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Items: 1 to 50 of 62

1.

NMR-based fragment screening and lead discovery accelerated by principal component analysis.

Namanja AT, Xu J, Wu H, Sun Q, Upadhyay AK, Sun C, Van Doren SR, Petros AM.

J Biomol NMR. 2019 Sep 20. doi: 10.1007/s10858-019-00279-9. [Epub ahead of print]

PMID:
31541395
2.

MT1-MMP Binds Membranes by Opposite Tips of Its β Propeller to Position It for Pericellular Proteolysis.

Marcink TC, Simoncic JA, An B, Knapinska AM, Fulcher YG, Akkaladevi N, Fields GB, Van Doren SR.

Structure. 2019 Feb 5;27(2):281-292.e6. doi: 10.1016/j.str.2018.10.008. Epub 2018 Nov 21.

PMID:
30471921
3.

Affinities and Comparisons of Enzyme States by Principal Component Analysis of NMR Spectra, Automated using TREND Software.

Xu J, Van Doren SR.

Methods Enzymol. 2018;607:217-240. doi: 10.1016/bs.mie.2018.05.016. Epub 2018 Jun 30.

PMID:
30149859
4.

Domain Gymnastics of an ABC Transporter.

Van Doren SR.

Structure. 2018 Jul 3;26(7):917-918. doi: 10.1016/j.str.2018.06.005.

5.

Phosphorylation-Dependent Effects on the Structural Flexibility of Phosphoglucosamine Mutase from Bacillus anthracis.

Stiers KM, Xu J, Lee Y, Addison ZR, Van Doren SR, Beamer LJ.

ACS Omega. 2017 Nov 29;2(11):8445-8452. doi: 10.1021/acsomega.7b01490. eCollection 2017 Nov 30.

6.

Multiple Ligand-Bound States of a Phosphohexomutase Revealed by Principal Component Analysis of NMR Peak Shifts.

Xu J, Sarma AVS, Wei Y, Beamer LJ, Van Doren SR.

Sci Rep. 2017 Jul 13;7(1):5343. doi: 10.1038/s41598-017-05557-w.

7.

Glycan Activation of a Sheddase: Electrostatic Recognition between Heparin and proMMP-7.

Fulcher YG, Prior SH, Masuko S, Li L, Pu D, Zhang F, Linhardt RJ, Van Doren SR.

Structure. 2017 Jul 5;25(7):1100-1110.e5. doi: 10.1016/j.str.2017.05.019. Epub 2017 Jun 22.

8.

Peripheral membrane associations of matrix metalloproteinases.

Van Doren SR, Marcink TC, Koppisetti RK, Jurkevich A, Fulcher YG.

Biochim Biophys Acta Mol Cell Res. 2017 Nov;1864(11 Pt A):1964-1973. doi: 10.1016/j.bbamcr.2017.04.013. Epub 2017 Apr 23. Review.

9.

Mapping Lipid Bilayer Recognition Sites of Metalloproteinases and Other Prospective Peripheral Membrane Proteins.

Marcink TC, Koppisetti RK, Fulcher YG, Van Doren SR.

Methods Mol Biol. 2017;1579:61-86. doi: 10.1007/978-1-4939-6863-3_5.

PMID:
28299733
10.

Tracking Equilibrium and Nonequilibrium Shifts in Data with TREND.

Xu J, Van Doren SR.

Biophys J. 2017 Jan 24;112(2):224-233. doi: 10.1016/j.bpj.2016.12.018.

11.

Noninvasive Recognition and Biomarkers of Early Allergic Asthma in Cats Using Multivariate Statistical Analysis of NMR Spectra of Exhaled Breath Condensate.

Fulcher YG, Fotso M, Chang CH, Rindt H, Reinero CR, Van Doren SR.

PLoS One. 2016 Oct 20;11(10):e0164394. doi: 10.1371/journal.pone.0164394. eCollection 2016.

12.

Binding Isotherms and Time Courses Readily from Magnetic Resonance.

Xu J, Van Doren SR.

Anal Chem. 2016 Aug 16;88(16):8172-8. doi: 10.1021/acs.analchem.6b01918. Epub 2016 Aug 5.

13.

Path to Collagenolysis: COLLAGEN V TRIPLE-HELIX MODEL BOUND PRODUCTIVELY AND IN ENCOUNTERS BY MATRIX METALLOPROTEINASE-12.

Prior SH, Byrne TS, Tokmina-Roszyk D, Fields GB, Van Doren SR.

J Biol Chem. 2016 Apr 8;291(15):7888-901. doi: 10.1074/jbc.M115.703124. Epub 2016 Feb 17.

14.

Charge-Triggered Membrane Insertion of Matrix Metalloproteinase-7, Supporter of Innate Immunity and Tumors.

Prior SH, Fulcher YG, Koppisetti RK, Jurkevich A, Van Doren SR.

Structure. 2015 Nov 3;23(11):2099-110. doi: 10.1016/j.str.2015.08.013. Epub 2015 Oct 1.

15.

Transient collagen triple helix binding to a key metalloproteinase in invasion and development.

