Department of Physiology and Biophysics

Publication Highlights

Publication Highlights in 2016-18

   
  Benoit MPMH, Sosa H. Use of Single Molecule Fluorescence Polarization Microscopy to Study Protein Conformation and Dynamics of Kinesin-Microtubule Complexes. Methods Mol Biol. 2018;1665:199-216.
  Nemeria NS, Gerfen G, Nareddy PR, Yang L, Zhang X, Szostak M, Jordan F. The mitochondrial 2-oxoadipate and 2-oxoglutarate dehydrogenase complexes share their E2 and E3 components for their function and both generate reactive oxygen species. Free Radic Biol Med. 2018 Feb 1;115:136-145.
  Hayama R, Sparks S, Hecht LM, Dutta K, Cabana CM, Karp JM, Rout MP, Cowburn D. Thermodynamic characterization of the multivalent interactions underlying rapid and selective translocation through the nuclear pore complex. J Biol Chem. 2018 Jan 26. [Epub ahead of print]
  Liu Z, Apontes P, Fomenko EV, Chi N, Schuster VL, Kurland IJ, Pessin JE, Chi Y. Mangiferin Accelerates Glycolysis and Enhances Mitochondrial Bioenergetics. Int J Mol Sci. 2018 Jan 9;19(1).
  Sparks S, Temel DB, Rout MP, Cowburn D. Deciphering the "Fuzzy" Interaction of FG Nucleoporins and Transport Factors Using Small-Angle Neutron Scattering. Structure. 2018 Jan 29. [Epub ahead of print]
  Tan K, Meiri A, Mowrey WB, Abbott R, Goodrich JT, Sandler AL, Suri AK, Lipton ML, Wagshul ME. Diffusion tensor imaging and ventricle volume quantification in patients with chronic shunt-treated hydrocephalus: a matched case-control study. J Neurosurg. 2018 Jan 19:1-12.
  Colas RA, Ashton AW, Mukherjee S, Dalli J, Akide-Ndunge OB, Huang H, Desruisseaux MS, Guan F, Jelicks LA, Matos Dos Santos F, Nagajyothi J, Zingman M, Reyes J, Weiss LM, Serhan CN, Tanowitz HB. Trypanosoma cruzi produces the specialized proresolving mediators Resolvin D1, Resolvin D5 and Resolvin E2. Infect Immun. 2018 Jan 22. [Epub ahead of print]
  Jana S, Meng F, Hirsch RE, Friedman JM, Alayash AI. Oxidized Mutant Human Hemoglobins S and E Induce Oxidative Stress and Bioenergetic Dysfunction in Human Pulmonary Endothelial Cells. Front Physiol. 2017 Dec 19;8:1082.
  Lewis-Ballester A, Pham KN, Batabyal D, Karkashon S, Bonanno JB, Poulos TL, Yeh SR. Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1. Nat Commun. 2017 Nov 22;8(1):1693.
  Wang Y, Deng GG, Davies KP. Urothelial MaxiK-activity regulates mucosal and detrusor metabolism. PLoS One. 2017 Dec 27;12(12):e0189387.
  Harding CV, Akabas MH, Andersen OS. History and Outcomes of 50 Years of Physician-Scientist Training in Medical Scientist Training Programs. Acad Med. 2017 Oct;92(10):1390-1398.
  Almeida-Paes R, Almeida-Silva F, Pinto GCM, Almeida MA, Muniz MM, Pizzini CV, Gerfen GJ, Nosanchuk JD, Zancopé-Oliveira RM. L-tyrosine induces the production of a pyomelanin-like pigment by the parasitic yeast-form of Histoplasma capsulatum. Med Mycol. 2017 Sep 12. [Epub ahead of print]
  Wang Y, Wu B, Lu P, Zhang D, Wu B, Varshney S, Del Monte-Nieto G, Zhuang Z, Charafeddine R, Kramer AH, Sibinga NE, Frangogiannis NG, Kitsis RN, Adams RH, Alitalo K, Sharp DJ, Harvey RP, Stanley P, Zhou B. Uncontrolled angiogenic precursor expansion causes coronary artery anomalies in mice lacking Pofut1. Nat Commun. 2017 Sep 18;8(1):578.
  Austin TO, Matamoros AJ, Friedman JM, Friedman AJ, Nacharaju P, Yu W, Sharp DJ, Baas PW. Nanoparticle Delivery of Fidgetin siRNA as a Microtubule-based Therapy to Augment Nerve Regeneration. Sci Rep. 2017 Aug 29;7(1):9675.
