Mattos Lab

Publications

Johnson, C. W., Fetics, S. K., Davis, K. P., Rodrigues, J. A. and Mattos, Allosteric site variants affect GTP hydrolysis on Ras, Protein Science, 32(10), e4767 (2023). https://doi.org/10.1002/pro.4767

Volmar, A. Y., Guterres, H., Zhou, H., Reid, D., Pavlopoulos, S., Makowski, L. and Mattos, Mechanism of isoform-specific residue influence on GTP-bound HRas, KRas, and NRas, Biophysical Journal, 121, 1-14 (2022).https://doi.org/10.1016/j.bpj.2022.07.005

Johnson, C.W., Seo, H.-S., Terrell, E.M., Feffken, E.A., Lakhani, J., Song, K., Popow, O., Liu, A., Mattos, C., Morrison, D.K., Dhe-Paganon, Haigis, K., Regulation of GTPase function by autophosphorylation, Molecular Cell 82(5), 950-968 (2022). https://doi.org/10.1016/j.molcel.2022.02.011

Li, Z., Mattos, C., and Buck, M., Computational studies of the principle of dynamic-change-driven protein interactions, Structure 30(6), 909-916 (2022). https://doi.org/10.1016/j.str.2022.03.008

Cookis, T. and Mattos, C., Crystal structure reveals full Ras:Raf interface and advances mechanistic understanding of Raf activation, Biomolecules, 11(7) 996 (2021). https://doi.org/10.3390/biom11070996

*Packer, M., *Parker, J. A., Chung, J. K., Li, Z., Lee, Y. K., Cookis, T., Guterres, H., Alvarez, S., Hossain, MDA, Donnelly, D. P., Agar, J. N., Makowski, L., Buck, M., Groves, J. T. and Mattos, C., Raf promotes dimerization of the Raf G-domain with increased allosteric connections, PNAS, 118(10) e2015648118; https://doi.org/10.1073/pnas.2015648118 (2021). (*Co-first authors)

Agarwal, S., Smith, M., De La Rosa, I., Verba, K.A., Swartz, P., Segura-Totten, M., and Mattos, C., Development of a structure-analysis pipeline using multiple solvent crystal structures of barrier-to-autointegration factor, Acta Cryst D: Structural Biology, 76, 1001-1014 (2020).

Kearney, B. M., Schwabe, Marcus, K., M. Roberts, D. M., Dechene, M., Swartz, P., and Mattos, C., DRoP: Automated detection of conserved solvent binding sites on proteins, Proteins: Structure, Function and Bioinformatics, 88, 152-165 (2020).

Reid, D. and Mattos, C., Targeting cancer from a structural biology perspective, in Unraveling Cancer Signaling Pathways: A Multidisciplinary Approach, Kakoli Bose and Pradip Chaudhari Editors, Springer (2019).

Jang, H., Banerjee, A., Marcus, K., Makowski, L., Mattos, C. Gaponenko, V. and Nussinov, R., The structural basis of the farnesylated and methylated KRas4B interaction with calmodulin, Structure, 27(11), 1647-1659 (2019).

Marcus, K. and Mattos, C., Water in Ras superfamily evolution, Journal of Computational Chemistry, 41(5), 402-414 (2019).

*Johnson, C. W., *Lin, Y.-J., Reid, D., Parker, J., Pavlopoulos, S., Dischinger, P., Graveel, C., Aguirre, A. J., Steensma, M., Haigis, K. M., Mattos, C., Isoform-specific destabilization of the active site reveals molecular mechanism of intrinsic activation of KRas G13D, Cell Reports, 28 (6), 1538-1550 (2019). (*Co-first authors)

Wadia-Fascetti, S., Mattos, C. and Cornwall, A., Advancing with the STARS: Fostering systemic inclusivity in Northeastern University’s STEM Ph.D. programs, in “Broadening STEM participation in academia: Documenting impact through empirical evidence”, Eds. Winfield, L., Wilson-Kennedy, Z., Thomas, G., and Watkins, L., ACS Books (2019).

Knihtila, R., Volmar, A., Meilleur, F. and Mattos, C., Titration of ionizable groups in proteins using multiple neutron data sets from a single crystal: application to the small GTPase Ras, Acta Crystallogr. F, 75, 111-115 (2019).

