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Structural Biophysics Laboratory (SBL)
Protein-Nucleic Acid Interaction Section
PublicationsPatents
1 - 44 of 44 results

1)  Chang FM, Coyne HJ, Cubillas C, Vinuesa P, Fang X, Ma Z, Ma D, Helmann JD, García-de Los Santos A, Wang YX, Dann CE, Giedroc DP.
Cu(I)-mediated Allosteric Switching in a Copper-sensing Operon Repressor (CsoR).
J. Biol. Chem. 289: 19204-17, 2014. [Journal]

2)  Fang X, Wang J, O'Carroll IP, Mitchell M, Zuo X, Wang Y, Yu P, Liu Y, Rausch JW, Dyba MA, Kjems J, Schwieters CD, Seifert S, Winans RE, Watts NR, Stahl SJ, Wingfield PT, Byrd RA, Le Grice SF, Rein A, Wang YX.
An unusual topological structure of the HIV-1 Rev response element.
Cell. 155: 594-605, 2013. [Journal]

3)  Giladi M, Sasson Y, Fang X, Hiller R, Buki T, Wang YX, Hirsch JA, Khananshvili D.
A Common Ca(2+)-Driven Interdomain Module Governs Eukaryotic NCX Regulation.
PLoS ONE. 7: e39985, 2012. [Journal]

4)  Chen B, Zuo X, Wang YX, Dayie TK.
Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy.
Nucleic Acids Res. 40: 3117-30, 2012. [Journal]

5)  Burke JE, Sashital DG, Zuo X, Wang YX, Butcher SE.
Structure of the yeast U2/U6 snRNA complex.
RNA. 18: 673-83, 2012. [Journal]

6)  Avvakumov GV, Walker JR, Xue S, Allali-Hassani A, Asinas A, Nair UB, Fang X, Zuo X, Wang YX, Wilkinson KD, Dhe-Paganon S.
Two ZnF-UBP domains in isopeptidase T (USP5).
Biochemistry. 51: 1188-98, 2012. [Journal]

7)  Liao JC, Lam R, Brazda V, Duan S, Ravichandran M, Ma J, Xiao T, Tempel W, Zuo X, Wang YX, Chirgadze NY, Arrowsmith CH.
Interferon-inducible protein 16: insight into the interaction with tumor suppressor p53.
Structure. 19: 418-29, 2011. [Journal]

8)  Ying J, Wang J, Grishaev A, Yu P, Wang YX, Bax A.
Measurement of (1)H-(15)N and (1)H-(13)C residual dipolar couplings in nucleic acids from TROSY intensities.
J. Biomol. NMR. 51: 89-103, 2011. [Journal]

9)  Nady N, Lemak A, Walker JR, Avvakumov GV, Kareta MS, Achour M, Xue S, Duan S, Allali-Hassani A, Zuo X, Wang Y, Bronner C, Chedin F, Arrowsmith CH, Dhe-Paganon S.
Recognition of multivalent histone states associated with heterochromatin by UHRF1.
J Biol Chem. 286: 24300-11, 2011. [Journal]

10)  Datta SA, Zuo X, Clark PK, Campbell SJ, Wang YX, Rein A.
Solution properties of murine leukemia virus gag protein: differences from HIV-1 gag.
J. Virol. 85: 12733-41, 2011. [Journal]

11)  Wang YX, Zuo X, Wang J, Yu P, Butcher SE.
Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering.
Methods. 52: 180-91, 2010. [Journal]

12)  Zuo X, Wang J, Yu P, Eyler D, Xu H, Starich MR, Tiede DM, Simon AE, Kasprzak W, Schwieters CD, Shapiro BA, Wang YX.
Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus.
Proc. Natl. Acad. Sci. U.S.A. 107: 1385-90, 2010. [Journal]

13)  Wang J, Zuo X, Yu P, Xu H, Starich MR, Tiede DM, Shapiro BA, Schwieters CD, Wang Y.
A method for helical RNA global structure determination in solution using small angle X-ray scattering and NMR measurements.
J. Mol. Biol. 393: 717-34, 2009. [Journal]

14)  Wang J, Zuo X, Yu P, Byeon I, Jung J, Wang X, Dyba M, Seifert S, Schwieters C, Qin J, Gronenborn A, Wang Y.
Determination of multicomponent protein structures in solution using global orientation and shape restraints.
J. Am. Chem. Soc. 131: 10507-15, 2009. [Journal]

