Publications Citing the Crystallization Center

2016 – 2022

Word cloud generated from publication titles of Crystallization Center users 2017-2022 (updated June 2022).

• Abrahams, GJ, Newman, J. BLASTing away preconceptions in crystallization trials.  Acta Crystallographica Section F: Structural Biology Communications. 2019; 75.
• Andreo-Vidal, A, Mamounis, KJ, Sehanobish, E, Avalos, D, Campillo-Brocal, JC, Sanchez-Amat, A, Yukl, ET, Davidson, VL. Structure and enzymatic properties of an unusual cysteine tryptophylquinone-dependent glycine oxidase from Pseudoalteromonas luteoviolacea.  Biochemistry. 2018; 57, 1155.
• Bailey DC, Alexander E, Rice MR, Drake EJ, Mydy LS, Aldrich CC, Gulick AM. Structural and functional delineation of aerobactin biosynthesis in hypervirulent Klebsiella pneumoniae.  Journal of Biological Chemistry. 2018; 293, 7841.
• Bailey DC, Drake EJ, Grant TD, Gulick AM. Structural and functional characterization of aerobactin synthetase IucA from a hypervirulent pathotype of Klebsiella pneumoniae. Biochemistry. 2016 Jun 28;55(25):3559-70.
• Barnier, JP, Meyer, J, Kolappan, S, Bouzinba-Ségard, H, Gesbert, G, Jamet, A, Frapy, E, Schönherr-Hellec, S, Capel, E, Virion, Z, Dupuis, M, Bille, E, Morand, P, Schmitt, T, Bourdoulous, S, Nassif, X, Craig, L, Coureuil, M. The minor pilin PilV provides a conserved adhesion site throughout the antigenically variable meningococcal type IV pilus. Proceedings of the National Academy of Sciences. 2021,118 (45) e2109364118.
• Bonneté F, Loll PJ. Characterization of New Detergents and Detergent Mimetics by Scattering Techniques for Membrane Protein Crystallization.  In Membrane Protein Structure and Function Characterization 2017 (pp. 169-193). Humana Press, New York, NY.
• Brambley, CA, Bolay, AL, Salvo, H, Jansch, AL, Yared, TJ, Miller, JM, Wallen, JR, Weiland, MH. Structural Characterization of Sphingomonas sp. KT-1 PahZ1-Catalyzed Biodegradation of Thermally Synthesized Poly(aspartic acid). ACS Sustainable Chem Eng. 2020, 8, 29.
• Brambley, CA, Yared, TJ, Gonzalez, M, Jansch, AL, Wallen, JR, Weiland, MH, Miller, JM. Sphingomonas sp. KT-1 PahZ2 Structure Reveals a Role for Conformational Dynamics in Peptide Bond Hydolysis. Journal of Physical Chemistry B. 2021; 125, 5722.
• Bremer PT, Pellett S, Carolan JP, Tepp WH, Eubanks LM, Allen KN, Johnson EA, Janda KD. Metal ions effectively ablate the action of botulinum neurotoxin A.  Journal of the American Chemical Society. 2017; 139, 7264.
• Bruno AE, Charbonneau P, Newman J, Snell EH, So DR, Vanhoucke V, Watkins CJ, Williams S, Wilson J. Classification of crystallization outcomes using deep convolutional neural networks.  PLOS One. 2018; 13, e0198883.
• Bruno AE, Soares AS, Owen RL, Snell EH. The use of haptic interfaces and web services in crystallography: an application for a ‘screen to beam’ interface. Journal of applied crystallography. 2016; 49, 2082.
• Clyde A, Galanie S, Kneller DW, Ma H, Babuji Y, Blaiszik B, Brace A, Brettin T, Chard K, Chard R, Coates L. High Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Non-Covalent Inhibitor. Journal of Chemical Information and Modeling. 2022, 62,1, 116-128.
