Due to a limited supply, we are unable to accept phone calls to schedule COVID-19 vaccinations.
For the most up-to-date information, please check our COVID-19 Vaccination Website.

 

Additional Coronavirus Updates >

MENU

Eileen K. Jaffe, PhD

Eileen Jaffe, PhD
About

Professor

Adjunct Professor, Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine, Temple University

Adjunct Professor, Department of Biochemistry and Molecular Biology, Drexel University College of Medicine

Research Program

Lab Overview

A dice based illustration of the morpheein phenomenon wherein alternate protomer conformations produce alternate assemblies that have alternate physiologically relevant functions. (A) Cubic and pyramidal dice are used as symbolic representations of alternate conformations of a protomer that can self-assemble through association of two complementary surfaces.  These are the die face with one and with four dots.  The tetramer resembles a stack of boxes; the pentamer resembles a flying saucer. The red dashed circle is a multimer-specific surface cavity that can serve as a ligand binding site. (B) The diamond shaped ligands can bind to the multimer-specific binding site and draw the equilibrium toward the assembly of cubic dice, thus dictating protein function. A dice based illustration of the morpheein phenomenon wherein alternate protomer conformations produce alternate assemblies that have alternate physiologically relevant functions. (A) Cubic and pyramidal dice are used as symbolic representations of alternate conformations of a protomer that can self-assemble through association of two complementary surfaces. These are the die face with one and with four dots. The tetramer resembles a stack of boxes; the pentamer resembles a flying saucer. The red dashed circle is a multimer-specific surface cavity that can serve as a ligand binding site. (B) The diamond shaped ligands can bind to the multimer-specific binding site and draw the equilibrium toward the assembly of cubic dice, thus dictating protein function.

The Jaffe laboratory is focused on the roles of protein quaternary structure and quaternary structure rearrangements in the control of protein function, disease mechanisms, and therapeutic potential.  We use both classic and cutting-edge biochemical and biophysical approaches, often involving both intra- and extramural collaborations. Our focus stems from our 2002 discovery that a homo-oligomeric protein can reversibly dissociate, the dissociated units can change conformation, and these altered conformations support association to a structurally, functionally, and physiologically relevant distinct oligomeric assembly (see Figure 1). In the past eighteen years we have associated this structural dynamic with allosteric regulation of protein function, with human disease, as a potential mechanism for off-target drug side effects, and with new opportunities for allosteric drug discovery. Seeing this protein structure dynamic as novel, we coined the term morpheein to describe proteins that could reversibly dissociate, change conformation, and assemble differently with finite stoichiometry.  The dynamic interchange of homomeric protein assemblies has now been termed the Fifth Level of Protein structure and important drug targets have been identified as morpheeins (HIV integrase, Ebola virus VP40, PKM2). Modulating protein quaternary structure dynamics is gaining traction as an approach to drug discovery. Our currently funded research is focused on mammalian phenylalanine hydroxylase where modulation of the quaternary structure dynamics is proposed as a basis for treating an inborn error of metabolism.

Figure 1 The structure of PAH.
Figure 1 The structure of PAH. (a) The annotated domain structure of mammalian PAH. (b) The 2.9 Å PAH crystal structure in orthogonal views, colored as in part a, subunit A is shown in ribbons; subunit B is as a C-alpha trace; subunit C is in sticks; and subunit D is in transparent spheres. In cyan the subunits are labeled near the catalytic domain (top); in red they are labeled near the regulatory domain (bottom). The dotted black circle illustrates the autoregulatory domain partially occluding the enzyme active site (iron, in orange sphere). (c) Comparison of the subunit structures of full length PAH and those of the composite homology model; the subunit overlay aligns residues 144-410. The four subunits of the full length PAH structure (the diagonal pairs of subunits are illustrated using either black or white) are aligned with the two subunits of 2PAH (cyan) and the one subunit of 1PHZ (orange). The catalytic domain is in spheres, the regulatory domain is in ribbons, and the multimerization domain is as a C-alpha trace. The arrow denotes where the ACT domain and one helix of 2PAH conflict.
A structural roll of the dice
Morpheeins challenge a protein-folding paradigm
An unusual phylogenetic variation in the active site and allosteric metal ions of PBGS
The equilibrium of morpheein forms observed for human PBGS
Three models for allosteric regulation
Targeting morpheeins for drug design or discovery

