Publications

Ma X, Baktina M, Shulgina I, Cantara WA, Nagy ABK, Goto Y, Suga H, Foster MP, Musier-Forsyth K. Structural basis of tRNAPro acceptor stem recognition by a bacterial trans-editing domain. Nucleic Acids Res. 2023 May 8; 51(8):3988-3999. doi: 10.1093/nar/gkad192.

Li W, Norris AS, Lichtenthal K, Kelly S, Ihms EC, Gollnick P, Wysocki VH, Foster MP. Thermodynamic coupling between neighboring binding sites in homo-oligomeric ligand sensing protiens from mass resolved ligand-dependent population distributions. Protein Science 2022 Sept. 27; 31(10): e4424. doi: 10.1002/pro.4424.

Stachowski K, Norris AS, Potter D, Wysocki V, Foster MP. Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM. Nucleic Acids Res. 2022 Feb. 1; gkac032. doi: 10.1093/nar/gkac032.

Wagner N, Foster MP. Nearest-Neighbor Effects Modulate loxP Spacer DNA Chemical Shifts and Guide Oligonucleotide Design for Nuclear Magnetic Resonance Studies. Biochem. 2022 Jan. 18; 61(2):67-76. doi: 10.1021/acs.biochem.1c00571.

Unnikrishnan A, Amero C, Yadav DK, Stachowski K, Potter D, Foster MP. DNA binding induces a cis-totrans switch in Cre recombinase to enable intasome assembly. PNAS. 2020 Oct. 6; 117(40):24849-24858. doi: 10.1073/pnas.2011448117.

Holmquist ML, Ihms EC, Gollnick P, Wysocki V, Foster MP. Population Distributions from Native Mass Spectrometry Titrations Reveal Nearest-Neighbor Cooperativity in the Ring-Shaped Oligomeric Protein TRAP. Biochem. 2020 June 19; 59(27):2518-2527. doi: 10.1021/acs.biochem.0c00352.

Ihms EC, Kleckner IR, Gollnick P, Foster MP. Mechanistic Models Fit to Variable Temperature Calorimetric Data Provide Insights into Cooperativity. Biophys J. 2017 Apr 11; 112(7):1328-1338. doi: 10.1016/j.bpj.2017.02.031.

Danhart EM, Bakhtina M, Cantara WA, Kuzmishin AB, Ma X, Sanford BL1,2, Vargas-Rodriguez O, Košutić, Goto Y, Suga H, Nakanishi K, Micura R, Foster MP, Musier-Forsyth K. Conformational and chemical selection by a trans-acting editing domain. Proc. Natl. Acad. Sci. USA. 2017 Aug 15; 114(33):E6774-E6783. doi: 10.1073/pnas.1703925114.

Crowe BL, Larue RC, Yuan C, Hess S, Kvaratskhelia M, Foster MP. Structure of the Brd4 ET domain bound to a C-terminal motif from γ-retroviral integrases reveals a conserved mechanism of interaction. PNAS. 2016; 113 (8):2086-91 10.1073/pnas.1516813113. (PDF) PMID: 26858406

Furman R, Danhart EM, NandyMazumdar M, Yuan C, Foster MP, Artsimovitch I. “pH Dependence of the Stress Regulator DksA” (2015) PLoS One 10 (3):e0120746. doi: 10.1371/journal.pone.0120746

Ihms EC, Foster MP. “MESMER: minimal ensemble solutions to multiple experimental restraints” (2015) Bioinformatics  2015 Jun 15;31(12):1951-8.  doi: 10.1093/bioinformatics/btv079 PMID: 863404

Ihms EC, Zhou M, Zhang Y, Kleckner IR, McElroy CA, Wysocki VH, Gollnick P, Foster MP. “Gene regulation by substoichiometric heterocomplex formation of undecameric TRAP and trimeric anti-TRAP” (2014) Proc Natl Acad Sci U S A 111 (9):3442-3447. doi: 10.1073/pnas.1315281111

