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ASBMB Today Sept 11, 2011
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Research Videos Featured in JoVE

Link to December JoVE viedo and article.

1. This December in JoVE
2. JoVE: Molecular Structures of HIV Envelope Glycoproteins
 
Intramural AIDS Research Fellowship 2011
Awarded to Gabriel Frank
 

IAVI Report:
July - August 2011
Artist's rendition of the 3D
surface HIV

Journal: IAVI Report cover July-August 2011

PNAS Cover
July 27, 2010
Artist's rendition of the
surface of dendritic cells

3D image of human melanoma cell

 

Nature Research Highlights
July 23, 2010
HIV Spread in 3D
Adobe Acrobat Reader icon get Adobe Reader
 

NCI in the Journals:
Visualizing High-Efficiency HIV Transfer
 

CCR Connections
High school students help accelerate HIV structural biology research.
CCR Connections, Vol. 4(1), 2010

  
 

IAVI Report:
Andreas von Bubnoff visits with Sriram Subramaniam

Journal: IAVI Report cover

 

NCI Cancer Bulletin:
A Conversation with Dr. Sriram Subramaniam
 

Press Releases: HIV Molecular Entry Claw
1. NIH News
2. NIH Research Matters

 

 

PUBLICATIONS

Selected Publications: 1999 - 2012

   
 

2012
 
Venkatesh M and Subramaniam S (2012) Chemoreceptor arrays.
Encyclopedia of Biophysics (in press)
 
J. Struct. Biol. (in press)
 Narayan K, Prosa T, Fu J, Kelly TF, and Subramaniam S (2012) Chemical mapping of mammalian cells by atom probe tomography.
J. Struct. Biol. (in press)
 
J. Struct. Biol. (in press)
 Frank GA, Bartesaghi A, Kuybeda O, Borgnia MJ, White TA, Sapiro G and Subramaniam S (2012) Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging.
J. Struct. Biol. (in press)
 

2011
 
J. of Vis. Exp. Dec 1(58: pii: 2770, doi: 10.3791/2770.
 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 (2011) Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging.
J. of Vis. Exp. Dec 1(58) pii: 2770, doi: 10.3791/2770.
 
J. Virol. 85(23): 12114-23.
 White TA, Bartesaghi A, Borgnia MJ, de la Cruz MJ, Nandwani R, Hoxi, JA, Bess JW, Lifson JD, Milne JLS and Subramaniam S (2011) 3D structures of sCD4-bound states of trimeric SIV envelope glycoproteins determined using cryo-electron tomography.
J. Virol. 85(23): 12114-23.
 
J. Struct. Biol. 176(3): 268-78.
 Murphy GE, Narayan K, Lowekamp BC, Hartnell LM, Heymann JAW, Fu J and Subramaniam S (2011) Correlative 3D imaging of Whole Mammalian Cells with Light and Electron Microscopy.
J. Struct. Biol. 176(3): 268-78.
 
PNAS 108(28): 11440-11445.
 Harris A, Shi D, Bartesaghi A, Borgnia MJ, He H, Pejchal R, Kang K, Depetris R, Marozsan A, Sanders RW, Klasse PJ, Milne JLS, Wilson IA, Olson W, Moore JP and Subramaniam S (2011) Trimeric HIV-1 gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.
PNAS 108(28): 11440-11445.
 
Blood118(18): 4841-52.
 Nikolic DS, Lehmann M, Felts RL, Garcia E, Blanchet FB, Subramaniam S and Piguet V (2011) HIV-1 activates Cdc42 and induces filopodia in immature dendritic cells to facilitate cell-to-cell virus propagation.
Blood 118(18): 4841-52.
 
PNAS, May 2011
 Tarasov SG, Gaponenko V, Howard Z, Chen Y, Oppenheim JJ, Dyba MA, Subramaniam S, Leeb Y, Michejdaa CJ, Tarasova NI (2011) Structural plasticity of a transmembrane peptide allows self-assembly into biologically active nanoparticles.
PNAS 108(24): 9798-9803.
 
