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Items: 1 to 50 of 54

1.

The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets.

Hegde RP, Fedorov AA, Sauder JM, Burley SK, Almo SC, Ramagopal UA.

Acta Crystallogr F Struct Biol Commun. 2017 Apr 1;73(Pt 4):184-195. doi: 10.1107/S2053230X17002680. Epub 2017 Mar 22.

2.

Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.

Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Chait BT, Almo SC, Rout MP, Sali A.

Mol Cell Proteomics. 2014 Nov;13(11):2911-26. doi: 10.1074/mcp.M114.040915. Epub 2014 Aug 19.

3.

Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate.

Korczynska M, Xiang DF, Zhang Z, Xu C, Narindoshvili T, Kamat SS, Williams HJ, Chang SS, Kolb P, Hillerich B, Sauder JM, Burley SK, Almo SC, Swaminathan S, Shoichet BK, Raushel FM.

Biochemistry. 2014 Jul 22;53(28):4727-38. doi: 10.1021/bi500595c. Epub 2014 Jul 9.

4.

Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.

Odokonyero D, Sakai A, Patskovsky Y, Malashkevich VN, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Agarwal R, Wang C, Ozerova ND, Yew WS, Sauder JM, Swaminathan S, Burley SK, Almo SC, Glasner ME.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8535-40. doi: 10.1073/pnas.1318703111. Epub 2014 May 28.

5.

Structural basis for the divergence of substrate specificity and biological function within HAD phosphatases in lipopolysaccharide and sialic acid biosynthesis.

Daughtry KD, Huang H, Malashkevich V, Patskovsky Y, Liu W, Ramagopal U, Sauder JM, Burley SK, Almo SC, Dunaway-Mariano D, Allen KN.

Biochemistry. 2013 Aug 13;52(32):5372-86. doi: 10.1021/bi400659k. Epub 2013 Jul 29.

6.

Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.

Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley SK, Sali A, Rout MP, Almo SC.

Structure. 2013 Apr 2;21(4):560-71. doi: 10.1016/j.str.2013.02.005. Epub 2013 Mar 14.

7.

Crystal structure of the human PRMT5:MEP50 complex.

Antonysamy S, Bonday Z, Campbell RM, Doyle B, Druzina Z, Gheyi T, Han B, Jungheim LN, Qian Y, Rauch C, Russell M, Sauder JM, Wasserman SR, Weichert K, Willard FS, Zhang A, Emtage S.

Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17960-5. doi: 10.1073/pnas.1209814109. Epub 2012 Oct 15.

8.

1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum.

Warlick BP, Evans BS, Erb TJ, Ramagopal UA, Sriram J, Imker HJ, Sauder JM, Bonanno JB, Burley SK, Tabita FR, Almo SC, Sweedler JS, Gerlt JA.

Biochemistry. 2012 Oct 23;51(42):8324-6. doi: 10.1021/bi301215g. Epub 2012 Oct 8.

9.

Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases.

Garside EL, Schellenberg MJ, Gesner EM, Bonanno JB, Sauder JM, Burley SK, Almo SC, Mehta G, MacMillan AM.

RNA. 2012 Nov;18(11):2020-8. doi: 10.1261/rna.033100.112. Epub 2012 Sep 24.

10.

Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata.

Sampathkumar P, Kim SJ, Manglicmot D, Bain KT, Gilmore J, Gheyi T, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Matsui T, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Almo SC, Burley SK.

Proteins. 2012 Aug;80(8):2110-6. doi: 10.1002/prot.24102. Epub 2012 Jun 4.

11.

Structure and catalytic mechanism of LigI: insight into the amidohydrolase enzymes of cog3618 and lignin degradation.

Hobbs ME, Malashkevich V, Williams HJ, Xu C, Sauder JM, Burley SK, Almo SC, Raushel FM.

Biochemistry. 2012 Apr 24;51(16):3497-507. doi: 10.1021/bi300307b. Epub 2012 Apr 9.

12.

The catalase activity of diiron adenine deaminase.

Kamat SS, Holmes-Hampton GP, Bagaria A, Kumaran D, Tichy SE, Gheyi T, Zheng X, Bain K, Groshong C, Emtage S, Sauder JM, Burley SK, Swaminathan S, Lindahl PA, Raushel FM.

