Daniel Southworth

Assistant Professor of Biological Chemistry

B.S., University of California, Santa Cruz, 1997
Ph.D., Johns Hopkins University, School of Medicine, 2004
Postdoctoral, University of California, San Francisco, 2010

Research Focus: Protein Macromolecular Structure and Function by Cryo-Electron Microscopy

Phone: 734.764.8938
Office: 6314A LSI
E-mail: dsouth@umich.edu

Mechanisms that maintain the properly folded state of proteins and promote the degradation of misfolded and denatured proteins are fundamental to the homeostasis of the crowded cellular environment. Malfunction of these processes leads to protein aggregation and the progression of many diseases including Alzheimer’s disease and cancer. Molecular chaperones are at the interface of these processes, serving as a critical triage center for numerous substrate ‘client’ proteins including transcription regulators and cell cycle kinases.

Our lab is focused on understanding at the structural level how molecular chaperones interact and coordinate decisions that determine the fate of a given client protein. Using cyro-electron microscopy (cryo-EM) we aim to determine the structure of functional molecular chaperone assemblies and identify protein:protein interactions and molecular mechanisms that are essential to the alternating pathways of protein degradation and activation.

The tumor suppressor p53 protein is a member of a growing class of proteins that are intrinsically unstable, containing unstructured regions in the native state that are essential in regulation. Hsp90 and Hsp70 are central in activation and signal transduction of p53, as well as proteasome-directed degradation by interactions with the Chip ubiquitin ligase. Mutations, including those that occur in many tumor cells alter the conformational state of p53 and ultimately shift the highly regulated equilibrium between degradation and activation. Our current goals are to investigate the mechanisms of this protein triage system and determine cryo-EM structures of protein complexes at distinct stages and conformational states critical to p53 turnover.

The dynamic protein:protein interactions central to molecular chaperone function and signal transduction mechanisms present tremendous challenges to structural studies. We employ powerful electron microscopy methods to visualize complex protein assemblies at the single molecule level that are otherwise impossible to dissect by other structural methods. Furthermore, we have developed key biochemical crosslinking methods to trap specific functional states and ensure homogeneity for 3-D structure determination.

Broadly our lab is interested in understanding macromolecular organization and function of essential protein-protein interaction networks. Through our coupled biochemical and structural approaches we hope to obtain a detailed understanding of the structural organization of these dynamic processes and identify novel mechanisms and therapeutic targets fundamental to biology.

Southworth Research Group



Biological Sciences Scholar, University of Michigan
American Cancer Society Postdoctoral Fellowship
2004 Paul Ehrlich Research Award, Johns Hopkins University


Representative Publications

  1. Southworth DR and Agard DA, “Client-loading conformation revealed in the cryo-EM structure of the human Hsp90:Hop molecular chaperone complex.” Molecular Cell, 2011 Jun 24;42(6): 771-81.

  2. Krukenberg KA, Southworth DR, Street TO, Agard DA, “pH-dependent conformational changes in bacterial Hsp90 reveal a Grp94-like conformation at pH 6 that is highly active in suppression of citrate synthase aggregation." Journal of Molecular Biology. 2009 Jul 10; 390(2): pp 278-91.

  3. Southworth DR and Agard DA, “Species-dependent ensembles of conserved conformational states define the Hsp90 chaperone ATPase cycle.” Molecular Cell, 2008 Dec. 5; 32(5):631-40.

  4. Shiau AK*, Harris SF*, Southworth DR and Agard, DA, “Structural analysis of a bacterial hsp90 reveals dramatic nucleotide-dependent conformational rearrangements.” Cell, 2006 Oct 20; 127(2):329-40.

  5. Cukras, AC*, Southworth, DR*, Brunelle, JL, Culver GM, and Green, R. “Ribosomal Proteins S12 and S13 Function as control elements for translocation of the mRNA:tRNA complex.” Molecular Cell, 2003 August; 12(2): 321-8.

  6. Southworth, DR, Brunelle, JL, Green, R. “EF-G-independent translocation of the mRNA:tRNA complex is promoted by modification of the ribosome with thiol-Specific reagents.” Journal of Molecular Biology, 2002 December 6; 324 (4): 611-23.