Department of Physiology and Biophysics

Publication Highlights

Publication Highlights in 2015-16

  Charafeddine RA, Nosanchuk JD, Sharp DJ. Targeting Microtubules for Wound Repair. Adv Wound Care (New Rochelle). 2016 Oct 1;5(10):444-454.
  Liu D, Cowburn D. Segmental Isotopic Labeling of Proteins for NMR Study Using Intein Technology. Methods Mol Biol. 2017; 1495:131-145.
  Lewis-Ballester A, Forouhar F, Kim SM, Lew S, Wang Y, Karkashon S, Seetharaman J, Batabyal D, Chiang BY, Hussain M, Correia MA, Yeh SR, Tong L. Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase. Sci Rep. 2016 Oct 20;6:35169.
  Stern JM, Moazami S, Qiu Y, Kurland I, Chen Z, Agalliu I, Burk R, Davies KP. Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers. Urolithiasis. 2016 Oct; 44(5):399-407.
  Malvestio LM, Celes MR, Jelicks LA, Tanowitz HB, Prado CM. Dantrolene improves in vitro structural changes induced by serum from Trypanosoma cruzi-infected mice. Parasitol Res. 2016 Oct 11.
  Kim N, Heo M, Fleysher R, Branch CA, Lipton ML. Two step Gaussian mixture model approach to characterize white matter disease based on distributional changes. J Neurosci Methods. 2016 Sep 1;270:156-64.
  Hirsch RE, Sibmooh N, Fucharoen S, Friedman JM. HbE/β-thalassemia and Oxidative Stress: The Key to Pathophysiological Mechanisms & Novel Therapeutics. Antioxid Redox Signal. 2016 Sep 21. [Epub ahead of print]
  Briggs KJ, Koivunen P, Cao S, Backus KM, Olenchock BA, Patel H, Zhang Q, Signoretti S, Gerfen GJ, Richardson AL, Witkiewicz AK, Cravatt BF, Clardy J, Kaelin WG Jr. Paracrine Induction of HIF by Glutamate in Breast Cancer: EglN1 Senses Cysteine. Cell. 2016 Jun 30; 166(1):126-39.
  Arora A, Deniskin R, Sosa Y, Nishtala SN, Henrich PP, Kumar TR, Fidock DA, Akabas MH. Substrate and inhibitor specificity of the Plasmodium berghei Equilibrative Nucleoside Transporter Type 1 (PbENT1). Mol Pharmacol. 2016 Jun; 89(6):678-85.
  Strauss SB, Kim N, Branch CA, Kahn ME, Kim M, Lipton RB, Provataris JM, Scholl HF, Zimmerman ME, Lipton ML. Bidirectional Changes in Anisotropy Are Associated with Outcomes in Mild Traumatic Brain Injury. AJNR Am J Neuroradiol. 2016 Jun 9.
  Nelson G, Kirian RA, Weierstall U, Zatsepin NA, Faragó T, Baumbach T, Wilde F, Niesler FB, Zimmer B, Ishigami I, Hikita M, Bajt S, Yeh SR, Rousseau DL, Chapman HN, Spence JC, Heymann M. Three-dimensional-printed gas dynamic virtual nozzles for x-ray laser sample delivery. Opt Express. 2016 May 30; 24(11):11515-30.
  Alvarez L, Lewis Ballester A, Roitberg AE, Estrin DA, Yeh SR, Marti MA, Capece L. Structural study of a flexible active site loop in human indoleamine 2,3-dioxygenase and its functional implications. Biochemistry. 2016 May 17; 55(19):2785-93
  Raveh B, Karp JM, Sparks S, Dutta K, Rout MP, Sali A, Cowburn D. Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. Proc Natl Acad Sci U S A. 2016 May 3; 113(18):E2489-97.
