Structure

Laboratory of Macromolecular Crystallography



This is a review of the works carried out in LMC of the IMPB RAS. Information on other papers in this field may be found in the original papers listed below.

Determining the structure of biological macromolecules

(1980-2002)

       The main LMC activities are concerned with mathematical and computational problems of X-ray crystallography. The investigations of particular macromolecular structures listed below were carried out in collaboration with laboratories studying these objects. Usually, LMC participated in the study in circumstances, when the standard methods failed to produce a suitable solution and some non-standard approaches were required. In different years Laboratory of Macromolecular Crystallography of the IMPB RAS collaborated with laboratories from:

  • Institute of Protein Research RAS, Pushchino, Russia; [1-2, 4, 7, 9, 10]
  • Institute of Biophysics RAS, Pushchino, Russia; [5, 6];
  • Institute of Crystallography RAS, Moscow, Russia; [12, 18, 20-22];
  • Institute of Bioorganic Chemistry RAS; Moscow, Russia; [3];
  • Institute of Molecular Genetics RAS; Moscow, Russia; [8];
  • Institut de Genetique et de Biologie Moleclaire et Cellulaire, Strasbourg, France; [13-17, 19];
  • Univrsité Henri Poincaré, Nancy I, Nancy, France; [23]
  • Medezinische Universitätsklinik Freiburg; Freiburg, Germany; [23].

       The titles of the listed below papers show the variety of the studied objects.

March, 24, 2003
V.Lunin

Publications

The full texts of papers

  1. Chirgadze, Yu.N., Sergeev, Yu.V., Fomenkova, N.P., Nikonov, S.V. & Lunin, V.Yu. (1980). "Structure determination of gamma-crystalline II from calf lens at 5Å resolution". Dokl.Akad.Nauk SSSR, 250, 3, 762-765. (In Russian).

  2. 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 5Å resolution". FEBS Letters, 118, 2, 296-298.

  3. Kuzin, A.P. & Urzhumtsev, A.G. (1983). "LSQ-refinement of actinoxanthin structure at 1.8Å resolution". All-Union Symp. on Chemistry of Proteins and Peptides, Riga, 1983, Coll. Abstr., 186. (In Russian)

  4. Urzhumtsev, A.G. & Lunin, V.Yu. (1982). "Electron-density-maps improvement by use of refinement of atomic model structure. II. Phase improvement for g-crystalline". Preprint, NCBI AN SSSR, Pushchino. (In Russian)

  5. Vazina, A.A., Koristova, A.F., Shelestov, V.M., Vernoslov, S.E., Lunin V.Yu , Kozlov M.A. & Kraisman, V.L.. (1984). "Investigation of Ca2+-binding centers of parvalbumine by distant fine structure of X-ray absorption spectra". Mol.Biol.(USSR), 18, 3, 681-684. (In Russian).

  6. Vazina, A.A., Korystova, A.F., Shelestov, V.M., Vernoslov, S.E., Lunin V.Yu., Kozlov M.A. & Kraizman, V.L. (1985). "Investigation of the structure of calmoduline metal-binding centers by EXAFS-spectroscopy". Mol.Biol.(USSR), 19, 6, 1643-1647. (In Russian).

  7. Chirgadze, Yu.N., Nevskaya, N.A., Fomenkova, N.P., Nikonov, S.V., Sergeev, Yu.V., Brazhnikov, E.V., Garber, M.B., Lunin, V.Yu., Urzhumtsev, A.G. & Vernoslova, E.A. (1986). "Spatial structure of gamma-crystalline IIIb from calf lens at 2.5Å resolution". Dokl.Akad.Nauk SSSR, 290, 2, 492-495. (In Russian).

  8. Lobsanov, Yu.D., Pletnev, V.Z., Vtyurin, N.N., Lubnin, M.Yu., Mokulskii, M.A., Urzhumtsev, A.G., Lunin, V.Yu. & Luzyanina, T.B. (1990). "X-ray study of the pea lectin-carbohydrate complex at 2.4Å resolution. I. Atomic model". Bioorganic Chemistry (USSR), 16, 12, 1589-1598. (In Russian).

