The p97-UBXD8 complex modulates ER-Mitochondria contact sites by modulating membrane lipid saturation and composition
Rakesh Ganji, Joao A. Paulo, Yuecheng Xi, Ian Kline, Jiang Zhu, Christoph S. Clemen, Conrad C. Weihl, John G. Purdy, Steve P. Gygi, Malavika Raman Nature communications, 14, Article number: 638 (2023)
The functional importance of VCP to maintaining cellular protein homeostasis.
Brittany Ahlstedt*, Rakesh Ganji* and Malavika Raman
Biochemical Society Transactions, October 2022,
* Equal contribution
The Cure VCP Scientific Conference 2021: Molecular and clinical insights into neurodegeneration and myopathy linked to multi-system proteinopathy-1 (MSP-1).
Michelle A.Johnson, Jacob A. Klickstein, Richa Khanna, Yunzi Gou, Cure VCP Disease Research Consortium, Malavika Raman.
Neurobiology or Disease, 2022, Volume 169
A reference induced pluripotent stem cell line for large-scale collaborative studies
Pantazis, CB, Yang, A, Lara, E, McDonough, JA., Blauwendraat, C, Peng, L, Oguro, H, Zou, J, Sebesta, D, Pratt, Gr, Cross, E, Blockwick, J, Buxton, P, Kinner-Bibeau, L, Medura, C, Tompkins, C, Hughes, S, Santiana, M, Faghri, , Nalls, M A., Vitale, D, Qi, YA., Ramos, D M., Anderson, K, Stadler, J, Narayan, P, Papademetriou, J, Reilly, L, Nelson, M P., Aggarwal, S, Rosen, L U., Kirwan, P, Pisupati, V, Coon, S L., Scholz, S W., Coccia, E, Sarrafha, L, Ahfeldt, T, Funes, S, Bosco, D A., Beccari, MS., Cleveland, DW., Zanellati, M C, Basundra, R, Deshmukh, M, Cohen, S, Nevin, Z S., Matia, M, Van Lent, J, Timmerman, V, Conklin, B R., Dou, D, Holzbaur, E L.F., L Emmy, R, Indigo V.L., Kampmann, M, Priebe, T, Öttl, M, Dong, J, van der Kant, R, Erlebach, L, Welzer, M, Kronenberg-Versteeg, D, Abu-Bonsrah, D, Parish, C L., Raman, M, Heinrich, L, Schüle, B, Aristoy, C Calatayud, V, Patrik, H, Aaron, W, Brian J., L, Guochang, A, Ernest, R, Ana-Caroline, B, Guojun, C, Dennis, P, Dominik, G, Rebecca M.C., Wray, S, Chase, K J, Zhang, K, Marioni, J C., Skarnes, W C., Cookson, M R., Ward, ME. and Merkle, F T. 2021, bioRxiv 2021.12.15.472643
The p97-UBXN1 complex regulates aggresome formation.
Sirisha Mukkavalli, Jacob Aaron Klickstein, Betty Ortiz, Peter Juo, Malavika Raman. 2021 Journal of Cell Science 134 (7).
AggreCount: An unbiased image analysis tool for identifying and quantifying cellular aggregates in a spatially-defined manner
Jacob Aaron Klickstein, Sirisha Mukkavalli, Malavika Raman. Journal of Biological Chemistry 2020 Dec 18;295(51):17672-17683
Download AggreCount here.
The WD40-repeat protein WDR-48 promotes the stability of the deubiquitinating enzyme USP-46 by inhibiting its ubiquitination and degradation.
Molly Hodul*, Rakesh Ganji *, Caroline L. Dahlberg , Malavika Raman , Peter Juo, J. Biol Chem. 2020 Jun 25:jbc.RA120.014590. doi: 10.1074/jbc.RA120.014590. Online ahead of print. PMID: 32587090* Equal contribution
The VCP-UBXN1 complex mediates triage of ubiquitylated cytosolic proteins bound to the BAG6 complex.
Rakesh Ganji, Sirisha Mukkavalli, Flavio Sonamji and Malavika Raman. Molecular and Celular Biology 2018. (38) 154-18. ( 2018)* Featured in MCB Spotlight.
Systematic proteomics of the VCP–UBXD adaptor network identifies a role for UBXN10 in regulating ciliogenesis
Malavika Raman, Mikhail Sergeev, Maija Garnaas, John R. Lydeard, Edward L. Huttlin, Wolfram Goessling, Jagesh V. Shah and J.Wade Harper. Nature Cell Biology 10, 1356-69 (2015).
Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
Shireen A. Sarraf, Malavika Raman, Virginia Pereira Guarani, Matthew E. Sowa, Edward L. Huttlin, Stephen P.Gygi, J. Wade Harper. Nature 496 (7445), 372-376 (2013).
A genome-wide screen identifies the p97 AAA-ATPase as an essential regulator of DNA damage-dependent CDT1 destruction.
Malavika Raman, Courtney G. Havens, Johannes C. Walter and J.Wade Harper. Molecular Cell 44(1): 72-84 (2011).
Stairway to the Proteasome.
Malavika Raman and J. Wade Harper. Nature 462, 585-586 (2009).
Differential regulation and properties of MAPKs.
Malavika Raman, Wei Chen and Melanie H. Cobb. Oncogene 26(22): 3100-12. (2007).
TAO kinases mediate activation of p38 in response to DNA damage.
Malavika Raman, Svetlana Earnest, Kai Zhang, Yingming Zhao, and Melanie H. Cobb. EMBO Journal 26, 2005-2014. (2007).
TGF-b regulation by Emilin1: new links in the etiology of hypertension.
Malavika Raman and Melanie H. Cobb. Cell 124, 893-895 (2006).
Crystal structure of the TAO2 kinase domain: activation and specificity of a Ste20p MAP3K
Tianjin Zhou, Malavika Raman, Yan Gao, Svetlana Earnest, Zhu Chen, Mischa Machius, Melanie H. Cobb and Elizabeth J. Goldsmith, Structure 12, 1891-1900(2004).
MAP kinase modules: many roads home.
Malavika Raman and Melanie H. Cobb. Current Biology 13, R886-888 (2003).
TAO (thousand-and-one amino acid) protein kinases mediate signaling from carbachol to p38 mitogen-activated protein kinase and ternary complex factors.
Zhu Chen, Malavika Raman, Linda Chen, Shuifen Lee, Alfred G. Gilman and Melanie H. Cobb. Journal of Biological Chemistry 278, 22278-22283 (2003).
Identification of novel point mutations in ERK2 that selectively disrupt binding to MEK1.
Fred L. Robinson, Angelique W. Whitehurst, Malavika Raman and Melanie H. Cobb. Journal of Biological Chemistry 277, 14844-14852 (2002).
Rakesh Ganji, Joao A. Paulo, Yuecheng Xi, Ian Kline, Jiang Zhu, Christoph S. Clemen, Conrad C. Weihl, John G. Purdy, Steve P. Gygi, Malavika Raman Nature communications, 14, Article number: 638 (2023)
The functional importance of VCP to maintaining cellular protein homeostasis.
Brittany Ahlstedt*, Rakesh Ganji* and Malavika Raman
Biochemical Society Transactions, October 2022,
* Equal contribution
The Cure VCP Scientific Conference 2021: Molecular and clinical insights into neurodegeneration and myopathy linked to multi-system proteinopathy-1 (MSP-1).
Michelle A.Johnson, Jacob A. Klickstein, Richa Khanna, Yunzi Gou, Cure VCP Disease Research Consortium, Malavika Raman.
Neurobiology or Disease, 2022, Volume 169
A reference induced pluripotent stem cell line for large-scale collaborative studies
Pantazis, CB, Yang, A, Lara, E, McDonough, JA., Blauwendraat, C, Peng, L, Oguro, H, Zou, J, Sebesta, D, Pratt, Gr, Cross, E, Blockwick, J, Buxton, P, Kinner-Bibeau, L, Medura, C, Tompkins, C, Hughes, S, Santiana, M, Faghri, , Nalls, M A., Vitale, D, Qi, YA., Ramos, D M., Anderson, K, Stadler, J, Narayan, P, Papademetriou, J, Reilly, L, Nelson, M P., Aggarwal, S, Rosen, L U., Kirwan, P, Pisupati, V, Coon, S L., Scholz, S W., Coccia, E, Sarrafha, L, Ahfeldt, T, Funes, S, Bosco, D A., Beccari, MS., Cleveland, DW., Zanellati, M C, Basundra, R, Deshmukh, M, Cohen, S, Nevin, Z S., Matia, M, Van Lent, J, Timmerman, V, Conklin, B R., Dou, D, Holzbaur, E L.F., L Emmy, R, Indigo V.L., Kampmann, M, Priebe, T, Öttl, M, Dong, J, van der Kant, R, Erlebach, L, Welzer, M, Kronenberg-Versteeg, D, Abu-Bonsrah, D, Parish, C L., Raman, M, Heinrich, L, Schüle, B, Aristoy, C Calatayud, V, Patrik, H, Aaron, W, Brian J., L, Guochang, A, Ernest, R, Ana-Caroline, B, Guojun, C, Dennis, P, Dominik, G, Rebecca M.C., Wray, S, Chase, K J, Zhang, K, Marioni, J C., Skarnes, W C., Cookson, M R., Ward, ME. and Merkle, F T. 2021, bioRxiv 2021.12.15.472643
The p97-UBXN1 complex regulates aggresome formation.