Zhao Y, Marcink TC, Sanganna Gari RR, Marsh BP, King GM, Stawikowska R, Fields GB, Van Doren SR.

Structure. 2015 Feb 3;23(2):257-69. doi: 10.1016/j.str.2014.11.021.

16.

Phosphorylation in the catalytic cleft stabilizes and attracts domains of a phosphohexomutase.

Xu J, Lee Y, Beamer LJ, Van Doren SR.

Biophys J. 2015 Jan 20;108(2):325-37. doi: 10.1016/j.bpj.2014.12.003.

17.

Matrix metalloproteinase interactions with collagen and elastin.

Van Doren SR.

Matrix Biol. 2015 May-Jul;44-46:224-31. doi: 10.1016/j.matbio.2015.01.005. Epub 2015 Jan 17. Review.

18.

Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12.

Koppisetti RK, Fulcher YG, Jurkevich A, Prior SH, Xu J, Lenoir M, Overduin M, Van Doren SR.

Nat Commun. 2014 Nov 21;5:5552. doi: 10.1038/ncomms6552.

19.

Heparinoids activate a protease, secreted by mucosa and tumors, via tethering supplemented by allostery.

Fulcher YG, Sanganna Gari RR, Frey NC, Zhang F, Linhardt RJ, King GM, Van Doren SR.

ACS Chem Biol. 2014 Apr 18;9(4):957-66. doi: 10.1021/cb400898t. Epub 2014 Feb 10.

20.

The role of collagen charge clusters in the modulation of matrix metalloproteinase activity.

Lauer JL, Bhowmick M, Tokmina-Roszyk D, Lin Y, Van Doren SR, Fields GB.

J Biol Chem. 2014 Jan 24;289(4):1981-92. doi: 10.1074/jbc.M113.513408. Epub 2013 Dec 2.

21.

Chemical shift assignments of domain 4 from the phosphohexomutase from Pseudomonas aeruginosa suggest that freeing perturbs its coevolved domain interface.

Wei Y, Marcink TC, Xu J, Sirianni AG, Sarma AV, Prior SH, Beamer LJ, Van Doren SR.

Biomol NMR Assign. 2014 Oct;8(2):329-33. doi: 10.1007/s12104-013-9511-5. Epub 2013 Jul 28.

22.

Solution NMR of a 463-residue phosphohexomutase: domain 4 mobility, substates, and phosphoryl transfer defect.

Sarma AV, Anbanandam A, Kelm A, Mehra-Chaudhary R, Wei Y, Qin P, Lee Y, Berjanskii MV, Mick JA, Beamer LJ, Van Doren SR.

Biochemistry. 2012 Jan 24;51(3):807-19. doi: 10.1021/bi201609n. Epub 2012 Jan 17.

23.

Remote exosites of the catalytic domain of matrix metalloproteinase-12 enhance elastin degradation.

Fulcher YG, Van Doren SR.

Biochemistry. 2011 Nov 8;50(44):9488-99. doi: 10.1021/bi2009807. Epub 2011 Oct 11.

25.

Solubilized elastin substrate for continuous fluorimetric assay of kinetics of elastases.

Palmier MO, Fulcher YG, Van Doren SR.

Anal Biochem. 2011 Jan 1;408(1):172-4. doi: 10.1016/j.ab.2010.09.001. Epub 2010 Sep 7.

26.

NMR and bioinformatics discovery of exosites that tune metalloelastase specificity for solubilized elastin and collagen triple helices.

Palmier MO, Fulcher YG, Bhaskaran R, Duong VQ, Fields GB, Van Doren SR.

J Biol Chem. 2010 Oct 1;285(40):30918-30. doi: 10.1074/jbc.M110.136903. Epub 2010 Jul 27.

27.

Apparent tradeoff of higher activity in MMP-12 for enhanced stability and flexibility in MMP-3.

Liang X, Arunima A, Zhao Y, Bhaskaran R, Shende A, Byrne TS, Fleeks J, Palmier MO, Van Doren SR.

Biophys J. 2010 Jul 7;99(1):273-83. doi: 10.1016/j.bpj.2010.04.002.

28.

Breaking the covalent connection: Chain connectivity and the catalytic reaction of PMM/PGM.

Schramm AM, Karr D, Mehra-Chaudhary R, Van Doren SR, Furdui CM, Beamer LJ.

Protein Sci. 2010 Jun;19(6):1235-42. doi: 10.1002/pro.402.

29.

An examination of the proteolytic activity for bovine pregnancy-associated glycoproteins 2 and 12.

Telugu BP, Palmier MO, Van Doren SR, Green JA.

Biol Chem. 2010 Feb-Mar;391(2-3):259-70. doi: 10.1515/BC.2010.016.

30.

Nuclear magnetic resonance captures the elusive.

Van Doren SR.

F1000 Biol Rep. 2009 Mar 24;1:24. doi: 10.3410/B1-24.

31.

Mechanistic insights into phosphoprotein-binding FHA domains.

Liang X, Van Doren SR.

Acc Chem Res. 2008 Aug;41(8):991-9. doi: 10.1021/ar700148u. Epub 2008 Jul 26. Review.

32.

