Structure and Function of Proteins: References

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• Rennell D, Bouvier SE, Hardy LW, Poteete AR (1991).
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• Brown BM, Sauer RT. (1999).
  Tolerance of Arc repressor to multiple-alanine substitutions. Proc Natl Acad Sci U S A96(5), 1983-8.

• Chou PY, Fasman GD (1974).
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• Garnier J, Osguthorpe DJ, Robson B (1978).
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• Salamov AA, Solovyev VV (1995).
  Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. J Mol Biol 247(1),11-5.
• Salamov AA, Solovyev VV (1997).
  Protein secondary structure prediction using local alignments.J Mol Biol 268(1),31-6
• Kabsch W, Sander C (1983).
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• Rost B, Sander C (1994).
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• Rost B, Sander C (1993).
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• Rost B, Sander C (1993).
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• Rost B (1996).
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• Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, Valencia A, Sali A, Rost B. (2001).
  EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics 17(12), 1242-3

• Kabsch W. & Sander C. (1984).
  On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci U S A 81, 1075-1078.
• Argos P (1987).
  Analysis of sequence-similar pentapeptides in unrelated protein tertiary structures. Strategies for protein folding and a guide for site-directed mutagenesis. J Mol Biol 197, 331-348.
• Cohen BI, Presnell SR, Cohen FE (1993).
  Origins of structural diversity within sequentially identical hexapeptides. Protein Sci 2, 2134-2145.
• Sudarsanam S (1998).
  Structural diversity of sequentially identical subsequences of proteins: identical octapeptides can have different conformations. Proteins 30, 228-231.
• Minor D.L. Jr & Kim P.S. (1996).
  Context-dependent secondary structure formation of a designed protein sequence. Nature 380, 730-734.
• Zhong L, Johnson WC Jr (1992).
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• Pearson WR (1990).
  Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol183, 63-98.
• Pearson WR, Lipman DJ (1988).
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• Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997).
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• Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C.(1998)
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• Swiss-model reference list.

• Relation between sequence and structure similarity
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    Proteins. One thousand families for the molecular biologist. Nature 357, 543-544.
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    Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9, 56-68.
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    The relation between the divergence of sequence and structure in proteins. EMBO J 5, 823-826
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    Expectations from structural genomics. Protein Sci 9, 197-200.
  • Koppensteiner WA, Lackner P, Wiederstein M, Sippl MJ (2000).
    Characterization of novel proteins based on known protein structures. J Mol Biol 296, 1139-52.
• Threading
  • Sippl MJ, Flockner H (1996).
    Threading thrills and threats. Structure 4, 15-19.
  • Jones DT, Taylor WR, Thornton JM (1992).
    A new approach to protein fold recognition. Nature 358, 86-89.
  • Bowie JU, Luthy R, Eisenberg D (1991).
    A method to identify protein sequences that fold into a known three-dimensional structure. Science 253, 164-170.
  • Fischer D, Eisenberg D (1997).
    Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci U S A 94, 11929-11934.
  • Fischer D, Eisenberg D (1996).
    Protein fold recognition using sequence-derived predictions. Protein Sci 5, 947-955.
  • Rice DW, Eisenberg D (1997).
    A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J Mol Biol 267, 1026-1038.
  • Rost B, Schneider R, Sander C (1997).
    Protein fold recognition by prediction-based threading. J Mol Biol 270, 471-480.
  • Jones DT (1999).
    GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287, 797-815.
  • LA Kelley, RM MacCallum, MJ Sternberg (2000).
    Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 299(2), 499-520.
  • Wolf YI, Grishin NV, Koonin EV.
    Estimating the number of protein folds and families from complete genome data. J Mol Biol 299(4), 897-905.
  • Sippl MJ, Lackner P, Domingues FS, Prlic A, Malik R, Andreeva A, Wiederstein M. (2001).
    Proteins Suppl 5, 55-67.
  • Rose GD, Creamer TP.(1994).
    Protein folding: predicting predicting. Proteins 19(1),1-3.
  • Ginalski K, Elofsson A, Fischer D, Rychlewski L. (2003).
    3D-Jury: a simple approach to improve protein structure predictions. Proteins Suppl 5, 55-67.

• F Frolow, M Harel, JL Sussman, M Mevarech, M Shoham (1996).
  Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin. Nat Struct Biol 3(5), 452-8.
• M Mevarech, F Frolow, LM Gloss (2000).
  Halophilic enzymes: proteins with a grain of salt. Biophys Chem 86(2-3), 155-64.
• RJ Russell, U Gerike, MJ Danson, DW Hough, GL Taylor (1998).
  Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium. Structure 6(3), 351-61.
• R Das and M Gerstein (2000).
  The stability of thermophilic proteins: a study based on comprehensive genome comparison. Funct Integr Genomics 1(1), 76-88.

