Intrinsically disordered protein

Journal of Molecular Graphics and Modelling - Tập 19 Số 1 - Trang 26-59 - 2001
A. Keith Dunker1, J. David Lawson1, Celeste J. Brown1, Ryan M. Williams1, Pedro Romero2, Jeong Seok Oh1, Christopher J. Oldfield1, Andrew Campen1, Catherine M Ratliff1, K. W. Hipps3, Juan Ausió4, M.S. Nissen1, Raymond Reeves1, ChulHee Kang1, Charles R. Kissinger5, Robert W. Bailey1, Michael D. Griswold1, Wah Chiu6, Ethan C. Garner1, Zoran Obradović7
1Schools of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USAand
2Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164-4660, USA and
3Department of Chemistry, Washington State University, Pullman, WA 99164-4660, USA
4Department of Biochemistry, University of Victoria, Victoria, BC V8W 3P6, Canada
5Pfizer Global Research & Development, La Jolla 11099 North Torrey Pines Road, La Jolla, CA 92037, USA
6National Center for Macromolecular Imaging, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
7Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA

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Fischer, 1894, Einfluss der configuration auf die wirkung der enzyme, Ber. Dt. Chem. Ges., 27, 2985, 10.1002/cber.18940270364

Lemieux, 1994, How Emil Fischer was led to the lock and key concept for enzyme specificity, Adv. Carbohydrate Chem. Biochem., 50, 1, 10.1016/S0065-2318(08)60149-3

Mirsky, 1936, On the structure of native, denatured and coagulated proteins, Proc. Natl. Acad. Sci. U.S.A., 22, 439, 10.1073/pnas.22.7.439

Northrop, 1930, Crystalline Pepsin. I. Isolation and tests of purity, J. Gen. Physiol., 13, 739, 10.1085/jgp.13.6.739

Anson, 1932, The effect of denaturation on the viscosity of protein systems, J. Gen. Physiol., 15, 341, 10.1085/jgp.15.3.341

Wu, 1931, Studies on denaturation of proteins XIII. A theory of denaturation, Chinese J. Physiol., 1, 219

Edsall, 1995, Hsien Wu and the first theory of protein denaturation (1931), Adv. Protein Chem., 46, 1, 10.1016/S0065-3233(08)60329-0

Anson, M.L., Protein denaturation and the properties of protein groups. In: Advances in Protein Chemistry, Anson, M.L., and Edsall, J.T., Eds. Academic Press, New York, 1945, pp. 361–384

Edsall, 1952, Some comments on proteins and protein structure, Proc. R. Soc. Lond., B147, 97

Phillips, 1986, Development of concepts of protein structure, Perspectives Biol. Med., 29, S124, 10.1353/pbm.1986.0064

Sela, 1957, Reductive cleavage of disulfide bridges in ribonuclease, Science, 125, 691, 10.1126/science.125.3250.691

Anfinsen, 1973, Principles that govern the folding of protein chains, Science, 181, 223, 10.1126/science.181.4096.223

Kendrew, 1960, Structure of myoglobin, Nature, 206, 757

Blake, 1965, Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution, Nature, 206, 757, 10.1038/206757a0

Berman, 2000, The protein data bank, Nucleic Acids Res, 28, 235, 10.1093/nar/28.1.235

Frishman, 1997, Protein structural classes in five complete genomes, Nat. Struct. Biol., 4, 626, 10.1038/nsb0897-626

Frishman, 1997, PEDANTic genome analysis, Trends in Genetics, 13, 416, 10.1016/S0168-9525(97)01224-9

Gerstein, 1998, How representative are the known structures of the proteins in a complete genome? A comprehensive structural census, Fold. Des., 3, 497, 10.1016/S1359-0278(98)00066-2

Gerstein, 1998, Comparing genomes in terms of protein structure, FEMS Microbiol. Rev., 22, 277, 10.1111/j.1574-6976.1998.tb00371.x

Karush, 1950, Heterogeneity of the binding sites of bovine serum albumin, J. Am. Chem. Soc., 72, 2705, 10.1021/ja01162a099

Lund, 1999, Structural heterogeneity of the binding sites of HSA for phenyl-groups and medium-chain fatty acids. Demonstration of equilibrium between different binding conformations, Eur. J. Biochem., 260, 470, 10.1046/j.1432-1327.1999.00175.x

Koshland, 1958, Application of a theory of enzyme specificity to protein synthesis, Proc. Natl. Acad. Sci. U.S.A., 44, 98, 10.1073/pnas.44.2.98

Bennett, 1978, Glucose-induced conformational change in yeast hexokinase, Proc. Natl. Acad. Sci. U.S.A., 75, 4848, 10.1073/pnas.75.10.4848

McDonald, 1979, Yeast hexokinase in solution exhibits a large conformational change upon binding glucose or glucose 6-phosphate, Biochemistry, 18, 338, 10.1021/bi00569a017

Koshland Jr., E., D. The key-lock theory and the induced fit theory. Angew. Chem. Int. Ed. Engl. 1994, 33, 2375–2378

Kawaguchi, 1997, Enzyme flexibility, J. Biochem. (Tokyo), 122, 55, 10.1093/oxfordjournals.jbchem.a021740

Monod, 1965, On the nature of allosteric transitions, J. Mol. Biol., 12, 88, 10.1016/S0022-2836(65)80285-6

Koshland, 1966, Comparison of experimental binding data and theoretical models in proteins containing subunits, Biochemistry, 5, 365, 10.1021/bi00865a047

Bloomer, 1978, Protein disk of tobacco mosiac virus at 2.8Å resolution showing the interactions within and between subunits, Nature, 276, 362, 10.1038/276362a0

Bode, 1978, The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. The refined crystal structures of the bovine trypsinogen-pancreatic trypsin inhibitor complex and of its ternary complex with Ile-Val at 1.9Å resolution, J. Mol. Biol., 118, 99, 10.1016/0022-2836(78)90246-2

Huber, 1979, Conformational flexibility and its functional significance in some protein molecules, TIBS, 4, 271

