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 macromolecular structures.

    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 subject.

  • 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.