School of biological ScienceS

50. Roca X, Karginov FV. (2012) RNA biology in a test tube-an overview of in vitro systems/assays. Wiley Interdiscip Rev RNA., 3, 509-527. 51...

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School of biological Sciences Publications January – July, 2012

Publications from January to July 2012 1. Kuss C, Gan CS, Gunalan K, Bozdech Z, Sze SK, Preiser PR. (2012) Quantitative Proteomics Reveals New Insights into Erythrocyte Invasion by Plasmodium falciparum. Mol Cell Proteomics. 11, M111.010645. 2. Andrews KT, Gupta AP, Tran TN, Fairlie DP, Gobert GN, Bozdech Z. (2012) Comparative Gene Expression Profiling of P. falciparum Malaria Parasites Exposed to Three Different Histone Deacetylase Inhibitors. PLoS One. 7, e31847. 3. Kraut R, Bag N, Wohland T. (2012) Fluorescence correlation methods for imaging cellular behavior of sphingolipid-interacting probes. Methods Cell Biol. 108, 395-427. 4. Yang R, Hou W, Zhang X, Liu CF. (2012) N-to-C sequential ligation using peptidyl N,N-bis(2-mercaptoethyl)amide building blocks. Org Lett. 14, 374-377. 5. Zhong Y, Liao Y, Fang S, Tam JP, Liu DX. (2012) Up-regulation of Mcl-1 and Bak by coronavirus infection of human, avian and animal cells modulates apoptosis and viral replication. PLoS One. 7,e30191. 6. Dai W, Zhang G, Makeyev EV. (2012) RNA-binding protein HuR autoregulates its expression by promoting alternative polyadenylation site usage. Nucleic Acids Res. 40, 787-800. 7. Lin X, Hong T, Mu Y, Torres J. (2012) Identification of residues involved in water versus glycerol selectivity in aquaporins by differential residue pair co-evolution. Biochim Biophys Acta 1818, 907-914. 8. Li W, Zhou R, Mu Y. (2012) Salting Effects on Protein Components in Aqueous NaCl and Urea Solutions: Toward Understanding of Urea-Induced Protein Denaturation. J Phys Chem B. 116, 1446-1151. 9. Li W, Mu Y. (2012) Dissociation of hydrophobic and charged nano particles in aqueous guanidinium chloride and urea solutions: A molecular dynamics study. Nanoscale 4, 1154-1159. 10. Korolev N, Zhao Y, Allahverdi A, Eom KD, Tam JP, Nordenskiöld L. (2012) The effect of salt on oligocation-induced chromatin condensation. Biochem Biophys Res Commun. 418, 205-210. 11. Yan J, Korolev N, Eom KD, Tam JP, Nordenskiöld L. (2012) Biophysical properties and supramolecular structure of self-assembled liposome/ε-peptide/DNA nanoparticles: correlation with gene delivery. Biomacromol. 13, 124-131. 12. Min L, Mohammad Isa SA, Fam WN, Sze SK, Beretta O, Mortellaro A, Ruedl C. (2012) Synergism between Curdlan and GM-CSF Confers a Strong Inflammatory Signature to Dendritic Cells. J Immunol. 188, 1789-1798.

