Publications

Angela Gronenborn

Guseman AJ, Gronenborn AM. Isomerization as the secret Achilles' heel of long-lived proteins. J Biol Chem. 2019 May 10;294(19):7556-7557. doi: 10.1074/jbc.H119.008716. PubMed PMID: 31076522; PMCID: PMC6514620.
Lu M, Wang M, Sergeyev IV, Quinn CM, Struppe J, Rosay M, Maas W, Gronenborn AM, Polenova T. 19F Dynamic Nuclear Polarization at Fast Magic Angle Spinning for NMR of HIV-1 Capsid Protein Assemblies. J Am Chem Soc. 2019 Apr 10;141(14):5681-5691. doi: 10.1021/jacs.8b09216. PubMed PMID: 30871317; PMCID: PMC6521953.
Russell RW, Fritz MP, Kraus J, Quinn CM, Polenova T, Gronenborn AM. Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some 'with a little help from a friend'. J Biomol NMR. 2019 Jul;73(6-7):333-346. doi: 10.1007/s10858-019-00233-9. PubMed PMID: 30847635; PMCID: PMC6693955.
Krzysiak TC, Thomas L, Choi YJ, Auclair S, Qian Y, Luan S, Krasnow SM, Thomas LL, Koharudin LMI, Benos PV, Marks DL, Gronenborn AM, Thomas G. An Insulin-Responsive Sensor in the SIRT1 Disordered Region Binds DBC1 and PACS-2 to Control Enzyme Activity. Mol Cell. 2018 Dec 20;72(6):985-998.e7. doi: 10.1016/j.molcel.2018.10.007. PubMed PMID: 30415949; PMCID: PMC6309500.
Quinn CM, Wang M, Fritz MP, Runge B, Ahn J, Xu C, Perilla JR, Gronenborn AM, Polenova T. Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations. Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):11519-11524. doi: 10.1073/pnas.1800796115. PubMed PMID: 30333189; PMCID: PMC6233135.
Wang M, Lu M, Fritz MP, Quinn CM, Byeon IL, Byeon CH, Struppe J, Maas W, Gronenborn AM, Polenova T. Fast Magic-Angle Spinning 19 F NMR Spectroscopy of HIV-1 Capsid Protein Assemblies. Angew Chem Int Ed Engl. 2018 Dec 10;57(50):16375-16379. doi: 10.1002/anie.201809060. PubMed PMID: 30225969; PMCID: PMC6279522.
Lu M, Sarkar S, Wang M, Kraus J, Fritz M, Quinn CM, Bai S, Holmes ST, Dybowski C, Yap GPA, Struppe J, Sergeyev IV, Maas W, Gronenborn AM, Polenova T. 19F Magic Angle Spinning NMR Spectroscopy and Density Functional Theory Calculations of Fluorosubstituted Tryptophans: Integrating Experiment and Theory for Accurate Determination of Chemical Shift Tensors. J Phys Chem B. 2018 Jun 14;122(23):6148-6155. doi: 10.1021/acs.jpcb.8b00377. PubMed PMID: 29756776; PMCID: PMC6203958.
Paramasivam S, Gronenborn AM, Polenova T. Backbone amide 15N chemical shift tensors report on hydrogen bonding interactions in proteins: A magic angle spinning NMR study. Solid State Nucl Magn Reson. 2018 Aug;921-6. doi: 10.1016/j.ssnmr.2018.03.002. PubMed PMID: 29579703; PMCID: PMC6261280.
Kraus J, Gupta R, Yehl J, Lu M, Case DA, Gronenborn AM, Akke M, Polenova T. Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations. J Phys Chem B. 2018 Mar 22;122(11):2931-2939. doi: 10.1021/acs.jpcb.8b00853. PubMed PMID: 29498857; PMCID: PMC5892201.
Debiec KT, Whitley MJ, Koharudin LMI, Chong LT, Gronenborn AM. Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein. Biophys J. 2018 Feb 27;114(4):839-855. doi: 10.1016/j.bpj.2018.01.001. PubMed PMID: 29490245; PMCID: PMC5985006.
Sharaf NG, Brereton AE, Byeon IL, Karplus PA, Gronenborn AM. Correction to: NMR structure of the HIV-1 reverse transcriptase thumb subdomain. J Biomol NMR. 2017 Dec;69(4):247. doi: 10.1007/s10858-017-0139-0. PubMed PMID: 29234947.
Nestor G, Anderson T, Oscarson S, Gronenborn AM. Direct Observation of Carbohydrate Hydroxyl Protons in Hydrogen Bonds with a Protein. J Am Chem Soc. 2018 Jan 10;140(1):339-345. doi: 10.1021/jacs.7b10595. PubMed PMID: 29227646.
Wang M, Quinn CM, Perilla JR, Zhang H, Shirra R Jr, Hou G, Byeon IJ, Suiter CL, Ablan S, Urano E, Nitz TJ, Aiken C, Freed EO, Zhang P, Schulten K, Gronenborn AM, Polenova T. Quenching protein dynamics interferes with HIV capsid maturation. Nat Commun. 2017 Nov 24;8(1):1779. doi: 10.1038/s41467-017-01856-y. PubMed PMID: 29176596; PMCID: PMC5701193.