• Beasley JR, Hecht MH (1997).
  Protein design: the choice of de novo sequences. J Biol Chem 272, 2031-2034.
• Cordes MH, Davidson AR, Sauer RT(1996).
  Sequence space, folding and protein design. Curr Opin Struct Biol 6, 3-10.
• West MW, Hecht MH (1995).
  Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins. Protein Sci 4, 2032-2039.
• Xiong H, Buckwalter BL, Shieh HM, Hecht MH (1995).
  Periodicity of polar and nonpolar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides. Proc Natl Acad Sci U S A 92, 6349-6353.
• Smith CK, Withka JM, Regan L. (1994).
  A thermodynamic scale for the beta-sheet forming tendencies of the amino acids. Biochemistry 33(18), 5510-7.
• Sudarsanam S. (1998).
  Structural diversity of sequentially identical subsequences of proteins: identical octapeptides can have different conformations. Proteins 30(3), 228-31.
• Schueler-Furman O, Altuvia Y, Margalit H. (2001).
  Examination of possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins. Proteins 45(1), 47-54.
• Young M, Kirshenbaum K, Dill KA, Highsmith S. (1999).
  Predicting conformational switches in proteins. Protein Sci. 8(9), 1752-64.
• Kuhlman B, Baker D. (2000).
  Proc Natl Acad Sci U S A. 97(19), 10383-8.
• Filikov AV, Hayes RJ, Luo P, Stark DM, Chan C, Kundu A, Dahiyat BI. (2002).
  Computational stabilization of human growth hormone. Protein Sci 11(6), 1452-61.

• Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH (1993).
  Protein design by binary patterning of polar and nonpolar amino acids. Science 262, 1680-1685.
• Vlassi M, Steif C, Weber P, Tsernoglou D, Wilson KS, Hinz HJ, Kokkinidis M (1994).
  Restored heptad pattern continuity does not alter the folding of a four-alpha-helix bundle. Nat Struct Biol 1, 706-716.
• Desjarlais JR, Handel TM (1995).
  De novo design of the hydrophobic cores of proteins. Protein Sci 4, 2006-2018.
• Rojas NR, Kamtekar S, Simons CT, McLean JE, Vogel KM, Spiro TG, Farid RS, Hecht MH (1997).
  De novo heme proteins from designed combinatorial libraries. Protein Sci 6, 2512-2524.
• Kamtekar S, Hecht MH (1995).
  Protein Motifs. 7. The four-helix bundle: what determines a fold? FASEB J 9, 1013-1022.
• Hellinga HW (1997).
  Rational protein design: combining theory and experiment. Proc Natl Acad Sci U S A 94 10015-10017.
• Dahiyat BI, Mayo SL (1997).
  De novo protein design: fully automated sequence selection. Science 278, 82-87.
• Dalal S, Balasubramanian S, Regan L (1997).
  Protein alchemy: changing beta-sheet into alpha-helix. Nat Struct Biol 4, 548-552.
  See also comment:
  • Rose GD (1997).
    Protein folding and the Paracelsus challenge. Nat Struct Biol 4, 512-514.
• MacBeath G, Kast P, Hilvert D (1998).
  Redesigning enzyme topology by directed evolution. Science 279, 1958-1961.

• Hubbard TJP, Murzin AG, Brenner SE, Chothia C (1997).
  SCOP: a structural classification of proteins database. Nucleic Acids Res 25, 236-239.
• Sonnhammer EL, Eddy SR, Durbin R (1997).
  Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28, 405-20
• Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R (1998).
  Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 26, 320-2
• Jeanette Tוngrot, Lixiao Wang1, Bo Kוgstrצm and Uwe H. Sauer.
  FISH -- family identification of sequence homologues using structure anchored hidden Markov models Nucleic Acids Res 34,
• Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL. (2000).
  The Pfam protein families database. Nucleic Acids Res 28(1), 263-6
• Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM (1997).
  CATH--a hierarchic classification of protein domain structures. Structure 5, 1093-1108.
• Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA. (2003).
  A rapid classification protocol for the CATH Domain Database to support structural genomics. Nucleic Acids Res 31(1), 452-457
• Apweiler et. al. (2001).
  The InterPro database, an integrated documentation resource for protein families, domains and functional sites.Nucleic Acids Res 29(1), 37-40
• Levitt M, Chothia C (1976).
  Structural patterns in globular proteins. Nature 261, 552-558.
• Timothy L. Bailey and William N. Grundy (1999).
  Classifying proteins by family using th e product of correlated p-values.Proceedings of the Third International Conference on Computational Mol ecular Biology (RECOMB99) , PP 10-14.
• Sujatha S, Balaji S, Srinivasan N. (2001).
  PALI: a database of alignme nts and phylogeny of homologous protein structures. Bioinformatics 17(4), 375-376 .
• Gowri VS, Pandit SB, Karthik PS, Srinivasan N, Balaji S. (2003).
  Integration of related seq uences with protein three-dimensional structural families in an updated version of PALI database. Nucl eic Acids Res. 31(3), 486-488.

