Deciphering the message in protein sequences: tolerance to amino acid substitutions.

An amino acid sequence encodes a message that determines the shape and function of a protein. This message is highly degenerate in that many different sequences can code for proteins with essentially the same structure and activity. Comparison of different sequences with similar messages can reveal key features of the code and improve understanding of how a protein folds and how it performs its function.

[1]  R. Sauer,et al.  NMR studies of Arc repressor mutants: proton assignments, secondary structure, and long-range contacts for the thermostable proline-8----leucine variant of Arc. , 1989, Biochemistry.

[2]  R. Kaptein,et al.  Sequence-specific 1H NMR assignment and secondary structure of the Arc repressor of bacteriophage P22, as determined by two-dimensional 1H NMR spectroscopy. , 1989, Biochemistry.

[3]  K. Dill,et al.  A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .

[4]  R. Sauer,et al.  Production and characterization of monoclonal antibodies to the N-terminal domain of lambda repressor. , 1989, The Journal of biological chemistry.

[5]  T C Terwilliger,et al.  Influence of interior packing and hydrophobicity on the stability of a protein. , 1989, Science.

[6]  J. Wells,et al.  High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. , 1989, Science.

[7]  A. Fersht,et al.  Energetics of complementary side-chain packing in a protein hydrophobic core. , 1989, Biochemistry.

[8]  W. Lim,et al.  Alternative packing arrangements in the hydrophobic core of λrepresser , 1989, Nature.

[9]  D. Shortle,et al.  Probing the determinants of protein folding and stability with amino acid substitutions. , 1989, The Journal of biological chemistry.

[10]  J U Bowie,et al.  Identifying determinants of folding and activity for a protein of unknown structure. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J Skolnick,et al.  Monte Carlo simulation of equilibrium globular protein folding: alpha-helical bundles with long loops. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[12]  P. Jhurani,et al.  Receptor and antibody epitopes in human growth hormone identified by homolog-scanning mutagenesis. , 1989, Science.

[13]  M. Navia,et al.  Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1 , 1989, Nature.

[14]  R. Sauer,et al.  Amino acid substitutions that increase the thermal stability of the λ Cro protein , 1989 .

[15]  Jordan,et al.  Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions , 1988, Science.

[16]  R. Sauer,et al.  Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. , 1988, Science.

[17]  W R Taylor,et al.  Pattern matching methods in protein sequence comparison and structure prediction. , 1988, Protein engineering.

[18]  Thomas R. Bürglin,et al.  The yeast regulatory gene PHO2 encodes a homeo box , 1988, Cell.

[19]  F. Sherman,et al.  Yeast iso‐l‐cytochrome c: Genetic analysis of structural requirements , 1988, FEBS Letters.

[20]  J. Berg,et al.  Proposed structure for the zinc-binding domains from transcription factor IIIA and related proteins. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[21]  R M Stroud,et al.  The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis. , 1988, Science.

[22]  William R. Taylor,et al.  A structural model for the retroviral proteases , 1987, Nature.

[23]  W. Rutter,et al.  The catalytic role of the active site aspartic acid in serine proteases. , 1987, Science.

[24]  A. Lesk,et al.  Determinants of a protein fold. Unique features of the globin amino acid sequences. , 1987, Journal of molecular biology.

[25]  B. Matthews,et al.  Temperature-sensitive mutations of bacteriophage T4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein. , 1987, Biochemistry.

[26]  J. Skolnick,et al.  Monte carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of β‐barrel proteins , 1987 .

[27]  J. Ponder,et al.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.

[28]  A M Lesk,et al.  The evolution of protein structures. , 1987, Cold Spring Harbor symposia on quantitative biology.

[29]  R. Sauer,et al.  Interaction of mutant λ repressors with operator and non-operator DNA , 1986 .

[30]  R. L. Baldwin,et al.  Temperature dependence of the hydrophobic interaction in protein folding. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[31]  W. Taylor,et al.  Identification of protein sequence homology by consensus template alignment. , 1986, Journal of molecular biology.

[32]  D. Eisenberg,et al.  Analysis of membrane and surface protein sequences with the hydrophobic moment plot. , 1984, Journal of molecular biology.

[33]  R. Sauer,et al.  Effect of single amino acid replacements on the thermal stability of the NH2-terminal domain of phage lambda repressor. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[34]  B. Matthews,et al.  Intrahelical hydrogen bonding of serine, threonine and cysteine residues within alpha-helices and its relevance to membrane-bound proteins. , 1984, Journal of molecular biology.

[35]  D. Eisenberg,et al.  The hydrophobic moment detects periodicity in protein hydrophobicity. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[36]  E. Baker,et al.  Hydrogen bonding in globular proteins. , 1984, Progress in biophysics and molecular biology.

[37]  D. Eisenberg,et al.  Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. , 1983, Journal of molecular biology.

[38]  David Eisenberg,et al.  The helical hydrophobic moment: a measure of the amphiphilicity of a helix , 1982, Nature.

[39]  A M Lesk,et al.  Evolution of proteins formed by beta-sheets. II. The core of the immunoglobulin domains. , 1982, Journal of molecular biology.

[40]  J. Greer Comparative model-building of the mammalian serine proteases. , 1981, Journal of molecular biology.

[41]  A. Lesk,et al.  How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. , 1980, Journal of molecular biology.

[42]  J H Miller,et al.  Genetic studies of the lac repressor. IX. Generation of altered proteins by the suppression of nonsence mutations. , 1979, Journal of molecular biology.

[43]  V. Lim Algorithms for prediction of α-helical and β-structural regions in globular proteins , 1974 .

[44]  V. Lim Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. , 1974, Journal of molecular biology.

[45]  F. Richards The interpretation of protein structures: total volume, group volume distributions and packing density. , 1974, Journal of molecular biology.

[46]  C. Anfinsen Principles that govern the folding of protein chains. , 1973, Science.

[47]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[48]  D. Phillips,et al.  A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme. , 1969, Journal of molecular biology.

[49]  M. Schiffer,et al.  Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. , 1967, Biophysical journal.

[50]  J. C. Kendrew,et al.  Structure and function of haemoglobin: II. Some relations between polypeptide chain configuration and amino acid sequence , 1965 .

[51]  C. Epstein,et al.  The Genetic Control of Tertiary Protein Structure: Studies With Model Systems , 1963 .

[52]  W. Kauzmann Some factors in the interpretation of protein denaturation. , 1959, Advances in protein chemistry.