Schulz, G.E., Nucleotide Binding Proteins. In: Molecular Mechanism of Biological Recognition, Balaban, M., Ed. Elsevier/North-Holland Biomedical Press, New York, 1979, pp. 79–94

Alber, 1982, The role of mobility in the substrate binding and catalytic machinery of enzymes, Ciba Found. Symp., 93, 4

Spolar, R.S., and Record II, M.T. Coupling of local folding to site-specific binding of proteins to DNA. Science 1994, 263, 777–784

Lewis, 1996, Crystal structure of the lactose operon repressor and its complexes with DNA and inducer, Science, 271, 1247, 10.1126/science.271.5253.1247

Dunker, 1997, On the importance of being disordered, PDB Newsletter, 81, 3

Aviles, 1978, The conformation of histone H5. Isolation and characterisation of the globular segment, Eur. J. Biochem., 88, 363, 10.1111/j.1432-1033.1978.tb12457.x

Muchmore, 1996, X-ray and NMR structure of human Bcl-xL, an inhibitor of programmed cell death, Nature, 381, 335, 10.1038/381335a0

Riek, 1996, NMR structure of the mouse prion protein domain PrP(121–321), Nature, 382, 180, 10.1038/382180a0

Kriwacki, 1996, Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state, Proc. Natl. Acad. Sci. U.S.A., 93, 11504, 10.1073/pnas.93.21.11504

Daughdrill, 1997, The C-terminal half of the anti-sigma factor, FlgM, becomes structured when bound to its target, sigma 28, Nat. Struct. Biol., 4, 285, 10.1038/nsb0497-285

Fletcher, 1998, The interaction of eIF4E with 4E-BP1 is an induced fit to a completely disordered protein, Protein Sci, 7, 1639, 10.1002/pro.5560070720

Plaxco, K.W., and Gross, M. The importance of being unfolded. Nature 1997, 386, 657, 659

Wright, 1999, Intrinsically unstructured proteins, J. Mol. Biol., 293, 321, 10.1006/jmbi.1999.3110

Tanford, 1968, Protein denaturation, Adv. Protein Chemistry, 23, 121, 10.1016/S0065-3233(08)60401-5

Kuwajima, 1976, Three-state denaturation of alpha-lactalbumin by guanidine hydrochloride, J. Mol. Biol., 106, 359, 10.1016/0022-2836(76)90091-7

Myer, 1968, Conformation of cytochromes. III. Effect of urea, temperature, extrinsic ligands, and pH variation on the conformation of horse heart ferricytochrome c, Biochemistry, 7, 765, 10.1021/bi00842a035

Dolgikh, 1981, Alpha-Lactalbumin, FEBS Lett, 136, 311, 10.1016/0014-5793(81)80642-4

Goto, 1989, Conformational states of beta-lactamase, Biochemistry, 28, 945, 10.1021/bi00429a004

Gast, 1994, Compactness of protein molten globules, Eur. Biophys. J., 23, 297, 10.1007/BF00213579

Nishii, 1994, Denaturation of the moltern globule states of apomyoglobin and a profile for protein folding, Biochemistry, 33, 4903, 10.1021/bi00182a019

Ohgushi, 1983, ’Molten-globule state’, FEBS Lett, 164, 21, 10.1016/0014-5793(83)80010-6

Kim, 1982, Specific Intermediates in the folding reactions of small proteins and the mechanism of protein folding, Annu. Rev. Biochem., 51, 459, 10.1146/annurev.bi.51.070182.002331

Kuwajima, 1989, The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure, Proteins, 6, 87, 10.1002/prot.340060202

Loh, 1995, Structure and stability of a second molten globule intermediate in the apomyoglobin folding pathway, Proc. Natl. Acad. Sci. U.S.A., 92, 5446, 10.1073/pnas.92.12.5446

Baum, J., Dobson C.M, Evans P.A., Hanley C. Characterization of a partly folded protein by NMR methods: studies on the molten globule state of guinea pig alpha-lactalbumin. Biochemistry 1989, 28, 7–13

Woodward, 2001, Experimental approaches to protein folding based on the concept of a slow hydrogen exchange core, J. Mol. Graphics Modell., 19, 94, 10.1016/S1093-3263(00)00131-5

Kim, 1990, Intermediates in the folding reactions of small proteins, Ann. Rev. Biochem., 59, 631, 10.1146/annurev.bi.59.070190.003215

Barrick, 1993, Stein and Moore Award address. The molten globule intermediate of apomyoglobin and the process of protein folding, Protein Sci, 2, 869, 10.1002/pro.5560020601

Peng, 1994, A protein dissection study of a molten globule, Biochemistry, 33, 2136, 10.1021/bi00174a021

Ptitsyn, 1994, The molten globule is a third thermodynamical state of protein molecules, FEBS Lett, 341, 15, 10.1016/0014-5793(94)80231-9

Kuwajima, 1996, The molten globule state of alpha-lactalbumin, FASEB J, 10, 102, 10.1096/fasebj.10.1.8566530

Bychkova, 1988, The ‘molten globule’ state is involved in the translocation of proteins across membranes?, FEBS Lett, 238, 231, 10.1016/0014-5793(88)80485-X

Bychkova, 1992, Retinol-binding protein is in the molten globule state at low pH, Biochemistry, 31, 7566, 10.1021/bi00148a018

Bychkova, 1998, Release of retinol and denaturation of its plasma carrier, retinol- binding protein, Fold. Des., 3, 285, 10.1016/S1359-0278(98)00039-X

Bychkova, 1993, The molten globule in vitro and in vivo, Chemtracts - Biochem. Mol. Biol., 4, 133

Seeley, 1996, The cytoplasmic fragment of the aspartate receptor displays globally dynamic behavior, Biochemistry, 35, 5199, 10.1021/bi9524979

Gursky, 1996, Thermal unfolding of human high-density apolipoprotein A-1, Proc. Natl. Acad. Sci. U.S.A., 93, 2991, 10.1073/pnas.93.7.2991

