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Our Science – Subramaniam Website

Sriram Subramaniam, Ph.D.

Selected Publications

1)  Bartesaghi A, Merk A, Borgnia MJ, Milne JL, Subramaniam S.
Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy.
Nat. Struct. Mol. Biol. 20: 1352-7, 2013.
[Journal]
2)  Meyerson JR, Tran EE, Kuybeda O, Chen W, Dimitrov DS, Gorlani A, Verrips T, Lifson JD, Subramaniam S.
Molecular structures of trimeric HIV-1 Env in complex with small antibody derivatives.
Proc. Natl. Acad. Sci. U.S.A. 110: 513-8, 2013.
[Journal]
3)  Schauder DM, Kuybeda O, Zhang J, Klymko K, Bartesaghi A, Borgnia MJ, Mayer ML, Subramaniam S.
Glutamate receptor desensitization is mediated by changes in quaternary structure of the ligand binding domain.
Proc. Natl. Acad. Sci. U.S.A. 110: 5921-6, 2013.
[Journal]
4)  Harris AK, Meyerson JR, Matsuoka Y, Kuybeda O, Moran A, Bliss D, Das SR, Yewdell JW, Sapiro G, Subbarao K, Subramaniam S.
Structure and accessibility of HA trimers on intact 2009 H1N1 pandemic influenza virus to stem region-specific neutralizing antibodies.
Proc. Natl. Acad. Sci. U.S.A. 110: 4592-7, 2013.
[Journal]
5)  Earl LA, Lifson JD, Subramaniam S.
Catching HIV "in the act" with 3D electron microscopy.
Trends Microbiol. 21: 397-404, 2013.
[Journal]
6)  Narayan K, Danielson CM, Lagarec K, Lowekamp BC, Coffman P, Laquerre A, Phaneuf MW, Hope TJ, Subramaniam S.
Multi-resolution correlative focused ion beam scanning electron microscopy: applications to cell biology.
J. Struct. Biol. 185: 278-84, 2014.
[Journal]
7)  Merk A, Subramaniam S.
HIV-1 envelope glycoprotein structure.
Curr. Opin. Struct. Biol. 23: 268-76, 2013.
[Journal]
8)  Harris AK, Bartesaghi A, Milne JL, Subramaniam S.
HIV-1 envelope glycoprotein trimers display open quaternary conformation when bound to the gp41 MPER-directed broadly neutralizing antibody Z13e1.
J. Virol. 87: 7191-6, 2013.
[Journal]
9)  Kuybeda O, Frank GA, Bartesaghi A, Borgnia M, Subramaniam S, Sapiro G.
A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography.
J. Struct. Biol. 181: 116-27, 2013.
[Journal]
10)  Subramaniam S.
Structure of trimeric HIV-1 envelope glycoproteins.
Proc. Natl. Acad. Sci. U.S.A. 110: E4172-4, 2013.
[Journal]
11)  Gustchina E, Li M, Ghirlando R, Schuck P, Louis JM, Pierson J, Rao P, Subramaniam S, Gustchina A, Clore GM, Wlodawer A.
Complexes of neutralizing and non-neutralizing affinity matured Fabs with a mimetic of the internal trimeric coiled-coil of HIV-1 gp41.
PLoS ONE. 8: e78187, 2013.
[Journal]
12)  Wang T, Choi E, Monaco MC, Campanac E, Medynets M, Do T, Rao P, Johnson KR, Elkahloun AG, Von Geldern G, Johnson T, Subramaniam S, Hoffman D, Major E, Nath A.
Derivation of neural stem cells from human adult peripheral CD34+ cells for an autologous model of neuroinflammation.
PLoS ONE. 8: e81720, 2013.
[Journal]
13)  Wu X, Subramaniam S, Case DA, Wu KW, Brooks BR.
Targeted conformational search with map-restrained self-guided Langevin dynamics: Application to flexible fitting into electron microscopic density maps.
J. Struct. Biol. 183: 429-40, 2013.
[Journal]
14)  Milne JL, Borgnia MJ, Bartesaghi A, Tran EE, Earl LA, Schauder DM, Lengyel J, Pierson J, Patwardhan A, Subramaniam S.
Cryo-electron microscopy--a primer for the non-microscopist.
FEBS J. 280: 28-45, 2013.
[Journal]
15)  Gopinath A, Xu G, Ress D, Öktem O, Subramaniam S, Bajaj C.
Shape-based regularization of electron tomographic reconstruction.
IEEE Trans Med Imaging. 31: 2241-52, 2012.
[Journal]
16)  Narayan K, Prosa TJ, Fu J, Kelly TF, Subramaniam S.
Chemical mapping of mammalian cells by atom probe tomography.
J. Struct. Biol. 178: 98-107, 2012.
[Journal]
17)  Frank GA, Bartesaghi A, Kuybeda O, Borgnia MJ, White TA, Sapiro G, Subramaniam S.
Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging.
J. Struct. Biol. 178: 165-76, 2012.
[Journal]
18)  Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-García E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ.
Data management challenges in three-dimensional EM.
Nat. Struct. Mol. Biol. 19: 1203-7, 2012.
[Journal]
19)  Bartesaghi A, Lecumberry F, Sapiro G, Subramaniam S.
Protein secondary structure determination by constrained single-particle cryo-electron tomography.
Structure. 20: 2003-13, 2012.
[Journal]
20)  Tran EE, Borgnia MJ, Kuybeda O, Schauder DM, Bartesaghi A, Frank GA, Sapiro G, Milne JL, Subramaniam S.
Structural Mechanism of Trimeric HIV-1 Envelope Glycoprotein Activation.
PLoS Pathog. 8: e1002797, 2012.
[Journal]
21)  Murphy GE, Narayan K, Lowekamp BC, Hartnell LM, Heymann JA, Fu J, Subramaniam S.
Correlative 3D imaging of whole mammalian cells with light and electron microscopy.
J. Struct. Biol. 176: 268-78, 2011.
[Journal]
22)  Meyerson JR, White TA, Bliss D, Moran A, Bartesaghi A, Borgnia MJ, de la Cruz MJ, Schauder D, Hartnell LM, Nandwani R, Dawood M, Kim B, Kim JH, Sununu J, Yang L, Bhatia S, Subramaniam C, Hurt DE, Gaudreault L, Subramaniam S.
Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging.
J Vis Exp. 58: 1-6, 2011.
[Journal]
23)  Khursigara CM, Lan G, Neumann S, Wu X, Ravindran S, Borgnia MJ, Sourjik V, Milne J, Tu Y, Subramaniam S.
Lateral density of receptor arrays in the membrane plane influences sensitivity of the E. coli chemotaxis response.
EMBO J. 30: 1719-29, 2011.
[Journal]
24)  Harris A, Borgnia MJ, Shi D, Bartesaghi A, He H, Pejchal R, Kang YK, Depetris R, Marozsan AJ, Sanders RW, Klasse PJ, Milne JL, Wilson IA, Olson WC, Moore JP, Subramaniam S.
Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.
Proc. Natl. Acad. Sci. U.S.A. 108: 11440-5, 2011.
[Journal]
25)  Felts RL, Narayan K, Estes JD, Shi D, Trubey CM, Fu J, Hartnell LM, Ruthel GT, Schneider DK, Nagashima K, Bess JW, Bavari S, Lowekamp BC, Bliss D, Lifson JD, Subramaniam S.
3D visualization of HIV transfer at the virological synapse between dendritic cells and T cells.
Proc. Natl. Acad. Sci. U.S.A. 107: 13336-41, 2010.
[Journal]
26)  Murphy GE, Lowekamp BC, Zerfas PM, Chandler RJ, Narasimha R, Venditti CP, Subramaniam S.
Ion-abrasion scanning electron microscopy reveals distorted liver mitochondrial morphology in murine methylmalonic acidemia.
J. Struct. Biol. 171: 125-32, 2010.
[Journal]
27)  White TA, Bartesaghi A, Borgnia MJ, Meyerson JR, de la Cruz MJ, Bess JW, Nandwani R, Hoxie JA, Lifson JD, Milne JL, Subramaniam S.
Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure.
PLoS Pathog. 6: e1001249, 2010.
[Journal]
28)  Heymann JA, Shi D, Kim S, Bliss D, Milne JL, Subramaniam S.
3D imaging of mammalian cells with ion-abrasion scanning electron microscopy.
J. Struct. Biol. 166: 1-7, 2009.
[Journal]
29)  Milne JL, Subramaniam S.
Cryo-electron tomography of bacteria: progress, challenges and future prospects.
Nat. Rev. Microbiol. 7: 666-75, 2009.
[Journal]
30)  Bennett AE, Narayan K, Shi D, Hartnell LM, Gousset K, He H, Lowekamp BC, Yoo TS, Bliss D, Freed EO, Subramaniam S.
Ion-abrasion scanning electron microscopy reveals surface-connected tubular conduits in HIV-infected macrophages.
PLoS Pathog. 5: e1000591, 2009.
[Journal]
31)  Bartesaghi A, Subramaniam S.
Membrane protein structure determination using cryo-electron tomography and 3D image averaging.
Curr. Opin. Struct. Biol. 19: 402-7, 2009.
[Journal]
32)  Hirai T, Subramaniam S.
Protein conformational changes in the bacteriorhodopsin photocycle: comparison of findings from electron and X-ray crystallographic analyses.
PLoS ONE. 4: e5769, 2009.