EMBO J. 30(9): 1719-1729
 Khursigara C, Lan G, Neumann S, Wu X, Ravindran S, Borgnia M J, Sourjik V, Milne JLS, Tu Y and Subramaniam S (2011) Lateral density of receptor arrays in the membrane plane influences sensitivity of the E.coli chemotaxis response.
EMBO J. 30(9): 1719-1729.
 
Anal. Chem. 83(4): 1207-1213.
 Szakal C, Narayan K, Fu J, Lefman J and Subramaniam S (2011) Compositional Mapping of the surface and interior of mammalian cells at submicrometer resolution.
Anal. Chem. 83(4): 1207-1213.
 
Mol. Microbiol. 79(3): 677-685.
 Li M, Khursigara CM, Subramaniam S and Hazelbauer G (2011)
Chemotaxis Kinase CheA is activated by three neighboring chemoreceptor dimers as effectively as by receptor clusters.
Mol. Microbiol. 79(3): 677-685.
 
J. Bact. 193(6): 1341-1350.
 Butan C, Hartnell LM,  Fenton AK, Bliss D, Sockett R E, Subramaniam S and Milne JLS (2011) Spiral architecture of the nucleoid in Bdellovibrio bacteriovorus .
J. Bact. 193(6): 1341-1350.
   
 

2010
 
FEMS Microbiology Letters 313(2): 89-95
 Fenton A, Butan C, Subramaniam S and Sockett RE (2010)
A Coiled-Coiled-Repeat-Protein ‘CCRP’ in Bdellovibrio bacteriovorus prevents cellular indentation but is not essential for vibroid cell morphology.
FEMS Microbiology Letters 313(2): 89-95.
 
PLoS Pathog. 6(12):e1001249

White TA, Bartesaghi A, Borgnia MJ, Meyerson JR, de la Cruz M JV, Bess JW, Lifson JD, Hoxie JA, Nandwani R, Milne JLS. and Subramaniam, S (2010) Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: Strain-dependent variation in quaternary structure.
PLoS Pathog. 6(12):e1001249.

 
PLoS Pathog. 6(12):e1001249
 Felts RL, Narayan K, Estes JD, Shi D, Trubey CM, Fu J, Hartnell L, Ruthe GT, Schneider DK, Nagashima K, Bess, Jr. JW, Bavari S, Lowekamp BC, Bliss D, Lifson JD and
Subramaniam S (2010)
3D visualization of HIV transfer at the virological synapse between dendritic cells and T- cells.
PNAS 107(30): 13336-13341.
 
J Struct Biol. 171(2): 125-32.
 Murphy GE, Lowekamp BC, Zerfas PM, Chandler RJ, Narasimha R, Venditti CP, Subramaniam S (2010) Ion-abrasion scanning electron microscopy reveals distorted liver mitochondrial morphology in murine methylmalonic acidemia.
J Struct Biol. 171(2): 125-32.
 
Milne, JLS (2010)
Structure and regulation of pyruvate dehydrogenase complexes. Encyclopedia of Biological Chemistry. M. Daniel Lane and William Lennarz, eds.
Elsevier Inc. In press.
   
 

2009
 
PLoS Pathog. 5(9):e1000591.
 Bennett AE, Narayan K, Shi D, Hartnell L, Gousset K, He H, Lowekamp BC, Yoo TS, Bliss D, Freed EO and Subramaniam S (2009)
Ion-abrasion scanning electron microscopy reveals surface-connected tubular conduits in HIV-infected macrophages.
PLoS Pathog. 5(9):e1000591.
 
Nature Rev. Microbiol. 7(9), 666-675.
 Milne JLS and Subramaniam S (2009)
Cryo-electron tomography of bacteria: progress, challenges and future prospects.
Nature Rev. Microbiol. 7(9), 666-675.
 
Curr Opin Struct Biol.(4):402-407.
 Bartesaghi A and Subramaniam S (2009)
Membrane protein structure determination using cryo-electron tomography and 3D image averaging.
Curr Opin Struct Biol.(4):402-407.
 
