Protein Crystallography Facility

  • Publications resulting from core engagement

    Laboratory
    Year
    Citation
    Technique(s)
    Washington 2008 Freudenthal BD, Ramaswamy S, Hingorani MM, Washington MT. Structure of a mutant form of proliferating cell nuclear antigen that blocks translesion DNA synthesis. Biochemistry. 2008 Dec 16;47(50):13354-61. doi: 10.1021/bi8017762. PubMed PMID: 19053247; PubMed Central PMCID: PMC2703463. Modeling
    Crystallography
    Purification/TPC 
    Artemyev 2009 Barren B, Gakhar L, Muradov H, Boyd KK, Ramaswamy S, Artemyev NO. Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit. EMBO J. 2009 Nov 18;28(22):3613-22. doi: 10.1038/emboj.2009.284. Epub 2009 Oct 1. PubMed PMID: 19798052; PubMed Central PMCID: PMC2782096. Modeling
    Crystallography
    Purification/TPC
    Light Scattering 
    McCray 2009  Jia HP, Look DC, Tan P, Shi L, Hickey M, Gakhar L, Chappell MC, Wohlford-Lenane C, McCray PB Jr. Ectodomain shedding of angiotensin converting enzyme 2 in human airway epithelia. Am J Physiol Lung Cell Mol Physiol. 2009 Jul;297(1):L84-96. doi: 10.1152/ajplung.00071.2009. Epub 2009 May 1. PubMed PMID: 19411314; PubMed Central PMCID: PMC2711803. Modeling
    Ramaswamy 2009 Little HJ, Rorick NK, Su LI, Baldock C, Malhotra S, Jowitt T, Gakhar L, Subramanian R, Schutte BC, Dixon MJ, Shore P. Missense mutations that cause Van der Woude syndrome and popliteal pterygium syndrome affect the DNA-binding and transcriptional activation functions of IRF6. Hum Mol Genet. 2009 Feb 1;18(3):535-45. doi: 10.1093/hmg/ddn381. Epub 2008 Nov 26. PubMed PMID: 19036739; PubMed Central PMCID: PMC2638798. Modeling
    CD 
    Ramaswamy 2009 Barren B, Gakhar L, Muradov H, Boyd KK, Ramaswamy S, Artemyev NO. Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit. EMBO J. 2009 Nov 18;28(22):3613-22. doi: 10.1038/emboj.2009.284. Epub 2009 Oct 1. PubMed PMID: 19798052; PubMed Central PMCID: PMC2782096. Modeling
    Crystallography
    Purification/TPC
    Light Scattering
    Washington 2009 Freudenthal BD, Gakhar L, Ramaswamy S, Washington MT. A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactions. Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):560-6. doi: 10.1107/S0907444909011329. Epub 2009 May 15. PubMed PMID: 19465770; PubMed Central PMCID: PMC2685733. Modeling
    Crystallography
    Purification/TPC
    McCray 2010 Gakhar L, Bartlett JA, Penterman J, Mizrachi D, Singh PK, Mallampalli RK, Ramaswamy S, McCray PB Jr. PLUNC is a novel airway surfactant protein with anti-biofilm activity. PLoS One. 2010 Feb 9;5(2):e9098. doi: 10.1371/journal.pone.0009098. PubMed PMID: 20161732; PubMed Central PMCID: PMC2817724. Purification/TPC
    CD
    Misc 
    Piper 2010 Pashkova N, Gakhar L, Winistorfer SC, Yu L, Ramaswamy S, Piper RC. WD40 repeat propellers define a ubiquitin-binding domain that regulates turnover of F box proteins. Mol Cell. 2010 Nov 12;40(3):433-43. doi: 10.1016/j.molcel.2010.10.018. PubMed PMID: 21070969; PubMed Central PMCID: PMC3266742. Modeling
    Crystallography
    Purification/TPC 
    Ramaswamy 2010 Pashkova N, Gakhar L, Winistorfer SC, Yu L, Ramaswamy S, Piper RC. WD40 repeat propellers define a ubiquitin-binding domain that regulates turnover of F box proteins. Mol Cell. 2010 Nov 12;40(3):433-43. doi: 10.1016/j.molcel.2010.10.018. PubMed PMID: 21070969; PubMed Central PMCID: PMC3266742. Misc
    Washington 2010 Freudenthal BD, Gakhar L, Ramaswamy S, Washington MT. Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange. Nat Struct Mol Biol. 2010 Apr;17(4):479-84. doi: 10.1038/nsmb.1776. Epub 2010 Mar 21. PubMed PMID: 20305653; PubMed Central PMCID: PMC2920209. Modeling
