current research

Gallery

1ihv 1neq 3czz

1996-2000

252. Frank MK, Clore GM, Gronenborn AM.  Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of Streptococcal protein G. Protein Sci 4: 2605-2615 (1996).

253. Clubb RT, Mizuuchi M, Huth JR, Omichinski JG, Savilahti H, Mizuuchi K, Clore GM, Gronenborn AM.  The wing of the enhancer binding domain of Mu phage transposase is flexible and essential for efficient transposition. Proc Natl Acad Sci USA 93: 1146-1150 (1996).

254. Qin J, Clore GM, Gronenborn AM.  Ionization equilibria for the side chain carboxyl groups in oxidized and reduced human thioredoxin and in the complex with its target peptide from the transcription factor NFkappaB. Biochemistry 35: 7-13 (1996).

255. Gronenborn AM, Clore GM.  Rapid screening for structural integrity of expressed proteins by heteronuclear NMR spectroscopy. Protein Sci 5: 174-177 (1996).

256. Pedone PV, Ghirlando R, Clore GM, Gronenborn AM, Felsenfeld G, Omichinski JG.  The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high affinity DNA binding. Proc Natl Acad Sci USA 93: 2822-2826 (1996).

257. Werner MH, Gronenborn AM, Clore GM.  Intercalation, DNA kinking and the control of transcription. Science 271, 778-784 (1996).

258. Clore GM, Gronenborn AM.  Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dimensional heteronuclear NMR.  Protein Sci 3: 372-390 (1994); Progr Biophys Mol Biol 62: 153-184 (1994); Encyclopedia of Nuclear Magnetic Resonance, vol. 7, pp. 4602-4622, (eds. Grant, D.M. & Harris, R.K.), John Wiley & Sons, New York (1996).

259. Clore GM, Gronenborn AM.  Multidimensional heteronuclear nuclear magnetic resonance of proteins. Meth Enzymol  239, 349-363 (1994); Spectroscopy 10: 32-38 (1995); Encyclopedia of Nuclear Magnetic Resonance, vol. 7, pp 4744-4752, (eds. Grant, D.M. & Harris, R.K.), John Wiley & Sons, New York (1996).

260. Grzesiek S, Bax A, Clore GM, Gronenborn AM, Hu J-H, Kaufman J, Palmer I, Stahl SJ, Wingfield PT.  The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase. Nat Struct Biol 3: 340-345 (1996).

261. Clore GM, Werner MH, Huth JR, Gronenborn AM.  Understanding 46X,Y sex reversal at the atomic level. In: Biological Structure and Dynamics  (eds. Sarma, R.H. & Sarma, M.H.), Vol. 1, pp. 35-40,  Adenine press, New York. (1996). In: Mechanisms of Transcription (eds. Eckstein, F. & Lilley, D.M.J.), vol. 11, p. 265-273, Springer, Berlin.

262. Trainor CD, Omichinski JG, Vandergon TL, Gronenborn AM, Clore GM, Felsenfeld G.  A palindromic regulatory site with vertebrate GATA-1 promoters requires both zinc fingers of the GATA-1 DNA binding domain for high affinity interaction. Mol Cell Biol 16: 2238-2247 (1996).

263. Qin J, Clore GM, Kennedy WP, Kuszewski J, Gronenborn AM.  The solution structure of human thioredoxin complexed with its target from Ref-1 reveals peptide chain reversal. Structure 4: 613-620 (1996).

264. Kuszewski J, Gronenborn AM, Clore GM. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases. Protein Sci 5: 1067-1080 (1996).

265. Werner MH, Huth JR, Gronenborn AM, Clore GM.  Molecular determinants of mammalian sex. Trends Biochem Sci 21: 302-308 (1996).

266. Kuszewski J, Gronenborn AM, Clore GM.  A potential involving multiple proton chemical shift restraints for non-stereospecifically assigned methyl and methylene protons. J Magn Reson Series B 112: 79-81 (1996).

267. Gronenborn AM, Frank MK, Clore GM.  Core mutants of the immunoglobulin binding domain of Streptococcal protein G: stability and structural integrity. FEBS Lett 398: 312-316 (1996).