  9. Chirgadze, Yu.N., Brazhnikov, E.V., Nikonov, S.V., Fomenkova, N.P., Garber, M.B., Lunin, V.Yu., Urzhumtsev, A.G. , Chirgadze, N.Yu. & Nekrasov, Yu.V. (1991). "Crystal structure of ribosomal factor G from bacteria Thermus thermophilus at low resolution". Dokl.Acad.Nauk SSSR, 320, 488-491 (In Russian).

  10. Chirgadze, Yu.N., Nevskaya, N.A., Vernoslova, E.A., Nikonov, S.V., Sergeev, Yu.V., Brazhnikov, E.V., Fomenkova, N.P., Lunin, V.Yu. & Urzhumtsev, A.G. (1991). "Crystal structure of calf eye lens gamma-crystallin IIIb at 2.5Å resolution: its relation to function". Experimental Eye Research, 53, 295-304.

  11. Urzhumtsev, A.G. (1992). "On the reliability of atomic models in the PDB: stereochemical point of view". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 27, 31-32.

  12. Morgunova, E.Yu., Mikhailov, A.M., Urzhumtsev, A.G. & Vainstein, B.K. (1992). "Crystal structure of the CMtV capsid at 6Å resolution". Kristallografiya (USSR), 37, 2, 396-404. (In Russian).

  13. Tete-Favier, F., Barth, P., Mitchler, A., Podjarny, A.D., Rondeau, J.-M., Urzhumtsev, A., Biellmann, J.-F. & Moras, D. (1995). "Aldose Reductase from Pig Lens". European Journal of Medicinal Chemistry, 30, S, 589-603.

  14. Urzhumtsev, A.G. & Podjarny, A.D. (1995). "On the problem of solvent modeling in macromolecular crystals using diffraction data: 1.The low-resolution range". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, 12-16.
  15. Volkmann, N., Schlunzen, F., Urzhumtsev, A.G., Vernoslova, E.A., Podjarny, A.D., Roth, M., Pebay-Peyroula , E., Berkovitch-Yellin, Z., Zaytzev-Bashan, A. & Yonath, A. (1995). "On ab-initio phasing of ribosomal particles at very low resolution". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, 23-32.

  16. 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.

  17. Urzhumtsev, A., Tete-Favier, F., Mitschler, A., Barbanton, J., Barth, P., Urzhumtseva, L., Biellmann, J-F., Podjarny, A.D. & Moras, D. (1997). "A 'specificity' pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil ". Structure, 5, 5, 601-612.

  18. Lunin, V.Yu., Levdikov, V.M., Shliapnikov, S.V., Blagova, E.V., Lunin, V.V., Wilson, K.S. & Mikhailov, A.M. (1997). "Three-dimensional structure of Serratia marcescens nuclease at 1.7Å resolution and mechanism of its action". FEBS Letters, 412, 217-222.

  19. Podjarny, A.D., Howard, E.I., Urzhumtsev, A.G. & Grigera, J.R. (1997). "A Multicopy Modeling of the Water Distribution in Macromolecular Crystals". Proteins, 28, 303-312.

  20. Lunin, V.Yu., Blagova, E.V., Levdikov, V.M., Lunin, V.V., Shlyapnikov, S.V., Perbandt, M., Raishankar, K.S., Betzel, H. & Mikhailov, A.M. (1999). "Extracellular Endonuclease of Serratia marcescens. I. Three-Dimensional Structure of Crystalline Protein at 1.7Å Resolution", Molecular Biology, 33, 2, 180-187.

  21. Shlyapnikov, S.V., Blagova, E.V., Levdikov, V.M., Lunin, V.Yu., Lunin, V.V., Mikhailov, A.M., Betzel, Ch., Rajashankar, K.S. & Perbandt, M. (1999). "Extracellular Endonuclease of Serratia marcescens. II. Active Site Amino Acid Residues and a Hypothetical Mechabism of Enzyme Functioning". Molecular Biology, 33, 3, 398-404

  22. 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 1.1Å resolution and the enzyme reaction mechanism." Acta Cryst. D56, 567-572.

  23. Lunin, V.Y., Lunina, N.L., Ritter, S., Frey, I., Berg, A., Diderichs, K., Podjarny, A.D., Urzhumtsev, A. & Baumstark M.W. (2001). "Low-resolution data analysis for low-density lipoprotein particle". Acta Cryst., D57, 108-121.