Protein–ligand interactions

Protein–ligand interactions are described and several of the unique interactions observed between proteins and other molecules are illustrated. The chapter covers protein–carbohydrate interactions, metal ions associated with proteins, protein–nucleic acid interactions, and sulfate and phosphate interactions.

[1]  S. Cusack RNA-protein complexes. , 1999, Current opinion in structural biology.

[2]  F. Quiocho,et al.  Dominant role of local dipolar interactions in phosphate binding to a receptor cleft with an electronegative charge surface: Equilibrium, kinetic, and crystallographic studies , 1998, Protein science : a publication of the Protein Society.

[3]  Reinhard Jahn,et al.  Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution , 1998, Nature.

[4]  J. Murray,et al.  Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments. , 1998, Nucleic acids research.

[5]  F A Quiocho,et al.  Structural basis for sequence-nonspecific recognition of 5'-capped mRNA by a cap-modifying enzyme. , 1998, Molecular cell.

[6]  G. Varani A cap for all occasions. , 1997, Structure.

[7]  F. Quiocho,et al.  Specific protein recognition of an mRNA cap through its alkylated base , 1997, Nature Structural Biology.

[8]  L. Mosyak,et al.  The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. , 1997, Structure.

[9]  Alexey Bochkarev,et al.  Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA , 1997, Nature.

[10]  A. Volbeda,et al.  Novel metal sites in protein structures. , 1996, Current opinion in structural biology.

[11]  S. Cusack,et al.  The crystal structures of T. thermophilus lysyl‐tRNA synthetase complexed with E. coli tRNA(Lys) and a T. thermophilus tRNA(Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl‐adenylate analogue. , 1996, The EMBO journal.

[12]  G. Verdine,et al.  Structural Basis for the Excision Repair of Alkylation-Damaged DNA , 1996, Cell.

[13]  F. Quiocho,et al.  Negative electrostatic surface potential of protein sites specific for anionic ligands. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[14]  S Cusack,et al.  The crystal structure of the ternary complex of T.thermophilus seryl‐tRNA synthetase with tRNA(Ser) and a seryl‐adenylate analogue reveals a conformational switch in the active site. , 1996, The EMBO journal.

[15]  F. Quiocho,et al.  Modulation of a salt link does not affect binding of phosphate to its specific active transport receptor. , 1996, Biochemistry.

[16]  A M Gronenborn,et al.  Intercalation, DNA Kinking, and the Control of Transcription , 1996, Science.

[17]  Xiaodong Cheng,et al.  DNA modification by methyltransferases. , 1995, Current opinion in structural biology.

[18]  C. Burd,et al.  Conserved structures and diversity of functions of RNA-binding proteins. , 1994, Science.

[19]  W. Cleland,et al.  Low-barrier hydrogen bonds and enzymic catalysis. , 1994, Science.

[20]  P. G. Gassman,et al.  Understanding the rates of certain enzyme-catalyzed reactions: proton abstraction from carbon acids, acyl-transfer reactions, and displacement reactions of phosphodiesters. , 1993, Biochemistry.

[21]  F. Quiocho,et al.  Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein , 1993, Protein science : a publication of the Protein Society.

[22]  S. Harrison,et al.  The phage 434 OR2/R1-69 complex at 2.5 A resolution. , 1993, Journal of molecular biology.

[23]  D. Vassylyev,et al.  DNA-repair enzymes. , 1993, Current opinion in structural biology.

[24]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[25]  J. Emsley,et al.  Hydrogen Bonding and Chemical Reactivity , 1991 .

[26]  H. Ueda,et al.  Cooperative stacking and hydrogen bond pairing interactions of fragment peptide in cap binding protein with mRNA cap structure. , 1991, Biochimica et biophysica acta.

[27]  N. Vyas Atomic features of protein-carbohydrate interactions , 1991 .

[28]  T. Steitz,et al.  Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase , 1991, Nature.

