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.

An overview

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.

An overview (DIFFC)

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.

Reference

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.

Availability

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.

System requirements

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.

Installation and initialization

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