  Sockolosky JT, Dougan M, Ingram JR, Ho CC, Kauke MJ, Almo SC, Ploegh HL, Garcia KC. Durable antitumor responses to CD47 blockade require adaptive immune stimulation. Proc Natl Acad Sci U S A. 2016 May 10; 113(19):E2646-54.
  Chatterjee C, Benoit MP, DePaoli V, Diaz-Valencia JD, Asenjo AB, Gerfen G, Sharp DJ, Sosa H. Distinct Interaction Modes of the Kinesin-13 Motor Domain with the Microtubule. Biophys J. 2016 Apr 12;110(7):1593-604.
  Liang Y, Zeng J, Jelicks L, Ma S, Liu J, Mei J, Perez-Soler R, Zou Y. Pax5 Re-Expression In H460 Cells Treated With The Combination Of Demethylating Agent And Histone Deacetylase Inhibitor Is Associated With The Enhancement Of P53 Binding To Pax5 Promoter Region. Curr Cancer Drug Targets. 2016 Mar 31. [Epub ahead of print]
  Strader MB, Kassa T, Meng F, Wood FB, Hirsch RE, Friedman JM, Alayash AI. Oxidative instability of hemoglobin E (ß26 Glu?Lys) is increased in the presence of free a subunits and reversed by a-hemoglobin stabilizing protein (AHSP): Relevance to HbE/ß-thalassemia. Redox Biol. 2016 Mar 10;8:363-374.
  Brodin NP, Partanen A, Asp P, Branch CA, Guha C, Tomé WA. A simple method for determining the coagulation threshold temperature of transparent tissue-mimicking thermal therapy gel phantoms: Validated by magnetic resonance imaging thermometry. Med Phys. 2016 Mar;43(3):1167-74.
  Smith TL, Yuan Z, Cardó-Vila M, Sanchez Claros C, Adem A, Cui MH, Branch CA, Gelovani JG, Libutti SK, Sidman RL, Pasqualini R, Arap W. AAVP displaying octreotide for ligand-directed therapeutic transgene delivery in neuroendocrine tumors of the pancreas. Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):2466-71.
  Stevens AJ, Brown ZZ, Shah NH, Sekar G, Cowburn D, Muir TW. Design of a Split Intein with Exceptional Protein Splicing Activity. J Am Chem Soc. 2016 Feb 24;138(7):2162-5.
  Choi E, Branch C, Cui MH, Yazdanbakhsh K, Mohandas N, Billett HH, Shi PA. No evidence for cell activation or brain vaso-occlusion with plerixafor mobilization in sickle cell mice. Blood Cells Mol Dis. 2016 Mar;57:67-70.
  Kerrigan N, Akabas MH, Betzler TF, Castaldi M, Kelly MS, Levy AS, Reichgott MJ, Ruberman L, Dolan SM. Implementing competency based admissions at the Albert Einstein College of Medicine. Med Educ Online. 2016 Feb 3;21:30000.
  Jerschow E, Ren Z, Hudes G, Sanak M, Morales E, Schuster V, Spivack SD, Rosenstreich D. Utility of low-dose oral aspirin challenges for diagnosis of aspirin-exacerbated respiratory disease. Ann Allergy Asthma Immunol. 2016 Apr;116(4):321-328.
  Kienker PK, Wu Z, Finkelstein A. Topography of the TH5 Segment in the Diphtheria Toxin T-Domain Channel. J Membr Biol. 2016 Apr;249(1-2):181-96.
  Ahmadi MS, Lee HH, Sanchez DA, Friedman AJ, Tar MT, Davies KP, Nosanchuk JD, Martinez LR. Sustained Nitric Oxide-Releasing Nanoparticles Induce Cell Death in Candida albicans Yeast and Hyphal Cells, Preventing Biofilm Formation In Vitro and in a Rodent Central Venous Catheter Model. Antimicrob Agents Chemother. 2016 Mar 25;60(4):2185-94.