Ashkar, R., Bilheux, H., Bordallo, H., Briber, R., Callaway, D., Cheng, X., Chu, X.-Q., Curtis, J., Dadmun, M., Fenimore, P., Fushman, D., Gabel, F., Gupta, K., Herberle, F., Heinrich, F., Hong, L., Datsaras, J., Kelman, Z., Kharlampieva, E., Kneller, G. R., Kovalevskyi, A., Krueger, S., Langan, P., Libermann, R., Liu, Y., Losche, M., Lyman, E., Mao, Y., Marino, J., Mattos, C., Meilleur, F., Moody, P., Nickels, J. D., O’Dell, W., O’Neill, H., Perez-Salas, U., Peters, J., Petridis, L., Sokolov, A., Stanley, C., Wagner, N., Weinrich, M., Weiss, K., Wymore, T., Zhang, Y., and Smith, J. C., Neutron scattering in the biological sciences: progress and prospects, Acta Crystallogr. D Structural Biology, 74, 1129-1168 (2018).

Zhou, H., Guterres, H., Mattos, C., Makowski, L., Predicting X-ray solution scattering from flexible macromolecules, Protein Science 12, 2023-2036 (2018).

Parker, J. A., Volmar, A., Y., Pavlopoulos, S. and Mattos, C., K-Ras populates conformational states differently from its isoform H-Ras and oncogenic mutant K-RasG12D, Structure 26, 810-820 (2018).

Parker, J. A. and Mattos, C., The K-Ras, N-Ras and H-Ras isoforms: Unique Conformational Preferences and Implications for Targeting Oncogenic Mutants, Ras in cancer and human disease. Cold Spring Harbor Perspect Med., 8(8) doi: 10.1101/cshperspect.a031427 (2018).

    *Johnson, C. W., *Reid, D., Parker, J. A., Salter, S., Knihtila, R., Kuzmic, P., and Mattos, C., The small GTPases K-Ras, N-Ras and H-Ras have distinct biochemical properties determined by allosteric effects, Journal of Biological Chemistry, 292(31), 12981-12993 (2017). (*Co-first authors).

      *Kauke, M. J., *Traxlmayr, M. W., *Parker, J. A., Kiefer, J. K., Knihtila, R., McGee, J., Mattos, C., and Wittrup, D. K., An engineered protein antagonist of K-Ras/B-Raf interaction, Scientific Reports, 7(1), 5831-5839 (2017). (*Co-first authors)

        Johnson, C. W., Buhrman, G., Ting, P.Y., Colicelli, J., and Mattos, C., Expression, Purification, Crystallization and X-ray data collection for RAS and its mutants, Data in Brief, 6, 423-427 (2016).

        Knihtila, R., Holzapfel, G., Weiss, K., Meilleur, F. and Mattos, C. Neutron Crystal Structure of RAS GTPase puts in question the Protonation State of the GTP γ-Phosphate J. Mol Bio 52, 31025-36 (2015).

        Mattos, C., Ras: structural details to guide direct targeting. Aging, 7(6), 344-345 (2015).

        Ting, P., Johnson, C., Mattos, C. and Colicelli, J., ABL phosphorylation of HRAS alters intrinsic hydrolysis and effector binding, FASEB (2015).

        Marcus, K. and Mattos, C., Direct attack on Ras: Targeting Communication Pathways and Mutation-specific Effects, Clinical Cancer Research, 21(8), 1810-1818 (2015).

        Parker, J. and Mattos, C., The Ras-membrane interface: isoform-specific differences in the catalytic domain, Molecular Cancer Research, 13(4), 595-603 (2015).

        Fetics, S. K., Guterres, H., Kearney, B. M., Buhrman, G. Ma, B., Nussinov, R. and Mattos, C., Allosteric effects of RasQ61L oncogenic mutation on Raf-RBD, Structure, 23(3), 505-516 (2015).

        Kearney, B. M., Johnson, C. W., Roberts, D. M., Swartz, P. and Mattos, C., DRoP: a water analysis program identifies Ras-GTP specific pathway of communication between membrane interacting regions and the active site, Journal of Molecular Biology, 426(3), 611-629 (2014).

        Johnson, C. W. and Mattos, C., The allosteric switch and conformational states in Ras-GTP affected by small molecules, in The Enzymes, Inhibitors of Ras Superfamily G-proteins, Editor Fuyu Tamanoi, Vol 33, 42-67 (2013).