Carroll, 1997, SKN-1 domain folding and basic region monomer stabilization upon DNA binding, Genes Dev, 11, 2227, 10.1101/gad.11.17.2227

Zurdo, 1997, The exchangeable yeast ribosomal acidic protein YP2β shows characteristics of a partly folded state under physiological conditions, Biochemistry, 36, 9625, 10.1021/bi9702400

Zhang, 1998, Ligand binding is the principal determinant of stability for the p21(H)- ras protein, Biochemistry, 37, 14881, 10.1021/bi9811157

Quintas, 1999, The tetrameric protein transthyretin dissociates to a non-native monomer in solution. A novel model for amyloidogenesis, J. Biol. Chem., 274, 32943, 10.1074/jbc.274.46.32943

Huber, 1983, Functional significance of flexibility in proteins, Biopolymers, 22, 261, 10.1002/bip.360220136

Douzou, 1984, Proteins at work, Adv. Protein Chem., 36, 245, 10.1016/S0065-3233(08)60299-5

Ishima, 2000, Protein dynamics from NMR, Nat. Struct. Biol., 7, 740, 10.1038/78963

Bracken, 2001, NMR spin relaxation methods for characterization of disorder and folding in proteins, J. Mol. Graphics Modell., 19, 3, 10.1016/S1093-3263(00)00136-4

Evans, 1995

Smith, 1999, Side-chain conformational disorder in a molten globule, J. Mol. Biol., 286, 1567, 10.1006/jmbi.1999.2545

Bai, 2000, Side chain accessibility and dynamics in the molten globule state of alpha-lactalbumin, Biochemistry, 39, 372, 10.1021/bi992056f

Eliezer, 1998, Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding, Nat. Struct. Biol., 5, 148, 10.1038/nsb0298-148

Eliezer, 2000, Native and non-native secondary structure and dynamics in the pH 4 intermediate of apomyoglobin, Biochemistry, 39, 2894, 10.1021/bi992545f

Fasman, 1996

Kuwajima, 1977, A folding model of alpha-lactalbumin deduced from the three-state denaturation mechanism, J. Mol. Biol., 114, 241, 10.1016/0022-2836(77)90208-X

Linderstrom-Lang, 1949, Structure and enzymatic break-down of proteins, Cold Spring Harbor Symp. Quant. Biol., 14, 117, 10.1101/SQB.1950.014.01.016

Markus, 1965, Protein Substrate Conformation and Proteolysis, Proc. Natl. Acad. Sci. U.S.A., 54, 253, 10.1073/pnas.54.1.253

Fontana, A., Polverino de Laureto, P., and De Filippis, V., Molecular Aspects of Proteolysis of Globular Proteins. In: Protein Stability and Stabilization, van den Tweel, W., Harder, A., and Buitelear, M., Eds. Elsevier Science Publ., Amsterdam, 1993

Fontana, 1997, Probing the conformational state of apomyoglobin by limited proteolysis, J. Mol. Biol., 266, 223, 10.1006/jmbi.1996.0787

Hubbard, 1994, Modeling studies of the change in conformation required for cleavage of limited proteolytic sites, Protein Sci, 3, 757, 10.1002/pro.5560030505

Hubbard, 1998, Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures, Protein Eng, 11, 349, 10.1093/protein/11.5.349

Honig, 1995, Free energy balance in protein folding, Adv. Protein Chem., 46, 27, 10.1016/S0065-3233(08)60331-9

Manalan, 1983, Activation of calcineurin by limited proteolysis, Proc. Natl. Acad. Sci. U.S.A., 80, 4291, 10.1073/pnas.80.14.4291

Kissinger, 1995, Crystal structures of human calcineurin and the human FKBP12-FK506- calcineurin complex, Nature, 378, 641, 10.1038/378641a0

Iakoucheva, 2001, Identification of intrinisc order and disorder in the DNA damage-recognition protein XPA by time-resolved proteolysis, prediction from sequence, and Fourier transform ion cyclotron resonance mass spectrometry, Protein Science, 10, 560, 10.1110/ps.29401

Schweers, 1994, Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for beta-structure, J. Biol. Chem., 269, 24290, 10.1016/S0021-9258(19)51080-8

Kriwacki, 1997, Probing protein structure using biochemical and biophysical methods. Proteolysis, matrix-assisted laser desorption/ionization mass spectrometry, high-performance liquid chromatography and size-exclusion chromatography of p21Waf1/Cip1/Sdi1, J. Chromatogr. A, 777, 23, 10.1016/S0021-9673(97)00527-X

Weinreb, 1996, NACP, a protein implicated in Alzheimer’s disease and learning, is natively unfolded, Biochemistry, 35, 13709, 10.1021/bi961799n

Ptitsyn, 1987, Protein Folding, J. Protein Chem., 6, 273, 10.1007/BF00248050

Ptitsyn, 1995, Molten globule and protein folding, Adv. Protein Chem., 47, 83, 10.1016/S0065-3233(08)60546-X

Handel, 1993, Metal ion-dependent modulation of the dynamics of a designed protein, Science, 261, 879, 10.1126/science.8346440

Betz, 1996, Controlling topology and native-like behavior of de novo-designed peptides, Biochemistry, 35, 6955, 10.1021/bi960095a

Ringe, 1986, Study of protein dynamics by X-ray diffraction, Methods Enzymol, 131, 389, 10.1016/0076-6879(86)31050-4

Parthasarathy, 2000, Protein thermal stability, Protein Eng, 13, 9, 10.1093/protein/13.1.9

McCammon, 1977, Dynamics of folded proteins, Nature, 267, 585, 10.1038/267585a0

Griffith, 1981, Filamentous bacteriophage contract into hollow spherical particles upon exposure to a chloroform-water interface, Cell, 23, 747, 10.1016/0092-8674(81)90438-4

Manning, 1981, Mechanism of coliphage M13 contraction, J. Virol., 40, 912, 10.1016/0042-6822(70)90137-6

