Laboratory of Macromolecular Crystallography
Head of laboratory: Vladimir Y. Lunin, Dr. Sci.
Postal address: IMPB RAS, Pushchino, Moscow Region, 142290, Russia
The work of the laboratory is concerned with the determination of three-dimensional structure of biological
macromolecules and their complexes on the base of the X-ray diffraction experiment. The laboratory specialises
in the developing of mathematical and computing method necessary to pass the way from the data measured in X-ray
experiment to an atomic model of the studied object.
This field of studies had appeared in Research Computing Centre of USSR Academy of Sciences in 1976 (this name
was changed in 1992 for Institute of Mathematical Problems of Biology). In those years the special program for
developing of Protein Crystallography in the USSR was launched by the Academy of Sciences. In particular, a
crystallographic laboratory (headed by Prof.Yu.N.Chirgadze) was created in the Institute of Protein Research
in Pushchino and it was decided to have a special mathematical group in the Research Computing Centre for
computational support of the studies. The goal of the first period of the work was to study the method and to
adapt the existing crystallographic software to the computers of RCC. This work was curried out in close
collaboration with the laboratory of Yu.N.Chirgadze and the department of computing machinery of RCC. This stage
was completed with creation in Pushchino of computing environment, which allowed performing of all main stages
of X-ray structure investigation of proteins.
Later the three main direction of the crystallographic work in the Research Computing Centre were raised as:
- development of mathematical and computing methods for the Protein crystallography;
- development of software for solution of crystallographic problems;
- computer and mathematical support of different projects concerned with the determination of
Last years the laboratory efforts were concentrated on the development of ab-initio approaches to the solution of
the main problem of Protein crystallography, namely the phase problem. By ab-initio method we mean here ones
designed for the solution of the structure immediately from the data of standard X-ray experiment, without the
use of additional experimental information. This work was curried out in collaboration with University of Nancy I,
(Nancy, France) and Institute of Genetics and Molecular and Cellular Biology (Strasbourg, France).
In different years the laboratory staff has published more then 100 full papers. The work of the laboratory was
supported by grants of Russian Foundation for Basic Researches, International Science Foundation, American
Crystallographic Association, Royal Society and Centre National de la Recherche Scientifique.
Some idea concerning the directions of the work of the laboratory may be got from the titles of some publications
listed below. The brief descriptions of laboratory projects, the full
list of laboratory publications as well as the
full texts of published papers provide with more information on this
- Chirgadze, Yu.N., Oreshin, V.D., Sergeev, Yu.V., Nikonov, S.V. & Lunin, V.Yu. (1980) "Structure of
gamma-crystallin IIIb from calf lens at 5 Å resolution". FEBS Letters, 118, 2, 296-298.
- Lunin, V.Yu., Urzhumtsev, A.G. (1984) "Improvement of Protein Phases by Coarse Model Modification".
Acta Cryst., A40, 269-277.
- Urzhumtsev, A.G., Lunin, V.Yu., Vernoslova, E.A. (1989) "FROG - high-speed restraint-constraint
refinement program for macromolecular structure". J.Appl.Cryst., 22, 500-506.
- Lunin, V.Yu. (1993) "Electron-Density Histograms and the Phase Problem". Acta Cryst. D49, 90-99.
- Navaza, J., Vernoslova, E. (1995) "On the Fast Translation Functions for Molecular Replacement". Acta
Crys. A51, 445-449.
- Lunin, V.Yu., Skovoroda, T.P. (1995) "R-free Likelihood-Based Estimates of Errors for Phases Calculated
from Atomic Models". Acta Cryst. A51, 880-887.
- Urzhumtsev, A.G., Vernoslova, E.A., Podjarny, A.D. (1996) "Approaches to Very Low Resolution Phasing of
the Ribosome 50S particle from Thermus thermophilus by the Few-Atoms-Models and Molecular-Replacement
Methods". Acta Cryst., D52,1092-1097.
- Shlyapnikov S.V., Lunin V.V., Perbandt M., Polyakov K.M., Lunin V.Yu., Levdikov V.M., Betzel Ch.,
Mikhailov A.M. (2000) "Atomic structure of the Serratia marcescens endonuclease at 1.1 Å resolution and the
enzyme reaction mechanism." Acta Cryst. D56, 567-572.
- Lunin V.Y., Lunina N.L., Petrova T.E., Skovoroda T.P., Urzhumtsev A.G., Podjarny A.D. (2000)
"Low-resolution ab initio phasing: problems and advances". Acta Cryst. D56, 1223-1232.
- Lunin, V.Y., Lunina, N.L., Ritter, S., Frey, I., Berg, A., Diderichs, K., Podjarny, A.D., Urzhumtsev, A.,
Baumstark M.W. "Low-resolution data analysis for low-density lipoprotein particle". (2001). Acta
Crys., D57, 108-121.
- Lunin, V.Y., Afonine P.V., A. G. Urzhumtsev, A.G. "Likelihood-based refinement. I. Irremovable
model errors". (2002). Acta Cryst. A58, 270-282.