Larue RC, Plumb MR, Crowe BL, Shkriabai N, Sharma A, Difiore J, Malani N, Aiyer SS, Roth MJ, Bushman FD, Foster MP, Kvaratskhelia M. “Bimodal high-affinity association of Brd4 with murine leukemia virus integrase and mononucleosomes” (2014) Nucleic Acids Res 42(8):4868-4881. doi: 10.1093/nar/gku135

Kleckner IR, McElroy CA, Kuzmic P, Gollnick P, Foster MP. “Homotropic cooperativity from the activation pathway of the allosteric ligand-responsive regulatory trp RNA-binding attenuation protein.” (2013) Biochemistry 52(49):8855-8865. doi: 10.1021/bi401364v

Eidahl JO, Crowe BL, North JA, McKee CJ, Shkriabai N, Feng L, Plumb M, Graham RL, Gorelick RJ, Hess S, Poirier MG, Foster MP, Kvaratskhelia M. “Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes.” (2013) Nucleic Acids Res. 41 (6):3924-36.  doi: 10.1093/nar/gkt074

Furman R, Biswas T, Danhart EM, Foster MP, Tsodikov OV, Artsimovitch I. “DksA2, a zinc-independent structural analog of the transcription factor DksA.”  (2013) FEBS Lett. 587 (6):614-9.  doi: 10.1016/j.febslet.2013.01.073

Larue R, Gupta K, Wuensch C, Shkriabai N, Kessl JJ, Danhart E, Feng L, Taltynov O, Christ F, Van Duyne GD, Debyser Z, Foster MP, Kvaratskhelia M. “Interaction of the HIV-1 intasome with Transportin 3 (TNPO3 or TRN-SR2).” (2012) J Biol Chem 287 (41):34044-58.  doi: 10.1074/jbc.M112.384669

Xu Y, Oruganti SV, Gopalan V, Foster MP. “Thermodynamics of Coupled Folding in the Interaction of Archaeal RNase P Proteins RPP21 and RPP29.” (2012) Biochemistry 51 (4):926–935. doi: 10.1021/bi201674d

Kleckner IR, Foster MP. “GUARDD: User-friendly MATLAB software for rigorous analysis of CPMG RD NMR data.” (2012) J Biomol NMR 52:11-22. doi: 10.1007/s10858-011-9589-y

Kleckner IR, Gollnick P, Foster MP. “Mechanisms of Allosteric Gene Regulation by NMR Quantification of μs-ms Protein Dynamics.” (2012) J Mol Biol 415(2): 372-381. doi: 10.1016/j.jmb.2011.11.019

Crowe BL, Bohlen CJ, Wilson RC, Gopalan V, Foster MP. “Assembly of the Complex between Archaeal RNase P Proteins RPP30 and Pop5.” (2011) Archaea 2011: Article ID 891531.doi:10.1155/2011/891531, (PDF)

Chen WY, Xu Y, Cho IM, Oruganti SV, Foster MP, Gopalan V. “Cooperative RNP assembly: complementary rescue of structural defects by protein and RNA subunits of archaeal RNase P.” (2011) J Mol Biol. 411(2):368-83.doi:10.1016/j.jmb.2011.05.012 (PubMed)

Wilson RC, Smith AM, Fuchs RT, Kleckner IR, Henkin TM, Foster MP. “Tuning Riboswitch Regulation through Conformational Selection.” (2011) J Mol Biol 405(4):926-38. doi:j.jmb.2010.10.056, (PDF)

Kleckner IR, Foster MP. “An Introduction to NMR-based Approaches for Measuring Protein Dynamics.” (2010) BBA – Proteins and Proteomics. Special Issue: Protein Dynamics.1841(8):942-968(http://dx.doi.org/10.1016/j.bbapap.2010.10.012), (PDF)