  Ishigami I, Zatsepin NA, Hikita M, Conrad CE, Nelson G, Coe JD, Basu S, Grant TD, Seaberg MH, Sierra RG, Hunter MS, Fromme P, Fromme R, Yeh SR, Rousseau DL. Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature. Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8011-8016.
  Ware JS, Wain LV, Channavajjhala SK, Jackson VE, Edwards E, Lu R, Siew K, Jia W, Shrine N, Kinnear S, Jalland M, Henry AP, Clayton J, O'Shaughnessy KM, Tobin MD, Schuster V, Cook S, Hall IP, Glover M. Phenotypic and pharmacogenetic evaluation of patients with thiazide-induced hyponatremia. J Clin Invest. 2017 Aug 7. pii: 89812. doi: 10.1172/JCI89812. [Epub ahead of print]
  Glass LN, Swapna G, Chavadi SS, Tufariello JM, Mi K, Drumm JE, Lam TT, Zhu G, Zhan C, Vilchéze C, Arcos J, Chen Y, Bi L, Mehta S, Porcelli SA, Almo SC, Yeh SR, Jacobs WR Jr, Torrelles JB, Chan J. Mycobacterium tuberculosis universal stress protein Rv2623 interacts with the putative ATP binding cassette (ABC) transporter Rv1747 to regulate mycobacterial growth. PLoS Pathog. 2017 Jul 28;13(7):e1006515.
  Stevens AJ, Sekar G, Shah NH, Mostafavi AZ, Cowburn D, Muir TW. A promiscuous split intein with expanded protein engineering applications. Proc Natl Acad Sci U S A. 2017 Aug 8;114(32):8538-8543.
  Mordorski B, Costa-Orlandi CB, Baltazar LM, Carreño LJ, Landriscina A, Rosen J, Navati M, Mendes-Giannini MJS, Friedman JM, Nosanchuk JD, Friedman AJ. Topical nitric oxide releasing nanoparticles are effective in a murine model of dermal Trichophyton rubrum dermatophytosis. Nanomedicine. 2017 Jul 13;13(7):2267-2270.
  Renda F, Pellacani C, Strunov A, Bucciarelli E, Naim V, Bosso G, Kiseleva E, Bonaccorsi S, Sharp DJ, Khodjakov A, Gatti M, Somma MP. The Drosophila orthologue of the INT6 onco-protein regulates mitotic microtubule growth and kinetochore structure. PLoS Genet. 2017 May 15;13(5):e1006784.
  Hirsch RE, Sibmooh N, Fucharoen S, Friedman JM. HbE/β-Thalassemia and Oxidative Stress: The Key to Pathophysiological Mechanisms and Novel Therapeutics. Antioxid Redox Signal. 2017 May 10;26(14):794-813.
  Cui MH, Suzuka SM, Branch NA, Ambadipudi K, Thangaswamy S, Acharya SA, Billett HH, Branch CA. Brain neurochemical and hemodynamic findings in the NY1DD mouse model of mild sickle cell disease. NMR Biomed. 2017 May;30(5). doi: 10.1002/nbm.3692.
  Nemeria NS, Gerfen G, Guevara E, Nareddy PR, Szostak M, Jordan F. The human Krebs cycle 2-oxoglutarate dehydrogenase complex creates an additional source of superoxide/hydrogen peroxide from 2-oxoadipate as alternative substrate. Free Radic Biol Med. 2017 Apr 21;108:644-654.
  Rodionova IA, Vetting MW, Li X, Almo SC, Osterman AL, Rodionov DA. A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. Nucleic Acids Res. 2017 Apr 20;45(7):3785-3799.
  Park HB, Sampathkumar P, Perez CE, Lee JH, Tran J, Bonanno JB, Hallem EA, Almo SC, Crawford JM. Stilbene epoxidation and detoxification in a Photorhabdus luminescens-nematode symbiosis. J Biol Chem. 2017 Apr 21;292(16):6680-6694.
  Draganski AR, Friedman JM, Ludescher RD. Solvent-Slaved Dynamic Processes Observed by Tryptophan Phosphorescence of Human Serum Albumin. Biophys J. 2017 Mar 14;112(5):881-891.
  Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Structure. 2017 Mar 7;25(3):434-445.
