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Harnessing the Combined Power of SAXS and NMR.

Gronenborn AM.

Adv Exp Med Biol. 2018;1105:171-180. doi: 10.1007/978-981-13-2200-6_11.


An Insulin-Responsive Sensor in the SIRT1 Disordered Region Binds DBC1 and PACS-2 to Control Enzyme Activity.

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.

Mol Cell. 2018 Dec 20;72(6):985-998.e7. doi: 10.1016/j.molcel.2018.10.007. Epub 2018 Nov 8.


Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations.

Quinn CM, Wang M, Fritz MP, Runge B, Ahn J, Xu C, Perilla JR, Gronenborn AM, Polenova T.

Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):11519-11524. doi: 10.1073/pnas.1800796115. Epub 2018 Oct 17.


Fast Magic-Angle Spinning 19 F NMR Spectroscopy of HIV-1 Capsid Protein Assemblies.

Wang M, Lu M, Fritz MP, Quinn CM, Byeon IL, Byeon CH, Struppe J, Maas W, Gronenborn AM, Polenova T.

Angew Chem Int Ed Engl. 2018 Dec 10;57(50):16375-16379. doi: 10.1002/anie.201809060. Epub 2018 Oct 19.


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.

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.

J Phys Chem B. 2018 Jun 14;122(23):6148-6155. doi: 10.1021/acs.jpcb.8b00377. Epub 2018 May 30.


Backbone amide 15N chemical shift tensors report on hydrogen bonding interactions in proteins: A magic angle spinning NMR study.

Paramasivam S, Gronenborn AM, Polenova T.

Solid State Nucl Magn Reson. 2018 Aug;92:1-6. doi: 10.1016/j.ssnmr.2018.03.002. Epub 2018 Mar 15.


Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM.

Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LMI, Struppe J, Case DA, Polenova T, Gronenborn AM.

Phys Chem Chem Phys. 2018 Apr 4;20(14):9543-9553. doi: 10.1039/c8cp00647d.


Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

Kraus J, Gupta R, Yehl J, Lu M, Case DA, Gronenborn AM, Akke M, Polenova T.

J Phys Chem B. 2018 Mar 22;122(11):2931-2939. doi: 10.1021/acs.jpcb.8b00853. Epub 2018 Mar 13.


Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.

Debiec KT, Whitley MJ, Koharudin LMI, Chong LT, Gronenborn AM.

Biophys J. 2018 Feb 27;114(4):839-855. doi: 10.1016/j.bpj.2018.01.001.


Correction to: NMR structure of the HIV-1 reverse transcriptase thumb subdomain.

Sharaf NG, Brereton AE, Byeon IL, Karplus PA, Gronenborn AM.

J Biomol NMR. 2017 Dec;69(4):247. doi: 10.1007/s10858-017-0139-0.


Direct Observation of Carbohydrate Hydroxyl Protons in Hydrogen Bonds with a Protein.

Nestor G, Anderson T, Oscarson S, Gronenborn AM.

J Am Chem Soc. 2018 Jan 10;140(1):339-345. doi: 10.1021/jacs.7b10595. Epub 2017 Dec 22.


Quenching protein dynamics interferes with HIV capsid maturation.

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.

Nat Commun. 2017 Nov 24;8(1):1779. doi: 10.1038/s41467-017-01856-y.


The HIV-1 p66 homodimeric RT exhibits different conformations in the binding-competent and -incompetent NNRTI site.

Sharaf NG, Xi Z, Ishima R, Gronenborn AM.

Proteins. 2017 Dec;85(12):2191-2197. doi: 10.1002/prot.25383. Epub 2017 Sep 26.


Expanding the horizons for structural analysis of fully protonated protein assemblies by NMR spectroscopy at MAS frequencies above 100 kHz.

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.

Solid State Nucl Magn Reson. 2017 Oct;87:117-125. doi: 10.1016/j.ssnmr.2017.07.001. Epub 2017 Jul 3.


Cataract-associated P23T γD-crystallin retains a native-like fold in amorphous-looking aggregates formed at physiological pH.

Boatz JC, Whitley MJ, Li M, Gronenborn AM, van der Wel PCA.

Nat Commun. 2017 May 5;8:15137. doi: 10.1038/ncomms15137.


Exploiting Uniformly 13C-Labeled Carbohydrates for Probing Carbohydrate-Protein Interactions by NMR Spectroscopy.

Nestor G, Anderson T, Oscarson S, Gronenborn AM.

J Am Chem Soc. 2017 May 3;139(17):6210-6216. doi: 10.1021/jacs.7b01929. Epub 2017 Apr 21.


A Combined NMR and SAXS Analysis of the Partially Folded Cataract-Associated V75D γD-Crystallin.

Whitley MJ, Xi Z, Bartko JC, Jensen MR, Blackledge M, Gronenborn AM.

