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Items: 1 to 50 of 81

1.

Activator Protein-1: redox switch controlling structure and DNA-binding.

Yin Z, Machius M, Nestler EJ, Rudenko G.

Nucleic Acids Res. 2017 Nov 2;45(19):11425-11436. doi: 10.1093/nar/gkx795.

2.

Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges.

Gangwar SP, Zhong X, Seshadrinathan S, Chen H, Machius M, Rudenko G.

Neuron. 2017 Jun 21;94(6):1132-1141.e4. doi: 10.1016/j.neuron.2017.06.009.

3.

TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis.

Nishimura MT, Anderson RG, Cherkis KA, Law TF, Liu QL, Machius M, Nimchuk ZL, Yang L, Chung EH, El Kasmi F, Hyunh M, Osborne Nishimura E, Sondek JE, Dangl JL.

Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E2053-E2062. doi: 10.1073/pnas.1620973114. Epub 2017 Jan 30.

4.

Discovery of Macrocyclic Pyrimidines as MerTK-Specific Inhibitors.

McIver AL, Zhang W, Liu Q, Jiang X, Stashko MA, Nichols J, Miley MJ, Norris-Drouin J, Machius M, DeRyckere D, Wood E, Graham DK, Earp HS, Kireev D, Frye SV, Wang X.

ChemMedChem. 2017 Feb 3;12(3):207-213. doi: 10.1002/cmdc.201600589. Epub 2017 Jan 9.

5.

Design and Synthesis of Novel Macrocyclic Mer Tyrosine Kinase Inhibitors.

Wang X, Liu J, Zhang W, Stashko MA, Nichols J, Miley MJ, Norris-Drouin J, Chen Z, Machius M, DeRyckere D, Wood E, Graham DK, Earp HS, Kireev D, Frye SV.

ACS Med Chem Lett. 2016 Sep 13;7(12):1044-1049. eCollection 2016 Dec 8.

6.

Functional analysis of rare variants found in schizophrenia implicates a critical role for GIT1-PAK3 signaling in neuroplasticity.

Kim MJ, Biag J, Fass DM, Lewis MC, Zhang Q, Fleishman M, Gangwar SP, Machius M, Fromer M, Purcell SM, McCarroll SA, Rudenko G, Premont RT, Scolnick EM, Haggarty SJ.

Mol Psychiatry. 2017 Mar;22(3):417-429. doi: 10.1038/mp.2016.98. Epub 2016 Jul 26.

PMID:
27457813
7.

Structural analyses to identify selective inhibitors of glyceraldehyde 3-phosphate dehydrogenase-S, a sperm-specific glycolytic enzyme.

Danshina PV, Qu W, Temple BR, Rojas RJ, Miley MJ, Machius M, Betts L, O'Brien DA.

Mol Hum Reprod. 2016 Jun;22(6):410-26. doi: 10.1093/molehr/gaw016. Epub 2016 Feb 26.

8.

Computational de novo design of a four-helix bundle protein--DND_4HB.

Murphy GS, Sathyamoorthy B, Der BS, Machius MC, Pulavarti SV, Szyperski T, Kuhlman B.

Protein Sci. 2015 Apr;24(4):434-45. doi: 10.1002/pro.2577. Epub 2014 Nov 6.

9.

Discovery of Mer specific tyrosine kinase inhibitors for the treatment and prevention of thrombosis.

Zhang W, McIver AL, Stashko MA, DeRyckere D, Branchford BR, Hunter D, Kireev D, Miley MJ, Norris-Drouin J, Stewart WM, Lee M, Sather S, Zhou Y, Di Paola JA, Machius M, Janzen WP, Earp HS, Graham DK, Frye SV, Wang X.

J Med Chem. 2013 Dec 12;56(23):9693-700. doi: 10.1021/jm4013888. Epub 2013 Nov 20.

10.

Pseudo-cyclization through intramolecular hydrogen bond enables discovery of pyridine substituted pyrimidines as new Mer kinase inhibitors.

Zhang W, Zhang D, Stashko MA, DeRyckere D, Hunter D, Kireev D, Miley MJ, Cummings C, Lee M, Norris-Drouin J, Stewart WM, Sather S, Zhou Y, Kirkpatrick G, Machius M, Janzen WP, Earp HS, Graham DK, Frye SV, Wang X.

J Med Chem. 2013 Dec 12;56(23):9683-92. doi: 10.1021/jm401387j. Epub 2013 Nov 20. Erratum in: J Med Chem. 2014 Aug 28;57(16):7141.

