ANDO LAB at CORNELL

Understanding Enzymes to Understand Life

Understanding Enzymes to Understand Life

Publications

  1. RC Miller*, MG Patterson*, N Bhatt, X Pei, and N Ando. "Mechanism of nucleotide-dependent allosteric regulation in Escherichia coli aspartate transcarbamoylase." (2024) Pre-print on bioRXiv.
    2. *equal contributions
  2. D Xu, WC Thomas, AA Burnim, and N Ando. "Conformational landscapes of a class I ribonucleotide reductase complex during turnover reveal intrinsic dynamics and asymmetry." Nature Communications (2025), 16: 2458. [web] Pre-print on bioRXiv.
  3. SP Meisburger* and N Ando*. "Scaling and merging macromolecular diffuse scattering with mdx2." Acta D (2024), 80" 299-313. [web] Pre-print on bioRXiv. *co-corresponding
  4. D Xu and N Ando. "Miffi: Improved accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information." J Struct Bio (2024) 216: 108072. [web] Pre-print on bioRXiv.
  5. X Sun, J Alfermann, H Li, MB Watkins, Y-T Chen, TE Morrell, F Mayerthaler, C-Y Wang, T Komatsuzaki, J-W Chu, N Ando, HD Mootz, and H Yang. Subdomain dynamics enable chemical chain reactions in non-ribosomal peptide synthetases. Nature Chemistry (2024) 16: 259-268. [web]
  6. D Nam*, JP Bacik*, RL Khade*, MC Aguilera, Y Wei, ML Neidig**, Y Zhang**, N Ando**, R Fasan**. “Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone.” Nature Communications (2023), 14: 7985. [web] Pre-print on ResearchSquare. *equal contributions, **co-corresponding.
  7. SP Meisburger* and N Ando*. “Processing macromolecular diffuse scattering data” Methods in Enzymology (2023), 688: 43-86. [web] Pre-print on bioRXiv. *co-corresponding
  8. X Pei*, N Bhatt*, H Wang, N Ando**, SP Meisburger**. "Introduction to diffuse scattering and data collection" Methods in Enzymology (2023), 688: 1-42. [web]*equal contributions, **co-corresponding.
  9. G Illava, RE Gillilan*, N Ando*. “Development of in-line anoxic small-angle X-ray scattering and structural characterization of an oxygen-sensing transcriptional regulator.” JBC (2023), 299(8)105039. [Editor's Pick] Pre-print on bioRXiv. *co-corresponding
  10. MB Watkins, H Wang, AA Burnim, N Ando. “Conformational switching and flexibility in cobalamin-dependent methionine synthase studied by small-angle X-ray scattering and cryo-electron microscopy.” PNAS (2023) 120 (26) e2302531120. [web] Pre-print on bioRXiv. [Commentary on PNAS]
  11. SP Meisburger, DA Case N Ando. "Robust total X-ray scattering workflow to study correlated motion of proteins in crystals." Nature Communications (2023) 14: 1228. [web] Pre-print on bioRXiv
  12. AA Burnim*, D Xu*, MA Spence, C Jackson, N Ando. "Analysis of insertions and extensions in the functional evolution of the ribonucleotide reductase family" Protein Science (2022), 31:e4483. [web], Protein Evolution Special Issue in Honor of Dan Tawfik. [Journal Cover] *equal contributions.
  13. AS Byer, X Pei*, MG Patterson*, N Ando. "Small-angle X-ray scattering studies of enzymes." Curr Op Chem Bio (2023), 72:102232. [web] *equal contributions.
  14. R Miller, C Cummings, Q Huang, N Ando, RE Gillilan. "Inline SAXS-coupled chromatography under extreme hydrostatic pressure." Protein Science (2022), 31:e4489. [web] Pre-print on bioRXiv.
  15. AA Burnim*, MA Spence*, D Xu*, C Jackson**, N Ando**. "Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade" eLife (2022) 11:e79790. [web] [eLife Digest] [Cornell Chronicle] *equal contributions, **co-corresponding. Pre-print on bioRXiv.
  16. JA Iannuzzelli, J-P Bacik, EJ Moore, Z Shen, EM Irving, DA Vargas, SD Khare*, N Ando, R Fasan*. "Tuning enzyme thermostability via computationally guided covalent stapling and structural basis of enhanced stabilization." Biochemistry (2021) 61, 1041–1054. [web] *co-corresponding.