Biophys J. 2017 Mar 28;112(6):1135-1146. doi: 10.1016/j.bpj.2017.02.010.


Human βB2-Crystallin Forms a Face-en-Face Dimer in Solution: An Integrated NMR and SAXS Study.

Xi Z, Whitley MJ, Gronenborn AM.

Structure. 2017 Mar 7;25(3):496-505. doi: 10.1016/j.str.2017.02.001. Epub 2017 Feb 23.


CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.

Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P.

J Phys Chem B. 2017 Apr 20;121(15):3853-3863. doi: 10.1021/acs.jpcb.6b13105. Epub 2017 Feb 22.


Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline Lectin.

Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LMI, Polenova T, Gronenborn AM.

J Phys Chem B. 2017 Apr 20;121(15):3574-3585. doi: 10.1021/acs.jpcb.6b09479. Epub 2016 Dec 21.


NMR structure of the HIV-1 reverse transcriptase thumb subdomain.

Sharaf NG, Brereton AE, Byeon IL, Karplus PA, Gronenborn AM.

J Biomol NMR. 2016 Dec;66(4):273-280. doi: 10.1007/s10858-016-0077-2. Epub 2016 Nov 17. Erratum in: J Biomol NMR. 2017 Dec 12;:.


HIV-1 Capsid Function is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD.

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.

J Am Chem Soc. 2016 Oct 5. [Epub ahead of print]


The DDB1-DCAF1-Vpr-UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction.

Wu Y, Zhou X, Barnes CO, DeLucia M, Cohen AE, Gronenborn AM, Ahn J, Calero G.

Nat Struct Mol Biol. 2016 Oct;23(10):933-940. doi: 10.1038/nsmb.3284. Epub 2016 Aug 29.


Structure and Glycan Binding of a New Cyanovirin-N Homolog.

Matei E, Basu R, Furey W, Shi J, Calnan C, Aiken C, Gronenborn AM.

J Biol Chem. 2016 Sep 2;291(36):18967-76. doi: 10.1074/jbc.M116.740415. Epub 2016 Jul 7.


Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model.

Debiec KT, Cerutti DS, Baker LR, Gronenborn AM, Case DA, Chong LT.

J Chem Theory Comput. 2016 Aug 9;12(8):3926-47. doi: 10.1021/acs.jctc.6b00567. Epub 2016 Jul 22.


Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity.

Byeon IJ, Byeon CH, Wu T, Mitra M, Singer D, Levin JG, Gronenborn AM.

Biochemistry. 2016 May 31;55(21):2944-59. doi: 10.1021/acs.biochem.6b00382. Epub 2016 May 19.


Conformational Plasticity of the NNRTI-Binding Pocket in HIV-1 Reverse Transcriptase: A Fluorine Nuclear Magnetic Resonance Study.

Sharaf NG, Ishima R, Gronenborn AM.

Biochemistry. 2016 Jul 19;55(28):3864-73. doi: 10.1021/acs.biochem.6b00113. Epub 2016 Jul 11.


Transmission electron microscopy for the evaluation and optimization of crystal growth.

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.

Acta Crystallogr D Struct Biol. 2016 May;72(Pt 5):603-15. doi: 10.1107/S2059798316001546. Epub 2016 Apr 26.


Molecular Architecture of the Retroviral Capsid.

Perilla JR, Gronenborn AM.

Trends Biochem Sci. 2016 May;41(5):410-420. doi: 10.1016/j.tibs.2016.02.009. Epub 2016 Mar 30. Review.


Crystal structure and interaction studies of the human FBxo3 ApaG domain.

Krzysiak TC, Chen BB, Lear T, Mallampalli RK, Gronenborn AM.

FEBS J. 2016 Jun;283(11):2091-101. doi: 10.1111/febs.13721. Epub 2016 Apr 22.


Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site.

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.

Nat Commun. 2016 Mar 4;7:10714. doi: 10.1038/ncomms10714.


Dynamic Nuclear Polarization Enhanced MAS NMR Spectroscopy for Structural Analysis of HIV-1 Protein Assemblies.

Gupta R, Lu M, Hou G, Caporini MA, Rosay M, Maas W, Struppe J, Suiter C, Ahn J, Byeon IJ, Franks WT, Orwick-Rydmark M, Bertarello A, Oschkinat H, Lesage A, Pintacuda G, Gronenborn AM, Polenova T.

J Phys Chem B. 2016 Jan 21;120(2):329-39. doi: 10.1021/acs.jpcb.5b12134. Epub 2016 Jan 12.


(19)F-modified proteins and (19)F-containing ligands as tools in solution NMR studies of protein interactions.

Sharaf NG, Gronenborn AM.

Methods Enzymol. 2015;565:67-95. doi: 10.1016/bs.mie.2015.05.014. Epub 2015 Jun 16.


Dynamic allostery governs cyclophilin A-HIV capsid interplay.

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.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14617-22. doi: 10.1073/pnas.1516920112. Epub 2015 Nov 9.