Curr Opin Struct Biol.19(4):433-439.
 Hirai T, Subramaniam S and Lanyi JK (2009)
Structural snapshots of conformational changes in a seven-helix membrane protein: lessons from bacteriorhodopsin.
Curr Opin Struct Biol.19(4):433-439.
 
Pattern Recognition 42(6), 1067-1079.
 Narasimha R, Ouyang H, Gray A, McLaughlin SW and Subramaniam S (2009)
Automatic joint classification and segmentation of whole cell 3D images.
Pattern Recognition 42(6), 1067-1079.
 
J. Struct. Biol. 166(1): 1-7.
 Heymann JAW, Shi D, Kim S, Bliss D, Milne JLS and Subramaniam S (2009)
3D Imaging of Mammalian Cells With Ion-Abrasion Scanning Electron Microscopy.
J. Struct. Biol. 166(1): 1-7.
 
J. Struct. Biol. 166(1): 1-7.
 Hildebrand M, Kim S, Shi D, Scott K and Subramaniam S (2009)
3D imaging of diatoms with ion-abrasion scanning electron microscopy.
J. Struct. Biol.166(3), 316-328.
 
PLoS ONE 4, e5769
 Hirai T and Subramaniam S (2009)
Protein conformational changes in the bacteriorhodopsin photocycle: Comparison of findings from electron and X-ray crystallographic analyses.
PLoS ONE 4, e5769.
 
PLoS ONE 4, e6188.
 Narayan K, Perkins EM, Murphy GE, Dalai SK, Edidin M, Subramaniam S and Sadegh-Nasseri S (2009)
Staphylococcal enterotoxin A induces small clusters of HLA-DR1 on B cells.
PLoS ONE 4, e6188.
 

2008
 
Link to: Proc. Natl. Acad. Sci. USA 105(43): 16555-16560.
 Khursigara C, Wu X, Zhang P, Lefman J and Subramaniam S (2008)
Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptors.
Proc. Natl. Acad. Sci. USA 105(43): 16555-16560.
 
Link to: J. Bacteriol. 190: 6805-6810.
 Khursigara CM, Wu X and Subramaniam S (2008)
Chemoreceptors in Caulobacter crescentus: trimers of receptor dimers in a partially ordered hexagonally packed array.
J. Bacteriol. 190(20): 6805-6810.
 
Link to: Nature 455: 109-113.
 Liu J, Bartesaghi A, Borgnia, MJ, Sapiro G and Subramaniam S (2008)
Molecular architecture of native gp120 trimers.
Nature 455: 109-113.
 
Link to: J. Struct. Biol. 164: 7-17.
 Narasimha R, Aganj I, Borgnia MJ, Bennett A, Zabransky D, Sapiro G, McLaughlin S, Milne JLS and Subramaniam S (2008)
Evaluation of denoising algorithms for biological electron tomography.
J. Struct. Biol. 164(1): 7-17.
 
Link to: J. Bact. 190(7): 2588-2596
 Borgnia MJ, Subramaniam S and Milne JLS (2008)
Three-Dimensional Imaging of the Highly Bent Architecture of Bdellovibrio bacteriovorus by Using Cryo-Electron Tomography.
J. Bacteriol. 190(7): 2588-2596.
 
Link to: . Struct. Biol. 162(3): 436-450
 Bartesaghi A, Sprechman P, Liu J, Randall G, Sapiro G and Subramaniam S (2008) Classification and 3D averaging with missing wedge correction in biological electron tomography.
J. Struct. Biol. 162(3): 436-450.
 
Link to: Mol. Cell. Proteomics 7: 442-447
 Nanavati, D, Gucek M, Milne JLS, Subramaniam S and Markey S (2008)
Stoichiometry and absolute quantification of proteins with mass spectrometry using fluorescent and isotope labeled concatenated peptide standards.
Mol. Cell. Proteomics 7: 442-447.
 