268. Miller M, Lubkowski J, Rao MJK, Danishefsky AT, Omichinski JG, Sakaguchi K, Sakamoto H, Appella E, Gronenborn AM, Clore GM. The oligomerization domain of p53: crystal structure of the trigonal form. FEBS Lett 399: 166-170 (1996).

269. Clore GM, Gronenborn AM. Dissecting intrinsic chaperonin activity.  Proc Natl Acad Sci USA 94: 7-8 (1997).

270. Omichinski JG, Pedone PV, Felsenfeld G, Gronenborn AM, Clore GM.  The solution structure of a specific GAGA factor/DNA complex reveals a modular binding mode. Nat Struct Biol 4: 222-232 (1997).

271. Garrett DS, Seok YJ, Liao DI, Peterkofsky A, Gronenborn AM, Clore GM.  Solution structure of the 30 kDa N-terminal domain of Enzyme I of the Escherichia coli phosphoenolpyruvate: sugar phosphotransferase system by multidimensional NMR. Biochemistry 36: 2517-2530 (1997).

272. Kuszewski J, Gronenborn AM, Clore GM. Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. J Magn Reson 125: 171-177 (1997).

273. Pedone PV, Omichinski JG, Nony P, Trainor C, Gronenborn AM, Clore GM, Felsenfeld G. The N-terminal fingers of cGATA-2 and cGATA-3 are independent sequence-specific DNA binding domains. EMBO J 16: 2874-2882 (1997).

274. Garrett DS, Seok YJ, Peterkofsky A, Clore GM, Gronenborn AM.  Identification by NMR of the binding surface for the histidine-containing phosphocarrier protein HPr on the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system. Biochemistry 36: 4393-4398 (1997).

275. Gronenborn AM, Clore GM. Water in and around proteins. The Biochemist 19(3): 18-21 (1997).

276. Tjandra N, Garrett DS, Gronenborn AM, Bax A, Clore GM. Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy. Nat Struct. Biol 4: 443-449 (1997).

277. Nagaich AK, Zhurkin VB, Sakamoto H, Gorin AA, Clore GM, Gronenborn AM, Appella E, Harrington RE.  Architectural accomodation in the complex of four p53 DNA binding domain peptides with the p21/Waf1/Cip1 DNA response element. J Biol Chem 272: 14830-14841 (1997).

278. Wingfield PT, Stahl SJ, Kaufman J, Zlotnick A, Hyde CC, Gronenborn AM, Clore GM. The extracellular domain of immunodeficiency virus gp41 protein: expression in Escherichia coli, purification and crystallization. Protein Sci 6: 1653-1660 (1997).

279. Cai M, Zheng R, Caffrey M, Craigie R, Clore GM, Gronenborn AM.  Solution structure of the N-terminal zinc binding domain of HIV-1 integrase. Nat Struct Biol 4: 567-577 (1997).

280. Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A. Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat Struct Biol 4: 732-738 (1997).

281. Werner MH, Clore GM, Fisher CL, Fisher RJ, Trinh L, Shiloach J, Gronenborn AM. The solution structure of the human ETS1/DNA complex reveals a novel mode of binding and true sidechain intercalation. Cell 83: 761-771 (1995); Erratum Cell 87, issue 2 (1996). Correction of the NMR structure of the ETS1/DNA complex. J Biomol NMR 10, 317-328 (1997).

282. Huth JR, Bewley CA, Nissen MS, Evans JNS, Reeves R, Gronenborn AM, Clore GM. The solution structure of an HMG-I(Y)/DNA complex defines a new architectural minor groove binding motif. Nat Sruct Biol 4: 657-665 (1997).

283. Caffrey M, Cai M, Kaufman J, Stahl SJ, Wingfield PT, Gronenborn AM, Clore GM.  Determination of the secondary structure and global topology of the 44 kDa ectodomain of gp41 of the simian immunodeficiency virus by multidimensional nuclear magnetic resonance spectroscopy. J Mol Biol 271: 819-826 (1997).

284. Clubb RT, Schumacher S, Mizuuchi K, Gronenborn AM, Clore GM. Solution structure of the I gamma subdomain of the Mu end DNA binding domain of Mu phage transposase. J Mol Biol 273: 19-25 (1997).

285. Huth JR, Bewley CA, Jackson BM, Hinnebusch AG, Clore GM, Gronenborn AM.  Design of an expression system for detecting folded protein domains and mapping macromolecular interactions by NMR. Protein Sci 6: 2359-2364 (1997).