Protein Sci. 2011 Dec;20(12):2080-94. doi: 10.1002/pro.748. Epub 2011 Nov 9.

13.

Structural variation in bacterial glyoxalase I enzymes: investigation of the metalloenzyme glyoxalase I from Clostridium acetobutylicum.

Suttisansanee U, Lau K, Lagishetty S, Rao KN, Swaminathan S, Sauder JM, Burley SK, Honek JF.

J Biol Chem. 2011 Nov 4;286(44):38367-74. doi: 10.1074/jbc.M111.251603. Epub 2011 Sep 13.

14.

Pa0148 from Pseudomonas aeruginosa catalyzes the deamination of adenine.

Goble AM, Zhang Z, Sauder JM, Burley SK, Swaminathan S, Raushel FM.

Biochemistry. 2011 Aug 2;50(30):6589-97. doi: 10.1021/bi200868u. Epub 2011 Jul 6.

15.

Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy.

Shi W, Punta M, Bohon J, Sauder JM, D'Mello R, Sullivan M, Toomey J, Abel D, Lippi M, Passerini A, Frasconi P, Burley SK, Rost B, Chance MR.

Genome Res. 2011 Jun;21(6):898-907. doi: 10.1101/gr.115097.110. Epub 2011 Apr 11.

16.

Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex.

Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley SK.

Proteins. 2011 May;79(5):1672-7. doi: 10.1002/prot.22973. Epub 2011 Mar 1. No abstract available.

17.

Enzymatic deamination of the epigenetic base N-6-methyladenine.

Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM.

J Am Chem Soc. 2011 Feb 23;133(7):2080-3. doi: 10.1021/ja110157u. Epub 2011 Jan 28.

18.

Catalytic mechanism and three-dimensional structure of adenine deaminase.

Kamat SS, Bagaria A, Kumaran D, Holmes-Hampton GP, Fan H, Sali A, Sauder JM, Burley SK, Lindahl PA, Swaminathan S, Raushel FM.

Biochemistry. 2011 Mar 22;50(11):1917-27. doi: 10.1021/bi101788n. Epub 2011 Feb 4.

19.

Structural and functional studies of fatty acyl adenylate ligases from E. coli and L. pneumophila.

Zhang Z, Zhou R, Sauder JM, Tonge PJ, Burley SK, Swaminathan S.

J Mol Biol. 2011 Feb 18;406(2):313-24. doi: 10.1016/j.jmb.2010.12.011. Epub 2010 Dec 23.

20.

Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.

Wisedchaisri G, Dranow DM, Lie TJ, Bonanno JB, Patskovsky Y, Ozyurt SA, Sauder JM, Almo SC, Wasserman SR, Burley SK, Leigh JA, Gonen T.

Structure. 2010 Nov 10;18(11):1512-21. doi: 10.1016/j.str.2010.08.014.

21.

Structural bases of PAS domain-regulated kinase (PASK) activation in the absence of activation loop phosphorylation.

Kikani CK, Antonysamy SA, Bonanno JB, Romero R, Zhang FF, Russell M, Gheyi T, Iizuka M, Emtage S, Sauder JM, Turk BE, Burley SK, Rutter J.

J Biol Chem. 2010 Dec 24;285(52):41034-43. doi: 10.1074/jbc.M110.157594. Epub 2010 Oct 13.

22.

Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.

Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, Burley SK.

Proteins. 2010 Nov 1;78(14):3056-62. doi: 10.1002/prot.22829. No abstract available.

23.

Mass spectrometry guided in situ proteolysis to obtain crystals for X-ray structure determination.

Gheyi T, Rodgers L, Romero R, Sauder JM, Burley SK.

J Am Soc Mass Spectrom. 2010 Oct;21(10):1795-801. doi: 10.1016/j.jasms.2010.06.015. Epub 2010 Jul 7.

24.

Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily .

Xiang DF, Patskovsky Y, Xu C, Fedorov AA, Fedorov EV, Sisco AA, Sauder JM, Burley SK, Almo SC, Raushel FM.

Biochemistry. 2010 Aug 10;49(31):6791-803. doi: 10.1021/bi100897u.

25.

Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase .

Hall RS, Agarwal R, Hitchcock D, Sauder JM, Burley SK, Swaminathan S, Raushel FM.

