Medicinal Chemistry
Andrei Lomize, PhD
Research Scientist
College of Pharmacy
428 Church St
Ann Arbor, MI 48109-1065
4056 Pharm
Role Overview and Bio
Andrei Lomize has research background and experience in computational modeling and theoretical analysis of protein structure, folding, stability and interactions. He has developed computational methods, software, empirical energy functions and bioinformatics resources to tackle a variety of problems, including conformational analysis of peptides from NMR spectroscopy data, thermodynamics of helix-coil transition in micelle and protein environments, influence of mutations on protein stability, energetics of protein-lipid interactions, positioning of proteins in biological membranes, and calculation of free energies of α-helix association in the lipid bilayer. He is the principal author of several bioinformatics resources: Orientations of Proteins in Membranes (OPM) database, Positioning of Proteins in Membranes (PPM) web server, and Membranome database. He participated in NMR studies of membrane peptides and proteins, including first experimental determination of cation-conducting structure of the gramicidin A. He has published over 45 papers in peer-reviewed journals and two book chapters.
He has been a successful participant of several community wide Critical Assessment of Techniques for Protein Structure Prediction (CASP) and GPCR structure modeling and docking experiments. He served as a reviewer for the NSF.
For the complete list of Lomize’s professional and organizational activities, refer to his CV.
Highlights
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The OPM database (http://opm.phar.umich.edu) of 3D structures of proteins and peptides positioned in membranes.
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The PPM server (http://opm.phar.umich.edu/server.php) for calculation of positions of membrane proteins and peptides in the lipid bilayer.
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The Membranome database (http://membranome.org/) of transmembrane domains of single-spanning membrane proteins.
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The Protein Data Bank entries: 1GRM, 1BCT, 1NOR, 1SIS.
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PhD Biophysics, Lomonosov Moscow State University, Moscow, Russia, 1983.
Research Interests
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Theoretical analysis of protein structure, folding, stability, evolution and interactions
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Development of new methods, software and empirical energy functions for computational modeling of peptides, proteins and small molecules in membranes
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Development of biological databases and other bioinformatics resources
Selected Publications
Lomize, A.L., Pogozheva, I.D., and Mosberg, H.I. (2011) 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
Lomize, A.L., Pogozheva, I.D., and Mosberg, H.I. (2011). 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
Ho, D., Lugo, M.R., Lomize, A.L., Pogozheva, I.D., Singh, S.P., Schwan, A.L., and Merrill, A.R. (2011) Membrane topology of the colicin E1 channel using genetically encoded fluorescence. Biochemistry, 50: 4830-4842
Lomize, M.A., Pogozheva, I.D., Joo, H., Mosberg, H.I., Lomize, A.L. (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res. 40 (Database issue): D370-D376
Pogozheva, I.D., Tristram-Nagle, S., Mosberg, H.I., Lomize, A.L. (2013) Structural adaptation of proteins to different biological membranes. BBA-Biomembranes, 1828: 2592–2608