Understanding how proteins fold is a central quest in biology. Studied for over 50 years, investigations of soluble protein folding have proven invaluable for dissecting the molecular basis of a multitude of diseases. By comparison, folding studies of membrane proteins (MPs) lag far behind. The knowledge gained from soluble protein studies cannot simply be transferred to inferences about MPs because their solvents are different. The balance of forces encoding a MP embedded in a lipid bilayer must be distinct from that of soluble proteins in water. Our research efforts contribute to filling this key gap in the understanding the physical chemistry of membrane proteins. We will experimentally determine of energetic forces stabilizing membrane proteins along the steeply changing polarity gradient of the phospholipid bilayer interface. These efforts will be complemented by molecular simulations and mathematic systems modeling. In addition, we aim to incorporate novel techniques to our toolbox to address the energetic importance of backbone hydrogen bonds in transmembrane proteins. Our results have broad ranging impact in the field at large through contributions to information databases used in training computational algorithms and by their incorporation in physically realistic mechanisms for protein folding catalysis by cellular machines.

Public Health Relevance

This discovery project will develop a fundamental understanding of the forces underlying folds and functions of membrane proteins. The knowledge gained from this research will contribute to the design of therapeutics to combat protein misfolding diseases, will be useful in the computational modeling of protein structures and of drug-binding to protein structures, and will inform on the design of proteins with novel functions.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM079440-09
Application #
9662061
Study Section
Biochemistry and Biophysics of Membranes Study Section (BBM)
Program Officer
Wehrle, Janna P
Project Start
2009-06-01
Project End
2022-11-30
Budget Start
2019-01-01
Budget End
2019-11-30
Support Year
9
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Johns Hopkins University
Department
Physiology
Type
Schools of Arts and Sciences
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21205
Fleming, Patrick J; Fleming, Karen G (2018) HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties. Biophys J 114:856-869
Fleming, Karen G (2018) Taking deterministic control of membrane protein monomer-dimer measurements. J Gen Physiol 150:181-183
Lessen, Henry J; Fleming, Patrick J; Fleming, Karen G et al. (2018) Building Blocks of the Outer Membrane: Calculating a General Elastic Energy Model for ?-Barrel Membrane Proteins. J Chem Theory Comput 14:4487-4497
Danoff, Emily J; Fleming, Karen G (2017) Novel Kinetic Intermediates Populated along the Folding Pathway of the Transmembrane ?-Barrel OmpA. Biochemistry 56:47-60
Mo, Gary C H; Ross, Brian; Hertel, Fabian et al. (2017) Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution. Nat Methods 14:427-434
Peterson, Janine H; Plummer, Ashlee M; Fleming, Karen G et al. (2017) Selective pressure for rapid membrane integration constrains the sequence of bacterial outer membrane proteins. Mol Microbiol 106:777-792
Marx, Dagen C; Fleming, Karen G (2017) Influence of Protein Scaffold on Side-Chain Transfer Free Energies. Biophys J 113:597-604
Costello, Shawn M; Plummer, Ashlee M; Fleming, Patrick J et al. (2016) Dynamic periplasmic chaperone reservoir facilitates biogenesis of outer membrane proteins. Proc Natl Acad Sci U S A 113:E4794-800
Zaccai, Nathan R; Sandlin, Clifford W; Hoopes, James T et al. (2016) Deuterium Labeling Together with Contrast Variation Small-Angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins. Methods Enzymol 566:159-210
Fleming, Patrick J; Patel, Dhilon S; Wu, Emilia L et al. (2016) BamA POTRA Domain Interacts with a Native Lipid Membrane Surface. Biophys J 110:2698-709

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