  Vetting MW, Bouvier JT, Gerlt JA, Almo SC. Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation. Acta Crystallogr F Struct Biol Commun. 2016 Jan 1;72(Pt 1):36-41.
  Vladimirova A, Patskovsky Y, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Hillerich B, Seidel RD, Richards NG, Almo SC, Raushel FM. Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase. J Am Chem Soc. 2016 Jan 27;138(3):826-36.
  Malachowski WP, Winters M, DuHadaway JB, Lewis-Ballester A, Badir S, Wai J, Rahman M, Sheikh E, LaLonde JM, Yeh SR, Prendergast GC, Muller AJ. O-alkylhydroxylamines as rationally-designed mechanism-based inhibitors of indoleamine 2,3-dioxygenase-1. Eur J Med Chem. 2016 Jan 27; 108:564-76.
  Deniskin R, Frame IJ, Sosa Y, Akabas MH. Targeting the Plasmodium vivax equilibrative nucleoside transporter 1 (PvENT1) for antimalarial drug development. Int J Parasitol Drugs Drug Resist. 2015 Nov 28;6(1):1-11.
  Liang H, Nacharaju P, Friedman A, Friedman JM. Nitric oxide generating/releasing materials. Future Sci OA. 2015;1(1).
  Akabas MH. Cysteine Modification: Probing Channel Structure, Function and Conformational Change. Adv Exp Med Biol. 2015; 869:25-54.
  Cabrales P, Ortiz D, Friedman JM. NO supplementation for transfusion medicine and cardiovascular applications. Future Sci OA. 2015; 1(1). pii: 51.
  Li X, Black M, Xia S, Zhan C, Bertisch HC, Branch CA, DeLisi LE. Subcortical structure alterations impact language processing in individuals with schizophrenia and those at high genetic risk. Schizophr Res. 2015 Dec; 169(1-3):76-82.
  Cui MH, Jayalakshmi K, Liu L, Guha C, Branch CA. In vivo (1) H MRS and (31) P MRSI of the response to cyclocreatine in transgenic mouse liver expressing creatine kinase. NMR Biomed. 2015 Dec; 28(12):1634-44.
  Cui MH, Branch CA, Cahill SM, Quinn TJ, Adem A, Libutti SK, Yuan Z. In vivo proton MR spectroscopy of pancreatic neuroendocrine tumors in a multiple endocrine neoplasia type 1 conditional knockout mouse model. Magn Reson Med. 2015 Nov; 74(5):1221-6.
  Ahn YO, Lee HJ, Kaluka D, Yeh SR, Rousseau DL, Ädelroth P, Gennis RB. The two transmembrane helices of CcoP are sufficient for assembly of the cbb3-type heme-copper oxygen reductase from Vibrio cholerae. Biochim Biophys Acta. 2015 Oct; 1847(10):1231-9.
  Leo L, Yu W, D'Rozario M, Waddell EA, Marenda DR, Baird MA, Davidson MW, Zhou B, Wu B, Baker L, Sharp DJ, Baas PW. Vertebrate Fidgetin Restrains Axonal Growth by Severing Labile Domains of Microtubules. Cell Rep. 2015 Sep 22; 12(11):1723-30.
  Hough LE, Dutta K, Sparks S, Temel DB, Kamal A, Tetenbaum-Novatt J, Rout MP, Cowburn D. The molecular mechanism of nuclear transport revealed by atomic scale measurements. Elife. 2015 Sep 15;4
  Giacco F, Du X, Carratú A, Gerfen GJ, D'Apolito M, Giardino I, Rasola A, Marin O, Divakaruni AS, Murphy AN, Shah MS, Brownlee M. GLP-1 Cleavage Product Reverses Persistent ROS Generation After Transient Hyperglycemia by Disrupting an ROS-Generating Feedback Loop. Diabetes. 2015 Sep; 64(9):3273-84.