[29]  N. Pavletich,et al.  Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A , 1991, Science.

[30]  T. Tanaka,et al.  Combination of Trp and Glu residues for recognition of mRNA cap structure Analysis of m7G base recognition site of human cap binding protein (IF‐4E) by site‐directed mutagenesis , 1991, FEBS letters.

[31]  H Luecke,et al.  Dipoles localized at helix termini of proteins stabilize charges. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Carl O. Pabo,et al.  Crystal structure of an engrailed homeodomain-DNA complex at 2.8 Å resolution: A framework for understanding homeodomain-DNA interactions , 1990, Cell.

[33]  F. Quiocho,et al.  High specificity of a phosphate transport protein determined by hydrogen bonds , 1990, Nature.

[34]  T. Steitz,et al.  Structural studies of protein–nucleic acid interaction: the sources of sequence-specific binding , 1990, Quarterly Reviews of Biophysics.

[35]  F. A. Quiocho,et al.  Substrate specificity and affinity of a protein modulated by bound water molecules , 1989, Nature.

[36]  F. Quiocho,et al.  Sulfate-binding protein dislikes protonated oxyacids. A molecular explanation. , 1988, Journal of molecular biology.

[37]  M. N. Vyas,et al.  Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. , 1988, Science.

[38]  T. Steitz,et al.  Cocrystal structure of an editing complex of Klenow fragment with DNA. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[39]  A. Joachimiak,et al.  Crystal structure of trp represser/operator complex at atomic resolution , 1988, Nature.

[40]  Florante A. Quiocho,et al.  Stabilization of charges on isolated ionic groups sequestered in proteins by polarized peptide units , 1987, Nature.

[41]  F. Quiocho,et al.  Sulphate sequestered in the sulphate-binding protein of Salmonella typhimurium is bound solely by hydrogen bonds , 1985, Nature.

[42]  C. Yanofsky,et al.  Functional inferences from crystals of Escherichia coli trp repressor. , 1983, The Journal of biological chemistry.

[43]  F. A. Cotton,et al.  Staphylococcal nuclease: proposed mechanism of action based on structure of enzyme-thymidine 3',5'-bisphosphate-calcium ion complex at 1.5-A resolution. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[44]  F. Cotton,et al.  Staphylococcal nuclease reviewed: A prototypic study in contemporary enzymology , 1979, Molecular and Cellular Biochemistry.

[45]  N. Seeman,et al.  Sequence-specific recognition of double helical nucleic acids by proteins. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[46]  H. Rosenberg,et al.  Phosphate transport in Escherichia coli. , 1971, Biochimica et biophysica acta.

[47]  D. Phillips,et al.  On the conformation of the hen egg-white lysozyme molecule , 1967, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[48]  A. Pardee Purification and properties of a sulfate-binding protein from Salmonella typhimurium. , 1966, The Journal of biological chemistry.

[49]  A. Gingras,et al.  X-ray studies of the messenger RNA 5' cap-binding protein (eIF4E) bound to 7-methyl-GDP. , 1997, Nucleic acids symposium series.

[50]  W. Weis,et al.  Structural basis of lectin-carbohydrate recognition. , 1996, Annual review of biochemistry.

[51]  P. Evans,et al.  Crystal structure of the U1A spliceosomal protein complexed with its cognate RNA hairpin. , 1995, Nucleic acids symposium series.

[52]  R E Harrington,et al.  New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility. , 1994, Progress in nucleic acid research and molecular biology.

[53]  R. Sauer,et al.  Transcription factors: structural families and principles of DNA recognition. , 1992, Annual review of biochemistry.

[54]  J. Glusker Structural aspects of metal liganding to functional groups in proteins. , 1991, Advances in protein chemistry.

[55]  F A Quiocho,et al.  Carbohydrate-binding proteins: tertiary structures and protein-sugar interactions. , 1986, Annual review of biochemistry.