We describe here a novel footprinting technique to probe the in vivo structural dynamics of membrane protein. This method utilized in situ generation of hydroxyl radicals to oxidize and covalently modify biomolecules on living Escherichia coli cell surface. After enriching and purifying the membrane proteome, the modified amino acid residues of the protein were identified with tandem mass spectrometry to map the solvent-accessible surface of the protein that will form the footprint of in vivo structure of the protein. Of about 100 outer membrane proteins identified, we investigated the structure details of a typical -barrel structure, the porin OmpF. We found that six modified tryptic peptides of OmpF were reproducibly detected with 19 amino acids modified under the physiological condition. The modified amino acid residues were widely distributed in the external loop area, -strands, and periplasmic turning area, and all of them were validated as solvent-accessible according to the crystallography data. We further extended this method to study the dynamics of the voltage gating of OmpF in vivo using mimic changes of physiological circumstance either by pH or by ionic strength. Our data showed the voltage gating of porin OmpF in vivo for the first time and supported the proposed mechanism that the local electrostatic field changes in the eyelet region may alter the porin channels to switch. Thus, this novel method can be a potentially efficient method to study the structural dynamics of the membrane proteins of a living cell. One of the most challenging problems in biological sciences is the correlation of the dynamic three-dimensional (3D) 1 structural changes in membrane proteins to their biological functions. Comprising about 30% of the human proteome, membrane proteins are critical mediators of material and information transfer between cells and their environment and are targets for many growth factors and pharmacologically active compounds. Signals from binding of ligands or drugs to receptors are transduced through conformational changes in the receptors. Therefore, understanding the dynamic conformational changes in the structure of membrane proteins is essential to the understanding of many biological processes and has important implications in human health.Although some methodologies including NMR and x-ray have been developed to study protein structures in atomic resolution, the determination of the structures of integral membrane proteins (IMPs) remains one of the most challenging problems in biological sciences (1). IMPs are usually insoluble low abundance proteins for which expression, purification, and crystallization are generally too inefficient to generate sufficient materials for conventional structural analysis techniques such as NMR and x-ray. Additionally, IMPs in living cells are constantly interacting with different molecules depending on the external environment and biological states of the cell such that the conformation of IMPs is highly dynamic. Hence monitoring real time conformationa...