• Costa DM, Gómez SV, de Araújo SS, Pereira MS, Alves RB, Favaro DC, Hengge AC, Nagem RA, Brandão TA. Catalytic mechanism for the conversion of salicylate into catechol by the flavin-dependent monooxygenase salicylate hydroxylase. International journal of biological macromolecules. 2019; 129, 588.
• Drake EJ, Miller BR, Shi C, Tarrasch JT, Sundlov JA, Allen CL, Skiniotis G, Aldrich CC, Gulick AM. Structures of two distinct conformations of holo-non-ribosomal peptide synthetases. Nature. 2016; 529, 235.
• Everett JK, Tejero R, Murthy SB, Acton TB, Aramini JM, Baran MC, Benach J, Cort JR, Eletsky A, Forouhar F, Guan R. A community resource of experimental data for NMR/X‐ray crystal structure pairs. Protein Science. 2016; 25, 30.
• Glaser J, Sedova A, Galanie S, Kneller DW, Davidson RB, Maradzike E, Del Galdo S, Labbé A, Hsu DJ, Agarwal R, Bykov D, Tharrington, A, Parks, JM, Smith, SMA, Daidone, I, Coates, L, Kovalevsky, A, Smith, JC. Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor. ACS Pharmacology & Translational Science. 2022, 5, 4, 255.
• González-Ramírez LA, Ruiz-Martínez CR, Estremera-Andújar RA, Nieves-Marrero CA, García-Caballero A, Gavira JA, López-Garriga J, García-Ruiz JM. Efficient Screening Methodology for Protein Crystallization Based on the Counter-Diffusion Technique.  Crystal Growth & Design. 2017; 17, 6780-6.
• Gorrec F, Löwe J. Automated Protocols for Macromolecular Crystallization at the MRC Laboratory of Molecular Biology. JoVE (Journal of Visualized Experiments). 2018; e55790.
• Guan R, Aiyer S, Cote ML, Xiao R, Jiang M, Acton TB, Roth MJ, Montelione GT.  X‐ray crystal structure of the N‐terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition. Proteins: Structure, Function, and Bioinformatics. 2017; 85, 647.
• Hall, D, Giaimo, BD, Park S, Hemmer, W, Friedrich, T, Ferrante, F, Bartkuhn, M, Yuan, Z, Oswald, F, Borggrefe, T, Rual, J, Koval, RA. The structure, binding and function of a Notch transcription complex involving RBPJ and the epigenetic reader protein L3MBTL3. bioRxiv. 2022. https://doi.org/10.1101/2022.02.09.479311.
• Holleman, ET, Duguid, E, Keefe, LK, Bowman, SEJ. Polo: an open-source graphical user interface for crystallization screening. J. Appl. Crystallogr. 2021; 54, 673-679
• Hou H, Shi M, Hu SY, Ahmad F, Zhang B, Chen ZH, Yin DC. A systematic comparison of sitting and hanging-drop crystallization using traditional and cross-diffusion microbatch crystallization plates.   Journal of Crystal Growth. 2019; 521, 1.
• Iketani, S, Forouhar, F, Liu, H, Hong, SJ, Lin, F-Y, Nair, MS, Zask, A, Huang, Y, Xing, L, Stockwell, BR, Chavez, A, Ho, DD. Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nature communications. 2021; 12.
• Kgosisejo O, Chen JA, Grochulski P, Tanaka T. Crystallographic structure of recombinant Lactococcus lactis prolidase to support proposed structure-function relationships.  Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics. 2017; 1865, 473.
• Kneller, DW, Phillips, G, O’Neill, HM, Jedrzejczak, R, Stols, L, Langan, P, Joachimiak, A, Coates, L, Kovalevsky, A. Structural Plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography. Nature Communications. 2020; 11, 3202.
• Kneller, DW, Phillips, G, Kovalevsky, A, Coates, L. Room-temperature neutron and X-ray data collection of 3CL Mpro from SARS-CoV-2. Acta Cryst. 2020; F76, 483.