• General reviews
  • Tan S, Richmond TJ (1998).
    Eukaryotic transcription factors. Curr Opin Struct Biol 8, 41-48.
  • Harrison SC (1991).
    A structural taxonomy of DNA-binding domains. Nature 353, 715-719.
  • Pabo CO, Sauer RT (1992).
    Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem 61, 1053-1095.
  • Seeman NC, Rosenberg JM, Rich A (1976).
    Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci U S A 73, 804-808.

• Reviews
  • Rhodes D, Klug A (1993).
    Zinc fingers. Sci Am 268, 56-59.
  • Klug A, Rhodes D (1987).
    Zinc fingers: a novel protein fold for nucleic acid recognition. Cold Spring Harb Symp Quant Biol 52, 473-482.
  • Choo Y, Klug A (1997).
    Physical basis of a protein-DNA recognition code. Curr Opin Struct Biol 7, 117-125.
  • Choo Y, Schwabe JW (1998).
    All wrapped up. Nat Struct Biol 5, 253-255.
  • Wolfe SA, Nekludova L, Pabo CO (2000).
    DNA recognition by Cys2His2 zinc finger proteins. Annu Rev Biophys Biomol Struct 29, 183-212 .
  • Laity JH, Lee BM, Wright PE (2001).
    Zinc finger proteins: new insights into structural and functional diversity. Curr Opin Struct Biol 11, 39-46.
  • Pabo CO, Peisach E, Grant RA (2001).
    DESIGN AND SELECTION OF NOVEL CYS2HIS2 ZINC FINGER PROTEINS. Annu Rev Biochem70, 313-340.
• Sequences and structures
  • Berg JM (1986).
    Potential metal-binding domains in nucleic acid binding proteins. Science 232, 485-487.
  • Gibson TJ, Postma JP, Brown RS, Argos P (1988).
    A model for the tertiary structure of the 28 residue DNA-binding motif ('zinc finger') common to many eukaryotic transcriptional regulatory proteins. Protein Eng 2, 209-218.
  • Parraga G, Horvath SJ, Eisen A, Taylor WE, Hood L, Young ET, Klevit RE (1988).
    Zinc-dependent structure of a single-finger domain of yeast ADR1. Science 241, 1489-1492.
  • Lee MS, Gippert GP, Soman KV, Case DA, Wright PE (1989).
    Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245, 635-637.
  • Pavletich NP, Pabo CO (1991).
    Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 252, 809-817.
  • Pavletich NP, Pabo CO (1993).
    Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science 261, 1701-1707.
  • Elrod-Erickson M, Benson TE, Pabo CO (1998).
    High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Structure 6, 451-464.
  • Nolte RT, Conlin RM, Harrison SC, Brown RS (1998).
    Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex. Proc Natl Acad Sci U S A 95, 2938-2943.
• Binding experiments
  • Jamieson AC, Kim SH, Wells JA (1994).
    In vitro selection of zinc fingers with altered DNA-binding specificity. Biochemistry 33, 5689-5695.
  • Rebar EJ, Pabo CO (1994).
    Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science 263, 671-673.
  • Choo Y, Klug A (1994).
    Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage. Proc Natl Acad Sci U S A 91, 11163-11167.
  • Choo Y, Klug A (1994).
    Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sci U S A 91, 11168-11172.
  • Desjarlais JR, Berg JM (1994).
    Length-encoded multiplex binding site determination: application to zinc finger proteins. Proc Natl Acad Sci U S A 91, 11099-11103.
  • Elrod-Erickson M, Pabo CO (1999).
    Binding Studies with Mutants of Zif268. Contribution of individual side chains to binding affinity and specificity in the zif268 zinc finger-dna complex. J Biol Chem 274, 19281-19285.
  • Segal DJ, Dreier B, Beerli RR, Barbas CF 3rd (1999).
    Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences. Proc Natl Acad Sci U S A 96, 2758-63.
  • Wolfe SA, Greisman HA, Ramm EI, Pabo CO (1999).
    Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J Mol Biol 285, 1917-34.
  • Liu Q, Segal DJ, Ghiara JB, Barbas CF 3rd (1997).
    Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. Proc Natl Acad Sci U S A 94, 5525-30.
  • Beerli RR, Segal DJ, Dreier B, Barbas CF 3rd (1998).
    Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks. Proc Natl Acad Sci U S A 95, 14628-33
  • Neely LS, Lee BM, Xu J, Wright PE, Gottesfeld JM.(1999).
    Identification of a minimal domain of 5 S ribosomal RNA sufficient for high affinity interactions with the RNA-specific zinc fingers of transcription factor IIIA. J Mol Biol 291, 549-560.
  • Moore M, Klug A, Choo Y.(2001).
    Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units. Proc Natl Acad Sci U S A 98, 1437-41.