        Mattos, C., Johnson, M., White, H., Sears, D., Bailey, C., Bell, E., Introduction: Promoting concept driven teaching strategies in Biochemistry and Molecular Biology, Biochemistry and Molecular Biology Education, 41(5), 287-288 (2013).

        Nussinov, R., Tsai, C.-J. and Mattos, C., Pathway drug cocktail: targeting Ras signaling based on structural pathways, Trends in Molecular Medicine, 19(11), 695-704 (2013).

        Holzapfel, G., Buhrman, G. and Mattos, C., Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition, Biochemistry, 51, 6114-6126 (2012).

        Walters, J., Schipper, J. L., Swartz, P., Mattos, C., and Clark, A. C., Allosteric Modulation of Caspase-3 through Mutagenesis, Bioscience Reports, 32, 401-411 (2012).

        Gagnon, K. T., Biswas, S., Zhang, X., Brown II, B. A., Wollenzien, P., Mattos, C. and Maxwell, E. S., The structurally conserved Nop56/58 N-terminal domain facilitates archaeal Box C/D sRNP-guided methyltransferase activity, Journal of Biological Chemistry, 287(23), 19418-19428 (2012).

        Prior, I. A., Lewis, P. D., Mattos, C., A comprehensive survey of Ras mutations in cancer, Cancer Research, 72(10): 2457-2467 (2012).

        Mattos C. and Ringe D.: Solvent Structure, In International Tables for Crystallography, Volume F, second edition, Crystallography of Biological Macromolecules. (Eddy Arnold, Daniel M. Himmel, Michael G. Rossman MG, Arnold E, Eds.) Wiley and Sons, 623-640 (2012).

        Buhrman, G., O’Connor, C., Zerbe, B., Kearney, B. M., Napoleon, R., Kovrigina, E. A., Vajda, S., Kozakov, D., Kovrigin, E. L., and Mattos, C., Analysis of binding site hot spots on the surface of Ras GTPase, Journal of Molecular Biology, 413, 773-789 (2011).

        Biswas, S., Buhrman, G., Gagnon, K., Mattos, C., Brown, B. and Maxwell, E., Comparative Analysis of the 15.5kD Box C/D snoRNP Core Protein in the Primitive Eukaryote Giardia lamblia Reveals Unique Structural and Functional Features, Biochemistry, 50, 2907-2918 (2011).

        Walters, J., Swartz, P., Mattos, C. and Clark, A.C., Thermodynamic, enzymatic and structural effects of removing a salt bridge at the base of loop 4 in (pro)caspase-3, Archives of Biochemistry and Biophysics, 508, 31-38 (2011).

        Burhman, G., Kumar, S., Cirit, M., Haugh, J. M., and Mattos, C. Allosteric modulation of Ras-GTP is linked to signal transduction through Raf kinase. Journal of Biological Chemistry, 286, 3323-3331 (2011).

        Buhrman, G., Holzapfel, G., Fetics, S. and Mattos, C., Allosteric modulation of Ras positions Q61 for a direct role in catalysis, PNAS, 107, 4931-4936 (2010).

        Walters, J., Pop, C., Scott, F.L., Drag, M., Swartz, P., Mattos, C., Salvesen, G.S., and Clark, A.C., A constitutively active and uninhibitable caspase-3 zymogen efficiently induces apoptosis, Biochemical Journal, 424, 335-345 (2009).

        Dechene, M., Wink, G., Smith, M., Swartz, P. and Mattos, C., Multiple Solvent Crystal Structures of Ribonuclease A: An Assessment of the Method, Proteins: Structure, Function and Bioinformatics, 76, 861-881 (2009).

        Brenke, R., Kozakov, D., Chuang, G.-Y., Beglov, D., Hall, D., Landon, M. R., Mattos, C. and Vajda, S., Fragment-based identification of druggable “hot spots” of proteins using Fourier domain correlation techniques, Bioinformatics, 25, 621-627 (2009).

        Mattos, C. Removing the Barrier between Teaching in the Classroom and Research in the Laboratory, ASBMB Today 17-19 (2008).

        Mattos, C. and Clark, A. C., Minimizing frustration by folding in an aqueous environment, Archives of Biochemistry and Biophysics, 469, 118-131 (2008).

        Buhrman, G., Wink, G. and Mattos, C., Transformation efficiency of RasQ61 mutants linked to structural features of the switch regions in the presence of Raf, Structure, 15, 1618-1629 (2007).