13. Rozen-Gagnon K, Moreland NJ, Ruedl C, Vasudevan SG. (2012) Expression and immunoaffinity purification of recombinant dengue virus 2 NS1 protein as a cleavable SUMOstar fusion. Protein Expr Purif. 82, 20-25. 14. Hao P, Qian J, Dutta B, Cheow ES, Sim KH, Meng W, Adav SS, Alpert A, Sze SK. (2012) Enhanced Separation and Characterization of Deamidated Peptides with RPERLIC- Based Multidimensional Chromatography Coupled with Tandem Mass Spectrometry. J Proteome Res. 11, 1804-1811. 15. Mishra M, Manavalan A, Sze SK, Heese K. (2012) Neuronal p60TRP expression modulates cardiac capacity. J Proteomics 75, 1600-1617. 16. Adav SS, Ravindran A, Sze SK. (2012) Quantitative proteomic analysis of lignocellulolytic enzymes by Phanerochaete chrysosporium on different lignocellulosic biomass. J Proteomics 75, 1493-1504. 17. Sundaramurthi H, Manavalan A, Ramachandran U, Hu JM, Sze SK, Heese K. (2012) Phenotyping of tianma-stimulated differentiated rat neuronal b104 cells by quantitative proteomics. Neurosignals 20, 48-60. 18. Kim W, Chakraborty G, Kim S, Shin J, Park CH, Jeong MW, Bharatham N, Yoon HS, Kim KT. (2012) Macro Histone H2A1.2 (MacroH2A1) Protein Suppresses Mitotic Kinase VRK1 during Interphase. J Biol Chem. 287, 5278-5289. 19. Saravanan R, Mohanram H, Joshi M, Domadia PN, Torres J, Ruedl C, Bhattacharjya S. (2012) Structure, activity and interactions of the cysteine deleted analog of tachyplesin-1 with lipopolysaccharide micelle: Mechanistic insights into outermembrane permeabilization and endotoxin neutralization. Biochim Biophys Acta 1818, 1613-1624. 20. Witmer K, Schmid CD, Brancucci NM, Luah YH, Preiser PR, Bozdech Z, Voss TS. (2012) Analysis of subtelomeric virulence gene families in Plasmodium falciparum by comparative transcriptional profiling. Mol Microbiol. 84, 243-259. 21. Rovira-Graells N, Gupta AP, Planet E, Crowley VM, Mok S, Ribas de Pouplana L, Preiser PR, Bozdech Z, Cortés A. (2012) Transcriptional variation in the malaria parasite Plasmodium falciparum. Genome Res. 22, 925-938. 22. Shin JS, Ha JH, He F, Muto Y, Ryu KS, Yoon HS, Kang S, Park SG, Park BC, Choi SU, Chi SW. (2012) Structural insights into the dual-targeting mechanism of Nutlin-3. Biochem Biophys Res Commun. 420, 48-53. 23. Liao YT, Chin KH, Kuo WT, Chuah ML, Liang ZX, Chou SH. (2012) Crystallization and preliminary X-ray diffraction characterization of the XccFimX(EAL)-c-di-GMP and XccFimX(EAL)-c-di-GMP-XccPilZ complexes from Xanthomonas campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun. 68, 301-315. 24. Yan J, Berezhnoy NV, Korolev N, Su CJ, Nordenskiöld L. (2012) Structure and internal organization of overcharged cationic-lipid/peptide/DNA self-assembly complexes. Biochim Biophys Acta 1818, 1794-1800.

25. Nikolaev Y, Pervushin K. (2012) Structural basis of RNA binding by leucine zipper GCN4. Protein Sci. 21, 667-676. 26. Lawton J, Brugat T, Yam XY, Reid AJ, Boehme U, Otto TD, Pain A, Jackson A, Berriman M, Cunningham D, Preiser P, Langhorne J. (2012) Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS). BMC Genomics 13, 125. 27. Watanabe S, Tan KH, Rathore AP, Rozen-Gagnon K, Shuai W, Ruedl C, Vasudevan SG. (2012) The Magnitude of Dengue Virus NS1 Protein Secretion Is Strain Dependent and Does Not Correlate with Severe Pathologies in the Mouse Infection Model. J Virol. 86, 5508-5514. 