  Hayden EY, Kaur P, Williams TL, Matsui H, Yeh SR, Rousseau DL. Heme Stabilization of α-Synuclein Oligomers during Amyloid Fibril Formation. Biochemistry. 2015 Aug 4; 54(30):4599-610.
  Davies KP. Development and therapeutic applications of nitric oxide releasing materials to treat erectile dysfunction. Future Sci OA. 2015 Aug;1(1). pii: FSO53.
  Egawa T, Haber J, Fee JA, Yeh SR, Rousseau DL. Interactions of Cu(B) with Carbon Monoxide in Cytochrome c Oxidase: Origin of the Anomalous Correlation between the Fe-CO and C-O Stretching Frequencies. J Phys Chem B. 2015 Jul 9; 119(27):8509-20.
  Frame IJ, Deniskin R, Arora A, Akabas MH. Purine import into malaria parasites as a target for antimalarial drug development. Ann N Y Acad Sci. 2015 Apr; 1342(1):19-28.
  Fu S, Davies KP. Opiorphin-dependent upregulation of CD73 (a key enzyme in the adenosine signaling pathway) in corporal smooth muscle cells exposed to hypoxic conditions and in corporal tissue in pre-priapic sickle cell mice. Int J Impot Res. 2015 Jul; 27(4):140-5.
  Thomas K, Cameron SA, Almo SC, Burgos ES, Gulab SA, Schramm VL. Active Site and Remote Contributions to Catalysis in Methylthioadenosine Nucleosidases. Biochemistry. 2015 Apr 21; 54(15):2520-9.
  Thomson R, Finkelstein A. Human trypanolytic factor APOL1 forms pH-gated cation-selective channels in planar lipid bilayers: Relevance to trypanosome lysis. Proc Natl Acad Sci U S A. 2015 Mar 3; 112(9):2894-9.
  Kaluka D, Batabyal D, Chiang BY, Poulos TL, Yeh SR. Spectroscopic and Mutagenesis Studies of Human PGRMC1. Biochemistry. 2015 Mar 3; 54(8):1638-47.
  Frame IJ, Deniskin R, Rinderspacher A, Katz F, Deng SX, Moir RD, Adjalley SH, Coburn-Flynn O, Fidock DA, Willis IM, Landry DW, Akabas MH. Yeast-Based High-Throughput Screen Identifies Plasmodium falciparum Equilibrative Nucleoside Transporter 1 Inhibitors That Kill Malaria Parasites. ACS Chem Biol. 2015 Mar 20; 10(3):775-83.
  Akhavan A, Murphy-Chutorian B, Friedman A. Pediatric Dermatology Training During Residency: A Survey of the 2014 Graduating Residents. Pediatr Dermatol. 2015 May-Jun; 32(3):327-32.
  Baltazar LM, Krausz AE, Souza AC, Adler BL, Landriscina A, Musaev T, Nosanchuk JD, Friedman AJ. Trichophyton rubrum is Inhibited by Free and Nanoparticle Encapsulated Curcumin by Induction of Nitrosative Stress after Photodynamic Activation. PLoS One. 2015 Mar 24; 10(3):e0120179.
  Krausz AE, Adler BL, Landriscina A, Rosen JM, Musaev T, Nosanchuk JD, Friedman AJ. Biafine topical emulsion accelerates excisional and burn wound healing in mice. Arch Dermatol Res. 2015 Sep; 307(7):583-94.
  Baltazar LM, Ray A, Santos DA, Cisalpino PS, Friedman AJ, Nosanchuk JD. Antimicrobial photodynamic therapy: an effective alternative approach to control fungal infections. Front Microbiol. 2015 Mar 13; 6:202.
  Schiffmiller A, Finkelstein A. Ion Conductance of the Stem of the Anthrax Toxin Channel during Lethal Factor Translocation. J Mol Biol. 2015 Mar 27; 427(6 Pt A):1211-23.
