Andrew P Capaldi

Andrew P Capaldi

Associate Professor, Molecular and Cellular Biology
Associate Professor, Genetics - GIDP
Associate Professor, BIO5 Institute
Member of the General Faculty
Member of the Graduate Faculty
Primary Department
(520) 626-9376

Research Interest

Andrew Capaldi, PhD, researches the signaling pathways and transcription factors in a cell that are organized into circuits. They allow cells to process information and make decisions. For Dr. Capaldi, the work arises in understanding both how these circuits are built from their components, and how they function and malfunction. To address these questions, he is working to reverse engineer the circuitry that controls cell growth in budding yeast using a combination of genomic, proteomic and computational methods.


Buchan, J. R., Capaldi, A. P., & Parker, R. (2012). TOR-tured yeast find a new way to stand the heat. Molecular cell, 47(2), 155-7.
BIO5 Collaborators
Ross Buchan, Andrew P Capaldi

In this issue, Takahara and Maeda (2012) discover that together, Pbp1 and sequestration of the TORC1 complex in cytoplasmic mRNP stress granules provides a negative regulatory mechanism for TORC1 signaling during stress.

Spence, G. R., Capaldi, A. P., & Radford, S. E. (2004). Trapping the on-pathway folding intermediate of Im7 at equilibrium. Journal of Molecular Biology, 341(1), 215-226.

PMID: 15312774;Abstract:

The four-helical protein Im7 folds via a rapidly formed on-pathway intermediate (kUI=3000 s-1 at pH 7.0, 10 °C) that contains three (helices I, II and IV) of the four native α-helices. The relatively slow (kIN=300 s-1) conversion of this intermediate into the native structure is driven by the folding and docking of the six residue helix III onto the developing hydrophobic core. Here, we describe the structural properties of four Im7* variants designed to trap the protein in the intermediate state by disrupting the stabilising interactions formed between helix III and the rest of the protein structure. In two of these variants (I54A and L53AI54A), hydrophobic residues within helix III have been mutated to alanine, whilst in the other two mutants the sequence encompassing the native helix III was replaced by a glycine linker, three (H3G3) or six (H3G6) residues in length. All four variants were shown to be monomeric, as judged by analytical ultracentrifugation, and highly helical as measured by far-UV CD. In addition, all the variants denature co-operatively and have a stability (ΔGUF) and buried hydrophobic surface area (M UF) similar to those of the on-pathway kinetic intermediate. Structural characterisation of these variants using 1-anilino-8-napthalene sulphonic acid (ANS) binding, near-UV CD and 1D 1H NMR demonstrate further that the trapped intermediate ensemble is highly structured with little exposed hydrophobic surface area. Interestingly, however, the structural properties of the variants I54A and L53AI54A differ in detail from those of H3G3 and H3G6. In particular, the single tryptophan residue, located near the end of helix IV, and distant from helix III, is in a distinct environment in the two sets of mutants as judged by fluorescence, near-UV CD and the sensitivity of tryptophan fluorescence to iodide quenching. Overall, the results confirm previous kinetic analysis that demonstrated the hierarchical folding of Im7 via an on-pathway intermediate, and show that this species is a highly helical ensemble with a well-formed hydrophobic core. By contrast with the native state, however, the intermediate ensemble is flexible enough to change in response to mutation, its structural properties being tailored by residues in the sequence encompassing the native helix III. © 2004 Elsevier Ltd. All rights reserved.

Capaldi, A. P., Kaplan, T., Liu, Y., Habib, N., Regev, A., Friedman, N., & O'Shea, E. K. (2008). Structure and function of a transcriptional network activated by the MAPK Hog1. Nature Genetics, 40(11), 1300-1306.

PMID: 18931682;PMCID: PMC2825711;Abstract:

Cells regulate gene expression using a complex network of signaling pathways, transcription factors and promoters. To gain insight into the structure and function of these networks, we analyzed gene expression in single- and multiple-mutant strains to build a quantitative model of the Hog1 MAPK-dependent osmotic stress response in budding yeast. Our model reveals that the Hog1 and general stress (Msn2/4) pathways interact, at both the signaling and promoter level, to integrate information and create a context-dependent response. This study lays out a path to identifying and characterizing the role of signal integration and processing in other gene regulatory networks. © 2008 Nature Publishing Group.

Sullivan, A., Wallace, R., Wellington, R., Luo, X., & Capaldi, A. P. (2018). EGOC and Pib2 Control Kog1-body Formation in S. Cerevisiae. eLife.

Paper describing a detailed mechanism underlying regulation of Kog1 body formation-explaining how both known and newly identified TORC1 regulators cooperate to control the reversible aggregation of the TOR complex will be submitted to eLife before Summer 2018

Capaldi, A. P., & Radford, S. E. (2001). An unfolding story. Trends in Biochemical Sciences, 26(12), 753-.