JOMfa1blu.gif (2406 bytes)

Mosberg

Lab Web

buttonAA.bmp (8838 bytes)button um.bmp (8838 bytes)buttonColPhar.bmp (8838 bytes)buttonMedChem.bmp (8838 bytes)

Home Up Mosberg Omnaas Sobczyk-Kojiro Lomize Pogozheva Gregson Fowler Ma Mousigian

Andrei L. Lomize
Ph.D., Assistant Research Scientist

Research Investigator, College of Pharmacy, University of Michigan (1993-1997)
Senior Research Fellow, College of Pharmacy, University of Michigan (1992-1993)
Researcher, NMR spectroscopy lab, Shemyakin Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow(1983-1992)
Ph.D., Biophysics, Lomonosov Moscow State University, Russia (1983)
M.S., Biophysics, Biological Department of Lomonosov Moscow State University, Russia (1979)

Phone: (734)647-5825
E-mail: almz@umich.edu

Research Interests

peptide/protein physics;
theory of protein structure;

wpe51406.gif (327522 bytes)     

In a local minimum near global maximum


 

Structures solved
Gramicidin A dimer in SDS micelles, double helices of gramicidin A in organic solvents, and succinyl-bis(desformil) gramicidin A (NMR and computational studies, 1grm PDB file and other structures), in collaboration with I.L. Barsukov, V.Y. Orekhov, A.S. Arseniev, and V.F. Bystrov
Insectotoxin I5 from Buthus eupeus (NMR and computational studies, 1sis PDB file), in collaboration with V. Kondakov, V. Maiorov, I.V. Maslennikov, A.S. Arseniev and V.F. Bystrov
Neurotoxin II from Naja naja oxiana (NMR study, 1nor PDB file), in collaboration with A.P. Golovanov and A.S. Arseniev
Several  fragments of bacterioopsin in organic solvents and in the presence of micelles (NMR and computational studies, 1bct PDB file and other structures), in collaboration with K.V. Pervushin, I.V. Maslennikov, I.L. Barsukov, D.E. Nolde, A.S. Arseniev and V.F. Bystrov.
Tyr-c[D-Cys-Phe-D-Pen]OH (JOM-13) and related peptides (theoretical conformational analysis; see crystal structure of JOM-13 determined by J. Flippen-Anderson and C. George in the neuropeptide database), in collaboration with I. Pogozheva and H.I. Mosberg.
Transmembrane 7 helix bundles of bovine rhodopsin and related G-protein coupled receptors  calculated by distance geometry with hydrogen bonding constrains (1bok and 1boj PDB files and other GPCR structures), in collaboration with I. Pogozheva and H.I. Mosberg.

Software developed
CONFORNMR, a program for conformational analysis of peptides by molecular mechanics with NMR spectroscopy data (in collaboration with A.G. Sobol and I.V. Maslennikov). The program includes the calculation and dynamic averaging of NOE cross-peak volumes using complete relaxation matrix approximation, the automated stereochemical assignment of chemical shifts, assignment of overlapped cross-peaks, determination of "local" (j , y , c) structure from NMR data, the search for low-energy NMR-consistent side-chain conformers in p - and a -helices and other features.
Software for analysis and optimum superposition of secondary structure packing motifs in proteins (in collaboration with D. Nolde,  D. Dementieva and V. Maiorov).
ADJUST, a set of programs for distance geometry docking of transmembrane helices using interhelical hydrogen bonds extracted from multiple sequence alignments (in collaboration with I.D. Pogozheva).
FRAMEWORK, a program that reproduces formation of secondary structure frameworks during protein folding (under development).


Selected publications

Protein structure theory.