    Crystallography
    Purification/TPC 
    Wold 2010 Hass CS, Gakhar L, Wold MS. Functional characterization of a cancer causing mutation in human replication protein A. Mol Cancer Res. 2010 Jul;8(7):1017-26. doi: 10.1158/1541-7786.MCR-10-0161. Epub 2010 Jun 29. PubMed PMID: 20587534; PubMed Central PMCID: PMC2905489. Modeling
    Fuentes 2011 Shepherd TR, Hard RL, Murray AM, Pei D, Fuentes EJ. Distinct ligand specificity of the Tiam1 and Tiam2 PDZ domains. Biochemistry. 2011 Mar 1;50(8):1296-308. doi: 10.1021/bi1013613. Epub 2011 Feb 4. PubMed PMID: 21192692; PubMed Central PMCID: PMC3059893. Crystallography
    Fuentes 2011 Shepherd TR, Fuentes EJ. Structural and thermodynamic analysis of PDZ-ligand interactions. Methods Enzymol. 2011;488:81-100. doi: 10.1016/B978-0-12-381268-1.00004-5. PubMed PMID: 21195225. Crystallography
    Horswill 2011 Kavanaugh JS, Gakhar L, Horswill AR. The structure of LsrB from Yersinia pestis complexed with autoinducer-2. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Dec 1;67(Pt 12):1501-5. doi: 10.1107/S1744309111042953. Epub 2011 Nov 29. PubMed PMID: 22139152; PubMed Central PMCID: PMC3232125. Crystallography
    Purification/TPC
    Light Scattering 
    McCray 2011 Bartlett JA, Gakhar L, Penterman J, Singh PK, Mallampalli RK, Porter E, McCray PB Jr. PLUNC: a multifunctional surfactant of the airways. Biochem Soc Trans. 2011 Aug;39(4):1012-6. doi: 10.1042/BST0391012. Erratum in: Biochem Soc Trans. 2011 Oct;39(5):1549. PubMed PMID: 21787339; PubMed Central PMCID: PMC3572202. Purification/TPC
    Misc 
    Washington 2011 Freudenthal BD, Brogie JE, Gakhar L, Kondratick CM, Washington MT. Crystal structure of SUMO modified proliferating cell nuclear antigen. J Mol Biol. 2011 Feb 11;406(1):9-17. doi: 10.1016/j.jmb.2010.12.015. Epub 2010 Dec 15. PubMed PMID: 21167178; PubMed Central PMCID: PMC3193175. Modeling
    Crystallography
    Purification/TPC 
    Washington 2011 Tsutakawa SE, Van Wynsberghe AW, Freudenthal BD, Weinacht CP, Gakhar L, Washington MT, Zhuang Z, Tainer JA, Ivanov I. Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA. Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17672-7. doi: 10.1073/pnas.1110480108. Epub 2011 Oct 17. PubMed PMID: 22006297; PubMed Central PMCID: PMC3203759. Purification/TPC
    SAXS 
    Plapp 2012 Plapp BV, Ramaswamy S. Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Biochemistry. 2012 May 15;51(19):4035-48. doi: 10.1021/bi300378n. Epub 2012 May 1. PubMed PMID: 22531044; PubMed Central PMCID: PMC3352959. Crystallography
    Misc 
    Subramanian 2012 Summers RM, Louie TM, Yu CL, Gakhar L, Louie KC, Subramanian M. Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purinealkaloids. J Bacteriol. 2012 Apr;194(8):2041-9. doi: 10.1128/JB.06637-11. Epub 2012 Feb 10. PubMed PMID: 22328667; PubMed Central PMCID: PMC3318484. Modeling
    Subramanian 2012 Mohanty SK, Yu CL, Das S, Louie TM, Gakhar L, Subramanian M. Delineation of the caffeine C-8 oxidation pathway in Pseudomonas sp. strain CBB1 via characterization of a new trimethyluric acid monooxygenase and genes involved in trimethyluric acid metabolism. J Bacteriol. 2012 Aug;194(15):3872-82. doi: 10.1128/JB.00597-12. Epub 2012 May 18. PubMed PMID: 22609920; PubMed Central PMCID: PMC3416557. Modeling
    Mahajan 2012 Mahajan VB, Skeie JM, Bassuk AG, Fingert JH, Braun TA, Daggett HT, Folk JC, Sheffield VC, Stone EM. Calpain-5 mutations cause autoimmune uveitis, retinal neovascularization, and photoreceptor degeneration. PLoS Genet.