Manning, 1982, Insertion of bacteriophage M13 coat protein into membranes, Biophys. J., 37, 28, 10.1016/S0006-3495(82)84583-9

Manning, 1985, Association of M13 I-forms and spheroids with lipid vesicles, Arch. Biochem. Biophys., 236, 297, 10.1016/0003-9861(85)90629-0

Roberts, 1993, Structural changes accompanying chloroform-induced contraction of the filamentous phage fd, Biochemistry, 32, 10479, 10.1021/bi00090a026

Dunker, 1991, A model for fd phage penetration and assembly, FEBS Lett, 292, 271, 10.1016/0014-5793(91)80882-4

Dunker, 1991, Proposed molten globule intermediates in fd phage penetration and assembly, FEBS Lett, 292, 275, 10.1016/0014-5793(91)80883-5

Ausio, 1989, Use of selectively trypsinized nucleosome core particles to analyze the role of the histone “Tails” in the stabilization of the nucleosome, J. Mol. Biol., 206, 451, 10.1016/0022-2836(89)90493-2

Luger, 1997, Crystal structure of the nucleosome core particle at 2.8 Å resolution, Nature, 389, 251, 10.1038/38444

Luger, 1998, The histone tails of the nucleosome, Curr. Opin. Genet. Dev., 8, 140, 10.1016/S0959-437X(98)80134-2

Waterborg, 1983, Intranuclear localization of histone acetylation in Physarum polycephalum and the structure of functionally active chromatin, Cell Biophys, 5, 265, 10.1007/BF02788625

Chahal, S., S., Matthews, H.R., and Bradbury, E.M. Acetylation of histone H4 and its role in chromatin structure and function. Nature 1980, 287, 76–79

Mizzen, 1998, Linking histone acetylation to transcriptional regulation, Cell Mol. Life Sci., 54, 6, 10.1007/s000180050121

Ausio, 1986, Histone hyperacetylation, Biochemistry, 25, 1421, 10.1021/bi00354a035

Imai, B., S., yau, P., Baldwin, J., P., Ibel, K., May, R., P., and Bradbury, E., Morton Hyperacetylation of core histones does not cause unfolding of nucleosomes. J. Biol. Chem. 1986, 261, 8784–8792

Oliva, 1990, Histone hyperacetylation can induce unfolding of the nucleosome core particle, Nucleic Acids Res, 18, 2739, 10.1093/nar/18.9.2739

Ji, 1998, Effects of relative humidity and applied force on atomic force microscopy images of the filamentous phage fd, Ultramicroscopy, 72, 165, 10.1016/S0304-3991(97)00169-1

Sertoli, 1865, e lesistenza di particulari cellule remificate nei canalicoli seminiferi dell’testicolo umano, Morgangni, 7, 31

Griswold, 1995, Interactions between germ cells and Sertoli cells in the testis, Biol. Reprod., 52, 211, 10.1095/biolreprod52.2.211

Kissinger, 1982, Analysis of Sertoli cell-secreted proteins by two-dimensional gel electrophoresis, Biol. Reprod., 27, 233, 10.1095/biolreprod27.1.233

Collard, 1988, Biosynthesis and molecular cloning of sulfated glycoprotein 1 secreted by rat Sertoli cells, Biochemistry, 27, 4557, 10.1021/bi00412a050

Bailey, 1999, Clusterin in the male reproductive system, Mol. Cell Endocrinol., 151, 17, 10.1016/S0303-7207(99)00016-7

Romero, 1997, Identifying disordered regions in proteins from amino acid sequences, Proc. I.E.E.E. International Conference on Neural Networks, 1, 90

Romero, 2001, Sequence complexity of disordered protein, Proteins: Struc. Funct. Gen., 42, 38, 10.1002/1097-0134(20010101)42:1<38::AID-PROT50>3.0.CO;2-3

Manalan, A.S., and Klee, C.B., Calcineurin, a calmodulin-stimulated protein phophatase. In: Calcium in Biological Systems, Rubin, R.P., Weiss, G.B., and Putney, J.W. Eds., Plenum Press, New York, 1985, pp. 307–315

Klee, 1979, Calcineurin, Proc. Natl. Acad. Sci. U.S.A., 76, 6270, 10.1073/pnas.76.12.6270

Liu, 1991, Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP- FK506 complexes, Cell, 66, 807, 10.1016/0092-8674(91)90124-H

McKeon, 1991, When worlds collide, Cell, 66, 823, 10.1016/0092-8674(91)90426-Y

Meador, 1992, Target enzymes recognition by calmodulin, Science, 257, 1251, 10.1126/science.1519061

MacLennan, 1971, Isolation of a calcium sequestering protein from sarcoplasmic reticulum, Proc. Natl. Acad. Sci. U.S.A., 68, 1231, 10.1073/pnas.68.6.1231

Krause, 1991, Thermodynamics of cation binding to rabbit skeletal muscle calsequestrin. Evidence for distinct Ca(2+)- and Mg(2+)-binding sites, J. Biol. Chem., 266, 9453, 10.1016/S0021-9258(18)92842-5

MacLennan, 1998, Ion Tamers, Nature Struct. Biol., 5 No. 6, 409, 10.1038/nsb0698-409

Wang, 1998, Crystal structure of calsequestrin from rabbit skeletal muscle sarcoplasmic reticulum, Nat. Struct. Biol., 5, 476, 10.1038/nsb0698-476

Huber, 1979, Conformational flexibility in protein molecules, Nature, 280, 538, 10.1038/280538a0

Kossiakoff, 1977, Structure of bovine trypsinogen at 1.9 A resolution, Biochemistry, 16, 654, 10.1021/bi00623a016

Bennett, 1984, Structural and functional aspects of domain motions in proteins, Crit. Rev. Biochem., 15, 291, 10.3109/10409238409117796

Holmes, 1983, Flexibility in tobacco mosaic virus, Ciba Found. Symp., 93, 116

Champness, 1976, The structure of the protein disk of tobacco mosaic virus to 5Å resolution, Nature, 259, 20, 10.1038/259020a0

