Publications

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Selected Publications by SCSB Faculty

Last Updated April 2023

2013

  • Zhou M, Guo J, Cha J, Chae M, Chen S, Barral JM, Sachs MS, Liu Y. "Non-optimal codon usage affects expression, structure and function of clock protein FRQ." Nature. 495(7439):111-5 (2013).
  • El Ayadi A, Stieren ES, Barral JM, Boehning D. "Ubiquilin-1 and protein quality control in Alzheimer disease." Prion. 7(2):164-9 (2013).
  • Akimzhanov AM, Barral JM, Boehning D. "Caspase 3 cleavage of the inositol 1,4,5-trisphosphate receptor does not contribute to apoptotic calcium release." Cell Calcium. 53(2):152-8 (2013).
  • Rana, T., Hasan, R.J., Nowicki, S., Venkatarajan, M.S., Singh, R., Urvil, P.T., Popov, V., Braun, W., Popik, W., Goodwin, J.S. and Nowicki, B.J. "Complement Protective Epitopes and CD55-Microtubule Complexes Facilitate the Invasion and Intracellular Persistence of Uropathogenic Escherichia coli." J. Infec. Dis. (in press) (2013).
  • Power, T.D, Ivanciuc, O., Schein, C.H. and Braun, W. "Assessment of 3D models for allergen research." PROTEINS: Struct. Funct. and Bioinf. 81(4):545-554 (2013).
  • Gottipati K, Ruggli N, Gerber M, Tratschin JD, Benning M, Bellamy H, Choi KH. "The structure of classical swine fever virus N(pro): a novel cysteine Autoprotease and zinc-binding protein involved in subversion of type I interferon induction." PLoS Pathog. 9(10):e1003704 (2013).
  • Zandarashvili L, Esadze A, Iwahara J. "NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins." Adv Protein Chem Struct Biol. 93:37-80 (2013).
  • Zandarashvili L, Sahu D, Lee K, Lee YS, Singh P, Rajarathnam K, Iwahara J. "Real-time kinetics of high-mobility group box 1 (HMGB1) oxidation in extracellular fluids studied by in situ protein NMR spectroscopy." J Biol Chem 288(17):11621-7 (2013).
  • Iwahara J, Levy Y. "Speed-stability paradox in DNA-scanning by zinc-finger proteins." Transcription. 4(2):58-61 (2013).
  • Anderson KM, Esadze A, Manoharan M, Brüschweiler R, Gorenstein DG, Iwahara J. "Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy." J Am Chem Soc. 135(9):3613-9 (2013).
  • Wu P, Zhao Y, Haidacher SJ, Wang E, Parsley MO, Gao J, Sadygov RG, Starkey JM, Luxon BA, Spratt H, Dewitt DS, Prough DS, Denner L. "Detection of structural and metabolic changes in traumatically injured hippocampus by quantitative differential proteomics." J Neurotrauma. 30(9):775-88 (2013).
  • Thomas S, Luxon BA. "Vaccines based on structure-based design provide protection against infectious diseases." Expert Rev Vaccines. 12(11):1301-11 (2013).
  • Xu M, Ma L, Bujalowski PJ, Qian F, Sutton RB, Oberhauser AF. "Analysis of the REJ Module of Polycystin-1 Using Molecular Modeling and Force-Spectroscopy Techniques." J Biophys. 2013:525231 (2013).
  • Bujalowski PJ, Oberhauser AF. "Tracking unfolding and refolding reactions of single proteins using atomic force microscopy methods." Methods. 60(2):151-60 (2013).
  • Infante SK, Oberhauser AF, Perez-Polo JR. "Bax phosphorylation association with nucleus and oligomerization after neonatal hypoxia-ischemia." J Neurosci Res. 91(9):1152-64 (2013).
  • Kokubo H, Harris RC, Asthagiri D, Pettitt BM. "Solvation free energies of alanine peptides: the effect of flexibility." J Phys Chem B. 117(51):16428-35 (2013).
  • Dyer KM, Pettitt BM. "Proximal distributions from angular correlations: a measure of the onset of coarse-graining." J Chem Phys. 139(21):214111 (2013).
  • Theruvathu JA, Yin YW, Pettitt BM, Sowers LC. "Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence." Biochemistry 52(47):8590-8 (2013).
  • Stoilova-McPhie S, Lynch GC, Ludtke S, Pettitt BM. "Domain organization of membrane-bound factor VIII" Biopolymers. 99(7):448-59 (2013).
  • Myers CG, Pettitt BM. "Communication: Origin of the contributions to DNA structure in phages." J Chem Phys. 138(7):071103 (2013).
  • Harrison A, Binder H, Buhot A, Burden CJ, Carlon E, Gibas C, Gamble LJ, Halperin A, Hooyberghs J, Kreil DP, Levicky R, Noble PA, Ott A, Pettitt BM, Tautz D, Pozhitkov AE. "Physico-chemical foundations underpinning microarray and next-generation sequencing experiments." Nucleic Acids Res. 41(5):2779-96 (2013).
  • Chaudhuri A, Basu P, Haldar S, Kombrabail M, Krishnamoorthy G, Rajarathnam K, Chattopadhyay A. "Organization and dynamics of the N-terminal domain of chemokine receptor CXCR1 in reverse micelles: effect of graded hydration." J Phys Chem B. 117(5):1225-33 (2013).