Sharaf NG, Xi Z, Ishima R, Gronenborn AM. The HIV-1 p66 homodimeric RT exhibits different conformations in the binding-competent and -incompetent NNRTI site. Proteins. 2017 Dec;85(12):2191-2197. doi: 10.1002/prot.25383. PubMed PMID: 28905420; PMCID: PMC5751703.
Struppe J, Quinn CM, Lu M, Wang M, Hou G, Lu X, Kraus J, Andreas LB, Stanek J, Lalli D, Lesage A, Pintacuda G, Maas W, Gronenborn AM, Polenova T. Expanding the horizons for structural analysis of fully protonated protein assemblies by NMR spectroscopy at MAS frequencies above 100 kHz. Solid State Nucl Magn Reson. 2017 Oct;87117-125. doi: 10.1016/j.ssnmr.2017.07.001. PubMed PMID: 28732673; PMCID: PMC5824719.
Nestor G, Anderson T, Oscarson S, Gronenborn AM. Exploiting Uniformly 13C-Labeled Carbohydrates for Probing Carbohydrate-Protein Interactions by NMR Spectroscopy. J Am Chem Soc. 2017 May 3;139(17):6210-6216. doi: 10.1021/jacs.7b01929. PubMed PMID: 28406013; PMCID: PMC5725960.
Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P. CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. J Phys Chem B. 2017 Apr 20;121(15):3853-3863. doi: 10.1021/acs.jpcb.6b13105. PubMed PMID: 28181439; PMCID: PMC5459578.
Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LMI, Polenova T, Gronenborn AM. Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline Lectin. J Phys Chem B. 2017 Apr 20;121(15):3574-3585. doi: 10.1021/acs.jpcb.6b09479. PubMed PMID: 28001418; PMCID: PMC5465307.
Sharaf NG, Brereton AE, Byeon IL, Karplus PA, Gronenborn AM. NMR structure of the HIV-1 reverse transcriptase thumb subdomain. J Biomol NMR. 2016 Dec;66(4):273-280. doi: 10.1007/s10858-016-0077-2. PubMed PMID: 27858311; PMCID: PMC5218889.
Zhang H, Hou G, Lu M, Ahn J, Byeon IL, Langmead CJ, Perilla JR, Hung I, Gor'kov PL, Gan Z, Brey WW, Case DA, Schulten K, Gronenborn AM, Polenova T. HIV-1 Capsid Function Is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD. J Am Chem Soc. 2016 Oct 26;138(42):14066-14075. doi: 10.1021/jacs.6b08744. PubMed PMID: 27701859; PMCID: PMC5380593.
Wu Y, Zhou X, Barnes CO, DeLucia M, Cohen AE, Gronenborn AM, Ahn J, Calero G. The DDB1-DCAF1-Vpr-UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction. Nat Struct Mol Biol. 2016 Oct;23(10):933-940. doi: 10.1038/nsmb.3284. PubMed PMID: 27571178; PMCID: PMC5385928.
Matei E, Basu R, Furey W, Shi J, Calnan C, Aiken C, Gronenborn AM. Structure and Glycan Binding of a New Cyanovirin-N Homolog. J Biol Chem. 2016 Sep 2;291(36):18967-76. doi: 10.1074/jbc.M116.740415. PubMed PMID: 27402833; PMCID: PMC5009269.
Debiec KT, Cerutti DS, Baker LR, Gronenborn AM, Case DA, Chong LT. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model. J Chem Theory Comput. 2016 Aug 9;12(8):3926-47. doi: 10.1021/acs.jctc.6b00567. PubMed PMID: 27399642; PMCID: PMC4980686.
Sharaf NG, Ishima R, Gronenborn AM. Conformational Plasticity of the NNRTI-Binding Pocket in HIV-1 Reverse Transcriptase: A Fluorine Nuclear Magnetic Resonance Study. Biochemistry. 2016 Jul 19;55(28):3864-73. doi: 10.1021/acs.biochem.6b00113. PubMed PMID: 27163463; PMCID: PMC4955860.
Stevenson HP, Lin G, Barnes CO, Sutkeviciute I, Krzysiak T, Weiss SC, Reynolds S, Wu Y, Nagarajan V, Makhov AM, Lawrence R, Lamm E, Clark L, Gardella TJ, Hogue BG, Ogata CM, Ahn J, Gronenborn AM, Conway JF, Vilardaga JP, Cohen AE, Calero G. Transmission electron microscopy for the evaluation and optimization of crystal growth. Acta Crystallogr D Struct Biol. 2016 May;72(Pt 5):603-15. doi: 10.1107/S2059798316001546. PubMed PMID: 27139624; PMCID: PMC4854312.
Perilla JR, Gronenborn AM. Molecular Architecture of the Retroviral Capsid. Trends Biochem Sci. 2016 May;41(5):410-420. doi: 10.1016/j.tibs.2016.02.009. PubMed PMID: 27039020; PMCID: PMC4879823.