  1. Lomize A.L. and Mosberg H.I. Thermodynamic model of secondary structure for a-helical peptides and proteins. Biopolymers. 42(2):239-269, 1997. Abstract.
  2. Lomize A.L. and Mosberg H.I. Thermodynamic model of a-helix in aqueous solution and micelle-bound state. In Peptides: Chemistry, Structure, and Biology, Proceedings of the 14th American Peptide Symposium, P. Kaumaya and R.S. Hodges, Eds., Mayflower Scientific, England, pp. 474-476, 1996 Abstract.
  3. Lomize A.L. Identification of unified coordinate frameworks for antiparallel and parallel helix to helix packing in peptides and proteins. In Peptides: Chemistry, Structure and Biology, Proceedings of the 13th American Peptide Symposium, R.S. Hodges and J.A. Smith, Eds., ESCOM. Leiden, pp 893-896.1994.
  4. Lomize A.L, Pogozheva I.D. and Mosberg H.I. Structural organization of G protein-coupled receptors. Perspectives in Drug Discovery and Design, in press, 1998. Abstract.
    5.

Modeling G-protein coupled receptors.

  1. Pogozheva I.D., Lomize A.L. and Mosberg H.I. The transmembrane 7-a-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints. Biophysical Journal. 72(5):1963-1985, 1997. Abstract.
    2.
  2. Pogozheva I.D., Lomize A.L. and Mosberg H.I. The origin of specificity in the opioid receptor family. Peptides: Chemistry, Structure, and Biology, Proceedings of the 15th American Peptide Symposium, in press, 1998. Abstract.
  3. Pogozheva I.D., Lomize A.L. and Mosberg H.I. Opioid receptor 3D structures from distance geometry calculations with hydrogen bonding constraints.Biophysical Journal, submitted 1998. Abstract.

Cyclic opioid peptides.

  1. Lomize A.L., Flippen-Anderson J.L, George C., and Mosberg H.I. Conformational analysis of the d receptor-selective, cyclic opioid peptide, Tyr-c[D-Cys-Phe-D-Pen]OH (JOM-13). Comparison of X-ray crystallographic structures, molecular mechanics simulations and 1H NMR data. J. Amer. Chem. Soc., 116:429-436, 1994. Abstract.
  2. Mosberg H.I., Lomize A.L., Wang C., Kroona H., Heyl D.L., Sobczyk-Kojiro K., Ma W., Mousigian C. and Porreca F. Development of a model for the d-opioid receptor pharmacophore. 1. Conformationally restricted Tyr1 replacements in the cyclic delta receptor selective tetrapeptide Tyr-c[D-Cys-Phe-D-Pen]OH (JOM-13) . Journal of Medicinal Chemistry. 37(25):4371-4383, 1994. Abstract.
  3. Mosberg H.I., Omnaas J.R., Lomize A.L., Heyl D.L., Nordan I., Mousigian C., Davis P. and Porreca F. Development of a model for the d-opioid receptor pharmacophore. 2. Conformationally restricted Phe3 replacements in the cyclic delta receptor selective tetrapeptide Tyr-c[D-Cys-Phe-D-Pen]OH (JOM-13). Journal of Medicinal Chemistry. 37(25): 4384-4391, 1994. Abstract.
  4. Lomize A.L., Pogozheva I.D. and Mosberg H.I. Development of a model for the d-opioid receptor pharmacophore: 3. Comparison of the cyclic tetrapeptide, Tyr-c[D-Cys-Phe-D-Pen]OH with other conformationally constrained d-receptor selective ligands.Biopolymers. 38(2):221-234, 1996.Abstract.
  5. Mosberg H.I., Dua R.K., Pogozheva I.D. and Lomize A.L. Development of a model for the d-opioid receptor pharmacophore. 4. Residue 3 dehydrophenylalanine analogues of Tyr-c[D-Cys-Phe-D-Pen]OH (JOM-13) confirm required gauche orientation of aromatic side chain. Biopolymers. 39(3):287-296, 1996. Abstract.
  6. Mosberg H.I., Omnaas J.R., Sobczyk-Kojiro K., Ho J.C., Ma W., Bush P., Mousigian C., and Lomize A.L. Pharmacophore elements of the TIPP (Tyr-Tic-Phe-Phe) class of d-opioid receptor antagonists, Letters in Peptide Science, 1:69-72, 1994. Abstract.