Stubbs, 1977, Structure of RNA and RNA binding site in tobacco mosaic virus from 4-Å map calculated from X-ray fibre diagrams, Nature, 267, 216, 10.1038/267216a0

Jardetzky, 1978, Unusual segmental flexibility in a region of tobacco mosaic virus coat protein, Nature, 273, 564, 10.1038/273564a0

Jacob, 1961, Genetic regulatory mechanisms in the synthesis of proteins, J. Mol. Biol., 3, 318, 10.1016/S0022-2836(61)80072-7

Slijper, 1997, Backbone and side chain dynamics of lac repressor headpiece (1-56) and its complex with DNA, Biochemistry, 36, 249, 10.1021/bi961670d

Babu, 1988, Structure of calmodulin refined at 2.2 Å resolution, J. Mol. Biol., 203, 191, 10.1016/0022-2836(88)90608-0

Wriggers, 1998, Structure and dynamics of calmodulin in solution, Biophys. J., 74, 1622, 10.1016/S0006-3495(98)77876-2

Ikura, 1992, Solution structure of a calmodulin-target peptide complex by multidimensional NMR, Science, 256, 632, 10.1126/science.1585175

Meador, 1993, Modulation of calmodulin plasticity in molecular recognition on the basis of X-ray structures, Science, 262, 1718, 10.1126/science.8259515

Dunker, 1998, Protein disorder and the evolution of molecular recognition, Pacific Symp. Biocomputing, 3, 473

Lee, 2000, Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex, Nat. Struct. Biol., 7, 72, 10.1038/71280

Gellman, 1991, On the role of methionine residues in the sequence-independent recognition of nonpolar protein surfaces, Biochemistry, 30, 6633, 10.1021/bi00241a001

Weliky, 1999, Solid-state NMR evidence for an antibody-dependent conformation of the V3 loop of HIV-1 gp120, Nat. Struct. Biol., 6, 141, 10.1038/5827

Stanfield, 1999, Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs, Structure Fold Des, 7, 131, 10.1016/S0969-2126(99)80020-3

Balbach, 2000, Probing hydrogen bonds in the antibody-bound HIV-1 gp120 V3 loop by solid state NMR REDOR measurements, J. Biomol. NMR, 16, 313, 10.1023/A:1008343623240

House-Pompeo, 1996, Conformational changes in the binding MSCRAMMs are induced by ligand binding, J. Biol. Chem., 271, 1379, 10.1074/jbc.271.3.1379

Penkett, 1997, NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein, J. Mol. Biol., 274, 152, 10.1006/jmbi.1997.1369

Lea, 1994, The structure and antigenicity of a type C foot-and-mouth disease virus, Structure, 2, 123, 10.1016/S0969-2126(00)00014-9

Romero, 1998, Thousands of proteins likely to have long disordered regions, Pacific Symp. Biocomputing, 3, 437

Boulikas, 1993, Nuclear localization signals (NLS), Crit. Rev. Eukaryot Gene Expr., 3, 193

Nolte, 1998, Differing roles for zinc fingers in DNA recognition, Proc. Natl. Acad. Sci. U.S.A., 95, 2938, 10.1073/pnas.95.6.2938

Choo, 1998, All wrapped up, Nat. Struct. Biol., 5, 253, 10.1038/nsb0498-253

Vajda, 1994, Effect of conformational flexibility and solvation on receptor-ligand binding free energies, Biochemistry, 33, 13977, 10.1021/bi00251a004

Rosenfeld, 1995, Flexible docking and design, Annu. Rev. Biophys. Biomol. Struct., 24, 677, 10.1146/annurev.bb.24.060195.003333

Novotny, 1989, On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5, Biochemistry, 28, 4735, 10.1021/bi00437a034

Noyes, 1961, Effects of diffusion rates on chemical kinetics, Prog. React. Kinet., 1, 129

Von Hippel, 1989, Facilitated target location in biological systems, J. Biol. Chem., 264, 675, 10.1016/S0021-9258(19)84994-3

Schreiber, 1996, Rapid, electrostatically assisted association of proteins, Nat. Struct. Biol., 3, 427, 10.1038/nsb0596-427

DeLisi, 1980, The biophysics of ligand-receptor interactions, Quart. Rev. Biophys., 13, 201, 10.1017/S0033583500001657

Berg, O.G., and Hippel, v. Diffusion-controlled macromolecular interactions. Ann. Rev. Biophys. Biophys. Chem. 1985, 14, 131–160

Pontius, 1993, Close encounters, Trends Biochem. Sci., 18, 181, 10.1016/0968-0004(93)90111-Y

Jeffery, 1999, Moonlighting proteins, Trends Biochem. Sci., 24, 8, 10.1016/S0968-0004(98)01335-8

Williams, 2001, Evolution of functionality in lattice proteins, J. Mol. Graphics Modell., 19, 150, 10.1016/S1093-3263(00)00125-X

Gast, 1995, Prothymosin alpha, Biochemistry, 34, 13211, 10.1021/bi00040a037

Fletcher, 1998, 4E binding proteins inhibit the translation factor eIF4E without folded structure, Biochemistry, 37, 9, 10.1021/bi972494r

Mader, 1995, The translation initiation factor eIF-4E binds to a common motif shared by the translation factor eIF-4 gamma and the translational repressors 4E-binding proteins, Mol. Cell. Biol., 15, 4990, 10.1128/MCB.15.9.4990

Marcotrigiano, 1999, Cap-dependent translation initiation in eukaryotes is regulated by a molecular mimic of eIF4G, Mol Cell, 3, 707, 10.1016/S1097-2765(01)80003-4

Bustin, 1996, HMG chromosomal proteins, Prog. Nucl. Acids Res. Molec. Biol., 54, 35, 10.1016/S0079-6603(08)60360-8

Huth, 1997, The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif, Nat. Struct. Biol., 4, 657, 10.1038/nsb0897-657

Zhang, 1994, Nuclear magnetic resonance studies of the structure of B50/neuromodulin and its interaction with calmodulin, Biochem. Cell Biol., 72, 109, 10.1139/o94-017

