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Congratulations
Salzman Award Winners!

3D structure of HIV-1 spike in complex with b12-Fab

The 2008 Norman P. Salzman Memorial Award in Virology
Albero Bartesaghi, Ph. D.
for his work
Molecular architecture of native HIV-1 gp120 trimers

The 2008 Norman P. Salzman Memorial Mentor Award in Virology
Sriram Subramaniam, Ph. D.

3D image of human melanoma cell

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 - 2009

   
 

2009
 
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. (in press).
 

2008
 
Heymann J, Shi D, Kim S, Bliss D, Milne JLS and Subramaniam S (2008)
3D Imaging of Mammalian Cells With Ion-Abrasion Scanning Electron Microscopy.
J. Struct. Biol. (in press).
 
Narasimha R, Ouyang H, Gray A, McLaughlin SW and Subramaniam S (2008)
Automatic joint classification and segmentation of whole cell 3D images.
Pattern Recognition (in press).
 
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 (in press).
 
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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