Bibliography

This bibliography includes all the papers referenced by DisProt, papers that have cited several key references on disordered proteins, and additional papers found by key word searches. The list is sorted by the first author's last name. Click here to see the distribution per year of the papers in the bibliography.
Last update on June 23rd, 2006. Total number of papers in this bibliography: 2785.

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Raab M, Schick G, Fondermann R, Dolg M, Henze W, Weynand U, Gschwind RM, Fischer K, Schmidt M, Niecke E. "A PH-Functionalized Polyphosphazene: A Macromolecule with a Highly Flexible Backbone." Angew Chem Int Ed Engl. 2006; 45(19): 3083-3086. PMID: 16586419
 
Raap J, Kerling KE, Vreeman HJ, Visser S. "Peptide substrates for chymosin (rennin): conformational studies of kappa-casein and some kappa-casein-related oligopeptides by circular dichroism and secondary structure prediction." Arch Biochem Biophys. 1983; 221(1): 117-24. PMID: 6402987
 
Rabzelj, S., Turk, V., Zerovnik, E. "In vitro study of stability and amyloid-fibril formation of two mutants of human stefin B (cystatin B) occurring in patients with EPM1." Protein Sci. 2005; 14(10): 2713-22. PMID: 16155205
 
Radhakrishnan I, Perez-Alvarado GC, Dyson HJ, Wright PE. "Conformational preferences in the Ser133-phosphorylated and non-phosphorylated forms of the kinase inducible transactivation domain of CREB." FEBS Lett. 1998; 430(3): 317-322. PMID: 9688563
 
Radhakrishnan I, Perez-Alvarado GC, Parker D, Dyson HJ, Montminy MR, Wright PE. "Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: a model for activator:coactivator interactions." Cell. 1997; 91(6): 741-752. PMID: 9413984
 
Radi AE, Acero Sanchez JL, Baldrich E, O'Sullivan CK. "Reagentless, reusable, ultrasensitive electrochemical molecular beacon aptasensor." J Am Chem Soc. 2006; 128(1): 117-24. PMID: 16390138
 
Radivojac P, Chawla NV, Dunker AK, Obradovic Z. "Classification and knowledge discovery in protein databases." J Biomed Inform. 2004; 37(4): 224-39. PMID: 15465476 zoran@ist.temple.edu
 
Radivojac P, Obradovic Z, Smith DK, Zhu G, Vucetic S, Brown CJ, Lawson JD, Dunker AK. "Protein flexibility and intrinsic disorder." Protein Sci. 2004; 13(1): 71-80. PMID: 14691223 kedunker@iupui.edu
 
Radivojac P, Vucetic S, O'Connor TR, Uversky VN, Obradovic Z, Dunker AK. "Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition." Proteins. 2006; 63(2): 398-410. PMID: 16493654 kedunker@iupui.edu
 
Raggett EM, Bainbridge G, Evans LJ, Cooper A, Lakey JH. "Discovery of critical Tol A-binding residues in the bactericidal toxin colicin N: a biophysical approach." Mol Microbiol. 1998; 28(6): 1335-43. PMID: 9680221
 
Raghuraman H, Chattopadhyay A. "Effect of ionic strength on folding and aggregation of the hemolytic peptide melittin in solution." Biopolymers. 2006. PMID: 16680713
 
Raha K, Merz KM Jr. "Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes." J Med Chem. 2005; 48(14): 4558-75. PMID: 15999994
 
Rajasekar K, Muntaha ST, Tame JR, Kommareddy S, Morris G, Wharton CW, Thomas CM, White SA, Hyde EI, Scott DJ. "Order and disorder in the domain organization of the plasmid partition protein KorB." J. Biol. Chem.. 2010; 285(20): 15440-9. PMID: 20200158
 
Rajendran C, Ermler U, Ludwig B, Michel H. "Structure at 1.5 A resolution of cytochrome c(552) with its flexible linker segment, a membrane-anchored protein from Paracoccus denitrificans." Acta Crystallogr. D Biol. Crystallogr.. 2010; 66(Pt 7): 850-4. PMID: 20606266
 
Rak A, Reents R, Pylypenko O, Niculae A, Sidorovitch V, Thoma NH, Waldmann H, Schlichting I, Goody RS, Alexandrov K. "Crystallization and preliminary X-ray diffraction analysis of the Rab escort protein-1 in complex with Rab geranylgeranyltransferase." J Struct Biol. 2001; 136(2): 158-61. PMID: 11886217
 
Rakow NA, Sen A, Janzen MC, Ponder JB, Suslick KS. "Molecular recognition and discrimination of amines with a colorimetric array." Angew Chem Int Ed Engl. 2005; 44(29): 4528-32. PMID: 16003792
 
Ralat LA, Funke T, Ren M, Guo Q, Dickey DM, Potter LR, Tang W-J. "Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human atrial natriuretic peptide (ANP)." PDB Primary Citation. 2010.
 
