Membrane transporters are principal players in active exchange of materials across the cellular membrane, one of the most fundamental and highly regulated processes in living cells. Investigating the molecular basis of their function, therefore, is of utmost importance in various disciplines of biological and biomedical research. These complex proteins provide highly sophisticated, operationally fine-tuned molecular machines to efficiently couple various sources of energy in the cell to vectorial translocation of various molecular species across the membrane against their chemical gradient. Investigation of the molecular details of the mechanism of membrane transporters poses a major challenge, primarily due to their structural complexity and the high dimensionality of the process of energy-dependent transport furnished by them. Substrate binding and translocation along the permeation pathway in membrane transporters is closely coupled to numerous stepwise protein conformational changes of various magnitudes that are induced and/or coordinated by the energy- providing mechanisms, e.g., binding and co-transport of protons and other ions, or binding and hydrolysis of ATP. A detailed description of the mechanism of transport in membrane transporters, therefore, relies on methods that can describe the dynamics of these processes at an atomic level. Molecular dynamics simulation remains a highly relevant approach with sufficient temporal and spatial resolutions to investigate such processes. Application of the method to membrane transporters is a very young area of research, since sufficient structural data required for such simulations has become available only recently. Furthermore, in order to describe biologically relevant events and steps involved in the function of membrane transporters, atomistic simulations of these large biomolecules on the orders of at least 0.1-1

Public Health Relevance

Membrane transporters are proteins that mediate selective transport of a wide range of materials, e.g., nutrients, hormones, and neurotransmitters, across the cellular membrane. They are essential to almost all aspects of human physiology, and their malfunction is associated with a large number of human diseases. The research proposed in this application will investigate the mechanism of function of several membrane transporters at a molecular level.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM086749-04
Application #
8310172
Study Section
Biochemistry and Biophysics of Membranes Study Section (BBM)
Program Officer
Chin, Jean
Project Start
2009-08-17
Project End
2014-07-31
Budget Start
2012-08-01
Budget End
2013-07-31
Support Year
4
Fiscal Year
2012
Total Cost
$297,971
Indirect Cost
$101,951
Name
University of Illinois Urbana-Champaign
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
041544081
City
Champaign
State
IL
Country
United States
Zip Code
61820
Baylon, Javier L; Vermaas, Josh V; Muller, Melanie P et al. (2016) Atomic-level description of protein-lipid interactions using an accelerated membrane model. Biochim Biophys Acta 1858:1573-83
Jiang, Tao; Han, Wei; Maduke, Merritt et al. (2016) Molecular Basis for Differential Anion Binding and Proton Coupling in the Cl(-)/H(+) Exchanger ClC-ec1. J Am Chem Soc 138:3066-75
Mayne, Christopher G; Arcario, Mark J; Mahinthichaichan, Paween et al. (2016) The cellular membrane as a mediator for small molecule interaction with membrane proteins. Biochim Biophys Acta 1858:2290-304
Baylon, Javier L; Tajkhorshid, Emad (2015) Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide. J Phys Chem B 119:7882-93
Denisov, Ilia G; Grinkova, Yelena V; Baylon, Javier L et al. (2015) Mechanism of drug-drug interactions mediated by human cytochrome P450 CYP3A4 monomer. Biochemistry 54:2227-39
Vermaas, Josh V; Baylon, Javier L; Arcario, Mark J et al. (2015) Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution. J Membr Biol 248:563-82
Moradi, Mahmoud; Enkavi, Giray; Tajkhorshid, Emad (2015) Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate antiporter. Nat Commun 6:8393
Li, Jing; Wen, Po-Chao; Moradi, Mahmoud et al. (2015) Computational characterization of structural dynamics underlying function in active membrane transporters. Curr Opin Struct Biol 31:96-105
Ahn, Young O; Mahinthichaichan, Paween; Lee, Hyun Ju et al. (2014) Conformational coupling between the active site and residues within the K(C)-channel of the Vibrio cholerae cbb3-type (C-family) oxygen reductase. Proc Natl Acad Sci U S A 111:E4419-28
Arcario, Mark J; Mayne, Christopher G; Tajkhorshid, Emad (2014) Atomistic models of general anesthetics for use in in silico biological studies. J Phys Chem B 118:12075-86

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