Department of Molecular and Cellular Biology, College of Biological Sciences
Proteome imaging of macromolecular systems - PIOMS
Our research aims to understand the structure and function of macromolecular interactions by selected model macromolecular systems. Viral structural proteins have the capacity to function both in assembly and in disassembly, which is made possible through a built-in flexibility triggered by cellular events. We observe conformational changes of viral particles at various states of their life cycle to analyze their assembly intermediates as well as the mature forms. Similarly, infectious virions can be treated with numerous conditions, e.g. receptor-mediated genome release or acid-activated membrane fusion, to observe the key steps of viral re-entry into host cells. Using electron microscopy, we apply a rapid-frozen and low-dose imaging procedure to best preserve the biological specimen in its native form. Computer image processing is developed to retrieve most of the useful signal from the low-contrast micrographs. Technical implementation of cryo-EM, cellular tomography, and computational modeling schemes also enables us to address interactions involved in complex biological molecules and/or nanoscale machines.
Editor-in-Chief: Developmental Microbiology and Molecular Biology
Grad Group Affiliations
- Computer Sciences; Biophotonics DE; Medical Microbiology and Immunology
Specialties / Focus
- Genomics, Proteomics and Metabolomics
- Molecular Medicine
- Spectroscopy and Imaging
- Structural Biology, Membranes and Macromolecular Assembly
- MCB 193 Advanced Research, Fall,Winter,Spring,Summer 1,Summer 2
- MCB 200A Current Technology in Cell Biology, Fall
- BIS 102 Structure and Function of Biomolecules, Winter,Spring
- MCB 220L Adv Biochem Lab, Fall
- MCB 200C Modern Techniques in Biophysics, Winter
- EMS 23x Electron Microscopy, Winter,Spring
- MCB 194H Honors Thesis, Fall,Winter,Spring
- BPH 290 Biophysics and Biophotonics, Fall,Spring
- MCB 298 TEM Case Studies, Fall
- MMI 208 Emerging Challenges in Microbiology and Immunology, Fall
- 056 Briggs Hall / Advanced Microscopy and Proteomics (amp) http://pioms.ucdavis.edu/members.htm
- American Academy of Nanomedicine
- 1992 PhD Structural Biology Purdue University
Miyazaki, N, Hagiwara, K, Naitow, H, Higashi, T, Cheng, RH, Tsukihara, T, Nakagawa, A, and Omura, T (2004). Transcapsidation and the conserved interactions of two major structural proteins of a pair of phytoreoviruses confirm the mechanism of assembly of the outer capsid layer. J. Mol. Biol. 345, 229-37
Gibbons, DL, A Ahn, M Liao, L Hammar, RH Cheng, and M Kielian (2004). Multistep regulation in membrane insertion of the fusion peptide with Semliki Forest virus. J Virol, 78, 3312-3318.
Hagiwara, K, Higashi, T, Miyazaki, N, Naitow, H, Cheng, RH, Nakagawa, A, Mizuno, H, Tsukihara, T and Omura, T (2004). The amino-terminal region of major capsid protein P3 is essential for self-assembly of single-shelled core-like particles of rice dwarf virus J Virol, 78, 3145-3148.
Cheng, RH and Miyamura, T (2007). Structure-based study of Virus Replication (pp560, ed), World Scientific Pub Co, ISBN 981-270-405-1
Wu SR, Haag L, Hammar L, Wu B, Garoff H, Xing L, Murata K, Cheng RH. (2007). The dynamic envelope of a fusion Class II virus: Prefusion stages of Semliki forest virus revealed by electron cryomicroscopy. J Biol Chem, 282, 6752-6762,
Noda, T, Sagara, H, Yen, A, Takada, A, Kida, H, Cheng, RH and Kawaoka, Y (2006). Architecture of ribonucleoprotein complexes in influenza A virus particles. Nature, 439, 490-2.
Nilsson, J, N Miyazaki, L Xing, B Wu, L Hammar, TC Li, N Takeda, T Miyamura, and RH Cheng (2005). Structure and assembly of a T=1 polyoma BK virus-like particle. J Virol, 79, 5337-45.