Rall SC Jr, Weisgraber KH, Mahley RW. "Human apolipoprotein E. The complete amino acid sequence." J Biol Chem. 1982; 257(8): 4171-8. PMID: 7068630
 
Ramadurai L, Jayaswal RK. "Molecular cloning, sequencing, and expression of lytM, a unique autolytic gene of Staphylococcus aureus." J Bacteriol. 1997; 179(11): 3625-31. PMID: 9171409
 
Ramakrishnan M, Jensen PH, Marsh D. "Association of alpha-synuclein and mutants with lipid membranes: spin-label ESR and polarized IR." Biochemistry. 2006; 45(10): 3386-95. PMID: 16519533
 
Ramakrishnan V, Finch JT, Graziano V, Lee PL, Sweet RM. "Crystal structure of globular domain of histone H5 and its implications for nucleosome binding." Nature. 1993; 362(6417): 219-223. PMID: 8384699
 
Ramamoorthy A, Thennarasu S, Tan A, Lee DK, Clayberger C, Krensky AM. "Cell selectivity correlates with membrane-specific interactions: A case study on the antimicrobial peptide G15 derived from granulysin." Biochim Biophys Acta. 2006; 1758(2): 154-63. PMID: 16579960
 
Ramelot TA, Cort JR, Yee AA, Semesi A, Edwards AM, Arrowsmith CH, Kennedy MA. "NMR structure of the Escherichia coli protein YacG: a novel sequence motif in the zinc-finger family of proteins." Proteins. 2002; 49(2): 289-293. PMID: 12211008
 
Ramelot TA, Nicholson LK. "Phosphorylation-induced structural changes in the amyloid precursor protein cytoplasmic tail detected by NMR." J Mol Biol. 2001; 307(3): 871-84. PMID: 11273707 lkn2@cornell.edu
 
Ramirez-Alvarado M, Serrano L, Blanco FJ. "Conformational analysis of peptides corresponding to all the secondary structure elements of protein L B1 domain: secondary structure propensities are not conserved in proteins with the same fold." Protein Sci. 1997; 6(1): 162-174. PMID: 9007989
 
Rantanen VV, Gyllenberg M, Koski T, Johnson MS. "A priori contact preferences in molecular recognition." J Bioinform Comput Biol. 2005; 3(4): 861-90. PMID: 16078365
 
Rao DK, Kumar R, Yadaiah M, Bhuyan AK. "The alkali molten globule state of ferrocytochrome c: extraordinary stability, persistent structure, and constrained overall dynamics." Biochemistry. 2006; 45(10): 3412-20. PMID: 16519536
 
Rao VD, Misra S, Boronenkov IV, Anderson RA, Hurley JH. "Structure of type IIbeta phosphatidylinositol phosphate kinase: a protein kinase fold flattened for interfacial phosphorylation." Cell. 1998; 94(6): 829-839. PMID: 9753329
 
Rashid F, Sharma S, Baig MA, Bano B. "Molten globule state of human placental cystatin (HPC) at low pH conditions and the effects of trifluoroethanol (TFE) and methanol." Biochem Cell Biol. 2006; 84(2): 126-134. PMID: 16609692
 
Rashid F, Sharma S, Bano B. "Comparison of guanidine hydrochloride (GdnHCl) and urea denaturation on inactivation and unfolding of human placental cystatin (HPC)." Protein J. 2005; 24(5): 283-92. PMID: 16284726
 
Rastinejad F, Perlmann T, Evans RM, Sigler PB. "Structural determinants of nuclear receptor assembly on DNA direct repeats." Nature. 1995; 375(6528): 203-11. PMID: 7746322
 
Ravanel K, Castelle C, Defrance T, Wild TF, Charron D, Lotteau V, Rabourdin-Combe C. "Measles virus nucleocapsid protein binds to FcgammaRII and inhibits human B cell antibody production." J Exp Med. 1997; 186(2): 269-278. PMID: 9221756
 
Rawat N, Biswas P. "Size, shape, and flexibility of proteins and DNA." J Chem Phys. 2009; 131(16): 165104. PMID: 19894979
 
Raychaudhuri S, Majumder P, Sarkar S, Giri K, Mukhopadhyay D, Bhattacharyya NP. "Huntingtin interacting protein HYPK is intrinsically unstructured." Proteins. 2008; 71(4): 1686-98. PMID: 18076027
 
Rechcinski T, Grebowska A, Kurpesa M, Rudnicka W, Krzeminska-Pakula M, Chmiela M. "Occurrence of serum class G immunoglobulins interacting with specific antigens of Helicobacter pylori in patients with unstable coronary artery disease and in symptomless individuals." Pol J Microbiol. 2005; 54(3): 221-5. PMID: 16450838
 