Link to: Nanomedicine 3(1): 125-131
 Lengyel JS, Milne JLS and Subramaniam S. (2008)
Electron tomography in Nanoparticle Imaging and Analysis.
Nanomedicine 3(1): 125-131.
 
Link to: Structure, 16: 93-103
 Lengyel S, Stott KM, Wu X, Brooks, BR, Balbo A, Schuck P, Perham RN, Subramaniam S and Milne JLS (2008)
Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase.
Structure, 16(1): 93-103.
 

2007
 
Link to: Current Opinion in Structural Biology 17(5): 596-602
 Subramaniam S, Bartesaghi A, Liu J, Bennett AE and Sougrat R (2007)
Electron tomography of viruses.
Current Opinion in Structural Biology 17(5): 596-602.
 
Link to: J. Bacteriol. 189(20): 7503-7506
 Liu J, McBride MJ, Subramaniam S (2007)
Cell-surface filaments of the gliding bacterium Flavobacterium johnsoniae revealed by cryo-electron tomography.
J. Bacteriol. 189(20): 7503-7506.
 
Link to: J. Biol. Chem. 282(38): 27754-27759
 Bennett AE, Liu J, Van Ryk D, Bliss D, Arthos J, Henderson RM and Subramaniam S (2007)
Cryoelectron tomographic analysis of an HIV neutralizing protein and its complex with native viral gp120.
J. Biol. Chem. 282(38): 27754-27759.
 
Link to: PLoS Pathogens 3(5): e63
 Sougrat R, Bartesaghi A, Lifson JD, Benett AE, Zabransky D and Subramaniam S (2007)
Electron tomography of the contact between T-cells and SIV/HIV-1: Implications for viral entry.
PLoS Pathogens 3(5): e63.
 
Link to: J. Struct. Biol. 158(3): 318-326
 Lefman J, Morrison R and Subramaniam S (2006)
Automated 100-Position Specimen Loader and Image Acquisition System for Transmission Electron Microscopy
J. Struct. Biol. 158(3): 318-326.
 
Link to: Proc. Natl. Acad. Sci. USA 104(10): 3777-3781
 Zhang P, Khursigara CM, Hartnell L and Subramaniam S (2007)
Direct visualization of E.coli chemotaxis receptor arrays using cryo-electron microscopy.
Proc. Natl. Acad. Sci. USA 104(10): 3777-3781.
 
Link to: Meth. Cell Biol. 79: 373-384
Zhang P, Weis RM, Peters PJ and Subramaniam S (2007)
Electron tomography of bacterial chemotaxis receptor assemblies.
Meth. Cell Biol. 79: 373-384.
 

2006
 
Link to: PLoS Pathog 2, e91
 Subramaniam S (2006)
The SIV surface spike imaged by electron tomography: One leg or three?
PLoS Pathog 2(8): e91.
 
Link to: J. Struct. Biol. 155: 63-73
 Heymann J, Hayles M, Gestmann I, Giannuzzi L, Lich L and Subramaniam S (2006)
Site-specific 3D Imaging of Cells and Tissues With a Dual Beam Microscope.
J. Struct. Biol. 155(1): 63-73.
 
Link to: J. Biol. Chem. 281: 4364-4370
 Milne JLS, Wu X, Borgnia MJB, Lengyel JS, Brooks BR, Shi D, Perham RN and Subramaniam S (2006)
Molecular Structure Of A 9 Mda Icosahedral Pyruvate Dehydrogenase Sub-Complex Containing The E2 And E3 Enzymes Using Cryo-Electron Microscopy.
J. Biol. Chem. 281(7): 4364-4370.
 

2005
 
Link to: IEEE Trans. Image Proc. 14: 1314-1323
 Bartesaghi A, Sapiro G and Subramaniam S (2005)
An energy-based 3D segmentation approach for the quantitative interpretation of electron tomograms.
IEEE Trans. Image Proc. 14(9): 1314-1323.
 
Link to: Curr. Opin.Microbiology 8: 316-322
 Subramaniam S (2005)
Bridging the imaging gap: Visualizing subcellular architecture with electron tomography.
Curr. Opin.Microbiology 8(3): 316-322.
 