  • Joseph PR, Poluri KM, Gangavarapu P, Rajagopalan L, Raghuwanshi S, Richardson RM, Garofalo RP, Rajarathnam K. "Proline substitution of dimer interface β-strand residues as a strategy for the design of functional monomeric proteins." Biophys J. 105(6):1491-501 (2013).
  • Joseph PR, Sawant KV, Isley A, Pedroza M, Garofalo RP, Richardson RM, Rajarathnam K. "Dynamic conformational switching in the chemokine ligand is essential for G-protein-coupled receptor activation." Biochem J. 456(2):241-51 (2013).
  • Poluri KM, Joseph PR, Sawant KV, Rajarathnam K. "Molecular basis of glycosaminoglycan heparin binding to the chemokine CXCL1 dimer." J Biol Chem. 288(35):25143-53 (2013).
  • Ravindran A, Sawant KV, Sarmiento J, Navarro J, Rajarathnam K. "Chemokine CXCL1 dimer is a potent agonist for the CXCR2 receptor." J Biol Chem. 288(17):12244-52 (2013).
  • Garces AP, Watowich SJ. "Intrinsic flexibility of West Nile virus protease in solution characterized using small-angle X-ray scattering." Biochemistry. 52(39):6856-65 (2013).
  • Chen R, Wang E, Tsetsarkin KA, Weaver SC "Chikungunya virus 3' untranslated region: adaptation to mosquitoes and a population bottleneck as major evolutionary forces." PLoS Pathog. 9(8):e1003591 (2013).
  • Weaver SC. " Urbanization and geographic expansion of zoonotic arboviral diseases: mechanisms and potential strategies for prevention." Trends Microbiol. 21(8):360-3 (2013).
  • Guerbois M, Volkova E, Forrester NL, Rossi SL, Frolov I, Weaver SC. "IRES-driven expression of the capsid protein of the Venezuelan equine encephalitis virus TC-83 vaccine strain increases its attenuation and safety." PLoS Negl Trop Dis. 7(5):e219 (2013).
  • Haddow AD, Guzman H, Popov VL, Wood TG, Widen SG, Haddow AD, Tesh RB, Weaver SC. "First isolation of Aedes flavivirus in the Western Hemisphere and evidence of vertical transmission in the mosquito Aedes (Stegomyia) albopictus (Diptera: Culicidae)." Virology. 440(2):134-9 (2013).
  • Seymour RL, Rossi SL, Bergren NA, Plante KS, Weaver SC. "The role of innate versus adaptive immune responses in a mouse model of O'nyong-nyong virus infection." Am J Trop Med Hyg. 88(6):1170-9 (2013).
  • Rossi SL, Guerbois M, Gorchakov R, Plante KS, Forrester NL, Weaver SC. "IRES-based Venezuelan equine encephalitis vaccine candidate elicits protective immunity in mice." Virology. 437(2):81-8 (2013).
  • Sherman MB, Trujillo J, Leahy I, Razmus D, Dehate R, Lorcheim P, Czarneski MA, Zimmerman D, Newton JT, Haddow AD, Weaver SC. "Construction and organization of a BSL-3 cryo-electron microscopy laboratory at UTMB." J Struct Biol. 181(3):223-33 (2013).
  • Vasilakis N, Forrester NL, Palacios G, Nasar F, Savji N, Rossi SL, Guzman H, Wood TG, Popov V, Gorchakov R, González AV, Haddow AD, Watts DM, da Rosa AP, Weaver SC, Lipkin WI, Tesh RB. "Negevirus: a proposed new taxon of insect-specific viruses with wide geographic distribution." J Virol. 87(5):2475-88 (2013).
  • Almahariq M, Tsalkova T, Mei FC, Chen H, Zhou J, Sastry SK, Schwede F, Cheng X. "A novel EPAC-specific inhibitor suppresses pancreatic cancer cell migration and invasion." Mol Pharmacol. 83(1):122-8 (2013).
  • Gong B, Shelite T, Mei FC, Ha T, Hu Y, Xu G, Chang Q, Wakamiya M, Ksiazek TG, Boor PJ, Bouyer DH, Popov VL, Chen J, Walker DH, Cheng X. "Exchange protein directly activated by cAMP plays a critical role in bacterial invasion during fatal rickettsioses." Proc Natl Acad Sci USA. 110(48):19615-20 (2013).
  • Gong B, Lee YS, Lee I, Shelite TR, Kunkeaw N, Xu G, Lee K, Jeon SH, Johnson BH, Chang Q, Ha T, Mendell NL, Cheng X, Bouyer DH, Boor PJ, Ksiazek TG, Walker DH. "Compartmentalized, functional role of angiogenin during spotted fever group rickettsia-induced endothelial barrier dysfunction: evidence of possible mediation by host tRNA-derived small noncoding RNAs." BMC Infect Dis. 13:285 (2013).
  • Chen H, Ding C, Wild C, Liu H, Wang T, White MA, Cheng X, Zhou J. "Efficient Synthesis of ESI-09, A Novel Non-cyclic Nucleotide EPAC Antagonist." Tetrahedron Lett. 54(12):1546-1549 (2013).
  • Chen H, Tsalkova T, Chepurny OG, Mei FC, Holz GG, Cheng X, Zhou J. "Identification and characterization of small molecules as potent and specific EPAC2 antagonists." J Med Chem. 56(3):952-62 (2013).
  • Jiang Y, Ou Y, Cheng X. "Role of TSG101 in cancer." Front Biosci (Landmark Ed). 18:279-88. Review. (2013).
  • Yan J, Mei FC, Cheng H, Lao DH, Hu Y, Wei J, Patrikeev I, Hao D, Stutz SJ, Dineley KT, Motamedi M, Hommel JD, Cunningham KA, Chen J, Cheng X. "Enhanced leptin sensitivity, reduced adiposity, and improved glucose homeostasis in mice lacking exchange protein directly activated by cyclic AMP isoform 1." Mol Cell Biol. 33(5):918-26 (2013).