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Andrei L.Lomize
Research Scientist
In a local minimum near global maximum
UofM Directory
Finger Information
Phone: (734)615-7194
almz@umich.edu
 
M.S.:
Department of Biophysics, Moscow State University, Moscow, Russia (1979 Biology, Biophysics)
Ph.D.:
Moscow State University, Moscow, Russia, (1981 Physics and Mathematics)
 

Research Interests

Protein structure, folding and thermodynamics.


Projects

Peptides and proteins in membranes

Homology modeling of GPCRs, important drug targets


Selected Publications

Lomize A.L., Pogozheva I.D.
TMDOCK: An energy-based method for modeling α-helical dimers in membranes.
J Mol Biol, 429: pii: S0022-2836(16)30369-2 [Epub] (2017)

 

Lomize A.L., Lomize M.A., Krolicki S.R., Pogozheva I.D.
Membranome: a database for proteome-wide analysis of single-pass membrane proteins.
Nucleic Acids Res, 45(D1): pii: gkw712 [Epub] (2017)

 

Pogozheva I.D., Mosberg H.I., Lomize A.L.
Life at the border: adaptation of proteins to anisotropic membrane environment
Protein Sci, 23: 1165-1196 (2014)

 

Lomize A.L., Pogozheva I.D.
Solvation models and computational prediction of orientations of peptides and proteins in membranes
Methods Mol Biol, 1063: 125-142 (2013)

 

Madhongsa K., Pasan S., Phophetleb O., Nasompag S., Thammasirirak S., Daduang S., Taweechaisupapong S., Lomize A.L., Patramanon R.
Antimicrobial action of the cyclic peptide bactenecin on Burkholderia pseudomallei correlates with efficient membrane permeabilization
PLoS Negl Trop Dis, 7: e2267 (2013)

 

Pogozheva I.D., Tristram-Nagle S., Mosberg H.I., Lomize A.L.
Structural adaptations of proteins to different biological membranes
Biochim Biophys Acta-Biomembranes, 1828: 2592-2608 (2013)

 

Lomize M.A., Pogozheva I.D., Joo H., Mosberg H.I., Lomize A.L.
OPM database and PPM web server: resources for positioning of proteins in membranes
Nucleic Acids Res, 40(Database issue): D370-D376 (2012)

 

Janovick J.A., Pogozheva I.D., Mosberg H.I., Cornea A., Conn P.M.
Rescue of misrouted GnRHR Mutants reveals its constitutive activity
Mol Endocrinol, 26: 1179-1188 (2012)

 

Anand J.P., Purington L.C., Pogozheva I.D., Traynor J.R., Mosberg H.I.
Modulation of opioid receptor ligand affinity and efficacy using active and inactive state receptor models
Chem Biol Drug Des, 80: 763-770 (2012)

 

Lomize AL, Pogozheva ID, Mosberg HI.
Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes.
J Chem Inf Model, 51: 930-946 (2011)

 

Lomize AL, Pogozheva ID, Mosberg HI.
Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.
J Chem Inf Model, 51: 918-929 (2011)

 

Ho D, Lugo MR, Lomize AL, Pogozheva ID, Singh SP, Schwan AL, Merrill AR.
Membrane topology of the colicin E1 channel using genetically encoded fluorescence.
Biochemistry, 50: 4830-4842 (2011)

 

Zhang WX, Thakur V, Lomize A, Pogozheva I, Panagabko C, Cecchini M, Baptist M, Morley S, Manor D, Atkinson J.
The contribution of surface residues to membrane binding and ligand transfer by the α-tocopherol transfer protein (α-TTP).
J Mol Biol, 405: 972-988 (2011)

 

Burman R, Herrmann A, Tran R, Kivelä JE, Lomize A, Gullbo J, Göransson U.
Cytotoxic potency of small macrocyclic knot proteins: structure-activity and mechanistic studies of native and chemically modified cyclotides.
Org Biomol Chem, 9: 4306-4314 (2011)

 

Purington L.C., Sobczyk-Kojiro K., Pogozheva I.D., Traynor J.R., Mosberg H.I.
Development and in vitro characterization of a novel bifunctional mu-agonist/delta-antagonist opioid tetrapeptide
ACS Chem Biol, 6: 1375-1381 (2011)

 