Redeker V, Lachkar S, Siavoshian S, Charbaut E, Rossier J, Sobel A, Curmi PA. "Probing the native structure of stathmin and its interaction domains with tubulin. Combined use of limited proteolysis, size exclusion chromatography, and mass spectrometry." J Biol Chem. 2000; 275(10): 6841-6849. PMID: 10702243
 
Redinbo MR, Champoux JJ, Hol WG. "Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA." Biochemistry. 2000; 39(23): 6832-6840. PMID: 10841763
 
Redinbo MR, Stewart L, Champoux JJ, Hol WG. "Structural flexibility in human topoisomerase I revealed in multiple non-isomorphous crystal structures." J Mol Biol. 1999; 292(3): 685-696. PMID: 10497031
 
Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG. "Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA." Science. 1998; 279(5356): 1504-1153. PMID: 9488644
 
Reed MA, Jelinska C, Syson K, Cliff MJ, Splevins A, Alizadeh T, Hounslow AM, Staniforth RA, Clarke AR, Craven CJ, Waltho JP. "The denatured state under native conditions: a non-native-like collapsed state of N-PGK." J Mol Biol. 2006; 357(2): 365-72. PMID: 16430920
 
Reeves R. "HMGA proteins: flexibility finds a nuclear niche?" Biochem Cell Biol. 2003; 81(3): 185-95. PMID: 12897853 reevesr@wsu.edu
 
Reeves R. "Molecular biology of HMGA proteins: hubs of nuclear function." Gene. 2001; 277(1-2): 63-81. PMID: 11602345 reevesr@wsu.edu
 
Reeves R, Beckerbauer L. "HMGI/Y proteins: flexible regulators of transcription and chromatin structure." Biochim Biophys Acta. 2001; 1519(1-2): 13-29. PMID: 11406267 reevesr@wsu.edu
 
Reeves, R. Nissen, M. S. "Purification and assays for high mobility group HMG-I(Y) protein function." Methods of Enzymology. 1996; 304: 155-188. PMID: 10372360
 
Reid AN, Whitfield C. "functional analysis of conserved gene products involved in assembly of Escherichia coli capsules and exopolysaccharides: evidence for molecular recognition between Wza and Wzc for colanic acid biosynthesis." J Bacteriol. 2005; 187(15): 5470-81. PMID: 16030241
 
Reid J, Betney R, Watt K, McEwan IJ. "The androgen receptor transactivation domain: the interplay between protein conformation and protein-protein interactions." Biochem Soc Trans. 2003; 31(Pt 5): 1042-6. PMID: 14505476 iain.mcewan@abdn.ac.uk
 
Reid J, Kelly SM, Watt K, Price NC, McEwan IJ. "Conformational analysis of the androgen receptor amino-terminal domain involved in transactivation. Influence of structure-stabilizing solutes and protein-protein interactions." J Biol Chem. 2002; 277(22): 20079-86. PMID: 11896058 iain.mcewan@abdn.ac.uk
 
Rekas A, Adda CG, Andrew Aquilina J, Barnham KJ, Sunde M, Galatis D, Williamson NA, Masters CL, Anders RF, Robinson CV, Cappai R, Carver JA. "Interaction of the molecular chaperone alphaB-crystallin with alpha-synuclein: effects on amyloid fibril formation and chaperone activity." J Mol Biol. 2004; 340(5): 1167-83. PMID: 15236975 john.carver@adelaide.edu.au
 
Remacha M, Saenz-Robles MT, Vilella MD, Ballesta JP. "Independent genes coding for three acidic proteins of the large ribosomal subunit from Saccharomyces cerevisiae." J Biol Chem. 1988; 263(19): 9094-9101. PMID: 2837476
 
Renault L, Kuhlmann J, Henkel A, Wittinghofer A. "Structural basis for guanine nucleotide exchange on Ran by the regulator of chromosome condensation (RCC1)." Cell. 2001; 105(2): 245-55. PMID: 11336674
 
Renault L, Nassar N, Vetter I, Becker J, Klebe C, Roth M, Wittinghofer A. "The 1.7 A crystal structure of the regulator of chromosome condensation (RCC1) reveals a seven-bladed propeller." Nature. 1998; 392(6671): 97-101. PMID: 9510255
 
Ren J, Kotaka M, Lockyer M, Lamb HK, Hawkins AR, Stammers DK. "GTP cyclohydrolase II structure and mechanism." J Biol Chem. 2005; 280(44): 36912-9. PMID: 16115872
 
Resende CG, Outeiro TF, Sands L, Lindquist S, Tuite MF. "Prion protein gene polymorphisms in Saccharomyces cerevisiae." Mol Microbiol. 2003; 49(4): 1005-17. PMID: 12890024
 