• Kneller, DW, Phillips, G, Weiss, KL, Pant, S, Zhang, Q, O’Neill, HM, Coates, L, Kovalevsky, A. Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography. Journal of Biological Chemistry. 2020; 295, 17365.
  
• Kneller, DW, Phillips, G, Weiss, KL, Zhang, Q, Coates, L, Kovalevsky, A. Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography. Journal of Medicinal Chemistry. 2021; 64, 4991.
• Kneller, D, Hui, L, Phillips, G, Weiss, K, Zhang Q, Amould, M, Jonsson, C, Surendranathan, S, Parvathareddy, J, Blakely, M, Coates, L, Lous, J, Bonnesen, P, Kovalevsky, A. Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease. Nature Communications. 2022; 13, 2268.
• Kneller DW, Li H, Galanie S, Phillips G, Labbé A, Weiss KL, Zhang Q, Arnould MA, Clyde A, Ma H, Ramanathan A, Jonsson, CB, Head, MS, Coates, L, Louis, JM, Bonnesen, PV, Kovalevsky. Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease. Journal of Medicinal Chemistry. 2021; 64, 23, 17366.
• Kneller, DW, Zhang, Q, Coates, L, Louis, JM & Kovalevsky, A. Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. IUCrJ. 2021; 8, 973.
• Kolappan S, Coureuil M, Yu X, Nassif X, Egelman EH, Craig L. Structure of the Neisseria meningitidis Type IV pilus. Nature communications. 2016; 7, 1.
• Krishnan, N, Bonham, CA, Rus, IA, Shrestha, OK, Gauss, CM, Haque, A, Tocilj, A, Joshua-Tor, L, Tonks, NK.  Harnessing insulin-and leptin-induced oxidation of PTP1B for therapeutic development. Nature Communications. 2018; 9, 283.
• Lattman EE, Grant TD, Snell EH. Biological Small Angle Scattering: Theory and Practice. Oxford University Press; 2018.
• Liu, H, Forouhar, F, Seibt, T, Saneto, R, Wigby, K, Friedman, J, Xia, X, Shchepinov, M, Ramesh SK, Conrad, M, Stockwell, BR. Characterization of a patient-derived variant of GPX4 for precision therapy. Nature Chemical Biology. 2022; 18, 91.
• Liu, H, Iketani, S, Zask, A, Khanizeman, N, Bednarova, E, Forouhar, F, Fowler, B, Hong, SJ, Mohri, H, Nair, MS, Huang, Y, Tay, NES, Lee, S, Karan, C, Resnick, SJ, Quinn, C, Li, W, Shion, H, Xia, X, Daniels JD, Bartolo-Cruz, M, Farina, M, Rajbhandari, P, Jurtschenko, C, Lauber, MA, McDonald, T, Stokes, ME, Hurst, BL, Rovis, T, Chavez, A, Ho, DD, Stockwell, BR. Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19. Nature Communications. 2022; 13, 1891.
• Lynch ML, Dudek MF, Bowman SEJ. A Searchable Database of Crystallization Cocktails in the PDB: Analyzing the Chemical Condition Space.  Patterns. 2020; 1(4), 10024.
• Lynch, ML, Snell, EH, Bowman, SEJ. Structural biology in the time of COVID-19: perspectives on methods and milestones. IUCrJ. 2021; 8, 3, 335-341.
• Ma LC, Guan R, Hamilton K, Aramini JM, Mao L, Wang S, Krug RM, Montelione GT. A second RNA-binding site in the NS1 protein of influenza B virus. Structure. 2016; 24, 1562.
• Marcos E, Basanta B, Chidyausiku TM, Tang Y, Oberdorfer G, Liu G, Swapna GV, Guan R, Silva DA, Dou J, Pereira JH, Xiao, R, Sankaran, B, Zwart, PH, Montelione, GT, Baker, D. Principles for designing proteins with cavities formed by β curved sheets.  Science. 2017; 355, 201.
• Mayer C. X-Ray Diffraction in Biology: How Can We See DNA and Proteins in Three Dimensions? X-ray Scattering. 2017, 207.