Smith, 1998, Identification of a neuronal calmodulin-binding peptide, CAP-19, containing an IQ motif, Brain Res. Mol. Brain Res., 62, 12, 10.1016/S0169-328X(98)00207-1

Alexander, 1988, Identification and characterization of the calmodulin-binding domain of neuromodulin, a neurospecific calmodulin-binding protein, J. Biol. Chem., 263, 7544, 10.1016/S0021-9258(18)68533-3

Wertz, 1996, Solution and membrane bound structure of a peptide derived from the protein kinase C substrate domain of neuromodulin, Biochemistry, 35, 11104, 10.1021/bi961248x

Gerendasy, 1999, Homeostatic tuning of Ca2+ signal transduction by members of the calpacitin protein family, J. Neurosci. Res., 58, 107, 10.1002/(SICI)1097-4547(19991001)58:1<107::AID-JNR11>3.0.CO;2-G

Rhoads, 1997, Sequence motifs for calmodulin recognition, FASEB J, 11, 331, 10.1096/fasebj.11.5.9141499

Sheu, 1995, Differential responses of protein kinase C substrates (MARCKS, neuromodulin, and neurogranin) phosphorylation to calmodulin and S100, Arch. Biochem. Biophys., 316, 335, 10.1006/abbi.1995.1045

Chakravarthy, 1999, Ca2+-calmodulin and protein kinase Cs, Trends. Neurosci., 22, 12, 10.1016/S0166-2236(98)01288-0

Marvin, 1998, Filamentous phage structure, infection and assembly, Curr. Opin. Struct. Biol., 8, 150, 10.1016/S0959-440X(98)80032-8

Marvin, 1969, Filamentous bacterial viruses, Bacteriol. Rev., 33, 172, 10.1128/BR.33.2.172-209.1969

Rossomando, 1970, Studies on the structural polarity of bacteriophage f1, Virology, 42, 681, 10.1016/0042-6822(70)90313-2

Gray, 1981, Adsorption complex of filamentous fd virus, J. Mol. Biol., 146, 621, 10.1016/0022-2836(81)90050-4

Stengele, 1990, Dissection of functional domains in phage fd adsorption protein. Discrimination between attachment and penetration sites, J. Mol. Biol., 212, 143, 10.1016/0022-2836(90)90311-9

Holliger, 1997, A conserved infection pathway for filamentous bacteriophages is suggested by the structure of the membrane penetration domain of the minor coat protein g3p from phage fd, Structure, 5, 265, 10.1016/S0969-2126(97)00184-6

Deng, 1999, Interaction of the globular domains of pIII protein of filamentous bacteriophage fd with the F-pilus of Escherichia coli, Virology, 253, 271, 10.1006/viro.1998.9509

Chatellier, 1999, Interdomain interactions within the gene 3 protein of filamentous phage, FEBS Lett, 463, 371, 10.1016/S0014-5793(99)01658-0

Lubkowski, 1998, The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p, Nat. Struct. Biol., 5, 140, 10.1038/nsb0298-140

Sutrina, 1990, The glucose permease of Bacillus subtilis is a single polypeptide chain that functions to energize the sucrose permease, J. Biol. Chem., 265, 18581, 10.1016/S0021-9258(17)44791-0

Wagenknecht, 1992, Configuration of interdomain linkers in pyruvate dehydrogenase complex of Escherichia coli as determined by cryoelectron microscopy, J. Struct. Biol., 109, 70, 10.1016/1047-8477(92)90069-M

Turner, 1993, Restructuring an interdomain linker in the dihydrolipoamide acetyltransferase component of the pyruvate dehydrogenase complex of Escherichia coli, Protein Eng, 6, 101, 10.1093/protein/6.1.101

Berger, 1996, Structure and mechanism of DNA topoisomerase II, Nature, 379, 225, 10.1038/379225a0

Reizer, 1993, Sequence analyses and evolutionary relationships among the energy- coupling proteins Enzyme I and HPr of the bacterial phosphoenolpyruvate, Protein Sci, 2, 506, 10.1002/pro.5560020403

Shamoo, 1995, Multiple RNA binding domains (RBDs) just don’t add up, Nucleic Acids Res, 23, 725, 10.1093/nar/23.5.725

Zhou, 1996, Phosphotransfer and CheY-binding domains of the histidine autokinase CheA are joined by a flexible linker, Biochemistry, 35, 433, 10.1021/bi951960e

Morais, 2000, The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase, Biochemistry, 39, 10385, 10.1021/bi001171j

Wang, 1999, Loss of the bcl-2 phosphorylation loop domain increases resistance of human leukemia cells (U937) to paclitaxel-mediated mitochondrial dysfunction and apoptosis, Biochem. Biophys. Res. Commun., 259, 67, 10.1006/bbrc.1999.0669

Srivastava, 1999, Deletion of the loop region of Bcl-2 completely blocks paclitaxel- induced apoptosis, Proc. Natl. Acad. Sci. U.S.A., 96, 3775, 10.1073/pnas.96.7.3775

Cheng, 1997, Conversion of Bcl-2 to a Bax-like death effector by caspases, Science, 278, 1966, 10.1126/science.278.5345.1966

Clem, 1998, Modulation of cell death by Bcl-xL through caspase interaction, Proc. Natl. Acad. Sci. U.S.A., 95, 554, 10.1073/pnas.95.2.554

Chang, 1997, Identification of a novel regulatory domain in Bcl-X(L) and Bcl-2, Embo. J., 16, 968, 10.1093/emboj/16.5.968

Yamamoto, 1999, BCL-2 is phosphorylated and inactivated by an ASK1/Jun N-terminal protein kinase pathway normally activated at G(2)/M, Mol. Cell. Biol., 19, 8469, 10.1128/MCB.19.12.8469

Knighton, D.R., Zheng, J.H., Ten Eyck, L.F., Xuong, N.H., Taylor, S.S., and Sowadski, J.M. Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science 1991, 253, 414–420