  17. D Xu*, SP Meisburger*, N Ando. "Correlated motions in structural biology." Biochemistry (2021) 60, 2331–2340. [web] *equal contributions.
  18. SP Meisburger*, D Xu*, N Ando. "REGALS: a general method to deconvolve X-ray scattering data from evolving mixtures." IUCrJ (2021) 8, 225-237. [web] *equal contributions. Pre-print on bioRXiv. Software on GitHub.
  19. EI Corless, SMS Imran*, MB Watkins*, J-P Bacik, JR Mattice, A Patterson, K Danyal, M Soffe, R Kitelinger, LC Seefeldt, S Origanti, B Bennett, B Bothner, N Ando**, E Antony**. "The flexible N-terminus of BchL autoinhibits activity through interaction with its [4Fe-4S] cluster and released upon ATP binding." J Mol. Biol. (2021) 296, 100107. [web] *equal contributions, **co-corresponding.
  20. N Ando, B Barquera, D Bartlett, E Boyd, AA Burnim, AS Byer, D Colman, RE Gillilan, M Gruebele, G Makhatadze, C Royer*, E Schock, AJ Wand, MB Watkins. "The molecular basis for life in extreme environments." Annual Review of Biophysics. (2020), 50, 343-372. [web]
  21. N Ando. "Thinking Outside of the Lattice." ACA RefleXions (2020) Spring Issue, p. 7-10. [web]
  22. SP Meisburger, DA Case, N Ando. "Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal." Nature Communications (2020) 11, Article number: 1271. [web] Pre-print on bioRXiv.Software on GitHub.
  23. WC Thomas, FP Brooks III, AA Burnim, JP Bacik, J Stubbe, JT Kaelber, JZ Chen, N Ando. "Convergent Allostery in Ribonucleotide Reductase." Nature Communications (2019), 10, Article number: 2653. [web] Pre-print on bioRXiv. [F1000 recommended]
  24. CA Khan, SP Meisburger, N Ando, and PF Fitzpatrick. "The phenylketonuria-associated substitution R68S converts phenylalanine hydroxylase to a constitutively active enzyme but reduces its stability." J Biol Chem (2019), 294: 4359-4367. [web]
  25. A Tinoco, Y Wei, DM Carminati, JP Bacik, EJ Moore, N Ando, Y Zhang, and R Fasan. "Origin of high stereocontrol in olefin cyclopropanation catalyzed by an engineered carbene transferase." ACS Catalysis (2019), 9: 1514–1524 [web]
  26. MJ Parker, AO Maggiolo*, WC Thomas*, A Kim, SP Meisburger, N Ando**, AK Boal**, and J Stubbe**. “An endogenous dAMP ligand in Bacillus subtilis class Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP”. PNAS (2018), 115: E4594-E4603. [web] *equal contributions, **co-corresponding
  27. S Shoemaker and N Ando. “X-rays in the cryo-electron microscopy era: Structural biology’s dynamic future”. Biochemistry (2018), 57: 277–285. [web]. (“Future of Biochemistry” special issue).
  28. KM Davis, KR Schramma, WA Hansen, JP Bacik, SD Khare, MR Seyedsayamdost, and N Ando. “Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition,” PNAS (2017), 114: 10420–10425 (2017). [web]
  29. SP Meisburger*, WC Thomas*, MB Watkins*, and N Ando. “X-ray scattering studies of protein structural dynamics,” Chemical Reviews (2017), 117: 7615-8480. *equal contributions [web] (invited) See also: Prologue by Susannah Shoemaker.
  30. SP Meisburger and N Ando. “Correlated motions from crystallography beyond diffraction,” Acc Chem Res (2017), 50: 580–583. [web] (invited commentary for “Holy Grails in Chemistry” special issue).
  31. JK Rustiguel, ROS Soares, SP Meisburger, KM Davis, KL Malzbender, N Ando, M Dias-Baruffi, and MC Nonato. “Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication.” Scientific Reports, 6: 33633 (2016). [web]
  32. SP Meisburger, AB Taylor, CA Khan, S Zhang, PF Fitzpatrick, and N Ando. “Domain movements upon activation of phenylalanine hydroxylase characterized by crystallography and chromatography-coupled small-angle X-ray scattering.” JACS (2016), 138: 6506–6516. [web]
  33. S Skou, RE Gillilan, N Ando. “Synchrotron-based small-angle X-ray scattering (SAXS) of biomacromolecules in solution.” Nature Protocols (2014), 9: 1727–1739. *corresponding. [web].