  Lázár-Molnár E, Scandiuzzi L, Basu I, Quinn T, Sylvestre E, Palmieri E, Ramagopal UA, Nathenson SG, Guha C, Almo SC. Structure-guided development of a high-affinity human Programmed Cell Death-1: Implications for tumor immunotherapy. EBioMedicine. 2017 Mar;17:30-44.
  Karp JM, Sparks S, Cowburn D. Effects of FGFR2 kinase activation loop dynamics on catalytic activity. PLoS Comput Biol. 2017 Feb 2;13(2):e1005360.
  Cui MH, Suzuka SM, Branch NA, Ambadipudi K, Thangaswamy S, Acharya SA, Billett HH, Branch CA. Brain neurochemical and hemodynamic findings in the NY1DD mouse model of mild sickle cell disease. NMR Biomed. 2017 Feb 10. doi: 10.1002/nbm.3692. [Epub ahead of print]
  Jani VP, Jelvani A, Moges S, Nacharaju P, Roche C, Dantsker D, Palmer A, Friedman JM, Cabrales P. Polyethylene Glycol Camouflaged Earthworm Hemoglobin. PLoS One. 2017 Jan 18;12(1):e0170041.
  Samanta D, Guo H, Rubinstein R, Ramagopal UA, Almo SC. Structural, mutational and biophysical studies reveal a canonical mode of molecular recognition between immune receptor TIGIT and nectin-2. Mol Immunol. 2017 Jan;81:151-159.
  Metcalf B, Chuang C, Dufu K, Patel MP, Silva-Garcia A, Johnson C, Lu Q, Partridge JR, Patskovska L, Patskovsky Y, Almo SC, Jacobson MP, Hua L, Xu Q, Gwaltney SL 2nd, Yee C, Harris J, Morgan BP, James J, Xu D, Hutchaleelaha A, Paulvannan K, Oksenberg D, Li Z. Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin. ACS Med Chem Lett. 2017 Jan 23;8(3):321-326.
  Jakes KS. The Colicin E1 TolC Box: Identification of a Domain Required for Colicin E1 Cytotoxicity and TolC Binding. J Bacteriol. 2016 Dec 13;199(1). pii: e00412-16.
  Mihu MR, Cabral V, Pattabhi R, Tar MT, Davies KP, Friedman AJ, Martinez LR, Nosanchuk JD. Sustained Nitric Oxide-Releasing Nanoparticles Interfere with Methicillin-Resistant Staphylococcus aureus Adhesion and Biofilm Formation in a Rat Central Venous Catheter Model. Antimicrob Agents Chemother. 2016 Dec 27;61(1).
  Jerschow E, Edin ML, Pelletier T, Abuzeid WM, Akbar NA, Gibber M, Fried M, Lih FB, Gruzdev A, Bradbury JA, Han W, Hudes G, Keskin T, Schuster VL, Spivack S, Zeldin DC, Rosenstreich D. Plasma 15-Hydroxyeicosatetraenoic Acid Predicts Treatment Outcomes in Aspirin-Exacerbated Respiratory Disease. J Allergy Clin Immunol Pract. 2016 Dec 29. pii: S2213-2198(16)30579-7. doi: 10.1016/j.jaip.2016.11.021. [Epub ahead of print]
  Liu W, Ramagopal U, Cheng H, Bonanno JB, Toro R, Bhosle R, Zhan C, Almo SC. Crystal Structure of the Complex of Human FasL and Its Decoy Receptor DcR3. Structure. 2016 Nov 1;24(11):2016-2023.
  Batabyal D, Lewis-Ballester A, Yeh SR, Poulos TL. A Comparative Analysis of the Effector Role of Redox Partner Binding in Bacterial P450s. Biochemistry. 2016 Nov 29;55(47):6517-6523.
  Wang Y, Wach JY, Sheehan P, Zhong C, Zhan C, Harris R, Almo SC, Bishop J, Haggarty SJ, Ramek A, Berry KN, O'Herin C, Koehler AN, Hung AW, Young DW. Diversity-Oriented Synthesis as a Strategy for Fragment Evolution against GSK3β. ACS Med Chem Lett. 2016 Jul 14;7(9):852-6.
  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]
  Wang Y, Deng GG, Davies KP. Novel insights into development of diabetic bladder disorder provided by metabolomic analysis of the rat nondiabetic and diabetic detrusor and urothelial layer. Am J Physiol Endocrinol Metab. 2016 Aug 1;311(2):E471-9.
  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.
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