    2012;8(10):e1003001. doi: 10.1371/journal.pgen.1003001. Epub 2012 Oct 4. PubMed PMID: 23055945; PubMed Central PMCID: PMC3464205.
    Modeling
    Li 2012 Chen L, Lin YL, Peng G, Li F. Structural basis for multifunctional roles of mammalian aminopeptidase N. Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17966-71. doi: 10.1073/pnas.1210123109. Epub 2012 Oct 15. PubMed PMID 23071329; PubMed Central PMCID: PMC3497818. Light Scattering
    Artemyev 2013 Majumder A, Gopalakrishna KN, Cheguru P, Gakhar L, Artemyev NO. Interaction of aryl hydrocarbon receptor-interacting protein-like 1 with the farnesyl moiety. J Biol Chem. 2013 Jun 4. [Epub ahead of print] PubMed PMID: 23737531. Modeling
    Purification/TPC
    Light Scattering
    SAXS
    CD 
    Fuentes 2013 Liu X, Shepherd TR, Murray AM, Xu Z, Fuentes EJ. The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics. Structure. 2013 Mar 5;21(3):342-54. doi: 10.1016/j.str.2013.01.004. Epub 2013 Feb 7. PubMed PMID: 23395182. Crystallography
    Fuentes 2013 Joshi M, Gakhar L, Fuentes EJ. High-resolution structure of the Tiam1 PHn-CC-Ex domain. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jul 1;69(Pt 7):744-52. doi: 10.1107/S1744309113014206. Epub 2013 Jun 27. PubMed PMID: 23832200. Modeling
    Crystallography
    Light Scattering
    SAXS 
    Bassuk 2013 Darbro BW, Mahajan VB, Gakhar L, Skeie JM, Campbell E, Wu S, Bing X, Millen KJ, Dobyns WB, Kessler JA, Jalali A, Cremer J, Segre A, Manak JR, Aldinger KA, Suzuki S, Natsume N, Ono M, Hai HD, Viet LT, Loddo S, Valente EM, Bernardini L, Ghonge N, Ferguson PJ, Bassuk AG. Mutations in Extracellular Matrix Genes NID1 and LAMC1 Cause Autosomal Dominant Dandy-Walker Malformation and Occipital Cephaloceles. Hum Mutat. 2013 May 14. doi: 10.1002/humu.22351. [Epub ahead of print] PubMed PMID: 23674478. Modeling
    McCray 2013
    Kohlgraf KG, Ackermann AR, Burnell KK, Srikantha RN, Joly SA, Bartlett JA, Gakhar L, Johnson GK, McCray PB Jr, Guthmiller JM, Brogden KA. Quantitation of SPLUNC1 in saliva with an xMAP particle-based antibody capture and detection immunoassay. Arch Oral Biol. 2012 Feb;57(2):197-204. doi: 10.1016/j.archoralbio.2011.08.013. Epub 2011 Sep 16. PubMed PMID: 21925642; PubMed Central PMCID: PMC3260398. Purification/TPC
    Piper 2013 Pashkova N, Gakhar L, Winistorfer SC, Sunshine AB, Rich M, Dunham MJ, Yu L, Piper RC. The yeast alix homolog bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes. Dev Cell. 2013 Jun 10;25(5):520-33. doi: 10.1016/j.devcel.2013.04.007. Epub 2013 May 30. PubMed PMID: 23726974. Modeling
    Crystallography
    Light Scattering
    SAXS 
    Washington 2013 Pryor JM, Gakhar L, Washington MT. Structure and functional analysis of the BRCT domain of translesion synthesis DNA polymerase Rev1. Biochemistry. 2013 Jan 8; 52(1):254-63. doi: 10.1021/bi301572z. Epub 2012 Dec 20. PubMed PMID: 23240687; PubMed Central PMCID: PMC3580236. Modeling
    Crystallography
    Purification/TPC
    Light Scattering 
    McCray 2013 Liu Y, Bartlett JA, Di ME, Bomberger JM, Chan YR, Gakhar L, Mallampalli RK, McCray PB Jr, Di YP. SPLUNC1/BPIFA1 contributes to pulmonary host defense against Klebsiella pneumoniae respiratory infection. Am J Pathol. 2013 May;182(5):1519-31. doi: 10.1016/j.ajpath.2013.01.050. Epub 2013 Mar 15. PubMed PMID: 23499554; PubMed Central PMCID: PMC3644735. Purification/TPC