• McPherson A. Protein crystallization. In Protein Crystallography. Humana Press, New York, NY; 2017, 17-50.
• Meng, Q, Moinuddin, SGA, Kim, S-J, Bedgar, DL, Costa, MA, Thomas, DG, Young, RP, Smith, CLA, Cort, JR, Davin, LB, Lewis, NG. Pterocarpan synthase (PTS) structures suggest a common quinone methid-stabilizing function in dirigent proteins and proteins with dirigent-like domains. Journal of Biological Chemistry. 2020; 295, 11584.
• Miller BR, Drake EJ, Shi C, Aldrich CC, Gulick AM. Structures of a nonribosomal peptide synthetase module bound to MbtH-like proteins support a highly dynamic domain architecture. Journal of Biological Chemistry. 2016; 291, 22559.
• Morales-Perez CL, Noviello CM, Hibbs RE. Manipulation of subunit stoichiometry in heteromeric membrane proteins. Structure. 2016; 24, 797.
• Moremen KW, Ramiah A, Stuart M, Steel J, Meng L, Forouhar F, Moniz HA, Gahlay G, Gao Z, Chapla D, Wang S, Yang, J-Y, Prabhakar, PK, Johnson, R, dela Rosa, M, Geisler, C, Nairn, A, Seetharaman, J, Wu, S-C, Tong, L, Gilbert, HJ, LaBaer, J, Jarvis, DL. Expression system for structural and functional studies of human glycosylation enzymes. Nature Chemical Biology. 2018; 14, 156.
• Mydy, LS, Cristobal, JR, Katigbak, RD, Bauer, P, Reyes, AC, Kamerlin, SCL, Richard, JP, Gulick, AM. Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies. 2019; 58, 1061.
• Neupane DP, Fullam SH, Chacón KN, Yukl ET. Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins.  Communications biology. 2019; 2, 1.
• Qin W, Xie SX, Zhang J, Zhao D, He CX, Li HJ, Xing L, Li PQ, Jin X, Yin DC, Cao HL. An Analysis on Commercial Screening Kits and Chemical Components in Biomacromolecular Crystallization Screening.  Crystal Research and Technology. 2019.
• Orlando BJ, Malkowski MG. Substrate-selective inhibition of cyclooxygeanse-2 by fenamic acid derivatives is dependent on peroxide tone. Journal of Biological Chemistry. 2016; 291, 15069.
• Orlando BJ, Malkowski MG. Crystal structure of rofecoxib bound to human cyclooxygenase-2. Acta Crystallographica Section F: Structural Biology Communications. 2016; 72, 772.
• Paddock C, Zhou D, Lertkiatmongkol P, Newman PJ, Zhu J. Structural basis for PECAM-1 homophilic binding. Blood. 2016; 127, 1052.
• Piserchio, A, Isiorho, EA, Long, K, Bohanon, AL, Kumar, EA, Will, N, Jeruzalmi, D, Dalby, KN, Ghose, R. Structural basis for the calmodulin-mediated activation of eEF-2K. bioRxiv. 2022. https://doi.org/10.1101/2022.01.15.476372
• Primi MC, Rangarajan ES, Patil DN, Izard T. Conformational flexibility determines the Nf2/merlin tumor suppressor functions. Matrix Biology Plus. 2021; 100074.
• Pusey ML, Aygün RS. Introduction to Protein Crystallization.  In Data Analytics for Protein Crystallization. Springer, Cham; 2017, 1-20.
• Pusey ML, Aygün RS.  Visualization. In Data Analytics for Protein Crystallization. Springer, Cham; 2017, 199-210.
• Rohner M, Medina-Molner A, Spingler B. N, N, O and N, O, N meridional cis coordination of two guanines to copper(II) by d(CGCGCG)2. Inorganic Chemistry. 2016; 55, 6130.