286. Schumacher S, Clubb RT, Cai M, Mizuuchi K, Clore GM, Gronenborn AM.  Solution structure of the Mu end DNA binding I beta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains. EMBO J. 16, 7532-7541 (1997).

287. Clore GM, Gronenborn AM.  Determining the structures of large proteins and protein complexes by NMR. Trends Biotechnol 16: 22-34 (1997); In: Modern Techniques in Protein NMR (eds. Krishnan, R.N. & Berliner, L.J. ), Plenum, New York, 3-26 (1998).

288. Bewley CA, Gronenborn AM, Clore GM. Minor-groove binding architectural proteins: structure, function and DNA recognition. Ann Rev Biophys Biomol Struct 27: 105-131 (1998).

289. Cai M, Huang Y, Sakaguchi K, Clore GM, Gronenborn AM, Craigie R. An efficient and cost-effective isotope labeling protocol for proteins expressed in Escherichia coli. J Biomol NMR 11: 97-102 (1998).

290. Louis JM, Martin R, Clore GM, Gronenborn AM.  Preparation of uniformly isotope labeled DNA oligonucleotides for NMR spectroscopy. J Biol Chem 273: 2374-2378 (1998).

291. Clore GM, Gronenborn AM. New methods of structure refinement for macromolecular structure determination by NMR. Proc Natl Acad Sci USA 95: 5891-5898 (1998).

292. Clore GM, Gronenborn AM, Tjandra N.  Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. J Magn Reson 131: 159-162 (1998).

293. Garrett DS, Seok Y-J, Peterkofsky A, Clore GM, Gronenborn AM.  Tautomeric state and pKa of the phosphorylated active site histidine in the N-terminal domain of Enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system. Protein Sci 7: 789-793 (1998).

294. Starich MR, Wikström M, Arst HN, Clore GM, Gronenborn AM.  The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors. J Mol Biol 277: 605-620 (1998).

295. Starich MR, Wikström M, Schumacher S, Arst HN, Gronenborn AM, Clore GM.  The solution structure of the Leu22→Val mutant of the AREA DNA binding domain complexed with a TGATA core element defines a role for hydrophobic packing in the determination of specificity.  J Mol Biol 277: 621-634 (1998).

296. Clore GM, Gronenborn AM, Bax A.  A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J Magn Reson 133: 216-221 (1998).

297. Clore GM, Gronenborn AM, Szabo A, Tjandra N.  Determining the magnitude of the fully asymmetric diffusion tensor from heteronuclear relaxation data in the absence of structural information. J Am Chem Soc 120: 4889-4890 (1998).

298. Clore GM, Murphy EC, Gronenborn AM, Bax A.  Determination of three-bond 1H3′-31P couplings in nucleic acids and protein-nucleic acid complexes by quantitative J correlation spectroscopy.  J Magn Reson 134: 164-167 (1998).

299. Bewley CA, Gustafson KR, Boyd MR, Covell DG, Bax A, Clore GM, Gronenborn AM.  Solution structure of cyanovirin-N, a potent HIV-inactivating protein. Nat Struct Biol 5: 571-578 (1998).

300. Caffrey M, Cai M, Kaufman J, Stahl SJ, Wingfield PT, Covell DG, Gronenborn AM, Clore GM.  Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41. EMBO J 17: 4572-4584 (1998).

301. Cai M, Huang Y, Zheng R, Wei S-Q, Ghirlando R, Lee MS, Craigie R, Gronenborn AM, Clore GM.  Solution structure of the cellular factor BAF responsible for protecting retroviral DNA from autointegration. Nat Struct Biol 5: 903-909 (1998).

302. Cai M, Huang Y, Caffrey M, Zheng R, Craigie R, Clore GM, Gronenborn AM.  Solution structure of the His12→Cys mutant of the N-terminal zinc binding domain of HIV-1 integrase complexed to cadmium.  Protein Sci 7: 2669-2674 (1998).

303. Clore GM, Starich MR, Gronenborn AM.  Measurement of residual dipolar couplings of macromolecules aligned in the nematic phase of a colloidal suspension of rod-shaped viruses.  J Am Chem Soc 120: 10571-10572 (1998).