Biochemistry. 2010 May 25;49(20):4374-82. doi: 10.1021/bi100252s.

26.

Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145.

Sampathkumar P, Ozyurt SA, Do J, Bain KT, Dickey M, Rodgers LA, Gheyi T, Sali A, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sauder JM, Burley SK.

Proteins. 2010 Jun;78(8):1992-8. doi: 10.1002/prot.22707. No abstract available.

27.

Structures of PHR domains from Mus musculus Phr1 (Mycbp2) explain the loss-of-function mutation (Gly1092-->Glu) of the C. elegans ortholog RPM-1.

Sampathkumar P, Ozyurt SA, Miller SA, Bain KT, Rutter ME, Gheyi T, Abrams B, Wang Y, Atwell S, Luz JG, Thompson DA, Wasserman SR, Emtage JS, Park EC, Rongo C, Jin Y, Klemke RL, Sauder JM, Burley SK.

J Mol Biol. 2010 Apr 9;397(4):883-92. doi: 10.1016/j.jmb.2010.02.017. Epub 2010 Feb 13.

28.

The hunt for 8-oxoguanine deaminase.

Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK, Almo SC, Raushel FM.

J Am Chem Soc. 2010 Feb 17;132(6):1762-3. doi: 10.1021/ja909817d.

29.

Structure and dynamics of NBD1 from CFTR characterized using crystallography and hydrogen/deuterium exchange mass spectrometry.

Lewis HA, Wang C, Zhao X, Hamuro Y, Conners K, Kearins MC, Lu F, Sauder JM, Molnar KS, Coales SJ, Maloney PC, Guggino WB, Wetmore DR, Weber PC, Hunt JF.

J Mol Biol. 2010 Feb 19;396(2):406-30. doi: 10.1016/j.jmb.2009.11.051. Epub 2009 Nov 26.

PMID:
19944699
30.

SGX523 is an exquisitely selective, ATP-competitive inhibitor of the MET receptor tyrosine kinase with antitumor activity in vivo.

Buchanan SG, Hendle J, Lee PS, Smith CR, Bounaud PY, Jessen KA, Tang CM, Huser NH, Felce JD, Froning KJ, Peterman MC, Aubol BE, Gessert SF, Sauder JM, Schwinn KD, Russell M, Rooney IA, Adams J, Leon BC, Do TH, Blaney JM, Sprengeler PA, Thompson DA, Smyth L, Pelletier LA, Atwell S, Holme K, Wasserman SR, Emtage S, Burley SK, Reich SH.

Mol Cancer Ther. 2009 Dec;8(12):3181-90. doi: 10.1158/1535-7163.MCT-09-0477.

31.

Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis .

Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA.

Biochemistry. 2009 Dec 8;48(48):11546-58. doi: 10.1021/bi901731c.

32.

Structural studies on cytosolic domain of magnesium transporter MgtE from Enterococcus faecalis.

Ragumani S, Sauder JM, Burley SK, Swaminathan S.

Proteins. 2010 Feb 1;78(2):487-91. doi: 10.1002/prot.22585. No abstract available.

33.

Structure of a microsporidian methionine aminopeptidase type 2 complexed with fumagillin and TNP-470.

Alvarado JJ, Nemkal A, Sauder JM, Russell M, Akiyoshi DE, Shi W, Almo SC, Weiss LM.

Mol Biochem Parasitol. 2009 Dec;168(2):158-67. doi: 10.1016/j.molbiopara.2009.07.008. Epub 2009 Aug 4.

34.

Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes.

Xiang DF, Xu C, Kumaran D, Brown AC, Sauder JM, Burley SK, Swaminathan S, Raushel FM.

Biochemistry. 2009 Jun 2;48(21):4567-76. doi: 10.1021/bi900453u.

35.

Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes.

Xiang DF, Patskovsky Y, Xu C, Meyer AJ, Sauder JM, Burley SK, Almo SC, Raushel FM.

Biochemistry. 2009 May 5;48(17):3730-42. doi: 10.1021/bi900111q.

36.

Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin.

Leiman PG, Basler M, Ramagopal UA, Bonanno JB, Sauder JM, Pukatzki S, Burley SK, Almo SC, Mekalanos JJ.

Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4154-9. doi: 10.1073/pnas.0813360106. Epub 2009 Feb 27.

37.

Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes.

Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, Rutter ME, Bain K, Chang S, Gheyi T, Sauder JM, Burley SK, Babbitt PC, Almo SC, Gerlt JA.

Biochemistry. 2009 Feb 24;48(7):1445-53. doi: 10.1021/bi802277h. Erratum in: Biochemistry. 2009 Mar 24;48(11):2569-70.

38.

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.

Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A.

J Struct Funct Genomics. 2009 Apr;10(2):107-25. doi: 10.1007/s10969-008-9056-5. Epub 2009 Feb 14.

39.

Protein production and purification.

Structural Genomics Consortium; China Structural Genomics Consortium; Northeast Structural Genomics Consortium, Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schütz A, Heinemann U, Yokoyama S, Büssow K, Gunsalus KC.

Nat Methods. 2008 Feb;5(2):135-46. doi: 10.1038/nmeth.f.202. Review. Erratum in: Nat Methods. 2008 Apr;5(4):369. Hallberg, B Martin [added].

40.

Structural genomics of protein phosphatases.

Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang ZY, Lawrence DS, Burley SK.

J Struct Funct Genomics. 2007 Sep;8(2-3):121-40. Epub 2007 Dec 5. Review.

41.

New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative.

Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, Burley SK.

J Struct Funct Genomics. 2005;6(2-3):225-32.

PMID:
16211523
42.

High-throughput limited proteolysis/mass spectrometry for protein domain elucidation.

Gao X, Bain K, Bonanno JB, Buchanan M, Henderson D, Lorimer D, Marsh C, Reynes JA, Sauder JM, Schwinn K, Thai C, Burley SK.

J Struct Funct Genomics. 2005;6(2-3):129-34.

PMID:
16211509
43.

Structural analysis of a set of proteins resulting from a bacterial genomics project.

Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ.

Proteins. 2005 Sep 1;60(4):787-96.

PMID:
16021622
44.

Impact of the deltaF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structure.

Lewis HA, Zhao X, Wang C, Sauder JM, Rooney I, Noland BW, Lorimer D, Kearins MC, Conners K, Condon B, Maloney PC, Guggino WB, Hunt JF, Emtage S.

J Biol Chem. 2005 Jan 14;280(2):1346-53. Epub 2004 Nov 3.

45.

Structure of nucleotide-binding domain 1 of the cystic fibrosis transmembrane conductance regulator.

Lewis HA, Buchanan SG, Burley SK, Conners K, Dickey M, Dorwart M, Fowler R, Gao X, Guggino WB, Hendrickson WA, Hunt JF, Kearins MC, Lorimer D, Maloney PC, Post KW, Rajashankar KR, Rutter ME, Sauder JM, Shriver S, Thibodeau PH, Thomas PJ, Zhang M, Zhao X, Emtage S.

EMBO J. 2004 Jan 28;23(2):282-93. Epub 2003 Dec 18.

46.

The promise of structural genomics in the discovery of new antimicrobial agents.

Buchanan SG, Sauder JM, Harris T.

Curr Pharm Des. 2002;8(13):1173-88. Review.

PMID:
12052226
47.

A structural genomics approach to the study of quorum sensing: crystal structures of three LuxS orthologs.

Lewis HA, Furlong EB, Laubert B, Eroshkina GA, Batiyenko Y, Adams JM, Bergseid MG, Marsh CD, Peat TS, Sanderson WE, Sauder JM, Buchanan SG.

Structure. 2001 Jun;9(6):527-37.

48.

Identification of a novel pre-TCR isoform in which the accessibility of the TCR beta subunit is determined by occupancy of the 'missing' V domain of pre-T alpha.

Berger MA, Carleton M, Rhodes M, Sauder JM, Trop S, Dunbrack RL, Hugo P, Wiest DL.

Int Immunol. 2000 Nov;12(11):1579-91.

PMID:
11058578
49.

Genomic fold assignment and rational modeling of proteins of biological interest.

Sauder JM, Dunbrack RL Jr.

Proc Int Conf Intell Syst Mol Biol. 2000;8:296-306.

PMID:
10977091
50.

Modeling of substrate specificity of the Alzheimer's disease amyloid precursor protein beta-secretase.

Sauder JM, Arthur JW, Dunbrack RL Jr.

J Mol Biol. 2000 Jul 7;300(2):241-8.

PMID:
10873463

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