28. Sutejo R, Yeo DS, Myaing MZ, Hui C, Xia J, Ko D, Cheung PC, Tan BH, Sugrue RJ. (2012) Activation of Type I and III Interferon Signalling Pathways Occurs in Lung Epithelial Cells Infected with Low Pathogenic Avian Influenza Viruses. PLoS One. 7, e33732. 29. Manavalan A, Feng L, Sze SK, Hu JM, Heese K. (2012) New insights into the brain protein metabolism of Gastrodia elata-treated rats by quantitative proteomics. J Proteomics 75, 2468-2479. 30. Zhu P, Goh YY, Chin HF, Kersten S, Tan NS. (2012) Angiopoietin-like 4: a decade of research. Biosci Rep. 32, 211-219. 31. Tan SM. (2012) The leucocyte β2 (CD18) integrins: the structure, functional regulation and signalling properties. Biosci Rep. 32, 241-269. 32. Misra A, George B, Rajmohan R, Jain N, Wong MH, Kambadur R, Thanabalu T. (2012) Insulin Receptor Substrate protein 53kDa (IRSp53) is a negative regulator of myogenic differentiation. Int J Biochem Cell Biol. 44, 928-941. 33. Mitra R, Sapolsky RM. (2012) Short-term enrichment makes male rats more attractive, more defensive and alters hypothalamic neurons. PLoS One. 7,e36092. 34. Raghunathan D, Gayen S, Kumar A, Hunke C, Grüber G, Verma CS. (2012) Subunit F modulates ATP binding and migration in the nucleotide-binding subunit B of the A(1) A(O) ATP synthase of Methanosarcina mazei Gö1. J Bioenerg Biomembr., 44, 213-224. 35. Heng YW, Lim HH, Mina T, Utomo P, Zhong S, Lim CT, Koh CG. (2012) TPPP acts downstream of RhoA-ROCK-LIMK2 to regulate astral microtubule organization and spindle orientation. J Cell Sci., 125, 1579-1590. 36. Korolev N, Fan Y, Lyubartsev AP, Nordenskiöld L. (2012) Modelling chromatin structure and dynamics: status and prospects. Curr Opin Struct Biol. 22, 151-159. 37. Ju PJ, Liu R, Yang HJ, Xia YY, Feng ZW. (2012) Clonal analysis for elucidating the lineage potential of embryonic NG2(+) cells. Cytotherapy 14, 608-620.

38. Decroly E, Ferron F, Lescar J, Canard B. (2012) Conventional and unconventional mechanisms for capping of virus mRNA. Nature Reviews Microbiology 10, 51-65. 39. Oglęcka, K., Sanborn, J., Parikh, A. N., Kraut, R. (2012). Osmotic Gradients Induce Bio-reminiscent Morphological Transformations in Giant Unilamellar Vesicles. Front. Membr. Physiol. Biophys. 3, 1-11. 40. Lu L, Kirchhausen T. (2012) Visualizing the high curvature regions of post-mitotic nascent nuclear envelope membrane. Commun. Integr. Biol. 5, 1-3. 41. Wong LE, Li Y, Pillay S, Frolova L, Pervushin K. (2012) Selectivity of stop codon recognition in translation termination is modulated by multiple conformations of GTS loop in eRF1. Nucleic Acids Res. 40, 5751-5765. 42. Feng C, Li YF, Yau YH, Lee HS, Tang XY, Xue ZH, Zhou YC, Lim WM, Cornvik C, Ruedl C, Shochat SG, Tan SM. (2012) Kindlin-3 mediates integrin αLβ2 outsidein signaling and it interacts with the scaffold protein receptor for activated-C kinase 1 (RACK1). J Biol Chem. 287, 10714-10726. 43. Fric J, Lim CX, Koh EG, Hofmann B, Chen J, Tay HS, Mohammad Isa SA, Mortellaro A, Ruedl C, Ricciardi-Castagnoli P. (2012) Calcineurin/NFAT signaling inhibits myeloid haematopoiesis. EMBO Mol Med. 4, 269-282. 44. Adav SS, Chao LT, Sze SK. (2012) Quantitative secretomic analysis of Trichoderma reesei strains reveals enzymatic composition for lignocellulosic biomass degradation. Mol Cell Proteomics 11, M111.012419 45. Li X, Arslan F, Yan R, Adav S, Poh KK, Sorokin V, Lee CN, de Kleijn DP, Lim SK, Sze SK. (2012) Metabolic Adaptation To A Disruption In Oxygen Supply During Myocardial Ischemia And Reperfusion Is Underpinned By Temporal And Quantitative Changes In The Cardiac Proteome. J Proteome Res. 11, 2331-2346. 