Sachleben JR, McElroy CA, Gollnick P, Foster MP. “Mechanism for pH-dependent gene regulation by amino-terminus-mediated homooligomerization of Bacillus subtilis anti-trp RNA-binding attenuation protein.” (2010) Proc Natl Acad Sci U S A 107(35):15385-90 doi: 10.1073/pnas.1004981107

Xu Y, Amero CD, Pulukkunat DK, Gopalan V, Foster MP. “Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions.” (2009) J Mol Biol. 393(5):1043-55. (PDF,http://dx.doi.org/10.1016/j.jmb.2009.08.068; PMC2782587)

Amero CD, Byerly DW, McElroy CA, Simmons A, Foster MP. “Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase.” (2009) Biochemistry. 48(32):7595-607. DOI: 10.1021/bi900600b (PDF, SI). Addendum.

Amero CD, Boomershine WP, Xu Y, Foster M. “Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner.” (2008) Biochemistry. 47(45):11704-10. DOI: 10.1021/bi8015982 (PDF, html)

Kamadurai HB, Jain R and Foster MP, “Crystallization and structure determination of the core-binding domain of bacteriophage lambda integrase.” (2008) Acta Crystallographica F, 64(6):470-473. (PDF, doi:10.1107/S174430910801381X)

Amero CD, Arnold JJ, Moustafa IM, Cameron CE, and Foster MP, “Identification of the oriI-binding site of poliovirus 3C protein by NMR spectroscopy.” (2008) J Virol, 82(9):4363-70, PMID: 18305026. (PubMed, doi:10.1128/JVI.02087-07, PDF)

Kamadurai HB, Foster MP, “DNA recognition via mutual-induced fit by the core-binding domain of bacteriophage lambda integrase.” (2007) Biochemistry, 46(49):13939-47. (PubMed, PDF) DOI: 10.1021/bi700974t

Subramaniam S, Kamadurai HB, Foster MP, “Trans Cooperativity by a Split DNA Recombinase: The Central and Catalytic Domains of Bacteriophage Lambda Integrase Cooperate in Cleaving DNA Substrates When the Two Domains Are not Covalently Linked.” (2007) J Mol Biol. 370(2):303 – 314. (PubMed, PDF) doi:10.1016/j.jmb.2007.04.024

Foster MP, McElroy CA, Amero CD, “Solution NMR of Large Molecules and Assemblies.” (2007) Biochemistry 46(2):331 – 340. (Pubmed, PDF)

McElroy CA, Manfredo A, Gollnick P, Foster MP, “Thermodynamics of tryptophan-mediated activation of the trp RNA-binding attenuation protein.” (2006) Biochemistry 45(25):7844-53. (Pubmed, PDF)

Wilson RC, Bohlen CJ, Foster MP, Bell CE, “Structure of Pfu Pop5, an archaeal RNase P protein.” (2006) Proc Natl Acad Sci U S A 103(4):873-8. (Pubmed, PDF)

Boomershine WP, McElroy CA, Tsai HY, Wilson RC, Gopalan V, Foster MP, “Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P.” (2003) Proc Natl Acad Sci U S A. 100(26), 15398-403. (Pubmed, PDF)

Subramaniam S, Tewari AK, Nunes-Duby SE, Foster MP, “Dynamics and DNA Substrate Recognition by the Catalytic Domain of Lambda Integrase.” (2003) J Mol Biol 329(3), 423-439. (Pubmed, PDF)

Kamadurai HB, Subramaniam S, Jones RB, Green-Church KB, Foster MP, “Protein folding coupled to DNA binding in the catalytic domain of bacteriophage lambda integrase detected by mass spectrometry.” (2003) Protein Science 12(3), 620-6.(PubMed, PDF)

McElroy C, Manfredo A, Wendt A, Gollnick P, Foster M. “TROSY-NMR of the 91 kDa TRAP Protein Reveals Allosteric Control of a Gene Regulatory Protein by Ligand-Altered Flexibility.” (2002) J. Mol. Biol. 323, 463-47. ( PubMed, PDF)