Chi H.-J., Bakolitsa C., Skerra A., Lomize A., Carlton D., Miller M.D., Krishna S.S., Abdubek P., Astakhova T., Axelrod H. L., Clayton T., et al.,
Structure of the first representative of Pfam familyPF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism.
Acta Crystallogr, F 66: doi:10.1107/S1744309109037749 (2010)

 

Kumar A., Lomize A., Jin K.K., Carlton D., Miller M.D., Jaroszewski L., Abdubek P., Astakhova T., Axelrod H. L., Chiu H.-J., Clayton T., Das D., et al
Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding.
Acta Crystallogr, F66: doi: 10.1107/S1744309109042481 (2010)

 

Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI
The role of hydrophobic interactions in positioning of peripheral proteins in membranes
BMC Struct Biol, 7: 44 (2007)

 

Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI
OPM: orientations of proteins in membranes database.
Bioinformatics, 22: 623-625 (2006)

 

Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI
Positioning of proteins in membranes: a computational approach
Protein Sci., 15: 1318-1333 (2006)

 

Pogozheva ID, Chai B-X, Lomize AL, Fong TM, Weinberg DH, Nargund RH, Mulholland MW, Gantz I, Mosberg HI
Interactions of human melanocortin receptor-4 with small-molecule agonists.
Biochemistry, 44: 11329-11341 (2005)

 

Fowler CB, Pogozheva ID, Lomize AL, LeVine H, Mosberg HI
Complex of active mu-opioid receptor with cyclic peptide agonist modeled from experimental constraints.
Biochemistry, 43: 15796-15810 (2004)

 

Lomize AL, Pogozheva ID, Mosberg HI
Quantification of helix-helix binding affinities in micelles and lipid bilayers.
Protein Sci., 13: 2600-2612 (2004)

 

Lomize AL, Reibarkh MY, Pogozheva ID
Interatomic potentials and solvation parameters from protein engineering data for buried residues.
Protein Sci., 11: 1984-2000 (2002)

 

Lomize AL, Pogozheva ID, Mosberg HI
Structural organization of G-protein-coupled receptors.
J. Comput. Aided Mol. Des., 13: 325-353 (1999)

 

Lomize AL, Pogozheva ID, Mosberg HI
Prediction of protein structure: The problem of fold multiplicity.
Proteins, 37: 199-203 (1999)

 

Pogozheva ID, Lomize AL, Mosberg HI
Opioid receptor three-dimensional structures from distance geometry calculations with hydrogen bonding constraints.
Biophys. J., 75: 612-634 (1998)

 

Pogozheva ID, Lomize AL, Mosberg HI
The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints.
Biophys. J., 72: 1963-1985 (1997)

 

Lomize AL, Mosberg HI
Thermodynamic model of secondary structure for alpha-helical peptides and proteins.
Biopolymers., 42: 239-269 (1997)

 

Mosberg HI, Dua RK, Pogozheva ID, Lomize AL
Development of a model for the delta-opioid receptor pharmacophore. 4. Residue 3dehydrophenylalanine analogues of Tyr-c[D-Cys-Phe-D-Pen]OH (JOM-13) confirmrequired gauche orientation of aromatic side chain.
Biopolymers, 39: 287-296 (1996)

 

Lomize AL, Pogozheva ID, Mosberg HI
Development of a model for the delta-opioid receptor pharmacophore: 3. Comparison of the cyclic tetrapeptide, Tyr-c[D-Cys-Phe-D-Pen]OH with other conformationally constrained delta-receptor selective ligands.
Biopolymers., 38: 221-234 (1996)

 

Mosberg HI, Omnaas JR, Lomize AL, Heyl DL, Nordan I, Mousigian C, Davis P, Porreca F
Development of a model for the delta 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).
J. Med. Chem., 37: 4384-4391 (1994)

 

Mosberg HI, Lomize AL, Wang C, Kroona H, Heyl DL, Sobczyk-Kojiro K, Ma W, Mousigian C, Porreca F
Development of a model for the delta 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).
J. Med. Chem., 37: 4371-4383 (1994)

 

People People
Henry I. Mosberg
Andrei L.Lomize
Irina D.Pogozheva
Katarzyna Sobczyk-Kojiro
Jessica Anand
Anthony F. Nastase
Sean P. Henry
Deanna Montgomery
Projects Projects
Publications Publications
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