Sirisha Mukkavalli, Jacob Aaron Klickstein, Betty Ortiz, Peter Juo, Malavika Raman. 2021 Journal of Cell Science 134 (7).
AggreCount: An unbiased image analysis tool for identifying and quantifying cellular aggregates in a spatially-defined manner
Jacob Aaron Klickstein, Sirisha Mukkavalli, Malavika Raman. Journal of Biological Chemistry 2020 Dec 18;295(51):17672-17683
Download AggreCount here.
The WD40-repeat protein WDR-48 promotes the stability of the deubiquitinating enzyme USP-46 by inhibiting its ubiquitination and degradation.
Molly Hodul*, Rakesh Ganji *, Caroline L. Dahlberg , Malavika Raman , Peter Juo, J. Biol Chem. 2020 Jun 25:jbc.RA120.014590. doi: 10.1074/jbc.RA120.014590. Online ahead of print. PMID: 32587090* Equal contribution
The VCP-UBXN1 complex mediates triage of ubiquitylated cytosolic proteins bound to the BAG6 complex.
Rakesh Ganji, Sirisha Mukkavalli, Flavio Sonamji and Malavika Raman. Molecular and Celular Biology 2018. (38) 154-18. ( 2018)* Featured in MCB Spotlight.
Systematic proteomics of the VCP–UBXD adaptor network identifies a role for UBXN10 in regulating ciliogenesis
Malavika Raman, Mikhail Sergeev, Maija Garnaas, John R. Lydeard, Edward L. Huttlin, Wolfram Goessling, Jagesh V. Shah and J.Wade Harper. Nature Cell Biology 10, 1356-69 (2015).
Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
Shireen A. Sarraf, Malavika Raman, Virginia Pereira Guarani, Matthew E. Sowa, Edward L. Huttlin, Stephen P.Gygi, J. Wade Harper. Nature 496 (7445), 372-376 (2013).
A genome-wide screen identifies the p97 AAA-ATPase as an essential regulator of DNA damage-dependent CDT1 destruction.
Malavika Raman, Courtney G. Havens, Johannes C. Walter and J.Wade Harper. Molecular Cell 44(1): 72-84 (2011).
Stairway to the Proteasome.
Malavika Raman and J. Wade Harper. Nature 462, 585-586 (2009).
Differential regulation and properties of MAPKs.
Malavika Raman, Wei Chen and Melanie H. Cobb. Oncogene 26(22): 3100-12. (2007).
TAO kinases mediate activation of p38 in response to DNA damage.
Malavika Raman, Svetlana Earnest, Kai Zhang, Yingming Zhao, and Melanie H. Cobb. EMBO Journal 26, 2005-2014. (2007).
TGF-b regulation by Emilin1: new links in the etiology of hypertension.
Malavika Raman and Melanie H. Cobb. Cell 124, 893-895 (2006).
Crystal structure of the TAO2 kinase domain: activation and specificity of a Ste20p MAP3K
Tianjin Zhou, Malavika Raman, Yan Gao, Svetlana Earnest, Zhu Chen, Mischa Machius, Melanie H. Cobb and Elizabeth J. Goldsmith, Structure 12, 1891-1900(2004).
MAP kinase modules: many roads home.
Malavika Raman and Melanie H. Cobb. Current Biology 13, R886-888 (2003).
TAO (thousand-and-one amino acid) protein kinases mediate signaling from carbachol to p38 mitogen-activated protein kinase and ternary complex factors.
Zhu Chen, Malavika Raman, Linda Chen, Shuifen Lee, Alfred G. Gilman and Melanie H. Cobb. Journal of Biological Chemistry 278, 22278-22283 (2003).
Identification of novel point mutations in ERK2 that selectively disrupt binding to MEK1.
Fred L. Robinson, Angelique W. Whitehurst, Malavika Raman and Melanie H. Cobb. Journal of Biological Chemistry 277, 14844-14852 (2002).