Publications (pre Ando Lab)

  1. N Ando*, H Li, EJ Brignole, S Thompson, MI McLaughlin, JE Page, FJ Asturias, J Stubbe, CL Drennan*. “Allosteric inhibition of human ribonucleotide reductase by dATP entails the stabilization of a hexamer.” Biochemistry (2016), 55: 373–381. *co-corresponding. [web].
  2. EC Minnihan, N Ando*, EJ Brignole*, L Olshansky*, J Chittuluru, FJ Asturias, CL Drennan, DG Nocera, J Stubbe. “Generation of a stable, aminotyrosyl radical-induced α2β2 complex of Escherichia coli class Ia ribonucleotide reductase,” PNAS (2013), 110: 3835-3840. [web].
  3. N Ando, Y Kung, M Can, G Bender, SW Ragsdale, CL Drennan. “Transient B12-dependent methyltransferase complexes revealed by small-angle X-ray scattering.” JACS (2012) 134: 17945–17954. [web]
  4. CM Zimanyi, N Ando, EJ Brignole, FJ Asturias, J Stubbe, CL Drennan. “Tangled up in knots: Structures of inactivated forms of E. coli class Ia ribonucelotide reductase.” Structure (2012) 20: 1374–1383. [web].
  5. S Wang, Y Meng, N Ando, MW Tate, S Krasnicki, C Yan, Q Liang, J Lai, H Mao, SM Gruner, RJ Hemley. “Single-crystal CVD diamonds as small-angle X-ray scattering windows for high-pressure research.” Journal of Applied Crystallography (2012) 45: 1–5. [web]
  6. Y Kung, N Ando, T Doukov, L Blasiak, G Bender, SW Ragsdale, CL Drennan. “Visualizing molecular juggling within a B12-dependent methyltransferase complex.” Nature (2012) 484: 265–269. [web].
  7. KD Bewley, MA Firer-Sherwood, J-Y Mock, N Ando, CL Drennan, SJ Elliott. “Mind the Gap: Diversity and reactivity relationships among multiheme cytochromes of the MtrA/DmsE family.” Biochemical Society Transactions (2012), 40: 1268–1273. [web].
  8. EJ Brignole*, N Ando, CM Zimanyi, CL Drennan. “The prototypic class Ia ribonucleotide reductase from Escherichia coli: Still surprising after all these years.” Biochemical Society Transactions (2012) 40: 523–530. *equal contributions [web]
  9. N Ando and B Barstow*. “High hydrostatic pressure effects on proteins: Fluorescence studies.” Encyclopedia of Analytical Chemistry, eds R.A. Meyers, John Wiley: Chichester. DOI: 10.1002/9780470027318.a9246. *co-corresponding, invited [web].
  10. N Ando*, EJ Brignole*, CM Zimanyi, MA Funk, K Yokoyama, FJ Asturias, J Stubbe, CL Drennan. “Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase.” PNAS (2011) 108: 21046–21051. *equal contributions [web].
  11. MA Firer-Sherwood*, N Ando*, SJ Elliott, CL Drennan. “Solution-based structural analysis of the decaheme cytochrome, MtrA, by small angle X-Ray scattering and analytical ultracentrifugation.” J. Phys. Chem. B (2011) 115: 11208–11214. *equal contributions [web]
  12. B Barstow, N Ando, CU Kim, SM Gruner. “Coupling of pressure-induced structural shifts to spectral changes in a Yellow Fluorescent Protein.” Biophysical Journal (2009) 97: 1719-1727. [web]
  13. N Ando, B Barstow, WA Baase, A Field, BW Matthews, Sol M. Gruner. “Structural and thermodynamic characterization of T4 lysozyme mutants and the contribution of internal cavities to pressure denaturation.” Biochemistry (2008) 47: 11097-11109. [web]
  14. B Barstow, N Ando, CU Kim, SM Gruner. “Alteration of Citrine structure by hydrostatic pressure explains accompanying spectral shift.” PNAS (2008) 105: 13362-13366. [web]
  15. N Ando, P Chenevier, M Novak, MW Tate, SM Gruner. “High hydrostatic pressure small-angle X-ray scattering cell for protein solution studies featuring diamond windows and disposable sample cells.” Journal of Applied Crystallography (2008) 41: 167-175. [web]
  16. A Batra, C Cohen; H Kim, KI Winey; N Ando, SM Gruner. “Counterion effect on the rheology and morphology of tailored poly(dimethylsiloxane) ionomers.” Macromolecules (2006) 39: 1630-1638. [web]
  1. A Polozova, X Lia, T Shangguana, P Meersa, DR Schuette, N Ando, SM Gruner, WR Perkins. “Formation of homogeneous unilamellar liposomes from an interdigitated matrix.” Biochimica et Biophysica Acta (2005) 1668: 117–125. [web]
  2. K Ito, J Chuang, C Alvarez-Lorenzo, T Watanabe, N Ando, AY Grosberg. “Multiple contact adsorption of target molecules by heteropolymer gels.” Macromolecular Symposia (2004) 207: 1. [web]
  3. K Ito, J Chuang, C Alvarez-Lorenzo, T Watanabe, N Ando, AY Grosberg. “Multiple point adsorption in a heteropolymer gel and the Tanaka approach to imprinting: experiment and theory.” Progress in Polymer Science (2003) 28: 1489-1515. [web]