46. Mukherjee M, Chow SY, Yusoff P, Seetharaman J, Ng C, Sinniah S, Koh XW, Asgar NF, Li D, Yim D, Jackson RA, Yew J, Qian J, Iyu A, Lim YP, Zhou X, Sze SK, Guy GR, Sivaraman J. (2012) Structure of a novel phosphotyrosine-binding domain in Hakai that targets E-cadherin. EMBO J. 31, 1308-1319. 47. Balakrishna AM, Hunke C, Grüber G. (2012) The Structure of Subunit E of the Pyrococcus horikoshii OT3 A-ATP Synthase Gives Insight into the Elasticity of the Peripheral Stalk. J Mol Biol. 420, 155-163. 48. Ge X, Vajjala A, McFarlane C, Wahli W, Sharma M, Kambadur R. (2012) Lack of Smad3 signaling leads to impaired skeletal muscle regeneration. Am J Physiol Endocrinol Metab. 303, E90-E102 49. Chuang LS, Lai SK, Murata-Hori M, Yamada A, Li HY, Gunaratne J, Ito Y. (2012) RUNX3 interactome reveals novel centrosomal targeting of RUNX family of transcription factors. Cell Cycle. 11, 1938-1947.

50. Roca X, Karginov FV. (2012) RNA biology in a test tube-an overview of in vitro systems/assays. Wiley Interdiscip Rev RNA., 3, 509-527. 51. Nguyen GK, Lim WH, Nguyen PQ, Tam JP. (2012) Novel cyclotides and uncyclotides with highly shortened precursors from Chassalia chartacea and effects of methionine oxidation on bioactivities. J Biol Chem. 287, 17598-17607. 52. Rajan S, Saw KQ, Nguyen QT, Baek K, Yoon HS. (2012) High resolution crystal structure of FKBP12 from Aedes aegypti. Protein Sci. 21, 1080-1084. 53. Dip, P. V., Saw, W. G., Roessle, M., Marshansky, V., Grüber, G. (2012) Solution structure of subunit a, a101-363, of the Saccharomyces cerevisiae V-ATPase and the importance of its C-terminus in structure formation. J. Bioenerg. Biomembr. 44, 341350. 54. Tibùrcio M, Niang M, Deplaine G, Perrot S, Bischoff E, Ndour PA, Silvestrini F, Khattab A, Milon G, David PH, Hardeman M, Vernick KD, Sauerwein RW, Preiser PR, Mercereau-Puijalon O, Buffet P, Alano P, Lavazec C. (2012) A switch in infected erythrocyte deformability at the maturation and blood circulation of Plasmodium falciparum transmission stages. Blood 119, e172-80 55. Wong CT, Rowlands DK, Wong CH, Lo TW, Nguyen GK, Li HY, Tam JP. (2012) Orally Active Peptidic Bradykinin B(1) Receptor Antagonists Engineered from a Cyclotide Scaffold for Inflammatory Pain Treatment. Angew Chem Int Ed Engl., 51, 5620-5624. 56. Yap K, Lim ZQ, Khandelia, P, Friedman B, Makeyev EV. (2012) Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention. Genes & Development 26, 1209-1223. 57. Lee WL, She YC, Widjaja E, Chong HC, Tan NS, Loo JSC. (2012) Fabrication and drug release study of double-layered microparticles of various sizes. J. Pharm. Sci. 101, 2787-2797. 58. Adav SS, Cheow ES, Ravindran A, Dutta B, Sze SK. (2012) Label free quantitative proteomic analysis of secretome by Thermobifida fusca on different lignocellulosic biomass. J Proteomics 75, 3694-3706. 59. Law AWL, Lescar J, Hao Q, Kotaka M. (2012) Expression, purification, crystallization and preliminary X-ray analysis of Plasmodium falciparum GTP:AMP phosphotransferase. Acta Cryst F. 68, 671-674. 60. Liew CW, Nilsson M, Chen MW, Sun H, Cornvik T, Liang ZX, Lescar J. (2012) Crystal structure of the acyltransferase domain of the iterative polyketide synthase in enediyne biosynthesis. J. Biol. Chem. 287, 23203-232015. 61. Tan YW, Hong W, Liu DX. (2012) Binding of the 5'-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription. Nucleic Acids Res. 40, 5065-5077.