• Ronayne EK, Peters SC, Gish JS, Wilson C, Spencer HT, Doering CB, Lollar P, Spiegel Jr PC, Childers KC. Structure of Blood Coagulation Factor VIII in Complex With an Anti-C2 Domain Non-Classical, Pathogenic Antibody Inhibitor. Frontiers in Immunology. 2021; 12, 2260.
• Russo TA, Manohar A, Beanan JM, Olson R, MacDonald U, Graham J, Umland TC. The response regulator BfmR is a potential drug target for Acinetobacter baumannii. MSphere. 2016;1.
• Senda M, Hayashi T, Hatakeyama M, Takeuchi K, Sasaki AT, Senda T. Use of multiple cryoprotectants to improve diffraction quality from protein crystals. Crystal Growth & Design. 2016; 16, 1565.
• Senda M, Senda T. Screening of Cryoprotectants and the Multistep Soaking Method. In Advanced Methods in Structural Biology Springer; 2016, 139-151.
• Shelby ML, Gilbile D, Grant TD, Bauer WJ, Segelke B, He W, Evans AC, Crespo N, Fischer P, Pakendorf T, Hennicke V, Hunter, MS, Batyuk, A, Barthelmess, M, Meents, A, Kuhl, TL, Frank, M, Coleman, MA.  Crystals. Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies. 2020; 10(10), 886.
• Stachowski TR, Snell ME, Snell EH. Structural insights into conformational switching in latency-associated peptide between transforming growth factor β-1 bound and unbound states. IUCrJ. 2020; 7, 238-252.
• Stachowski TR, Snell ME, Snell EH. SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique. PLOS ONE. 2020; 15(11), e0239702.
• Stetsenko A, Guskov A. An overview of the top ten detergents used for membrane protein crystallization.  Crystals. 2017; 7, 197.
• Subedi S, Dinc I, Tran TX, Sharma D, Shrestha BR, Pusey ML, Aygün, RS. Visual-X2: interactive visualization and analysis tool for protein crystallization.  Network Modeling Analysis in Health Informatics and Bioinformatics. 2020; 9, 15.
• Sutton KA, Breen J, Russo TA, Schultz LW, Umland TC. Crystal structure of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase from the ESKAPE pathogen Acinetobacter baumannii. Acta Crystallographica Section F: Structural Biology Communications. 2016; 72, 179.
• Ran, Y, Zheng, A, Thibodeau, PH.  Structural analysis reveals pathomechanisms associated with pseudoxanthoma elasticum-causing mutations in the ABCC6 transporter. Journal of Biological Chemistry. 2018; 293, 15855.
• Ray LC, Das D, Entova S, Lukose V, Lynch AJ, Imperiali B, Allen KN. Membrane association of monotopic phosphoglycosyl transferase underpins function.  Nature Chemical Biology. 2018; 14, 538. 
• Wlodarchak, N, Teachout, N, Beczkiewicz, J, Rocknow, R, Schaenzer, AJ, Satyshur, K, Pavelka, M, Zuercher, W, Drewry, D, Sauer, J-D, Striker, R. In silico screen and structural analysis identifies bacterial kinase inhibitors witch act with β-lactams to inhibit mycobacterial growth.  Molecular Pharmaceutics. 2018; 15, 5410.
• Yang, H, Huang, L, Zhang, F, Karde, V, Yang, Z, Heng, JY. Gravity on Crystallization of Lysozyme: Slower or Faster?  Crystal Growth & Design. 2019; 19, 7402.
• Ye, G, Gallant, JP, Zheng, J, Massey, C, Shi, K, Tai, W, Odle, A, Vickers, M, Shang, J, Wan, Y, Du, L, Aihara, H, Perlman, S, LeBeau, AM, Li, F.  The development of Nanosota-1 as anti-SARS-CoV-2 nanobody drug candidates. ELife. 2021; 10, e64815.
  
• Yekwa, EL, Serrano, FA, Yukl, E. Conformational flexibility in the zinc solute-binding protein ZnuA. Acta Cryst F. 2022; 78, 128.