Link to: J. Struct. Biol. 150: 144-153
 Zhang P, Land W, Lee S, Juliani J, Lefman J, Smith S, Germain D, Kessel M, Leapman R, Rouault TA and Subramaniam S (2005)
Electron tomography of degenerating neurons in mice with abnormal regulation of iron metabolism.
J. Struct. Biol. 150(2): 144-153.
 

2004
 
Link to: Tsr J. Microsc. 216: 76-83
 Zhang P, Bos E, Heymann J, Gnaegi H, Kessel M, Peters P and Subramaniam S (2004)
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(1): 76-83.
 
Link to: J. Bacteriol 186: 5052-5061
 Lefman J, Zhang P, Hirai T, Weis RM, Juliani J, Bliss D, Kessel M, Bos E, Peters PJ and Subramaniam S (2004)
3D electron microscopic imaging of membrane invaginations in E.coli overproducing the chemotaxis receptor Tsr.
J. Bacteriol 186(15): 5052-5061.
 
Shen W, Zhang P, Germain D, Rouault T and Subramaniam S (2004)
A template propagation method for segmentation of filamentous structures in electron tomograms.
IEEE ISBI 2004 (Biomedical Imaging).
 
Bartesaaghi A, Sapiro G, Lee S, Lefman J and Subramaniam S (2004)
A new approach for 3D segmentation of cellular tomograms obtained using three-dimensional electron microscopy.
IEEE ISBI 2004 (Biomedical Imaging).
 
Link to: J. Struct. Biol 147: 136-145
Borgnia MJ, Shi D, Zhang P and Milne JLS (2004)
Visualization of a-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(2): 136-145.
 

Link to: Ann. Rev. Biophys. Biomol. Struct . 33: 141-155

 Subramaniam S and Milne JLS (2004)
Three-dimensional electron microscopy at molecular resolution.
Ann. Rev. Biophys. Biomol. Struct. 33: 141-155.
 
2003
 
Link to: J Struct Biol.141(1): 63-76
 Wu X, Milne JLS, Borgnia M, Rostapshov A, Subramaniam S and Brooks BR (2003)
A core-weighted fitting method for docking atomic structures into low resolution maps: Application to electron cryo-microscopy.
J Struct Biol. 141(1): 63-76.
 
Link to: J Bacteriol. 185(5): 1712-1718
 Hirai T, Heymann J and Subramaniam S (2003)
A structural model for 12-helix transporters in the Major Facilitator Superfamily.
J Bacteriol. 185(5): 1712-1718.
 
Link to: J Struct Biol. 143(2): 135-144
 Zhang P, Borgnia M, Mooney P, Shi D, Pan M, O'Herron P, Mao A, Brogan D, Milne JLS and Subramaniam S (2003)
Automated image acquisition and processing using a new generation of 4K x 4K CCD cameras for cryo electron microscopic studies of macromolecular assemblies.
J Struct Biol. 143(2): 135-144.
 
Link to: J Bacteriol. 185(12): 3636-3643
 Weis RM, Hirai T, Chalah A, Kessel M, Peters PJ and Subramaniam S (2003)
Electron microscopic analysis of membrane assemblies formed by the bacterial chemotaxis receptor Tsr.
J Bacteriol. 185(12): 3636-3643.
 
Subramaniam S, Zhang P, Lefman J, Juliani J and Kessel M (2003)
Electron tomography: A powerful tool for three-dimensional cellular microscopy.
ASM News 60: 240-245.
 
Link to: FEBS Lett. 545(1): 2-8
 Hirai T and Subramaniam S (2003)
Structural insights into the mechanism of proton pumping by bacteriorhodopsin.
FEBS Lett. 545(1): 2-8.
 
Link to: J Struct Biol. 144(3): 320-326
 Heymann J, Hirai T, Shi D and Subramaniam S (2003)
Projection structure of the bacterial oxalate transporter at 3.4 Å resolution.
J Struct Biol. 144(3): 320-326.
 