NMR and theoretical conformational analysis.

  1. Golovanov, A. P, Lomize, A. L., Arseniev, A. S., Utkin, Y. N. and Tsetlin, V. I. Two-dimensional 1H-NMR study of neurotoxin II Naja naja oxiana spatial structure, Eur.J.Biochem., 213:1213-1223, 1993.
  2. Maslennikov, I. V., Lomize, A. L. and Arseniev, A. S. Structure refinement of (34-65) bacterioopsin from NMR data in solution, Bioorgan. Chemistry (USSR), 17:1456-1469, 1991.
  3. Barsukov, I. L., Nolde, D. E., Lomize, A. L. and Arseniev, A.S. Three-dimensional structure of proteolytic fragment 163-231 of bacterioopsin determined from nuclear magnetic resonance data in solution, Eur.J. Biochem., 206:665-672, 1992.
  4. Lomize, A. L., Pervushin, K. V. and Arseniev, A. S. Spatial structure of (34-65)bacterioopsin polypeptide in SDS micelles determined from nuclear magnetic resonance data, J. Biomol. NMR, 2: 361-372, 1992.
  5. Lomize, A. L., Maiorov, V. N. and Arseniev, A. S. Spatial structure of insectotoxin I5A Buthus eupeus by 1H Nuclear magnetic resonance spectroscopy, Bioorgan. Chemistry (USSR), v.17:1613-1632, 1991.
  6. Lomize, A. L., Sobol, A. G. and Arseniev, A. S. Determination of local structure of proteins from two-dimensional NMR data. Bioorgan. Chemistry (USSR), 16:179-201, 1990.
  7. Lomize, A. L., Arseniev, A. S., Maslennikov, I. V. and Bystrov, V.F. Determination of the local structure of the protein insectotoxin I5A from the scorpion Buthus eupeus from 1H-NMR spectroscopy data, Bioorgan. Chemistry (USSR), 16:1310-1324, 1990.
  8. Arseniev, A. S., Barsukov, I. L., Bystrov, V. F., Lomize, A.L. and Ovchinnikov, Y. A. NMR study of gramicidin A transmembrane ion channel. Head-to-head right-handed, single-stranded helices, FEBS Lett., 186:168-174, 1985.
  9. Bystrov, V. F., Arseniev, A., S., Barsukov, I. L. and Lomize, A.L. 2D NMR of single and double stranded helices of gramicidin A in micelles and solutions, Bulletin of Magnetic Resonance, 8:84-94, 1986.
  10. Arseniev, A. S., Lomize, A. L., Barsukov, I. L. and Bystrov, V. F. Gramicidin A transmembrane ion-channel. Three-dimensional structure reconstruction based on NMR spectroscopy and energy refinement, Biol. Membr. (USSR), 3:1077-1104, 1986.
  11. Barsukov, I. L., Lomize, A. L., Arseniev, A. S. and Bystrov, V. F. Spatial structure of succinyl-bis(desformil)gramicidin A in micelles. NMR conformational analysis. Biol. Membr. (USSR), 4:171-193, 1987.
  12. Bystrov, V. F., Arseniev, A. S., Barsukov, I. L., Lomize, A. L., Abdulaeva, G. V., Sobol, A. G., Maslennikov, I. V. and Golovanov, A. P. 2D-NMR for 3D-structure of membrane spanning polypeptides: gramicidin A and fragments of bacteriorhodopsin, In: Protein Structure and Engineering (ed. by O.Jardetzky) NATO ASI Series, Series A, 183:111-138, 1989.
  13. Lomize, A. L., Orekhov, V. Yu. and Arseniev, A. S. Refinement of the spatial structure of the gramicidin A transmembrane ion-channel, Bioorgan. Chemistry (USSR), 18:182-200 (1992).

 
Finger information

This page was last updated 05/01/98 by Irina D. Pogozheva.