  Charafeddine RA, Makdisi J, Schairer D, O'Rourke BP, Diaz-Valencia JD, Chouake J, Kutner A, Krausz A, Adler B, Nacharaju P, Liang H, Mukherjee S, Friedman JM, Friedman A, Nosanchuk JD, Sharp DJ. Fidgetin-Like 2: A Microtubule-Based Regulator of Wound Healing. J Invest Dermatol. 2015 Sep; 135(9):2309-18.
  Malashkevich VN, Higgins CD, Almo SC, Lai JR. A Switch from Parallel to Antiparallel Strand Orientation in a Coiled-Coil X-Ray Structure via Two Core Hydrophobic Mutations. Biopolymers. 2015 May;104(3):178-85.
  Kienker PK, Wu Z, Finkelstein A. Mapping the membrane topography of the TH6-TH7 segment of the diphtheria toxin T-domain channel. J Gen Physiol. 2015 Feb; 145(2):107-25.
  Zhang X, Kumar R, Vetting MW, Zhao S, Jacobson MP, Almo SC, Gerlt JA. A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily. J Am Chem Soc. 2015 Feb 4; 137(4):1388-91.
  Mordorski B, Pelgrift R, Adler B, Krausz A, da Costa Neto AB, Liang H, Gunther L, Clendaniel A, Harper S, Friedman JM, Nosanchuk JD, Nacharaju P, Friedman AJ. S-nitrosocaptopril nanoparticles as nitric oxide-liberating and transnitrosylating anti-infective technology. Nanomedicine. 2015 Feb; 11(2):283-91.
  Chitu V, Gokhan S, Gulinello M, Branch CA, Patil M, Basu R, Stoddart C, Mehler MF, Stanley ER. Phenotypic characterization of a Csf1r haploinsufficient mouse model of adult-onset leukodystrophy with axonal spheroids and pigmented glia (ALSP). Neurobiol Dis. 2015 Feb;74:219-28.
  Samanta D, Almo SC. Nectin family of cell-adhesion molecules: structural and molecular aspects of function and specificity. Cell Mol Life Sci. 2015 Feb; 72(4):645-58.
  Fedorov AA, Martí-Arbona R, Nemmara VV, Hitchcock D, Fedorov EV, Almo SC, Raushel FM. Structure of N-formimino-L-glutamate iminohydrolase from Pseudomonas aeruginosa. Biochemistry. 2015 Jan 27; 54(3):890-7.
  Ishigami I, Hikita M, Egawa T, Yeh SR, Rousseau DL. Proton translocation in cytochrome c oxidase: insights from proton exchange kinetics and vibrational spectroscopy. Biochim Biophys Acta. 2015 Jan; 1847(1):98-108.
  Karp JM, Erylimaz E, Cowburn D. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins. J Biomol NMR. 2015 Jan; 61(1):35-45.
  Roche CJ, Talwar A, Palmer AF, Cabrales P, Gerfen G, Friedman JM. Evaluating the capacity to generate and preserve nitric oxide bioactivity in highly purified earthworm erythrocruorin: a giant polymeric hemoglobin with potential blood substitute properties. J Biol Chem. 2015 Jan 2; 290(1):99-117.
  Krausz AE, Adler BL, Cabral V, Navati M, Doerner J, Charafeddine RA, Chandra D, Liang H, Gunther L, Clendaniel A, Harper S, Friedman JM, Nosanchuk JD, Friedman AJ. Curcumin-encapsulated nanoparticles as innovative antimicrobial and wound healing agent. Nanomedicine. 2015 Jan; 11(1):195-206.
  London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry. 2015 Jan 20; 54(2):528-37.
  Morrill GA, Kostellow AB, Gupta RK. Computational analysis of the extracellular domain of the Ca(2+)-sensing receptor: An alternate model for the Ca(2+) sensing region. Biochem Biophys Res Commun. 2015 Mar 27; 459(1):36-41.
  Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC. Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry. 2015 Jan 27; 54(3):909-31.
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