15)  Yang Y, Wang X, Hawkins CA, Chen K, Vaynberg J, Mao X, Tu Y, Zuo X, Wang J, Wang YX, Wu C, Tjandra N, Qin J.
Structural basis of focal adhesion localization of LIM-only adaptor PINCH by integrin-linked kinase.
J. Biol. Chem. 284: 5836-44, 2009. [Journal]

16)  Zuo X, Wang J, Foster TR, Schwieters CD, Tiede DM, Butcher SE, Wang YX.
Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data.
J. Am. Chem. Soc. 130: 3292-3, 2008. [Journal]

17)  Wang J, Walsh J, Kuszewski J, Wang Y.
Periodicity, planarity, and pixel (3P): A program using the intrinsic residual dipolar coupling periodicity-to-peptide plane correlation and phi/psi angles to derive protein backbone structures.
J. Magn. Res. 189: 90-103, 2007. [Journal]

18)  Lee D, Walsh JD, Yu P, Markus MA, Choli-Papadopoulou T, Schwieters CD, Krueger S, Draper DE, Wang YX.
The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.
J. Mol. Biol. 367: 1007-22, 2007. [Journal]

19)  Lee D, Walsh JD, Migliorini M, Yu P, Cai T, Schwieters CD, Krueger S, Strickland DK, Wang Y.
The structure of receptor-associated protein (RAP).
Protein Sci. 16: 1628-40, 2007. [Journal]

20)  Walsh JD, Lee D, Yu P, Migliorini M, Strickland DK, Wang YX.
NMR assignment of domain 2 of the receptor-associated protein.
J. Biomol. NMR. 36 Suppl 1: 54, 2006. [Journal]

21)  Lee D, Walsh JD, Yu P, Migliorini M, Wu Y, Strickland DK, Wang YX.
NMR assignment of domain 3 of the receptor-associated protein (RAP).
J. Biomol. NMR. 36 Suppl 1: 56, 2006. [Journal]

22)  Lee D, Walsh JD, Mikhailenko I, Yu P, Migliorini M, Wu Y, Krueger S, Curtis JE, Harris B, Lockett S, Blacklow SC, Strickland DK, Wang YX.
RAP uses a histidine switch to regulate its interaction with LRP in the ER and Golgi.
Mol. Cell. 22: 423-30, 2006. [Journal]

23)  Reiter NJ, Lee D, Wang YX, Tonelli M, Bahrami A, Cornilescu CC, Butcher SE.
Resonance assignments for the two N-terminal RNA recognition motifs (RRM) of the S. cerevisiae pre-mRNA processing protein Prp24.
J. Biomol. NMR. 36 Suppl 1: 58, 2006. [Journal]

24)  Walsh JD, Kuszweski J, Wang Y.
Determining a helical protein structure using peptide pixels.
J Magn Reson. 177(1): 155-9, 2005. [Journal]

25)  Walsh JD, Wang YX.
Periodicity, planarity, residual dipolar coupling, and structures.
J Magn Reson. 174: 152-62, 2005. [Journal]

26)  Wu Y, Migliorini M, Walsh J, Yu P, Strickland DK, Wang YX.
NMR structural studies of domain 1 of receptor-associated protein.
J Biomol NMR. 29: 271-9, 2004. [Journal]

27)  Walsh JD, Cabello-Villegas J, Wang YX.
Periodicity in residual dipolar couplings and nucleic acid structures.
J Am Chem Soc. 126: 1938-9, 2004. [Journal]

28)  Cabello-Villegas J, Giles KE, Soto AM, Yu P, Mougin A, Beemon KL, Wang YX.
Solution structure of the pseudo-5' splice site of a retroviral splicing suppressor.
RNA. 10: 1388-98, 2004. [Journal]

29)  Wu Y, Migliorini M, Yu P, Strickland DK, Wang YX.
1H, 13C and 15N resonance assignments of domain 1 of receptor associated protein.
J. Biomol. NMR. 26: 187-8, 2003. [Journal]

30)  Neamati N, Murthy M, Wang YX.
Preparation of DNA-protein complexes suitable for spectroscopic analysis.
Methods Mol. Med. 85: 185-202, 2003. [Journal]

