Francesca Massi, Ph.D.

Academic Role: Assistant Professor

Faculty Appointment(s) In:
   Biochemistry and Molecular Pharmacology

From protein dynamics to protein function and stability using NMR spectroscopy and computer simulation.

Proteins are flexible molecules that often undergo conformational changes to perform biological functions. For this reason, knowledge of the internal dynamics of proteins is crucial to an understanding of the details of their functions and mechanisms of action.

The focus of my laboratory is the relationship between structure, stability, and dynamics of proteins. The fundamental phenomena that we investigate are:

• The role of enzyme dynamics in catalysis.
• The contribution of conformational dynamics to molecular recognition in proteins.
• Protein aggregation in amyloidosis.

We study these phenomena by solution nuclear magnetic resonance (NMR) spectroscopy and by computational methods. NMR spectroscopy is a powerful technique that can monitor protein motions over a broad range of time scales with atomic resolution. Computer simulations offer additional insight into the details of protein structure and dynamics in solution.

Specific targets of our research program:

1.  Orotidine 5-monophosphate decarboxylase (ODCase).
ODCase catalyzes the decarboxylation of orotidine 5’-monophosphate (OMP) to uridine 5’-monophosphate (UMP). This reaction is the last step in the de novo synthesis of pyrimidine nucleotides. Among protein catalysts that do not use metal ions or other cofactors, ODCase is the most proficient enzyme identified to date, and it enhances the uncatalyzed reaction rate by a factor of 10¹⁷. The detailed reaction mechanism of ODCase is still unknown. The enzyme undergoes a significant conformational change upon ligand binding, from an “open” state to a “closed” catalytically active state. We monitor the protein motions promoted by the binding of the ligand in order to understand the details of their essential role in the catalysis, and to elucidate the catalytic mechanism.

2.  b ₂-microglobulin (b ₂m)
A number of human diseases originate from the deposition of stable, ordered protein aggregates called amyloid fibrils. Approximately 20 different amyloidogenic proteins have been identified and associated with diseases. Each of these amyloidogenic proteins has a different native structure, but all of the diverse amyloid fibers are composed by b strands. b ₂-microglobulin is a 12 kD protein that folds as a seven-stranded antiparallel b sandwich. As a consequence of its dissociation from the MHCI, b ₂m is present in the plasma under physiological conditions. After prolonged hemodialysis, individuals with renal dysfunction show an anomalous increase of concentration of b ₂m in the plasma, which can lead to pathogenic amyloid fibril formation.  In order to understand what causes the aggregation of b ₂-microglobulin into amyloid deposits, we are studying the relationship between conformational flexibility and aggregation.

3.  Scapharca dimeric hemoglobin (HbI)
Hemoglobin from Scapharca inaequivalvis is a homodimer that cooperatively binds oxygen and carbon monoxide.  The arrangement of monomers is different from that of mammalian hemoglobins, allowing the two heme groups to be in closer proximity and in more direct communication. Ligand binding produces only a moderate structural change.  Our goal is to use NMR spectroscopy to understand how HbI achieves cooperative ligand binding.

Publications

E. R. Valentine, F. Ferrage, F. Massi, D. Cowburn and A. G. Palmer III. Joint composite-rotation adiabatic-sweep isotope filtration. J. Biomol. NMR 38, 11-22 (2007).

F. Massi, C. Wang, and A. G. Palmer III. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 45, 10787-10794 (2006).

A. G. Palmer III and F. Massi. Characterization of the Dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700-1719 (2006).

F. Massi, M. J. Grey and A. G. Palmer III. Microsecond time-scale conformational dynamics in ubiquitin studied with NMR R_1r relaxation experiments. Protein Sci. 14, 735-742 (2005).

F. Massi , E. Johnson, C.Wang, M. Rance, and A. G. Palmer III. NMR R_1r rotating-frame relaxation with weak radio frequency fields. J. Am. Chem. Soc. 126, 2247-2256 (2004).

F. Massi and A. G. Palmer III. Temperature dependence of NMR order parameters and protein dynamics. J. Am. Chem. Soc. 125, 11158-11159 (2003).

F. Massi and J. E. Straub. Structural and dynamical analysis of the hydration of the Alzheimer's b-amyloid peptide. J. Comp. Chem. 24, 143-153 (2003).

F. Massi, D. Klimov, D. Thirumalai, and J. E. Straub. Charge states rather than propensity for b-structure determine enhanced fibrillogenesis in the wild type Alzheimer's b-amyloid peptide compared to E22Q Dutch mutant. Protein Sci. 11, 1639-1647 (2002).

F. Massi and J. E. Straub. Probing the origins of increased activity of the E22Q Dutch mutant of the Alzheimer's b-amyloid peptide. Biophys. J. 81,697-709 (2001).

F. Massi and J. E. Straub. Energy landscape theory for Alzheimer's amyloid b-peptide fibril elongation. Proteins 42, 217-229 (2001).

F. Massi, J. W. Peng, J. P. Lee, and J. E. Straub. Simulation study of the structure and dynamics of the Alzheimer's amyloid peptide congener in solution. Biophys. J. 80, 31-44 (2001).

Rotation Projects

Rotation projects are available to understand:

1. The effect of enzyme loop motions on catalysis.
Ligand binding promotes a structural transition in ODCase between an open and a closed state. What are the kinetic and thermodynamic properties of this transition? We will perform NMR relaxation experiments to monitor enzyme motions on different time scales. These results will provide direct insight into the opening and closing transitions of the enzyme and will correlate these transitions with the microscopic rate of catalytic turnover.

2. The relationship between flexibility and aggregation propensity in b₂-microglobulin. The presence of conformational flexibility indicates the transition between two or more states, one of which might be an intermediate that drives the monomeric b₂m to associate into insoluble aggregates. In order to fully explore the connection between dynamics and aggregation propensity, we will study the structure and dynamics of the wild type b₂m and different mutants that show different aggregation properties relative to the wild type protein.

Academic Background

Laurea, University of Rome “La Sapienza”, 1995
Ph.D., Boston University , 2002
Postdoctoral Fellow, Columbia University, 2002-2007

Office: LRB 925
Phone: 508-856-4501
E-mail: Francesca.Massi@umassmed.edu
Keywords: Protein Folding, Biophysics, Structural Biology, Biochemistry

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