The methods developed in the course of our earlier work with pyruvate dehydrogenase has served as a platform for studies on HIV and SIV envelope glycoproteins and have resulted in a number of new structures. These studies, which produced the first structures of trimeric Env immunogens a couple of years ago, are now leading to new insights that could be invaluable for rational vaccine design. Two examples are listed below. In one instance, we reported cryo-electron microscopic studies of the interaction between the ectodomain of trimeric HIV-1 envelope glycoprotein (Env) and Z13e1, a broadly neutralizing antibody that targets the membrane proximal external region (MPER) of the gp41 subunit. We showed that Z13e1-bound Env displays an open quaternary conformation similar to the CD4-bound conformation. Our results support the idea that MPER directed antibodies, such as Z13e1, block viral entry by interacting with Env at a step after CD4 activation. In another example, we carried out cryo-electron microscopic analysis at sub-nanometer resolution of a cleaved, soluble version of trimeric Env to explore structural changes that take place with ligand activation. We showed that Env in the open, activated conformation has highly conserved elements of gp41 organized in a three-helix motif in the central portion of the envelope glycoprotein complex. The N-terminal gp41 helices in this novel, activated Env conformation are much less compactly packed than in the post-fusion, six-helix bundle state, suggesting a new structural template for designing immunogens that can elicit antibodies targeting HIV at a vulnerable, pre-entry stage.

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Merk, Alan; Bartesaghi, Alberto; Banerjee, Soojay et al. (2016) Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery. Cell 165:1698-707
Banerjee, Soojay; Bartesaghi, Alberto; Merk, Alan et al. (2016) 2.3 Ã… resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. Science 351:871-5
Bartesaghi, Alberto; Merk, Alan; Banerjee, Soojay et al. (2015) 2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor. Science 348:1147-51
Merk, Alan; Subramaniam, Sriram (2013) HIV-1 envelope glycoprotein structure. Curr Opin Struct Biol 23:268-76
Harris, Audray K; Bartesaghi, Alberto; Milne, Jacqueline L S et al. (2013) HIV-1 envelope glycoprotein trimers display open quaternary conformation when bound to the gp41 membrane-proximal external-region-directed broadly neutralizing antibody Z13e1. J Virol 87:7191-6
Bartesaghi, Alberto; Merk, Alan; Borgnia, Mario J et al. (2013) Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy. Nat Struct Mol Biol 20:1352-7
Tran, Erin E H; Borgnia, Mario J; Kuybeda, Oleg et al. (2012) Structural mechanism of trimeric HIV-1 envelope glycoprotein activation. PLoS Pathog 8:e1002797
White, Tommi A; Bartesaghi, Alberto; Borgnia, Mario J et al. (2011) Three-dimensional structures of soluble CD4-bound states of trimeric simian immunodeficiency virus envelope glycoproteins determined by using cryo-electron tomography. J Virol 85:12114-23
Khursigara, Cezar M; Lan, Ganhui; Neumann, Silke et al. (2011) Lateral density of receptor arrays in the membrane plane influences sensitivity of the E. coli chemotaxis response. EMBO J 30:1719-29
Butan, Carmen; Hartnell, Lisa M; Fenton, Andrew K et al. (2011) Spiral architecture of the nucleoid in Bdellovibrio bacteriovorus. J Bacteriol 193:1341-50

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