        Milam, S.L., Nicely, N.I., Feeney, B., Mattos, C., Clark, A.C., Rapid Folding and Unfolding of Apaf-1 CARD, Journal of Molecular Biology, 369, 290-304 (2007).

        Ringe, D. and Mattos, C., Location of Binding Sites on Proteins by the Multiple Solvent Crystal Structure Method, In Fragment-based Approaches in Drug Discovery, Methods and Principles in Medicinal Chemistry (Jahnke, W., Erlanson, D. A., Eds) Wiley-VCH; vol 34, 67-88 (2006).

        Feeney, B., Pop, C., Swartz, P., Mattos, C. and Clark, A.C., The Role of Loop Bundle Hydrogen Bonds in the Maturation and Activity of (Pro)caspase-3, Biochemistry, 45, 13249-13263 (2006).

        Mattos, C., Bellamacina, C., Peisach, E., Pereira, A., Vitkup, D., Petsko, G.A. and Ringe, D., Multiple Solvent Crystal Structures: Probing Binding Sites, Plasticity and Hydration, Journal of Molecular Biology, 357, 1471-1482 (2006).

        Buhrman, G., Parker, B., Sohn, J., Rudolph, J. and Mattos, C., Structural mechanism of oxidative regulation of the phosphatase Cdc25B via an intramolecular disulfide bond, Biochemistry, 44, 5307-5316 (2005).

        Nicely, N., Kosak, J., de Serrano, V., and Mattos, C., Crystal Structures of Ral-GppNHp and Ral-GDP Reveal Two Binding Sites That Are Also Present in Ras and Rap, Structure, 12, 2025-2036 (2004).

        Mattos, C., Cohen, J.D., Green, D.F., Tidor, B., and Karplus, M., X-ray Structural and Simulation Analysis of a Protein Mutant: The Value of a Combined Approach, Proteins: Structure, Function, and Bioinformatics 55, 733-742 (2004).

        Buhrman, G., de Serrano, V., and Mattos, C., Organic Solvents Order the Dynamic Switch II in Ras Crystals, Structure 11, 747-751 (2003).

        Mattos, C., Protein-Water Interactions in a Dynamic World, Trends in Biochemical Sciences 27, 203-208 (2002).

        Mattos, C. and Ringe D., Proteins in Organic Solvents, Curr. Opin. Struct. Biol. 11, 761-764 (2001).

        Mattos C. and Ringe D.: Solvent Structure, In International Tables for Crystallography. (Rossman MG, Arnold E, Eds.) Kluwer Academic Publishers; vol F, 623-640 (2001)

        Ringe, D. and Mattos, C., Analysis of the Binding Surfaces of Proteins, Med. Res. Rev. 19, 321-331 (1999).

        MacKerell Jr., A. D., Bashford, D., Bellott, M., Dunbrack Jr., R. L., Evanseck, J., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher III, W. E., Roux, B., Schlenkrich, M., Smith, J., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M., All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B 102, 3586-3616 (1998).

        Mattos, C. and Ringe D., Locating and Characterizing Binding Sites on Proteins, Nature Biotech. 14, 595-599 (1996).

        Allen, K. N., Bellamacina, C. R., Ding, X., Jeffery, C. J., Mattos, C., Petsko, G. A., and Ringe, D., An Experimental Approach to Mapping the Binding Surfaces of Crystalline Proteins, J. Phys. Chem. 100, 2605-2611 (1996).

        Mattos, C., Giammona, D., Petsko, G.A., and Ringe, D., Structural Analysis of the Active Site of Porcine Pancreatic Elastase Based on the X-Ray Crystal Structure of Complexes with Trifluoroacetyl-Dipeptide-Anilide Inhibitors, Biochemistry 34, 3193-3203 (1995).

        Mattos, C., Petsko, G. A., and Karplus, M., Analysis of Two-Residue Turns in Proteins, J. Mol. Biol. 238, 733-747 (1994).

        Mattos, C., Rasmussen, B., Ding, X., Petsko, G. A., and Ringe, D., Analogous Inhibitors of Elastase Do Not Always Bind Analogously, Nature Struct. Biol. 1, 55-58 (1994).

        Mattos, C., and Ringe, D., Multiple Binding Modes, In 3D QSAR in Drug Design — Theory, Methods and Applications, (H. Kubinyi, ed.) ESCOM Science Publisher, Leiden (1993).