Inactivation of N-TIMP-1 by N-terminal acetylation when expressed in bacteria.

Van Doren SR, Wei S, Gao G, DaGue BB, Palmier MO, Bahudhanapati H, Brew K.

Biopolymers. 2008 Nov;89(11):960-8. doi: 10.1002/bip.21043.

33.

MMP-12 catalytic domain recognizes triple helical peptide models of collagen V with exosites and high activity.

Bhaskaran R, Palmier MO, Lauer-Fields JL, Fields GB, Van Doren SR.

J Biol Chem. 2008 Aug 1;283(31):21779-88. doi: 10.1074/jbc.M709966200. Epub 2008 Jun 6.

34.

Solution structure of inhibitor-free human metalloelastase (MMP-12) indicates an internal conformational adjustment.

Bhaskaran R, Palmier MO, Bagegni NA, Liang X, Van Doren SR.

J Mol Biol. 2007 Dec 14;374(5):1333-44. Epub 2007 Oct 16.

35.

Rapid determination of enzyme kinetics from fluorescence: overcoming the inner filter effect.

Palmier MO, Van Doren SR.

Anal Biochem. 2007 Dec 1;371(1):43-51. Epub 2007 Jul 18.

36.

Phosphoprotein and phosphopeptide interactions with the FHA domain from Arabidopsis kinase-associated protein phosphatase.

Ding Z, Wang H, Liang X, Morris ER, Gallazzi F, Pandit S, Skolnick J, Walker JC, Van Doren SR.

Biochemistry. 2007 Mar 13;46(10):2684-96. Epub 2007 Feb 16.

PMID:
17302430
37.
38.

Eukaryotic cyclophilin as a molecular switch for effector activation.

Coaker G, Zhu G, Ding Z, Van Doren SR, Staskawicz B.

Mol Microbiol. 2006 Sep;61(6):1485-96.

39.

1H, 13C, and 15N peak assignments and secondary structure of human macrophage metalloelastase (MMP-12) in its inhibitor-free state.

Bhaskaran R, Van Doren SR.

J Biomol NMR. 2006;36 Suppl 1:55. Epub 2006 Jul 20. No abstract available.

40.

Hsc70 contacts helix III of the J domain from polyomavirus T antigens: addressing a dilemma in the chaperone hypothesis of how they release E2F from pRb.

Garimella R, Liu X, Qiao W, Liang X, Zuiderweg ER, Riley MI, Van Doren SR.

Biochemistry. 2006 Jun 6;45(22):6917-29.

PMID:
16734427
41.

PhosphoThr peptide binding globally rigidifies much of the FHA domain from Arabidopsis receptor kinase-associated protein phosphatase.

Ding Z, Lee GI, Liang X, Gallazzi F, Arunima A, Van Doren SR.

Biochemistry. 2005 Aug 2;44(30):10119-34.

42.

NMR structure of the forkhead-associated domain from the Arabidopsis receptor kinase-associated protein phosphatase.

Lee GI, Ding Z, Walker JC, Van Doren SR.

Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11261-6. Epub 2003 Sep 18.

43.

Global orientation of bound MMP-3 and N-TIMP-1 in solution via residual dipolar couplings.

Arumugam S, Van Doren SR.

Biochemistry. 2003 Jul 8;42(26):7950-8.

PMID:
12834347
44.

1H, 13C and 15N resonance assignments of the kinase-interacting FHA domain of Arabidopsis thaliana kinase-associated protein phosphatase.

Lee GI, Li J, Walker JC, Van Doren SR.

J Biomol NMR. 2003 Mar;25(3):253-4. No abstract available.

PMID:
12652139
45.

Increased backbone mobility in beta-barrel enhances entropy gain driving binding of N-TIMP-1 to MMP-3.

Arumugam S, Gao G, Patton BL, Semenchenko V, Brew K, Van Doren SR.

J Mol Biol. 2003 Mar 28;327(3):719-34.

PMID:
12634064
46.

Structural basis for a lethal mutation in U6 RNA.

Sashital DG, Allmann AM, Van Doren SR, Butcher SE.

Biochemistry. 2003 Feb 18;42(6):1470-7.

47.

Hsc70-interacting HPD loop of the J domain of polyomavirus T antigens fluctuates in ps to ns and micros to ms.

Berjanskii M, Riley M, Van Doren SR.

J Mol Biol. 2002 Aug 16;321(3):503-16.

PMID:
12162962
48.

Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action.

Leeper TC, Martin MB, Kim H, Cox S, Semenchenko V, Schmidt FJ, Van Doren SR.

Nat Struct Biol. 2002 May;9(5):397-403.

PMID:
11927952
49.

The FHA domain mediates phosphoprotein interactions.

Li J, Lee GI, Van Doren SR, Walker JC.

J Cell Sci. 2000 Dec;113 Pt 23:4143-9. Review.

50.

NMR structure of the N-terminal J domain of murine polyomavirus T antigens. Implications for DnaJ-like domains and for mutations of T antigens.

Berjanskii MV, Riley MI, Xie A, Semenchenko V, Folk WR, Van Doren SR.

J Biol Chem. 2000 Nov 17;275(46):36094-103.

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