62. Li X, Wang R, Tang C, Vararattanavech A, Zhao Y, Torres J, Fane T. (2012) Preparation of supported lipid membranes for aquaporin Z incorporation. Colloids Surf B Biointerfaces 94, 333-340. 63. Bhunia A, Mohanram H, Bhattacharjya S. (2012) Structural determinants of the specificity of a membrane binding domain of the scaffold protein Ste5 of budding yeast: Implications in signaling by the scaffold protein in MAPK pathway. Biochim Biophys Acta.1818, 1250-1260. 64. Bonala S, Lokireddy S, Arigela H, Teng S, Wahli W, Sharma M, McFarlane C, Kambadur R. (2012) Peroxisome Proliferator Activated Receptor β/δ induces myogenesis by modulating Myostatin activity. J Biol Chem. 287, 12935-12951. 65. Zhang C, Tan CK, McFarlane C, Sharma M, Tan NS, Kambadur R. (2012) MyostatinNull Mice Exhibit Delayed Skin Wound Healing through The Blockade of Transforming Growth Factor-β Signaling by Decorin. Am J Physiol Cell Physiol. 302, C1213-1225. 66. Roca X, Akerman M, Gaus H, Berdeja A, Bennett CF, and Krainer AR. (2012) Widespread recognition of 5' splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides. Genes & Development 16, 1098-1099. 67. K-G Lee, S. Xu, Z-H Kang, J. Huo, M. Huang, D. X. Liu, O. Takeuchi, S. Akira, and K-P. Lam. (2012). Bruton's tyrosine kinase phosphorylates Toll-like receptor 3 to initiate anti-viral response. PNAS USA 109, 5791-5796 68. Ramachandran, U., Manavalan, A., Sundaramurthi, H., Sze, S. K., Feng, Z. W., Hu, J. M., and Heese, K. (2012) Tianma modulates proteins with various neuro-regenerative modalities in differentiated human neuronal SH-SY5Y cells. Neurochem Int. 60, 827836. 69. Yang, P. Y., Wang, M., Liu, K., Ngai, M. H., Sheriff, O., Lear, M. J., Sze, S. K., He, C. Y., and Yao, S. Q. (2012) Parasite-Based Screening and Proteome Profiling Reveal Orlistat, an FDA-Approved Drug, as a Potential Anti Trypanosoma brucei Agent. Chemistry. 18, 8403-8413. 70. Manavalan, A., Ramachandran, U., Sundaramurthi, H., Mishra, M., Sze, S. K., Hu, J. M., Feng, Z. W., and Heese, K. (2012) Gastrodia elata Blume (tianma) mobilizes neuro-protective capacities. Int J Biochem Mol Biol. 3, 219-241. 71. Feng, L., Manavalan, A., Mishra, M., Sze, S. K., Hu, J. M., and Heese, K. (2012) Tianma Modulates Blood Vessel Tonicity. Open Biochem J. 6, 56-65. 72. Selmer, M., Gao, Y.G., Weixlbaumer, A., Ramakrishnan, V. (2012) Ribosome engineering to promote new crystal forms. Acta Crystallographica Section D. 68, 578583

73. Ruenn Chai Lai, Soon Sim Tan, Bao Ju Teh, Siu Kwan Sze, Fatih Arslan, Dominique P. de Kleijn, Andre Choo and Sai Kiang Lim. (2012) Proteolytic potential of the MSC exosome proteome: implications for an exosome-mediated delivery of therapeutic proteasome, Intern. J. Proteomics, in press. 74. Dutta, B., Adav, S. S., Koh, C. G., Lim, S. K., Meshorer, E., and Sze, S. K. (2012) Elucidating the Temporal Dynamics of Chromatin-Associated Protein Release Upon DNA Digestion by Quantitative Proteomics Approach. J Proteomics, in press. 