(19)F Paramagnetic Relaxation Enhancement: A Valuable Tool for Distance Measurements in Proteins.

Matei E, Gronenborn AM.

Angew Chem Int Ed Engl. 2016 Jan 4;55(1):150-4. doi: 10.1002/anie.201508464. Epub 2015 Oct 29.


Structural Insight into Fungal Cell Wall Recognition by a CVNH Protein with a Single LysM Domain.

Koharudin LM, Debiec KT, Gronenborn AM.

Structure. 2015 Nov 3;23(11):2143-54. doi: 10.1016/j.str.2015.07.023. Epub 2015 Oct 9.


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.

Wu Y, Koharudin LM, Mehrens J, DeLucia M, Byeon CH, Byeon IJ, Calero G, Ahn J, Gronenborn AM.

J Biol Chem. 2015 Jul 17;290(29):17935-45. doi: 10.1074/jbc.M115.665513. Epub 2015 Jun 4.


Sampling of Glycan-Bound Conformers by the Anti-HIV Lectin Oscillatoria agardhii agglutinin in the Absence of Sugar.

Carneiro MG, Koharudin LM, Ban D, Sabo TM, Trigo-Mourino P, Mazur A, Griesinger C, Gronenborn AM, Lee D.

Angew Chem Int Ed Engl. 2015 May 26;54(22):6462-5. doi: 10.1002/anie.201500213. Epub 2015 Apr 14.


(1)H, (13)C and (15)N resonance assignment of the anti-HIV lectin from Oscillatoria agardhii.

Carneiro MG, Koharudin LM, Griesinger C, Gronenborn AM, Lee D.

Biomol NMR Assign. 2015 Oct;9(2):317-9. doi: 10.1007/s12104-015-9600-8. Epub 2015 Feb 14.


Sequence and structural determinants of human APOBEC3H deaminase and anti-HIV-1 activities.

Mitra M, Singer D, Mano Y, Hritz J, Nam G, Gorelick RJ, Byeon IJ, Gronenborn AM, Iwatani Y, Levin JG.

Retrovirology. 2015 Jan 22;12:3. doi: 10.1186/s12977-014-0130-8.


Dissection of binding between a phosphorylated tyrosine hydroxylase peptide and 14-3-3zeta: A complex story elucidated by NMR.

Hritz J, Byeon IJ, Krzysiak T, Martinez A, Sklenar V, Gronenborn AM.

Biophys J. 2014 Nov 4;107(9):2185-94. doi: 10.1016/j.bpj.2014.08.039.


Structural basis of allosteric activation of sterile α motif and histidine-aspartate domain-containing protein 1 (SAMHD1) by nucleoside triphosphates.

Koharudin LM, Wu Y, DeLucia M, Mehrens J, Gronenborn AM, Ahn J.

J Biol Chem. 2014 Nov 21;289(47):32617-27. doi: 10.1074/jbc.M114.591958. Epub 2014 Oct 6.


Antiviral lectins as potential HIV microbicides.

Koharudin LM, Gronenborn AM.

Curr Opin Virol. 2014 Aug;7:95-100. doi: 10.1016/j.coviro.2014.05.006. Epub 2014 Jul 8. Review.


Broad anti-HIV activity of the Oscillatoria agardhii agglutinin homologue lectin family.

Férir G, Huskens D, Noppen S, Koharudin LM, Gronenborn AM, Schols D.

J Antimicrob Chemother. 2014 Oct;69(10):2746-58. doi: 10.1093/jac/dku220. Epub 2014 Jun 25.


Weak protein complexes: challenging to study but essential for life.

Qin J, Gronenborn AM.

FEBS J. 2014 Apr;281(8):1948-9. Review. No abstract available.


The p66 immature precursor of HIV-1 reverse transcriptase.

Sharaf NG, Poliner E, Slack RL, Christen MT, Byeon IJ, Parniak MA, Gronenborn AM, Ishima R.

Proteins. 2014 Oct;82(10):2343-52. doi: 10.1002/prot.24594. Epub 2014 May 12.


Evaluating the strength of salt bridges: a comparison of current biomolecular force fields.

Debiec KT, Gronenborn AM, Chong LT.

J Phys Chem B. 2014 Jun 19;118(24):6561-9. doi: 10.1021/jp500958r. Epub 2014 Apr 17.


Magic angle spinning NMR reveals sequence-dependent structural plasticity, dynamics, and the spacer peptide 1 conformation in HIV-1 capsid protein assemblies.

Han Y, Hou G, Suiter CL, Ahn J, Byeon IJ, Lipton AS, Burton S, Hung I, Gor'kov PL, Gan Z, Brey W, Rice D, Gronenborn AM, Polenova T.

J Am Chem Soc. 2013 Nov 27;135(47):17793-803. doi: 10.1021/ja406907h. Epub 2013 Nov 13.

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