Hauer, 1999, Binding-dependent disorder-order transition in PKI alpha, Biochemistry, 38, 6774, 10.1021/bi983074k

Johnson, 1996, Control by phosphorylation, Curr. Opin. Struct. Biol., 6, 762, 10.1016/S0959-440X(96)80005-4

Ohmori, 1993, Apoptosis of lung cancer cells caused by some anti-cancer agents (MMC, CPT-11, ADM) is inhibited by bcl-2, Biochem. Biophys. Res. Commun., 192, 30, 10.1006/bbrc.1993.1377

Tang, 1994, High levels of p26BCL-2 oncoprotein retard taxol-induced apoptosis in human pre-B leukemia cells, Leukemia, 8, 1960

Fang, 1998, “Loop” domain is necessary for taxol-induced mobility shift and phosphorylation of Bcl-2 as well as for inhibiting taxol-induced cytosolic accumulation of cytochrome c and apoptosis, Cancer Res, 58, 3202

Rodi, 1999, Screening of a library of phage-displayed peptides identifies human bcl- 2 as a taxol-binding protein, J. Mol. Biol., 285, 197, 10.1006/jmbi.1998.2303

Rodi, 1999, Similarity between sequences of the taxol-selected peptides and the disordered loop of the anti-apoptotic protein, Bcl-2, Pacific Symp. Biocomputing, 4, 532

Rice, 1999, A structural change in the kinesin motor protein that drives motility, Nature, 402, 778, 10.1038/45483

Kozielski, 1997, The crystal structure of dimeric kinesin and implications for microtubule-dependent motility, Cell, 91, 985, 10.1016/S0092-8674(00)80489-4

Kull, 1996, Crystal structure of the kinesin motor domain reveals a structural similarity to myosin, Nature, 380, 550, 10.1038/380550a0

Sack, 1997, X-ray structure of motor and neck domains from rat brain kinesin, Biochemistry, 36, 16155, 10.1021/bi9722498

Thomas, 1995, The mechanism of force generation in myosin, Biophys. J., 68, 135S

Houdusse, 1999, Atomic structure of scallop myosin subfragment S1 complexed with MgADP, Cell, 97, 459, 10.1016/S0092-8674(00)80756-4

Wahlstrom, J., Randall, A., Lawson, J.D., Lyons, D., Crouch, G., and Cremo, C.R. Sites of interaction between the regulatory light chains of dephosphorylated smooth muscle myosin. J. Biol. Chem. submitted

Lawson, J.D., Grammer, J.C., and Yount, R.G. Inter-head photoaffinity labeling in scallop myosin. J. Biol. Chem. submitted

Trombitas, 1998, Titin extensibility in situ, J. Cell Biol., 140, 853, 10.1083/jcb.140.4.853

Armstrong, 1977, Inactivation of the sodium channel. II. Gating current experiments, J. Gen. Physiol., 70, 567, 10.1085/jgp.70.5.567

Antz, 1997, NMR structure of inactivation gates from mammalian voltage-dependent potassium channels, Nature, 385, 272, 10.1038/385272a0

Lee, 1992, On the activation-inactivation coupling in Shaker potassium channels, FEBS Lett, 306, 95, 10.1016/0014-5793(92)80976-N

Brown, 1997, Entropic exclusion by neurofilament sidearms, Biochemistry, 36, 15035, 10.1021/bi9721748

Hoh, 1998, Functional protein domains from the thermally driven motion of polypeptide chains, Proteins, 32, 223, 10.1002/(SICI)1097-0134(19980801)32:2<223::AID-PROT8>3.0.CO;2-L

Lakoff, 1987

Linderstrom-Lang, 1952, Structure and enzymatic break-down of proteins, Lane Medical Lectures, 6, 117

Linderstrom-Lang, K.U., and Schellman, J.A., Protein structure and enzyme activity. In: The Enzymes, Boyer, P.D., Lardy, H., and Myrback, K., Eds. Academic Press, New York, 1959, pp. 443–510

Blow, 1982, Hard facts on structure, Nature, 297, 454, 10.1038/297454a0

Dunker, 1982, Lipid dependent structural changes of an amphomorphic membrane protein, Biophys. J., 37, 201, 10.1016/S0006-3495(82)84669-9

Rosenblatt, 1980, Conformational studies of the synthetic precursor-specific region of preproparathyroid hormone, Proc. Natl. Acad. Sci. U.S.A., 77, 3983, 10.1073/pnas.77.7.3983

Stein, 1991, Serpin tertiary structure transformation, J. Mol. Biol., 221, 615, 10.1016/0022-2836(91)80076-7

Potempa, 1994, The serpin superfamily of proteinase inhibitors, J. Biol. Chem., 269, 15957, 10.1016/S0021-9258(17)33954-6

Young, 1999, Predicting conformational switches in proteins, Protein Sci, 8, 1752, 10.1110/ps.8.9.1752

Kirshenbaum, 1999, Predicting allosteric switches in myosins, Protein Sci, 8, 1806, 10.1110/ps.8.9.1806

Hobohm, 1994, Enlarged representative set of protein structures, Protein Sci, 3, 522, 10.1002/pro.5560030317

Garner, 1999, Predicting binding regions within disordered proteins, Genome Informatics, 10, 41

Vihinen, 1994, Accuracy of protein flexibility predictions, Proteins, 19, 141, 10.1002/prot.340190207

Williams, 2001, The protein non-folding problem, Pacific Symp. Biocomp., 6, 89

Xie, 1998, The sequence attribute method for determining relationships between sequence and protein disorder, Genome Info, 9, 193

Li, 2000, Comparing predictors of disordered protein, Genome Informatics, 11, 172

Romero, 1997, Sequence data analysis for long disordered regions prediction in the calcineurin family, Genome Informatics, 8, 110

Garner, 1998, Predicting disordered regions from amino acid sequence, Genome Informatics, 9, 201

Li, 1999, Predicting protein disorder for N-, C-, and internal regions, Genome Informatics, 10, 30