304. Caffrey M, Kaufman J, Stahl SJ, Wingfield PT, Gronenborn AM, Clore GM.  3D NMR experiments for measuring 15N relaxation data of large proteins: application to the 44 kDa ectodomain of SIV gp41. J Magn Reson 135: 368-372 (1998).

305. Yu B, Blaber M, Gronenborn AM, Clore GM, Caspar DLD.  Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography. Proc Natl Acad Sci USA 96(1): 103-108 (1999).

306. Gronenborn AM, Clore GM, Louis JM, Wingfield PT.  Is human thioredoxin monomeric or dimeric?  Protein Sci 8, 1-4 (1999).

307. Garrett DS, Seok Y-J, Peterkofsky A, Gronenborn AM, Clore GM.  Solution structure of the 40,000 Mr phosphoryl transfercomplex between the N-terminal domain of enzyme I and HPr.  Nat Struct Biol 6: 166 – 173 (1999).

308. Kuszewski J, Gronenborn AM, Clore GM.  Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration.  J Am Chem Soc 121: 2337-2338 (1999).

309. Clore GM, Gronenborn AM.  NMR structures of proteins and protein complexes beyond 20 kDA.  Curr Opin Chem Biol 2(5): 564-570 (1998).

310. Yang F, Bewley CA, Louis JM, Gustafson KR, Boyd MR, Gronenborn AM, Clore GM, Wlodawer A. Crystal Structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping. J Mol Biol 288: 403-412 (1999).

311. Cornilescu G, Ramirez BE, Frank MK, Clore GM, Gronenborn AM, Bax A.Correlation between 3hJNC’ and hydrogen bond length in proteins. Am Chem Soc 121: 6275-6279 (1999).

312. Caffrey M, Kaufman J, Stahl SJ, Wingfield PT, Gronenborn AM, Clore GM.  Monomer-trimer equilibrium of the SIV gp41 ectodomain: insight into the mechanism of peptide inhibition of HIV infection.  Protein Sci 8: 1904-1907 (1999).

313. Louis JM, Clore GM, Gronenborn AM.  Autoprocessing of HIV-1 protease is tightly coupled to protein folding. Nat Struct Biol 6: 868-875 (1999).

314. Castagne C, Murphy EC, Gronenborn AM, Delepierre M. 31P NMR analysis of the DNA conformation induced by protein binding: SRY-DNA complexes. Eur J Biochem 207: 1223-1229 (2000).

315. Barrientos LG, Dolan,C, Gronenborn AM.  Characterization of surfactant liquid crystal phases suitable for molecular alignment and measurement of dipolar couplings. J Biomol NMR 16: 329-337 (2000).

316. Gakh YG, Gakh AA, Gronenborn AM. Fluorine as a NMR probe for structural studies of chemical and biological systems. Magn Reson Chem 38: 551-558 (2000).

317. Tcherkasskaya O, Bychkova VE, Uversky VN, Gronenborn AM.  Multi-site fluorescence in proteins with multiple tryptophan residues: Apomyoglobin natural variants and site directed mutants. J Biol Chem 275: 36285-36294 (2000).

318. Louis JM, Clore GM, Gronenborn AM.  Enzyme studies by NMR: Promise and limitations – HIV-1 protease maturation; a case study.  In: Improving enzyme catalysis: screening, evolution & rational redesign. (Ornstein, R.L. ed.), Marcel Dekker Inc. (2000).

319. Tcherkasskaya O, Knutson JR, Bowley SA, Frank MK, Gronenborn AM.  Nanosecond dynamics of the single tryptophan reveals multi-state equilibrium unfolding of protein GB1. Biochemistry 39: 11216-11226 (2000).

320. Qin J, Yang Y, Velyvis A, Gronenborn AM.  Molecular views of redox-regulation: three dimensional structures of redox regulatory proteins and protein complexes. J Antioxidants and Redox Signalling 2: 827-840 (2000).

321. Louis JM, Weber IT, Tözsér J, Clore GM, Gronenborn AM.  HIV-1 Protease: Maturation, enzyme specificity and drug resistance.  Adv Pharmacol 49: 111-146 (2000).

322. Li H, Yamada H, Akasaka K, Gronenborn AM.  Pressure alters electronic orbital overlap in hydrogen bonds. J Biol NMR 18: 207-216 (2000).