Krzysiak TC, Chen BB, Lear T, Mallampalli RK, Gronenborn AM. Crystal structure and interaction studies of the human FBxo3 ApaG domain. FEBS J. 2016 Jun;283(11):2091-101. doi: 10.1111/febs.13721. PubMed PMID: 27010866; PMCID: PMC5065005.
Liu C, Perilla JR, Ning J, Lu M, Hou G, Ramalho R, Himes BA, Zhao G, Bedwell GJ, Byeon IJ, Ahn J, Gronenborn AM, Prevelige PE, Rousso I, Aiken C, Polenova T, Schulten K, Zhang P. Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site. Nat Commun. 2016 Mar 4;710714. doi: 10.1038/ncomms10714. PubMed PMID: 26940118; PMCID: PMC4785225.
Liu X, Hillwig ML, Koharudin LM, Gronenborn AM. Unified biogenesis of ambiguine, fischerindole, hapalindole and welwitindolinone: identification of a monogeranylated indolenine as a cryptic common biosynthetic intermediate by an unusual magnesium-dependent aromatic prenyltransferase. Chem Commun (Camb). 2016 Jan 28;52(8):1737-40. doi: 10.1039/c5cc10060g. PubMed PMID: 26740122; PMCID: PMC4720564.
Sharaf NG, Gronenborn AM. (19)F-modified proteins and (19)F-containing ligands as tools in solution NMR studies of protein interactions. Methods Enzymol. 2015;56567-95. doi: 10.1016/bs.mie.2015.05.014. PubMed PMID: 26577728.
Lu M, Hou G, Zhang H, Suiter CL, Ahn J, Byeon IJ, Perilla JR, Langmead CJ, Hung I, Gor'kov PL, Gan Z, Brey W, Aiken C, Zhang P, Schulten K, Gronenborn AM, Polenova T. Dynamic allostery governs cyclophilin A-HIV capsid interplay. Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14617-22. doi: 10.1073/pnas.1516920112. PubMed PMID: 26553990; PMCID: PMC4664340.
Matei E, Gronenborn AM. (19)F Paramagnetic Relaxation Enhancement: A Valuable Tool for Distance Measurements in Proteins. Angew Chem Int Ed Engl. 2016 Jan 4;55(1):150-4. doi: 10.1002/anie.201508464. PubMed PMID: 26510989; PMCID: PMC4715678.
Wu Y, Koharudin LM, Mehrens J, DeLucia M, Byeon CH, Byeon IJ, Calero G, Ahn J, Gronenborn AM. Structural Basis of Clade-specific Engagement of SAMHD1 (Sterile α Motif and Histidine/Aspartate-containing Protein 1) Restriction Factors by Lentiviral Viral Protein X (Vpx) Virulence Factors. J Biol Chem. 2015 Jul 17;290(29):17935-45. doi: 10.1074/jbc.M115.665513. PubMed PMID: 26045556; PMCID: PMC4505041.
Carneiro MG, Koharudin LM, Ban D, Sabo TM, Trigo-Mourino P, Mazur A, Griesinger C, Gronenborn AM, Lee D. Sampling of Glycan-Bound Conformers by the Anti-HIV Lectin Oscillatoria agardhii agglutinin in the Absence of Sugar. Angew Chem Int Ed Engl. 2015 May 26;54(22):6462-5. doi: 10.1002/anie.201500213. PubMed PMID: 25873445; PMCID: PMC4480366.
Carneiro MG, Koharudin LM, Griesinger C, Gronenborn AM, Lee D. (1)H, (13)C and (15)N resonance assignment of the anti-HIV lectin from Oscillatoria agardhii. Biomol NMR Assign. 2015 Oct;9(2):317-9. doi: 10.1007/s12104-015-9600-8. PubMed PMID: 25680849; PMCID: PMC4537409.
Koharudin LM, Wu Y, DeLucia M, Mehrens J, Gronenborn AM, Ahn J. Structural basis of allosteric activation of sterile α motif and histidine-aspartate domain-containing protein 1 (SAMHD1) by nucleoside triphosphates. J Biol Chem. 2014 Nov 21;289(47):32617-27. doi: 10.1074/jbc.M114.591958. PubMed PMID: 25288794; PMCID: PMC4239615.
Sharaf NG, Poliner E, Slack RL, Christen MT, Byeon IJ, Parniak MA, Gronenborn AM, Ishima R. The p66 immature precursor of HIV-1 reverse transcriptase. Proteins. 2014 Oct;82(10):2343-52. doi: 10.1002/prot.24594. PubMed PMID: 24771554; PMCID: PMC4441793.
Debiec KT, Gronenborn AM, Chong LT. Evaluating the strength of salt bridges: a comparison of current biomolecular force fields. J Phys Chem B. 2014 Jun 19;118(24):6561-9. doi: 10.1021/jp500958r. PubMed PMID: 24702709; PMCID: PMC4064690.

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