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Publications

Tavella D, Ertekin A, Schaal H, Ryder SP, Massi F.
A Disorder-to-Order Transition Mediates RNA Binding of the Caenorhabditis elegans Protein MEX-5.
Biophys J. 2020 Apr 21;118(8):2001-2014. doi: 10.1016/j.bpj.2020.02.032. Epub 2020 Mar 19.

Basak S, Nobrega RP, Tavella D, Deveau LM, Koga N, Tatsumi-Koga R, Baker D, Massi F, Matthews CR.
Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein.
Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):6806-6811. doi: 10.1073/pnas.1818744116. Epub 2019 Mar 15.

Tavella D, Zitzewitz JA, Massi F. 
Characterization of TDP-43 RRM2 Partially Folded States and Their Significance to ALS.
Pathogenesis Biophys J. 2018 Nov 6;115(9):1673-1680

Morgan, B. R.; Zitzewitz, J. A.; Massi, F.
Structural Rearrangement upon Fragmentation of the Stability Core of the ALS-linked protein TDP-43.
Biophys. J. 113, 540-549 (2017).

Massi, F.; Peng, J. W.
Characterizing protein dynamics with NMR R1r relaxation experiments.
Methods Mol. Biol. 1688, 205-221 (2018).

Tavella, D.; Deveau, L. M.; Massi, F.
Understanding the origin of the disorder of the tandem zinc finger domain of TTP.
J. Chem. Theory Comput. 12, 4717-4725 (2016).

Deveau, L. M.; Massi, F.
Three residues make an evolutionary switch for folding and RNA-destabilizing activity in the TTP family of protein.
ACS Chem. Biol. 11, 435-43 (2016).

Morgan, B. R.; Deveau, L. M.; Massi, F.
Probing the structural and dynamical effects of the charged residues of the TZF domain of TIS11d.
Biophys. J. 108, 1503-1515 (2015).

Zearfoss, N.R.; Deveau, L. M.; Clingman, C. C.; Schmidt, E.; Johnson, E.S.; Massi, F.; Ryder, S. P.
A Conserved three-nucleotide core motif defines Musashi RNA-binding specificity. 
J. Biol. Chem. 289, 35530–35541  (2014).

Laine, J. M.; Amat, M.; Morgan, B. R.; Royer, W. E.; Massi, F. 
Insight into the allosteric mechanism of Scapharca dimeric hemoglobin.
Biochemistry 53, 7199–7210 (2014).

Ertekin, A.; Massi, F.
Understanding the role of conformational dynamics in protein-ligand interactions using NMR relaxation methods.
eMagRes 3, 255-266 (2014).

Clingman, C. C.; Deveau, L. M.; Hay, S.; Shandilya, S.; Massi, F.; Ryder, S. P.
Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite. eLife ;10.7554/eLife.02848 (2014).

Basavanapura, G. P.; Laine, J. M.; Kathuria, S. V.; Massi, F.*; Matthews, C. R.*
Clusters of branched aliphatic side chains serve as cores of stability in the native state of the HisF TIM barrel protein.
J. Mol. Biol. 425, 1065–1081 (2013) (* corresponding authors).

Romano, K. P.; Jennifer M. Laine, J. M.; Deveau, L. M.; Cao, H.; Massi, F.; Schiffer, C. A.
Molecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease.
J.Virol. 85, 6106-6116 (2011).

Stewart, M. D.; Morgan, B. R.; Massi, F.*; Igumenova, T. I.*
Probing the Determinants of Diacylglycerol Binding Affinity in a Lipid Binding Module of Protein Kinase Cα.
J. Mol. Biol. 408, 949-970 (2011). (* corresponding authors)

Ryder, S.P.; Massi, F. 
Insights into the structural basis of RNA Recognition by STAR domain proteins. 
Adv. Exp. Med. Biol. 693, 37-53 (2010).

Morgan, B. R.; Massi, F.
Accurate estimates of free energy changes in charge mutations.
J. Chem. Theory Comput. 6, 1884-1893 (2010).

Morgan, B. R.; Massi, F.
A computational study of RNA binding specificity in the tandem zinc finger domain of TIS11d.
Protein Sci. 19, 1222-1234 (2010).

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

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

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

Massi, F.; Grey, M. J.; Palmer, A. G.
Microsecond time-scale conformational dynamics in ubiquitin studied with NMR R1ρ relaxation experiments.
Protein Sci. 14, 735-742 (2005).

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

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

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

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

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

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

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