2002
 
Link to: Philos Transact Ser A Math Phys Eng Sci. 360(1794): 859-874
 Subramaniam S, Hirai T and Henderson R (2002)
From structure to mechanism: Electron crystallographic analysis of bacteriorhodopsin.
Philos Transact Ser A Math Phys Eng Sci. 360(1794): 859-874.
 
Link to: Nat Struct Biol. 9(8): 597-600
 Hirai T, Heymann J, Shi D, Sarker R, Maloney PC and Subramaniam S (2002)
Three dimensional structure of a bacterial oxalate transporter.
Nat Struct Biol. 9(8): 597-600.
 
Link to: EMBO J. 21(21): 5587-5598
 Milne JLS, Shi D, Rosenthal PB, Sunshine J, Domingo G, Wu X, Broooks BR, Perham RN, Henderson R and Subramaniam S (2002)
Molecular architecture and functional mechanism of an icosahedral pyruvate dehydrogenase multienzyme complex.
EMBO J. 21(21): 5587-5598.
 
Link to: J Mol Biol. 319(2): 555-65
 Tittor J, Paula S, Subramaniam S, Heberle J, Henderson R and Oesterhelt D (2002)
Proton Translocation by Bacteriorhodopsin in the Absence of Substantial Conformational Changes.
J Mol Biol. 319(2): 555-65.
 
2001
 
Link to: J Struct Biol. 135(3): 251-261
 Zhang P, Beatty A, Milne JLS and Subramaniam S (2001)
Automated data collection with a Tecnai 12 electron microscope:
Applications for molecular imaging by cryo-microscopy.
J Struct Biol. 135(3): 251-261.
 
Link to: EMBO J. 20(16): 4408-4413
 Heymann J, Sarker R, Hirai T, Shi D, Milne JLS, Maloney PC and Subramaniam S (2001)
Projection structure and molecular architecture of OxlT, a membrane transporter.
EMBO J. 20(16): 4408-4413.
 
2000
 
Link to: Biochim Biophys Acta 1460(1): 157-165
 Subramaniam S and Henderson R (2000)
Crystallographic Analysis of Protein Conformational Changes in the Bacteriorhodopsin Photocycle.
Biochim Biophys Acta 1460(1): 157-165.
 
Link to: Nature 406(6796): 653-657
 Subramaniam S and Henderson R (2000)
Molecular mechanism for vectorial proton translocation by bacteriorhodopsin.
Nature 406(6796): 653-657.
 
Link to: Mol Membr Biol 17(3): 165-174
 Heymann J and Subramaniam S (2000)
Integration of deletion mutants of bovine rhodopsin into the membrane of the endoplasmic reticulum.
Mol Membr Biol 17(3): 165-174.
 
Link to: Q Rev Biophys 33: 1-27
 Faruqi AR and Subramaniam S (2000)
Applications of CCD detectors in high resolution electron microscopy.
Q Rev Biophys 33(1): 1-27.
 
1999
 
Link to: J Struct Biol 128(1): 19-25
 Subramaniam S and Henderson R (1999)
Electron Crystallography of Bacteriorhodopsin with Millisecond Time Resolution
J Struct Biol 128(1): 19-25.
 
Link to: Curr Opin Struct Biol 9(4): 462-468
 Subramaniam S (1999)
The Structure of Bacteriorhodopsin: An Emerging Consensus.
Curr Opin Struct Biol 9(4): 462-468.
 
Link to: J Mol Biol 287(1): 145-61
 Subramaniam S, Lindahl M, Bullough P, Faruqi AR, Tittor J, Oesterhelt D, Lanyi J and Henderson R (1999)
Protein Conformational Changes in the Bacteriorhodopsin Photocycle.
J Mol Biol 287(1): 145-61.
 
Link to: Ultramicroscopy 75: 235-250
 Faruqi AR, Henderson R and Subramaniam S (1999)
Cooled CCD Detector with Tapered Fibre Optics for Recording Electron Diffraction Patterns.
Ultramicroscopy 75(4): 235-250.
   
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