75. Vyas, A. (2012) Parasite augmented mate choice and reduction in innate fear of rats infected by Toxoplasma gondii. J Exp. Biol. in press 76. Juvvuna PK, Khandelia P, Lee LM, Makeyev EV. (2012) Argonaute identity defines the length of mature mammalian microRNAs. Nucleic Acids Res., in press 77. Chua EY, Vasudevan D, Davey GE, Wu B, Davey CA. (2012) The mechanics behind DNA sequence-dependent properties of the nucleosome. Nucleic Acids Res., in press 78. Morshedi A, Ren Z, Li J, Dröge P. (2012) Probing into the Biological Processes Influenced by ESC Factor and Oncoprotein HMGA2 Using iPSCs. Stem Cell Rev., in press 79. Guo T, Fan L, Ng WH, Zhu Y, Ho M, Wan WK, Lim KH, Ong WS, Lee SS, Huang S, Kon OL, Sze SK. (2012) Multidimensional Identification of Tissue Biomarkers of Gastric Cancer. J Proteome Res., in press 80. Chong HC, Tan CK, Huang RL, Tan NS. (2012) Matricellular proteins: a sticky affair with cancers. J Oncol., in press 81. Morshedi A, Soroush Noghabi M, Dröge P. (2012) Use of UTF1 Genetic Control Elements as iPSC Reporter. Stem Cell Rev., in press 82. Bag N, Sankaran J, Paul A, Kraut R S, Wohland T. (2012) Calibration and limits of camera–based fluorescence correlation spectroscopy: A supported lipid bilayer study. Phys Chem., in press 83. Xu QC, Zhang Y, Tan MJ, Liu Y, Yuan S, Choong C, Tan NS and Tan TTY. (2012) Anti-cAngptl4 Ab-conjugated N-TiO2/NaYF4:Yb,Tm Nanocomposite for Near Infrared-Triggered Drug Release and Enhanced Targeted Cancer Cell Ablation. Adv. Healthcare Mater., in press 84. Chebaro Y, Jiang P, Zang T, Mu Y, Nguyen PH, Mousseau N, Derreumaux P. (2012) Structures of Aβ17-42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure. J Phys Chem B., in press 85. Gao X, Tan B-H, Sugrue R J. Tang K. (2012) MALDI mass spectrometry for nucleic acid analysis. Top. Curr. Chem., in press.

86. Gan SW, Tan E, Lin X, Yu D, Wang J, Tan GM, Vararattanavech A, Yeo CY, Soon CH, Soong TW, Pervushin K, Torres J. (2012) The small hydrophobic protein of the human respiratory syncytial virus forms pentameric ion channels. J Biol Chem., in press 87. Chen L, Zhang L-F. (2012) A balanced network: transcriptional regulation in pluripotent stem cells. Stem Cell Res. & Therapy, in press 88. Basak S, Balakrishna AM, Manimekalai MSS, Grüber G. (2012) Crystallization and preliminary X-ray crystallographic analysis of subunit F, F1-94, an essential coupling subunit of the eukaryotic V1VO ATPase from Saccharomyces cerevisiae. Acta Cryst. Section F., in press 89. Grüber A, Manimekalai MSS, Preiser, PR, Grüber G. (2012) Structural architecture and interplay of the nucleotide- and erythrocyte binding domain of the reticulocyte binding protein Py235 from Plasmodium yoelii. Internat. J. Parasitol., in press. 90. Sun, H., Ho, C-L, Ding, F., Soehano, I., Liu, X. Liang, Z.-X. (2012) Synthesis of (R)mellein by a partially reducing iterative polyketide synthase. J. Am. Chem. Soc., in press 91. Chen, M. W., Kotaka, M., Vonrhein, C., Bricogne, G., Rao, F., Chuah, M. L. C., Liang, Z.-X, Lescar, J. (2012) Structural insights into the regulatory mechanism of the response regulator RocR in cyclic di-GMP singaling. J. Bacteriol., in press