• Sequences and structures
  • Sauer RT, Yocum RR, Doolittle RF, Lewis M, Pabo CO (1982).
    Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature 298, 447-451.
  • Jordan SR, Pabo CO (1988).
    Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions. Science 242, 893-899.
  • Beamer LJ, Pabo CO (1992).
    Refined 1.8 A crystal structure of the lambda repressor-operator complex. J Mol Biol 227, 177-196.
  • Pabo CO, Aggarwal AK, Jordan SR, Beamer LJ, Obeysekare UR, Harrison SC (1990).
    Conserved residues make similar contacts in two repressor-operator complexes. Science 247, 1210-1213.
  • Albright RA, Matthews BW (1998).
    How Cro and lambda-repressor distinguish between operators: the structural basis underlying a genetic switch. Proc Natl Acad Sci U S A 95, 3431-3436.
  • Schultz SC, Shields GC, Steitz TA (1991).
    Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253, 1001-1007.
  • Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB (1988).
    Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335, 321-329.
• Swap experiments
  • Wharton RP, Brown EL, Ptashne M (1984).
    Substituting an alpha-helix switches the sequence-specific DNA interactions of a repressor. Cell 38, 361-369.
  • Wharton RP, Ptashne M (1985).
    Changing the binding specificity of a repressor by redesigning an alpha-helix. Nature 316, 601-605.
• Homeodomain proteins
  • Kissinger CR, Liu BS, Martin-Blanco E, Kornberg TB, Pabo CO (1990).
    Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. Cell 63, 579-590.
  • Klemm JD, Rould MA, Aurora R, Herr W, Pabo CO (1994).
    Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell 77, 21-32.
  • Draganescu A, Levin JR, Tullius TD (1995).
    Homeodomain proteins: what governs their ability to recognize specific DNA sequences? J Mol Biol 250, 595-608.
• Lac repressor
  • Lewis M, Chang G, Horton NC, Kercher MA, Pace HC, Schumacher MA, Brennan RG, Lu P (1996).
    Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science 271, 1247-1254.
  • Miller JH (1996).
    Structure of a paradigm. Nat Struct Biol 3, 310-312.

• Reviews
  • Alber T (1993).
    How GCN4 binds DNA? Curr Biol 3, 182.
  • Ellenberger T (1994).
    Getting a grip on DNA recognition: structures of the basic helix-loop-helix DNA-binding domains. Curr Opin Struct Biol. 4, 12-21.
• Sequences and structures
  • Landschulz WH, Johnson PF, McKnight SL (1988).
    The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240, 1759-1764.
  • Landschulz WH, Johnson PF, McKnight SL (1989).
    The DNA binding domain of the rat liver nuclear protein C/EBP is bipartite. Science 243, 1681-1688.
  • Agre P, Johnson PF, McKnight SL (1989).
    Cognate DNA binding specificity retained after leucine zipper exchange between GCN4 and C/EBP. Science 246, 922-926.
  • Sellers JW, Struhl K (1989).
    Changing fos oncoprotein to a jun-independent DNA binding protein with GCN4 dimerization specificity by swapping "leucine zippers". Nature 341, 74-76.
  • O'Shea EK, Klemm JD, Kim PS, Alber T (1991).
    X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254, 539-544.
  • O'Shea EK, Rutkowski R, Kim PS (1992).
    Mechanism of specificity in the Fos-Jun oncoprotein heterodimer. Cell 68, 699-708.
  • Ellenberger TE, Brandl CJ, Struhl K, Harrison SC (1992).
    The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. Cell 71, 1223-1237.
  • Konig P, Richmond TJ (1993).
    The X-ray structure of the GCN4-bZIP bound to A TF/CREB site DNA shows the complex depends on DNA flexibility. J Mol Biol 233, 139-154.
  • Harbury PB, Zhang T, Kim PS, Alber T (1993).
    A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262, 1401-1407.

• Nagano N, Orengo CA, Thornton JM. (2002).
  One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.J Mol Biol. 321, 741-65.
• Lang D, Thoma R, Henn-Sax M, Sterner R, Wilmanns M. (2000).
  Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion.Science 289, 1546-50.

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