Romero, 2001, Intelligent data analysis for protein disorder prediction, Artificial Intelligence Reviews, 14, 447, 10.1023/A:1006678623815

Wootton, 1993, Statistic of local complexity in amino acid sequences and sequence databases, Computers Chem, 17, 149, 10.1016/0097-8485(93)85006-X

Wootton, 1994, Non-globular domains in protein sequences, Comput. Chem., 18, 269, 10.1016/0097-8485(94)85023-2

Wootton, 1994, Sequences with ’unusual’ amino acid compositions, Curr. Opin. Struct. Biol., 4, 413, 10.1016/S0959-440X(94)90111-2

Wootton, 1996, Analysis of compositionally biased regions in sequence databases, Methods Enzymol, 266, 554, 10.1016/S0076-6879(96)66035-2

Karlin, 1992, Chance and statistical significance in protein and DNA sequence analysis, Science, 257, 39, 10.1126/science.1621093

Karlin, 1995, Statistical significance of sequence patterns in proteins, Curr. Opin. Struct. Biol., 5, 360, 10.1016/0959-440X(95)80098-0

Romero, 1999, Folding minimal sequences, FEBS Lett, 462, 363, 10.1016/S0014-5793(99)01557-4

Riddle, 1997, Functional rapidly folding proteins from simplified amino acid sequences, Nat. Struct. Biol., 4, 805, 10.1038/nsb1097-805

Dunker, 2000, Intrinsic protein disorder in complete genomes, Genome Informatics, 11, 161

Schoenheimer, 1942

Bond, 1987, Proteolysis and physiological regulation, Molec. Aspects Med., 9, 173, 10.1016/0098-2997(87)90021-5

Rogers, 1986, Amino acid sequences common to rapidly degraded proteins, Science, 234, 364, 10.1126/science.2876518

Rechsteiner, M., and Rogers, S.W. PEST sequences and regulation by proteolysis. Trends Biochem. Sci. 1996, 21, 267–27

Ciechanover, 1994, The ubiquitin-proteasome proteolytic pathway, Cell, 79, 13, 10.1016/0092-8674(94)90396-4

Hochstrasser, 1996, Ubiquitin-dependent protein degradation, Annu. Rev. Genet., 30, 405, 10.1146/annurev.genet.30.1.405

Dahlqvist-Edberg, U., and Ekman, P. Purification of a Ca2+-activated protease from rat erythrocytes and its possible effect on pyruvate kinase in vivo. Biochim. Biophys. Acta. 1981, 660, 96–10

Chan, 1999, Caspase and calpain substrates, J. Neurosci. Res., 58, 167, 10.1002/(SICI)1097-4547(19991001)58:1<167::AID-JNR16>3.0.CO;2-K

Murray, 1997, The calpain-calpastatin system and cellular proliferation and differentiation in rodent osteoblastic cells, Exp. Cell Res., 233, 297, 10.1006/excr.1997.3550

Neurath, 1976, Role of proteolytic enzymes in biological regulation (a review), Proc. Natl. Acad. Sci. U.S.A., 73, 3825, 10.1073/pnas.73.11.3825

Salama, 1994, G1 cyclin degradation, Mol. Cell Biol., 14, 7953, 10.1128/MCB.14.12.7953

Santella, 1998, The role of calcium in the cell cycle, Biochem. Biophys. Res. Commun., 244, 317, 10.1006/bbrc.1998.8086

Kitamura, 1998, Alteration of proteins regulating apoptosis, Bcl-2, Bcl-x, Bax, Bak, Bad, ICH-1 and CPP32, in Alzheimer’s disease, Brain Res, 780, 260, 10.1016/S0006-8993(97)01202-X

Brown, 1999, A proteolytic pathway that controls the cholesterol content of membranes, cells, and blood, Proc. Natl. Acad. Sci. U.S.A., 96, 11041, 10.1073/pnas.96.20.11041

Hubbard, 1998, The structural aspects of limited proteolysis of native proteins, Biochim. Biophys. Acta., 1382, 191, 10.1016/S0167-4838(97)00175-1

Hemmingsen, 1988, Homologous plant and bacterial proteins chaperone oligomeric protein assembly, Nature, 333, 330, 10.1038/333330a0

Hartl, 1991, Heat shock proteins in protein folding and membrane translocation, Semin. Immunol., 3, 5

Shapiro, 1998, The Argonne Structural Genomics Workshop, Structure, 6, 265, 10.1016/S0969-2126(98)00030-6

Gaasterland, 1998, Structural genomics, Nat. Biotechnology, 16, 625, 10.1038/nbt0798-625

Goldstein, 1998, An unacknowledged problem for structural genomics?, Nat. Biotechnol., 16, 696, 10.1038/nbt0898-696

Sweet, 1983, Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure, J. Mol. Biol., 171, 479, 10.1016/0022-2836(83)90041-4

Kyte, 1982, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol., 157, 105, 10.1016/0022-2836(82)90515-0

Chechetkin, 1999, Characterization and comparison of protein structures. Part I- characterization, J. Theor. Biol., 198, 197, 10.1006/jtbi.1999.0910

Jamin, 2000, The unfolding enthalpy of the pH 4 molten globule of apomyoglobin measured by isothermal titration calorimetry, Protein Sci, 9, 1340, 10.1110/ps.9.7.1340

Baldwin, 2000, Are denatured proteins ever random coils?, Proc. Natl. Acad. Sci. USA, 97, 12391, 10.1073/pnas.97.23.12391

Ratliff, C., Hipps, K.W., Nissen, M., Reeves, R., Ausio, J., and Dunker, A.K. Atomic force microscopy of nucleosomes: evidence for softening by hyperacetylation. Protein Science 2000, 9, Suppl. 1, 125

Bailey, 2000, Clusterin binds through the action of natively disordered regions, Biophysical Journal, 78, 152A

Uversky, N.V., Gillespie, R.J., and Fink, L.A. Why are “natively unfolded” proteins unstructured under physiological conditions? Proteins: structure, function, and genetics 2000, 41, 415–427.