[Journal]
33)  Narayan K, Perkins EM, Murphy GE, Dalai SK, Edidin M, Subramaniam S, Sadegh-Nasseri S.
Staphylococcal enterotoxin A induces small clusters of HLA-DR1 on B cells.
PLoS ONE. 4: e6188, 2009.
[Journal]
34)  Lengyel JS, Stott KM, Wu X, Brooks BR, Balbo A, Schuck P, Perham RN, Subramaniam S, Milne JL.
Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complex.
Structure. 16: 93-103, 2008.
[Journal]
35)  Liu J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S.
Molecular architecture of native HIV-1 gp120 trimers.
Nature. 455: 109-13, 2008.
[Journal]
36)  Khursigara CM, Wu X, Zhang P, Lefman J, Subramaniam S.
Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptors.
Proc. Natl. Acad. Sci. U.S.A. 105: 16555-60, 2008.
[Journal]
37)  Sougrat R, Bartesaghi A, Lifson JD, Bennett AE, Bess JW, Zabransky DJ, Subramaniam S.
Electron tomography of the contact between T cells and SIV/HIV-1: implications for viral entry.
PLoS Pathog. 3: e63, 2007.
[Journal]
38)  Subramaniam S, Bartesaghi A, Liu J, Bennett AE, Sougrat R.
Electron tomography of viruses.
Curr. Opin. Struct. Biol. 17: 596-602, 2007.
[Journal]
39)  Milne JL, Wu X, Borgnia MJ, Lengyel JS, Brooks BR, Shi D, Perham RN, Subramaniam S.
Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy.
J. Biol. Chem. 281: 4364-70, 2006.
[Journal]
40)  Heymann JA, Hayles M, Gestmann I, Giannuzzi LA, Lich B, Subramaniam S.
Site-specific 3D imaging of cells and tissues with a dual beam microscope.
J Struct Biol. 155: 63-73, 2006.
Full Text Article. [Journal]
41)  Subramaniam S.
Bridging the imaging gap: visualizing subcellular architecture with electron tomography.
Curr Opin Microbiol. 8: 316-22, 2005.
[Journal]
42)  Zhang P, Land W, Lee S, Juliani J, Lefman J, Smith SR, Germain D, Kessel M, Leapman R, Rouault TA, Subramaniam S.
Electron tomography of degenerating neurons in mice with abnormal regulation of iron metabolism.
J Struct Biol. 150: 144-53, 2005.
[Journal]
43)  Zhang P, Bos E, Heymann J, Gnaegi H, Kessel M, Peters PJ, Subramaniam S.
Direct visualization of receptor arrays in frozen-hydrated sections and plunge-frozen specimens of E. coli engineered to overproduce the chemotaxis receptor Tsr.
J Microsc. 216: 76-83, 2004.
[Journal]
44)  Subramaniam S, Milne JL.
Three-dimensional electron microscopy at molecular resolution*.
Annu Rev Biophys Biomol Struct. 33: 141-55, 2004.
[Journal]
45)  Borgnia MJ, Shi D, Zhang P, Milne JL.
Visualization of alpha-helical features in a density map constructed using 9 molecular images of the 1.8 MDa icosahedral core of pyruvate dehydrogenase.
J Struct Biol. 147: 136-45, 2004.
[Journal]
46)  Agard D, Cheng Y, Glaser RM, Subramaniam S.
Single particle cryo-electron microscopy: progress, challenges, and perspectives for further improvement.
Advanced Imaging Electron Physics. 2014.
In Press. [Journal]
47)  Meyerson JR, Kumar J, Chittori S, Rao P, Pierson J, Bartesaghi A, Mayer ML, Subramaniam S.
Structural mechanism of glutamate receptor activation and desensitization.
Nature. 2014.
In Press. [Journal]
48)  Risco C, de Castro I, Sanz-Sanchez L, Narayan K, Grandinetti G, Subramaniam S.
Three-dimensional imaging of viral infections.
Annual Review of Virology. 2014.
In Press. [Journal]
49)  Do T, Murphy G, Earl LA, Del Prete GQ, Grandinetti G, Li G, Estes JD, Rao P, Trubey CM, Thomas J, Spector J, Bliss D, Nath A, Lifson JD, Subramaniam S.
3D imaging of HIV-1 virological synapses reveals membrane architectures involved in virus transmission.
J. Virol. 2014.
[Journal]
50)  Tran EE, Simmons JA, Bartesaghi A, Shoemaker CJ, Nelson E, White JM, Subramaniam S.
Spatial localization of the Ebola glycoprotein mucin-like domain using cryo-electron tomography.
J. Virol. 2014.
[Journal]
51)  Bartesaghi A, Matthies D, Banerjee S, Merk A, Subramaniam S.
Structure of ß-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy.
Proc. Natl. Acad. Sci. U.S.A. 2014.
[Journal]
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This page was last updated on 8/13/2014.