Johansson, ES, Xing, L, Cheng, RH, and Shafren, DR (2004). Enhanced cellular receptor usage by a bioselected variant of Coxsackievirus A21. J Virol, 78,12603-12
Cheng, R H, and L Hammar (2004). Conformational Proteomics of Macromolecular Architectures. 420pp. World Scientific Publishing Co. ISBN 981-238-614-9
Li, Tian-Cheng, Naokazu Takeda, Kenzo Kato, Josefina Nilsson, Li Xing, Lars Haag, R. Holland Cheng and Tatsuo Miyamura (2003). Characterization of self-assembled virus-like particles of human polyomavirus BK generated by recombinant baculoviruses. Virology 311, 115-124.
Wartiovaara, J, L-G Ofverstedt, J Khoshnoodi, J Zhang, E Makela, S Sandin, V Ruotsalainen, RH Cheng, H Jalanko, U Skoglund, and K Tryggvason (2004). Nephrin strands contribute to a porous scaffold in the renal glomerular slit diaphragm. J Clin Invest, 114, 1475-83
Xing, L, Huhtala, M, Pietainen, V, Kapyla, J, Vuorinen, K, Heino, J, Johnson, MS, Hyypia, T, and Cheng RH (2004). Structural and functional analysis of integrin alpha2I domain interaction with echovirus 1. J Biol Chem, 279, 11632-11638.
Sedzik, J, L Hammar, L Haag, U Skoging-Nyberg, K Tars, M Marko, and RH Cheng (2001). Structural proteomics of enveloped viruses: Crystallization, crystallography, mutagenesis and cryo-electron microscopy. Recent Res Devel Virol 3, 41-60.
Hammar, L, S Markarian, L Haag, H Lankinen, A Salmi, and R. H. Cheng (2003). Prefusion rearrangements resulting in fusion peptide exposure in Semliki Forest virus. J Biol Chem, 277, 7189-7198.
Xing, Li, Jose M. Casasnovas, and R. Holland Cheng (2003). Structural analysis of human rhinovirus complex with ICAM-1 reveals the dynamics of receptor-mediated virus uncoating. J Virol. 77, 6101-6107.
Silberstein, Erica, Li Xing, Willem van de Beek, Jinhua Lu, R. Holland Cheng, and Gerardo G. Kaplan (2003). Alteration of hepatitis A virus (HAV) particles by a soluble form of HAV cellular receptor 1 containing the immunoglobin-and mucin-like regions. J Virol. 77, 8765-74.
Haag L, Garoff H, Xing L, Hammar L, Kan ST, Cheng RH (2002). Acid-induced movements in the glycoprotein shell of an alphavirus turn the spikes into membrane fusion-mode. EMBO J. 21, 4402-4410.
Cheng, RH, Hultenby, K, Haag, L, Forsell, K, Garoff, H, Hsieh, C, and Marko, M (2001). Bring together high- and low-resolution data: Electron tomography of budding enveloped alphavirus. Microsc Microanal, 7S, 104-105.
Garoff H, Cheng RH (2001). The missing link between envelope formation and fusion in alphaviruses. Trend Microbiol 9, 408-410.
Nakagawa, Atsushi, Naoyuki Miyazaki, Junichiro Taka, Hisashi Naitow, Akira Ogawa, Zui Fujimoto, Hiroshi Mizuno, Takahiko Higashi, Yasuo Watanabe, Toshihiro Omura, R. Holland Cheng and Tomitake Tsukihara (2003). The Atomic Structure of Rice dwarf Virus Reveals the Self-Assembly Mechanism of Component Proteins. Structure 11, 1227-1238.
Forsell K, Xing L, Kozlovska T, Cheng RH, Garoff H (2000). Membrane proteins organize a symmetrical virus. EMBO J. 19, 5081-91.
Xing L, Tjarnlund K, Lindqvist B, Kaplan GG, Feigelstock D, Cheng RH, Casasnovas JM (2000). Distinct cellular receptor interactions in poliovirus and rhinoviruses. EMBO J. 19, 1207-16.