11.

Structural determinants of RGS-RhoGEF signaling critical to Entamoeba histolytica pathogenesis.

Bosch DE, Kimple AJ, Manning AJ, Muller RE, Willard FS, Machius M, Rogers SL, Siderovski DP.

Structure. 2013 Jan 8;21(1):65-75. doi: 10.1016/j.str.2012.11.012. Epub 2012 Dec 20.

12.

Heterotrimeric G-protein signaling is critical to pathogenic processes in Entamoeba histolytica.

Bosch DE, Kimple AJ, Muller RE, Giguère PM, Machius M, Willard FS, Temple BR, Siderovski DP.

PLoS Pathog. 2012;8(11):e1003040. doi: 10.1371/journal.ppat.1003040. Epub 2012 Nov 15.

13.

Biophysical and bioinformatic analyses implicate the Treponema pallidum Tp34 lipoprotein (Tp0971) in transition metal homeostasis.

Brautigam CA, Deka RK, Ouyang Z, Machius M, Knutsen G, Tomchick DR, Norgard MV.

J Bacteriol. 2012 Dec;194(24):6771-81. doi: 10.1128/JB.01494-12. Epub 2012 Oct 5.

14.

Discovery of Novel Small Molecule Mer Kinase Inhibitors for the Treatment of Pediatric Acute Lymphoblastic Leukemia.

Liu J, Yang C, Simpson C, Deryckere D, Van Deusen A, Miley MJ, Kireev D, Norris-Drouin J, Sather S, Hunter D, Korboukh VK, Patel HS, Janzen WP, Machius M, Johnson GL, Earp HS, Graham DK, Frye SV, Wang X.

ACS Med Chem Lett. 2012 Feb 9;3(2):129-134.

15.

Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core.

Murphy GS, Mills JL, Miley MJ, Machius M, Szyperski T, Kuhlman B.

Structure. 2012 Jun 6;20(6):1086-96. doi: 10.1016/j.str.2012.03.026. Epub 2012 May 24.

16.

Computational design of a symmetric homodimer using β-strand assembly.

Stranges PB, Machius M, Miley MJ, Tripathy A, Kuhlman B.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20562-7. doi: 10.1073/pnas.1115124108. Epub 2011 Dec 5.

17.

Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer.

Der BS, Machius M, Miley MJ, Mills JL, Szyperski T, Kuhlman B.

J Am Chem Soc. 2012 Jan 11;134(1):375-85. doi: 10.1021/ja208015j. Epub 2011 Dec 15.

18.

A single active-site mutation of P450BM-3 dramatically enhances substrate binding and rate of product formation.

Haines DC, Hegde A, Chen B, Zhao W, Bondlela M, Humphreys JM, Mullin DA, Tomchick DR, Machius M, Peterson JA.

Biochemistry. 2011 Oct 4;50(39):8333-41. doi: 10.1021/bi201099j. Epub 2011 Sep 6.

19.

Computational design of the sequence and structure of a protein-binding peptide.

Sammond DW, Bosch DE, Butterfoss GL, Purbeck C, Machius M, Siderovski DP, Kuhlman B.

J Am Chem Soc. 2011 Mar 30;133(12):4190-2. doi: 10.1021/ja110296z. Epub 2011 Mar 9.

20.

The crystal structure of a self-activating G protein alpha subunit reveals its distinct mechanism of signal initiation.

Jones JC, Duffy JW, Machius M, Temple BR, Dohlman HG, Jones AM.

Sci Signal. 2011 Feb 8;4(159):ra8. doi: 10.1126/scisignal.2001446.

21.

Structural determinants of affinity enhancement between GoLoco motifs and G-protein alpha subunit mutants.

Bosch DE, Kimple AJ, Sammond DW, Muller RE, Miley MJ, Machius M, Kuhlman B, Willard FS, Siderovski DP.

J Biol Chem. 2011 Feb 4;286(5):3351-8. doi: 10.1074/jbc.M110.190496. Epub 2010 Nov 29.

22.

Crystal structure of the Formin mDia1 in autoinhibited conformation.

Otomo T, Tomchick DR, Otomo C, Machius M, Rosen MK.

PLoS One. 2010 Sep 30;5(9). pii: e12896. doi: 10.1371/journal.pone.0012896.

23.

Diffraction data analysis in the presence of radiation damage.

Borek D, Cymborowski M, Machius M, Minor W, Otwinowski Z.

Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):426-36. doi: 10.1107/S0907444909040177. Epub 2010 Mar 24.

24.

Munc13 C2B domain is an activity-dependent Ca2+ regulator of synaptic exocytosis.

Shin OH, Lu J, Rhee JS, Tomchick DR, Pang ZP, Wojcik SM, Camacho-Perez M, Brose N, Machius M, Rizo J, Rosenmund C, Südhof TC.

Nat Struct Mol Biol. 2010 Mar;17(3):280-8. doi: 10.1038/nsmb.1758. Epub 2010 Feb 14.

25.

Structural and energetic mechanisms of cooperative autoinhibition and activation of Vav1.

Yu B, Martins IR, Li P, Amarasinghe GK, Umetani J, Fernandez-Zapico ME, Billadeau DD, Machius M, Tomchick DR, Rosen MK.

Cell. 2010 Jan 22;140(2):246-56. doi: 10.1016/j.cell.2009.12.033.

26.

Structure and mechanism of a eukaryotic FMN adenylyltransferase.

Huerta C, Borek D, Machius M, Grishin NV, Zhang H.

J Mol Biol. 2009 Jun 5;389(2):388-400. doi: 10.1016/j.jmb.2009.04.022. Epub 2009 Apr 16.

27.

Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor.

Scheuermann TH, Tomchick DR, Machius M, Guo Y, Bruick RK, Gardner KH.

Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):450-5. doi: 10.1073/pnas.0808092106. Epub 2009 Jan 7.

28.

Localization and structure of the ankyrin-binding site on beta2-spectrin.

Davis L, Abdi K, Machius M, Brautigam C, Tomchick DR, Bennett V, Michaely P.

J Biol Chem. 2009 Mar 13;284(11):6982-7. doi: 10.1074/jbc.M809245200. Epub 2008 Dec 20.

29.

Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.

Kato M, Wynn RM, Chuang JL, Tso SC, Machius M, Li J, Chuang DT.

Structure. 2008 Dec 10;16(12):1849-59. doi: 10.1016/j.str.2008.10.010.

30.

Structure and substrate recruitment of the human spindle checkpoint kinase Bub1.

Kang J, Yang M, Li B, Qi W, Zhang C, Shokat KM, Tomchick DR, Machius M, Yu H.

Mol Cell. 2008 Nov 7;32(3):394-405. doi: 10.1016/j.molcel.2008.09.017.

31.

Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates.

Rezácová P, Kozísek M, Moy SF, Sieglová I, Joachimiak A, Machius M, Otwinowski Z.

Mol Microbiol. 2008 Aug;69(4):895-910. doi: 10.1111/j.1365-2958.2008.06318.x. Epub 2008 Jun 28.

32.

Changes at the KinA PAS-A dimerization interface influence histidine kinase function.

Lee J, Tomchick DR, Brautigam CA, Machius M, Kort R, Hellingwerf KJ, Gardner KH.

Biochemistry. 2008 Apr 1;47(13):4051-64. doi: 10.1021/bi7021156. Epub 2008 Mar 7.

PMID:
18324779
33.

Insights into mad2 regulation in the spindle checkpoint revealed by the crystal structure of the symmetric mad2 dimer.

Yang M, Li B, Liu CJ, Tomchick DR, Machius M, Rizo J, Yu H, Luo X.

PLoS Biol. 2008 Mar 4;6(3):e50. doi: 10.1371/journal.pbio.0060050.

34.

Crystal structure of inhibitor-bound P450BM-3 reveals open conformation of substrate access channel.

Haines DC, Chen B, Tomchick DR, Bondlela M, Hegde A, Machius M, Peterson JA.

Biochemistry. 2008 Mar 25;47(12):3662-70. doi: 10.1021/bi7023964. Epub 2008 Feb 26.

PMID:
18298086
35.

p31comet blocks Mad2 activation through structural mimicry.

Yang M, Li B, Tomchick DR, Machius M, Rizo J, Yu H, Luo X.

Cell. 2007 Nov 16;131(4):744-55.

36.

Interactions of substrates at the surface of P450s can greatly enhance substrate potency.

Hegde A, Haines DC, Bondlela M, Chen B, Schaffer N, Tomchick DR, Machius M, Nguyen H, Chowdhary PK, Stewart L, Lopez C, Peterson JA.

Biochemistry. 2007 Dec 11;46(49):14010-7. Epub 2007 Nov 16.

PMID:
18004886
37.