Rezler EM, Seenisamy J, Bashyam S, Kim MY, White E, Wilson WD, Hurley LH. "Telomestatin and diseleno sapphyrin bind selectively to two different forms of the human telomeric G-quadruplex structure." J Am Chem Soc. 2005; 127(26): 9439-47. PMID: 15984871
 
Rhoden JB, Bouvet M, Izenwasser S, Wade D, Lomenzo SA, Trudell ML. "Structure-activity studies of 3'-4'-dichloro-meperidine analogues at dopamine and serotonin transporters." Bioorg Med Chem. 2005; 13(19): 5623-34. PMID: 15993612
 
Riccio, M., Di Giaimo, R., Pianetti, S., Palmieri, P. P., Melli, M., Santi, S. "Nuclear localization of cystatin B, the cathepsin inhibitor implicated in myoclonus epilepsy (EPM1)." Exp Cell Res. 2001; 262(2): 84-94. PMID: 11139332
 
Rice LM, Brennwald P, Brunger AT. "Formation of a yeast SNARE complex is accompanied by significant structural changes." FEBS Lett. 1997; 415(1): 49-55. PMID: 9326367 brunger@stanford.edu
 
Rice RH, Green H. "Presence in human epidermal cells of a soluble protein precursor of the cross-linked envelope: activation of the cross-linking by calcium ions." Cell. 1979; 18(3): 681-694. PMID: 42494
 
Richard A, Delvaux J, Bourel-Bonnet L. "Effects of sterilizing-grade filters on the physico-chemical properties of onion-like vesicles." Int J Pharm. 2006; 312(1-2): 144-50. PMID: 16480839
 
Richards JP, Bachinger HP, Goodman RH, Brennan RG. "Analysis of the structural properties of cAMP-responsive element-binding protein (CREB) and phosphorylated CREB." J Biol Chem. 1996; 271(23): 13716-13723. PMID: 8662719
 
Richardson LG, Jelokhani-Niaraki M, Smith MD. "The acidic domains of the Toc159 chloroplast preprotein receptor family are intrinsically disordered protein domains." BMC Biochem. 2009; 10(1): 35. PMID: 20042108
 
Rico M, Bruix M, Santoro J, Gonzalez C, Neira JL, Nieto JL, Herranz J. "Sequential 1H-NMR assignment and solution structure of bovine pancreatic ribonuclease A." Eur. J. Biochem.. 1989; 183(3): 623-38. PMID: 2776756
 
Rico M, Santoro J, González C, Bruix M, Neira JL, Nieto JL, Herranz J. "3D structure of bovine pancreatic ribonuclease A in aqueous solution: an approach to tertiary structure determination from a small basis of 1H NMR NOE correlations." J. Biomol. NMR. 1991; 1(3): 283-98. PMID: 1841699
 
Riek R, Hornemann S, Wider G, Glockshuber R, Wuthrich K. "NMR characterization of the full-length recombinant murine prion protein, mPrP(23-231)." FEBS Lett. 1997; 413(2): 282-8. PMID: 9280298
 
Riley LG, Junius FK, Swanton MK, Vesper NA, Williams NK, King GF, Weiss AS. "Cloning, expression, and spectroscopic studies of the Jun leucine zipper domain." Eur J Biochem. 1994; 219(3): 877-886. PMID: 8112339
 
Rimsay R, Robinson JJ. "Biochemical analysis of hyalin gelation: an essential step in the assembly of the sea urchin extraembryonic matrix, the hyaline layer." Arch Biochem Biophys. 2003; 414(2): 279-86. PMID: 12781780
 
Ringstad L, Schmidtchen A, Malmsten M. "Effect of Peptide Length on the Interaction between Consensus Peptides and DOPC/DOPA Bilayers." Langmuir. 2006; 22(11): 5042-50. PMID: 16700592
 
Ritter LM, Arakawa T, Goldberg AF. "Predicted and measured disorder in peripherin/rds, a retinal tetraspanin." Protein Pept Lett. 2005; 12(7): 677-86. PMID: 16522184 goldberg@oakland.edu
 
Robson CN, Hickson ID. "Isolation of cDNA clones encoding a human apurinic/apyrimidinic endonuclease that corrects DNA repair and mutagenesis defects in E. coli xth (exonuclease III) mutants." Nucleic Acids Res. 1991; 19(20): 5519-5523. PMID: 1719477
 
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Rochel N, Wurtz JM, Mitschler A, Klaholz B, Moras D. "The crystal structure of the nuclear receptor for vitamin D bound to its natural ligand." Mol Cell. 2000; 5(1): 173-9. PMID: 10678179
 
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Rodi DJ, Agoston GE, Manon R, Lapcevich R, Green SJ, Makowski L. "Identification of small molecule binding sites within proteins using phage display technology." Comb Chem High Throughput Screen. 2001; 4(7): 553-72. PMID: 11562259
 
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