31)  Freedberg DI, Ishima R, Jacob J, Wang YX, Kustanovich I, Louis JM, Torchia DA.
Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations.
Protein Sci. 11: 221-32, 2002. [Journal]

32)  Wang YX, Jacob J, Wingfield PT, Palmer I, Stahl SJ, Kaufman JD, Huang PL, Huang PL, Lee-Huang S, Torchia DA.
Anti-HIV and anti-tumor protein MAP30, a 30 kDa single-strand type-I RIP, shares similar secondary structure and beta-sheet topology with the A chain of ricin, a type-II RIP.
Protein Sci. 9: 138-44, 2000. [Journal]

33)  Ishima R, Freedberg DI, Wang YX, Louis JM, Torchia DA.
Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function.
Structure. 7: 1047-55, 1999. [Journal]

34)  Wang YX, Jacob J, Cordier F, Wingfield P, Stahl SJ, Lee-Huang S, Torchia D, Grzesiek S, Bax A.
Measurement of 3hJNC' connectivities across hydrogen bonds in a 30 kDa protein.
J. Biomol. NMR. 14: 181-4, 1999. [Journal]

35)  Wang YX, Neamati N, Jacob J, Palmer I, Stahl SJ, Kaufman JD, Huang PL, Huang PL, Winslow HE, Pommier Y, Wingfield PT, Lee-Huang S, Bax A, Torchia DA.
Solution structure of anti-HIV-1 and anti-tumor protein MAP30: structural insights into its multiple functions.
Cell. 99: 433-42, 1999. [Journal]

36)  Freedberg DI, Wang YX, Stahl S, Kaufman JD, Wingfield PT, Kiso Y, Torchia DA.
Flexibility and function in HIV protease: Dynamics of the HIV-1 protease bound to the asymmetric inhibitor kynostatin 272 (KNI-272).
J. Am. Chem. Soc. 120(31): 7916-23, 1998. [Journal]

37)  Wang YX, Marquardt JL, Wingfield P, Stahl SJ, Lee-Huang S, Torchia D, Bax A.
Simultaneous measurement of H-1-N-15, H-1-C-13', and N-15-C-13' dipolar couplings in a perdeuterated 30 kDa protein dissolved in a dilute liquid crystailine phase.
J. Am. Chem. Soc. 120(29): 7385-6, 1998. [Journal]

38)  Wang YX, Freedberg DI, Wingfield PT, Stahl SJ, Kaufman JD, Kiso Y, Bhat TN, Erickson JW, Torchia DA.
Bound water molecules at the interface between the HIV-1 protease and a potent inhibitor, KNI-272, determined by NMR.
J. Am. Chem. Soc. 118(49): 12287-90, 1996. [Journal]

39)  Wang YX, Freedberg DI, Grzesiek S, Torchia DA, Wingfield PT, Kaufman JD, Stahl SJ, Chang CH, Hodge CN.
Mapping hydration water molecules in the HIV-1 protease/DMP323 complex in solution by NMR spectroscopy.
Biochemistry. 35: 12694-704, 1996. [Journal]

40)  Wang YX, Freedberg DI, Yamazaki T, Wingfield PT, Stahl SJ, Kaufman JD, Kiso Y, Torchia DA.
Solution NMR evidence that the HIV-1 protease catalytic aspartyl groups have different ionization states in the complex formed with the asymmetric drug KNI-272.
Biochemistry. 35: 9945-50, 1996. [Journal]

41)  Huang S, Wang YX, Draper DE.
Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs.
J. Mol. Biol. 258: 308-21, 1996. [Journal]

42)  Wang YX, Huang S, Draper DE.
Structure of a U.U pair within a conserved ribosomal RNA hairpin.
Nucleic Acids Res. 24: 2666-72, 1996. [Journal]

43)  Yamazaki T, Hinck AP, Wang YX, Nicholson LK, Torchia DA, Wingfield P, Stahl SJ, Kaufman JD, Chang CH, Domaille PJ, Lam PY.
Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy.
Protein Sci. 5: 495-506, 1996. [Journal]

44)  Wang YX, Lu M, Draper DE.
Specific ammonium ion requirement for functional ribosomal RNA tertiary structure.
Biochemistry. 32: 12279-82, 1993. [Journal]

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