Structural and biochemical basis for polyamine binding to the Tp0655 lipoprotein of Treponema pallidum: putative role for Tp0655 (TpPotD) as a polyamine receptor.

Machius M, Brautigam CA, Tomchick DR, Ward P, Otwinowski Z, Blevins JS, Deka RK, Norgard MV.

J Mol Biol. 2007 Oct 26;373(3):681-94. Epub 2007 Aug 21.

38.

Crystal structure of the RIM1alpha C2B domain at 1.7 A resolution.

Guan R, Dai H, Tomchick DR, Dulubova I, Machius M, Südhof TC, Rizo J.

Biochemistry. 2007 Aug 7;46(31):8988-98. Epub 2007 Jul 14.

39.

Structural basis for the inhibition of the LSD1 histone demethylase by the antidepressant trans-2-phenylcyclopropylamine.

Yang M, Culhane JC, Szewczuk LM, Jalili P, Ball HL, Machius M, Cole PA, Yu H.

Biochemistry. 2007 Jul 10;46(27):8058-65. Epub 2007 Jun 15.

PMID:
17569509
40.

Structural basis of histone demethylation by LSD1 revealed by suicide inactivation.

Yang M, Culhane JC, Szewczuk LM, Gocke CB, Brautigam CA, Tomchick DR, Machius M, Cole PA, Yu H.

Nat Struct Mol Biol. 2007 Jun;14(6):535-9. Epub 2007 May 27.

PMID:
17529991
41.

The two active sites in human branched-chain alpha-keto acid dehydrogenase operate independently without an obligatory alternating-site mechanism.

Li J, Machius M, Chuang JL, Wynn RM, Chuang DT.

J Biol Chem. 2007 Apr 20;282(16):11904-13. Epub 2007 Feb 27.

42.

Structural analysis of Xanthomonas XopD provides insights into substrate specificity of ubiquitin-like protein proteases.

Chosed R, Tomchick DR, Brautigam CA, Mukherjee S, Negi VS, Machius M, Orth K.

J Biol Chem. 2007 Mar 2;282(9):6773-82. Epub 2007 Jan 3.

43.

Crystal structure of the Tp34 (TP0971) lipoprotein of treponema pallidum: implications of its metal-bound state and affinity for human lactoferrin.

Deka RK, Brautigam CA, Tomson FL, Lumpkins SB, Tomchick DR, Machius M, Norgard MV.

J Biol Chem. 2007 Feb 23;282(8):5944-58. Epub 2006 Dec 27.

44.

Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase.

Yang M, Gocke CB, Luo X, Borek D, Tomchick DR, Machius M, Otwinowski Z, Yu H.

Mol Cell. 2006 Aug 4;23(3):377-87.

45.

A proximal arginine R206 participates in switching of the Bradyrhizobium japonicum FixL oxygen sensor.

Gilles-Gonzalez MA, Caceres AI, Sousa EH, Tomchick DR, Brautigam C, Gonzalez C, Machius M.

J Mol Biol. 2006 Jun 30;360(1):80-9. Epub 2006 May 11.

PMID:
16813836
46.

Structural basis for a Munc13-1 homodimer to Munc13-1/RIM heterodimer switch.

Lu J, Machius M, Dulubova I, Dai H, Südhof TC, Tomchick DR, Rizo J.

PLoS Biol. 2006 Jul;4(7):e192.

47.

A versatile conformational switch regulates reactivity in human branched-chain alpha-ketoacid dehydrogenase.

Machius M, Wynn RM, Chuang JL, Li J, Kluger R, Yu D, Tomchick DR, Brautigam CA, Chuang DT.

Structure. 2006 Feb;14(2):287-98. Erratum in: Structure. 2006 Mar;14(3):625.

48.

Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex.

Brautigam CA, Wynn RM, Chuang JL, Machius M, Tomchick DR, Chuang DT.

Structure. 2006 Mar;14(3):611-21. Epub 2006 Jan 26.

49.

The PnrA (Tp0319; TmpC) lipoprotein represents a new family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC)-like operon in Treponema pallidum.

Deka RK, Brautigam CA, Yang XF, Blevins JS, Machius M, Tomchick DR, Norgard MV.

J Biol Chem. 2006 Mar 24;281(12):8072-81. Epub 2006 Jan 16.

50.

Crystal structure of the RIM2 C2A-domain at 1.4 A resolution.

Dai H, Tomchick DR, García J, Südhof TC, Machius M, Rizo J.

Biochemistry. 2005 Oct 18;44(41):13533-42.

PMID:
16216076

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