recent publications

• academic article

  • Hayashi, Y., Caboni, L., Das, D., Yumoto, F., Clayton, T., Deller, M. C., Nguyen, P., Farr, C. L., Chiu, H. J., Miller, M. D., Elsliger, M. A., Deacon, A. M., et al. Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells Proceedings of the National Academy of Sciences of the United States of America  2015 112:4666-4671  DOI:10.1073/pnas.1502855112  PMID:25825768  PMCID:PMC4403148
  • Das, D., Chiu, H. J., Farr, C. L., Grant, J. C., Jaroszewski, L., Knuth, M. W., Miller, M. D., Tien, H. J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A., et al. Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family Proteins-Structure Function and Bioinformatics  2014 82:1086-1092  DOI:10.1002/prot.24455  PMID:24174223  PMCID:PMC4006323
  • Kumar, A., Punta, M., Axelrod, H. L., Das, D., Farr, C. L., Grant, J. C., Chiu, H. J., Miller, M. D., Coggill, P. C., Klock, H. E., Elsliger, M. A., Deacon, A. M., et al. Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake Protein Science  2014 23:1380-1391  DOI:10.1002/pro.2522  PMID:25044324  PMCID:PMC4287006
  • Das, D., Herve, M., Elsliger, M. A., Kadam, R. U., Grant, J. C., Chiu, H. J., Knuth, M. W., Klock, H. E., Miller, M. D., Godzik, A., Lesley, S. A., Deacon, A. M., et al. Structure and function of a novel LD-carboxypeptidase A involved in peptidoglycan recycling Journal of Bacteriology  2013 195:5555-5566  DOI:10.1128/jb.00900-13  PMID:24123814
  • Das, D., Lee, W. S., Grant, J. C., Chiu, H. J., Farr, C. L., Vance, J., Klock, H. E., Knuth, M. W., Miller, M. D., Elsliger, M. A., Deacon, A. M., Godzik, A., et al. Structure and function of the DUF2233 domain in bacteria and in the human mannose 6-phosphate uncovering enzyme Journal of Biological Chemistry  2013 288:16789-16799  DOI:10.1074/jbc.M112.434977  PMID:23572527  PMCID:PMC3675612
  • Das, D., Herve, M., Feuerhelm, J., Farr, C. L., Chiu, H. J., Elsliger, M. A., Knuth, M. W., Klock, H. E., Godzik, A., Lesley, S. A., Deacon, A. M., Mengin-Lecreulx, D., et al. Structure and function of the first full-length murein peptide ligase (mpl) cell wall recycling protein PLoS One  2011 6:e17624  DOI:10.1371/journal.pone.0017624  PMID:21445265  PMCID:PMC3060825
  • Xu, Q. P., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X. H., Carlton, D., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Das, D., et al. A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from bacteroides thetaiotaomicron at 2.2 A resolution Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1281-1286  DOI:10.1107/s1744309110006548  PMID:20944223  PMCID:PMC2954217
  • Xu, Q., Bateman, A., Finn, R. D., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Carlton, D., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., et al. Bacterial pleckstrin homology domains: A prokaryotic origin for the PH domain Journal of Molecular Biology  2010 396:31-46  DOI:10.1016/j.jmb.2009.11.006  PMID:19913036  PMCID:PMC2817789
  • Das, D., Moiani, D., Axelrod, H. L., Miller, M. D., McMullan, D., Jin, K. K., Abdubek, P., Astakhova, T., Burra, P., Carlton, D., Chiu, H. J., Clayton, T., et al. Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair Journal of Molecular Biology  2010 397:647-663  DOI:10.1016/j.jmb.2010.01.049  PMID:20122942  PMCID:PMC2839085
  • Kumar, A., Lomize, A., Jin, K. K., Carlton, D., Miller, M. D., Jaroszewski, L., Abdubek, P., Astakhova, T., Axelrod, H. L., Chiu, H. J., Clayton, T., Das, D., et al. Open and closed conformations of two SpoiiAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1245-1253  DOI:10.1107/s1744309109042481  PMID:20944218  PMCID:PMC2954212
  • Bakolitsa, C., Xu, Q. P., Rife, C. L., Abdubek, P., Astakhova, T., Axelrod, H. L., Carlton, D., Chen, C., Chiu, H. J., Clayton, T., Das, D., Deller, M. C., et al. Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1274-1280  DOI:10.1107/s1744309110032999  PMID:20944222  PMCID:PMC2954216
  • Yeh, A. P., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X. H., Carlton, D., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Das, D., et al. Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 A resolution: The first structural representative of a new protein family that may play a role in carbohydrate metabolism Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1287-1296  DOI:10.1107/s1744309110028228  PMID:20944224  PMCID:PMC2954218
  • Xu, Q. P., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X. H., Carlton, D., Chen, C., Chiu, H. J., Clayton, T., Das, D., Deller, M. C., et al. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1297-1305  DOI:10.1107/s1744309110023055  PMID:20944225  PMCID:PMC2954219
  • Han, G. W., Elsliger, M. A., Yeates, T. O., Xu, Q. P., Murzin, A. G., Krishna, S. S., Jaroszewski, L., Abdubek, P., Astakhova, T., Axelrod, H. L., Carlton, D., Chen, C., et al. Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15 Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1237-1244  DOI:10.1107/s1744309110025534  PMID:20944217  PMCID:PMC2954211