 

Education and Training

Educational Background

  • Postdoctoral, Chemistry/Enzymology, Harvard University, 1979-1981
  • PhD, Biochemistry, University of Pennsylvania, 1979
  • BS, Chemistry, State University New York, Cortland, 1975

Memberships

  • American Chemical Society 1975 - present
  • American Society for Biochemistry and Molecular Biology, 1986 - present
  • AAAS membership 1979 - present
  • Association for Women in Science 1982 - present
  • Sigma Xi 1979 - present
  • UPENN Biomedical Graduate Studies Advisory Board, 1992-1996Referee Panel X6A National Synchrotron Light Source, 2002-date
  • Advisory Board, Partnership for Cancer Research Education, FCCC, 1998 - 2006
  • Dean of Arts & Sciences Advisory Board, SUNY Cortland, 1999-2004
  • NIH Physiological Chemistry Study Section, 1997-2001

Honors & Awards

  • Elizabeth Bingham Award, AWIS-PHL, 2006
  • Academic Hall of Fame Inaugural Inductee, State University New York, Cortland, 2006
Research Profile

Research Program

Research Interests

Quaternary structure dynamics and the control of protein function

  • Morpheein model for protein allostery, for which the prototype is porphobilinogen synthase
  • Allosteric regulation of phenylalanine hydroxylase, a putative morpheein
  • Multimer-specific surface cavities as targets for the discovery of allosteric modulators (e.g. drugs)

Lab Description

The Jaffe Laboratory studies protein structure-function relationships using both biochemical and biophysical approaches. We are focused on the roles of protein quaternary structure dynamics in the control of protein function. This follows our discovery that multimeric proteins can come apart, the dissociated units can change conformation, and these altered conformations can come back together differently to form a structurally and functionally distinct assembly.

Unlike amyloid, the changes in subunit structure are subtle, such as a hinge movement between folded domains, the oligomeric stoichiometry is finite, and the process is freely reversible. This structural dynamic can be the basis for allosteric regulation of protein function (the morpheein model of protein allostery). Disregulation of the equilibrium of assemblies is responsible for some human disease. Designed regulation of the equilibrium of assemblies provides a basis for allosteric drug discovery. The now well-established structural dynamic was originally unexpected, but new examples are being discovered regularly, as in the Ebola virus VP40 protein (E. Ollmann-Saphire, Scripps Institute).

Although we coined the term morpheein to describe proteins that could reversibly dissociate, change conformation and assemble differently with finite stoichiometry and alternate functionality, the term "transformers" has also been used. This fifth level of protein structure (functionally distinct alternate assemblies with alternate protomer conformations) may be closely related to other protein structure function phenomena such as filamentation and moonlighting.  In the case of filamentation, it is well established that some proteins that function as enzymes can reversibly form filaments as a function of the cell cycle or metabolic state.  In general, it remains unknown if the conformation of the protomer in the filament is the same as the conformation of the protomer in the non-filamentous assembly.  The moonlighting phenomenon is established for nearly 500 different proteins, many of which are ancient metabolic enzymes which have been discovered as able to moonlight with different functions (e.g. transcription factors, alternate enzymatic activities, etc.), often in different cellular compartments.  A prime cancer-relevant example is PKM2, which has alternate functions in the cytosol vs. nucleus.  In general, it remains unknown if moonlighting functions correlate with alternate protomer conformations and/or alternate assemblies.  Jaffe is working with experts in these related phenomena to promote a consolidated view of the 5th level of protein structure.  To date, we have organized symposia at national and international meetings (American Crystallography Association meeting in Toronto (2018), American Society of Biochemistry and Molecular Biology (2020, online), and the Protein Society (planned for 2021)).

