license for DASHA are available for free world wide. You get the
source code, and you can also get executables. Academic licenses cannot be used
for projects that are supported by a "for profit" organization. Academic users
can get DASHA here
.Signed license form should be send by mail to
Prof. Arseniev as soon as the software is installed. The license form can be
found in the DASHA package in PostScipt format (file license.ps in DASHA
home directory).
You can download the whole package here
For other licenses please contact Prof. Alexander Arseniev.
DASHA is writen in ANSI C. It was extensively tested on various Sun and SGI
workstations. No basic problems are known that would prevent it from running on
other UNIX systems.
Algorithms implemented in this program are not undue time-consuming, so for
vide variety of computers this program seems to be suitable. At least Sun Sparc
and SGI IRIS-220 work well. Since the program has been written in ANSI C
programming language it is usually straightforward to implement the program on
other UNIX machines.
DASHA is available in the form of compressed tar file dashaXX.tar.Z (XX
- is to be substituted for the particular version number).
To install the DASHA
a. Put dashaXX.tar.Z file to the directory where you want
to install DASHA program.
b. Type the following commands:
uncompress dashaXX.tar.Z
tar xvf dashaXX.tar
cd dashaXX
c. If you are using SUN or SGI computers, the program is
ready. If you use another system or want to recompile the executables, use the
install shell in the DASHA directory. To compile the program you need C
and F77 compillers installed on your system.
d. For the proper usage of the DASHA program each user should
modify his shell environment. The directory where the DASHA is installed should
be included in path variable and the environment variable DASHA_DIR
should be defined for the the DASHA directory. For example if the DASHA is
installed in /usr/home/dasha directory the following lines could be
inserted into the user .cshrc file:
set path=($path /usr/home/dasha)
setenv DASHA_DIR /usr/home/dasha
After the modification of .cshrc file you should type
source .cshrc