  • Xu, Q. P., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X. H., Carlton, D., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Das, D., et al. Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1354-1364  DOI:10.1107/s1744309110021214  PMID:20944232  PMCID:PMC2954226
  • Bakolitsa, C., Kumar, A., Jin, K. K., McMullan, D., Krishna, S. S., Miller, M. D., Abdubek, P., Acosta, C., Astakhova, T., Axelrod, H. L., Burra, P., Carlton, D., et al. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1182-1189  DOI:10.1107/s1744309109050647  PMID:20944209  PMCID:PMC2954203
  • Han, G. W., Bakolitsa, C., Miller, M. D., Kumar, A., Carlton, D., Najmanovich, R. J., Abdubek, P., Astakhova, T., Axelrod, H. L., Chen, C., Chiu, H. J., Clayton, T., et al. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1218-1225  DOI:10.1107/s1744309109050416  PMID:20944214  PMCID:PMC2954208
  • Axelrod, H. L., Das, D., Abdubek, P., Astakhova, T., Bakolitsa, C., Carlton, D., Chen, C., Chiu, H. J., Clayton, T., Deller, M. C., Duan, L. A., Ellrott, K., et al. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved alpha plus beta core domain and an auxiliary C-terminal treble-clef zinc finger Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1335-1346  DOI:10.1107/s1744309110020166  PMID:20944230  PMCID:PMC2954224
  • Das, D., Finn, R. D., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X. H., Carlton, D., Chen, C. N., Chiu, H. J., Chiu, M., Clayton, T., et al. The crystal structure of a bacterial sufu-like protein defines a novel group of bacterial proteins that are similar to the n-terminal domain of human sufu Protein Science  2010 19:2131-2140  DOI:10.1002/pro.497  PMID:20836087  PMCID:PMC3005784
  • Das, D., Finn, R. D., Carlton, D., Miller, M. D., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., et al. The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1265-1273  DOI:10.1107/s1744309109046788  PMID:20944221  PMCID:PMC2954215
  • Chiu, H. J., Abdubek, P., Astakhova, T., Axelrod, H. L., Carlton, D., Clayton, T., Das, D., Deller, M. C., Duan, L. A., Feuerhelm, J., Grant, J. C., Grzechnik, A., et al. The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1317-1325  DOI:10.1107/s1744309110021688  PMID:20944228  PMCID:PMC2954222
  • Bakolitsa, C., Bateman, A., Jin, K. K., McMullan, D., Krishna, S. S., Miller, M. D., Abdubek, P., Acosta, C., Astakhova, T., Axelrod, H. L., Burra, P., Carlton, D., et al. The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 A resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1198-1204  DOI:10.1107/s1744309109025196  PMID:20944211  PMCID:PMC2954205
  • Das, D., Kozbial, P., Han, G. W., Carlton, D., Jaroszewski, L., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Chen, C., Chiu, H. J., Chiu, M., et al. The structure of KPN03535 (gi vertical bar 152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1254-1260  DOI:10.1107/s1744309109018168  PMID:20944219  PMCID:PMC2954213
  • Das, D., Grishin, N. V., Kumar, A., Carlton, D., Bakolitsa, C., Miller, M. D., Abdubek, P., Astakhova, T., Axelrod, H. L., Burra, P., Chen, C., Chiu, H. J., et al. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation Acta Crystallographica Section F-Structural Biology and Crystallization Communications  2010 66:1174-1181  DOI:10.1107/s1744309109022672  PMID:20944208  PMCID:PMC2954202
  • Xu, Q. P., McMullan, D., Abdubek, P., Astakhova, T., Carlton, D., Chen, C., Chiu, H. J., Clayton, T., Das, D., Deller, M. C., Duan, L., Elsliger, M. A., et al. A structural basis for the regulatory inactivation of DnaA Journal of Molecular Biology  2009 385:368-380  DOI:10.1016/j.jmb.2008.10.059  PMID:19000695  PMCID:PMC2667141
  • Das, D., Kozbial, P., Axelrod, H. L., Miller, M. D., McMullan, D., Krishna, S. S., Abdubek, P., Acosta, C., Astakbova, T., Burra, P., Carlton, D., Chen, C., et al. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution Proteins-Structure Function and Bioinformatics  2009 75:296-307  DOI:10.1002/prot.22360  PMID:19173316  PMCID:PMC2785455
  • Das, D., Krishna, S. S., McMullan, D., Miller, M. D., Xu, Q., Abdubek, P., Acosta, C., Astakhova, T., Axelrod, H. L., Burra, P., Carlton, D., Chiu, H. J., et al. Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution Proteins-Structure Function and Bioinformatics  2009 75:264-271  DOI:10.1002/prot.22338  PMID:19127588  PMCID:PMC2674511
  • Xu, Q., Traag, B. A., Willemse, J., McMullan, D., Miller, M. D., Elsliger, M. A., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Carlton, D., Chen, C., et al. Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes Journal of Biological Chemistry  2009 284:25268-25279  DOI:10.1074/jbc.M109.018564  PMID:19567872  PMCID:PMC2757229