What we have learned from the prototype morpheein, porphobilinogen synthase, allows us to mine the literature and protein structure databases in search of other proteins that function as morpheeins. A family of putative morpheeins includes many drug targets, including cancer chemotherapeutic targets. The putative morpheein currently under most active investigation in the laboratory is phenylalanine hydroxylase (PAH), where the dysregulation of the interchange between various multimers is proposed to account for phenylketonuria in some patients.  The commonality between cancers and inborn error of metabolism is the dysfunction (often due to single amino acid substitutions) of the patients own proteins. 

Our current experimental focus on PAH resulted in an innovative mechanism for its allosteric regulation, the first X-ray crystal structure of the resting-state tetrameric assembly, and significant advances towards defining the structure of the architecturally alternative activated assembly.  Collaborative work with V. Voelz (Temple U, Chemistry) merged computational and experimental studies to establish a conformational selection mechanism for the allosteric process.  Collaborative computational docking studies (J. Karanicolas, FCCC; J. Kulp, Fox Chase Chemical Diversity Center) has revealed two sets of small molecules (akin to the diamonds in Fig 1) that may serve to stabilize PAH in the activated conformation, thus providing a small molecule therapeutic option for individuals living with PKU. The lab is currently developing methods for screening these compounds. 

">
Lab Staff

George W. Merkel, MS

Research Specialist

Room: R452
215-728-5268
Publications

Selected Publications

Jaffe, E. K. (2020) Wrangling Shape-Shifting Morpheeins to Tackle Disease and Approach Drug Discovery. Front Mol Biosci 7, 582966

Arturo, E. C., Merkel, G. W., Hansen, M. R., Lisowski, S., Almeida, D., Gupta, K., and Jaffe, E. K. (2020) Manipulation of a cation-pi sandwich reveals conformational flexibility in phenylalanine hydroxylase. Biochimie

Arturo, E. C., Gupta, K., Hansen, M. R., Borne, E., and Jaffe, E. K. (2019) Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium. J Biol Chem 294, 10131-10145

Ge, Y., Borne, E., Stewart, S., Hansen, M. R., Arturo, E. C., Jaffe, E. K., and Voelz, V. A. (2018) Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding. J Biol Chem 293, 19532-19543

Jaffe, E. K. (2017) New protein structures provide an updated understanding of phenylketonuria. Mol Genet Metab 121, 289-296

Jaffe, E. K. (2016) The Remarkable Character of Porphobilinogen Synthase. Acc Chem Res 49, 2509-2517

Lawrence, S. H., Selwood, T., and Jaffe, E. K. (2013) Environmental contaminants perturb fragile protein assemblies and inhibit normal protein function. Curr Chem Biol 7, 196-206

Selwood, T., and Jaffe, E. K. (2012) Dynamic dissociating homo-oligomers and the control of protein function. Arch Biochem Biophys 519, 131-143

Lawrence, S. H., Selwood, T., and Jaffe, E. K. (2011) Diverse clinical compounds alter the quaternary structure and inhibit the activity of an essential enzyme. ChemMedChem 6, 1067-1073

Lawrence, S. H., Ramirez, U. D., Tang, L., Fazliyez, F., Kundrat, L., Markham, G. D., and Jaffe, E. K. (2008) Shape shifting leads to small-molecule allosteric drug discovery. Chem Biol 15, 586-596

Jaffe, E. K., and Stith, L. (2007) ALAD porphyria is a conformational disease. Am J Hum Genet 80, 329-337

Jaffe, E. K. (2005) Morpheeins--a new structural paradigm for allosteric regulation. Trends Biochem Sci 30, 490-497

Additional Publications

My NCBI

This Fox Chase professor participates in the Undergraduate Summer Research Fellowship
Learn more about Research Volunteering.

Connect with Fox Chase