The minimum information required for reporting a molecular interaction experiment (MIMIx). (2007)
Orchard, S., Salwinski, L., Kerrien, S., Montecchi-Palazzi, L., Oesterheld, M., Stümpflen, V., ...
Nature Biotechnology, 25(2007) S.894-98
Packed protein bilayers in the 0.90 A resolution structure of a designed alpha helical bundle (1999)
of a designed alpha helical bundle (1998)
Gg Prive, Dh Anderson, L Wesson, D Cascio, D Eisenberg, Email Alerting, ...
Packed protein bilayers in the 0.90 A resolution structure of a
A missing link in cupredoxins: Crystal structure of cucumber stellacyanin at 1.6 A resolution (1996)
HART, P. J., NERSISSIAN, A. M., HERRMANN, R. G., NALBANDYAN, R. M., VALENTINE, J. S., EISENBERG, D.
Discovery of the ammonium substrate site on glutamine synthetase, a third cation binding site (1995)
Caenorhabditis elegans embryos contain only one major species of Ro RNP (1995)
Van Horn, D. J., Eisenberg, D., O'Brien, C. A., Wolin, S. L.
Crystallization of proton channel peptides (1992)
LOVEJOY, B., AKERFELDT, K. S., DEGRADO, W. F., EISENBERG, D.
X-ray grade crystals of a designed {alpha}-helical coiled coil (1992)
LOVEJOY, B., CHAU-LE, T., LUTHY, R., CASCIO, D., O'NEIL, K. T., DEGRADO, W. F., ...
Dielectric polarization of thermochemically treated MgO : Li+ crystals (1980)
Dielectric loss (DL) and thermally stimulated depolarization measurements (TSD) on MgO : Li crystals, thermochemically treated at 1 400 K in oxidizing atmospheres, have been used to investigate the...
Dielectric polarization of thermochemically treated MgO : Li+ crystals (1980)
Dielectric loss (DL) and thermally stimulated depolarization measurements (TSD) on MgO : Li crystals, thermochemically treated at 1 400 K in oxidizing atmospheres, have been used to investigate the...
Dielectric polarization of thermochemically treated MgO : Li+ crystals (1980)
Dielectric loss (DL) and thermally stimulated depolarization measurements (TSD) on MgO : Li crystals, thermochemically treated at 1 400 K in oxidizing atmospheres, have been used to investigate the...
Weiss, M S, Anderson, D H, Raffioni, S, Bradshaw, R A, Ortenzi, C, Luporini, P, ...
The crystal structure of the pheromone Er-1 from the unicellular eukaryotic organism Euplotes raikovi was determined at 1.6 A resolution and refined to a crystallographic R factor of 19.9%. In the...
Domain swapping: entangling alliances between proteins.
Bennett, M J, Choe, S, Eisenberg, D
The comparison of monomeric and dimeric diphtheria toxin (DT) reveals a mode for protein association which we call domain swapping. The structure of dimeric DT has been extensively refined against...
Three short protein sequences have been guided by computer to folds resembling their crystal structures. Initially, peptide fragment conformations ranging in size from 9 to 25 residues were selected...
The three-dimensional profile method expresses the three-dimensional structure of a protein as a table, the profile, which represents the local environment of each residue. The score of an amino acid...
Liaw, S H, Pan, C, Eisenberg, D
Bacterial glutamine synthetase (GS; EC 6.3.1.2) was previously shown to be inhibited by nine end products of glutamine metabolism. Here we present four crystal structures of GS, complexed with the...
The structure of granulocyte-colony-stimulating factor and its relationship to other growth factors.
Hill, C P, Osslund, T D, Eisenberg, D
We have determined the three-dimensional structure of recombinant human granulocyte-colony-stimulating factor by x-ray crystallography. Phases were initially obtained at 3.0-A resolution by multiple...
Schreuder, H A, Knight, S, Curmi, P M, Andersson, I, Cascio, D, Brändén, C I, ...
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the key first step in photosynthetic CO2 fixation, the reaction that incorporates CO2 into sugar. In this study, refined crystal...
Where metal ions bind in proteins.
Yamashita, M M, Wesson, L, Eisenman, G, Eisenberg, D
The environments of metal ions (Li+, Na+, K+, Ag+, Cs+, Mg2+, Ca2+, Mn2+, Cu2+, Zn2+) in proteins and other metal-host molecules have been examined. Regardless of the metal and its precise pattern of...
B29: a member of the immunoglobulin gene superfamily exclusively expressed on beta-lineage cells.
Hermanson, G G, Eisenberg, D, Kincade, P W, Wall, R
A number of the glycoproteins identified on the surfaces of cells of the immune response belong to the immunoglobulin superfamily. We have isolated and characterized cDNA clones and the complete...
Profile analysis: detection of distantly related proteins.
Gribskov, M, McLachlan, A D, Eisenberg, D
Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the...
The hydrophobic moment detects periodicity in protein hydrophobicity.
Eisenberg, D, Weiss, R M, Terwilliger, T C
Periodicities in the polar/apolar character of the amino acid sequence of a protein can be examined by assigning to each residue a numerical hydrophobicity and searching for periodicity in the...
Fisher, P B, Weinstein, I B, Eisenberg, D, Ginsberg, H S
The tumor-promoting agent 12-O-tetradecanoyl-phorbol-13-acetate (TPA) caused a 2- to 3-fold enhancement of transformation of secondary rat embryo cells that had been injected with a...
O'Keefe, D O, Cabiaux, V, Choe, S, Eisenberg, D, Collier, R J
To investigate how diphtheria toxin (DT) undergoes pH-dependent membrane translocation in mammalian cells, we have isolated and characterized mutants of the toxin that are defective in...
Glutamine synthetase forms three- and seven-stranded helical cables.
Frey, T G, Eisenberg, D, Eiserling, F A
When cobaltous ion is bound to glutamine synthetase [L-glutamate:ammonia ligase (ADP-forming), EC 6.3.1.2], the two-layered hexagonal molecules polymerize face-to-face, to form long strands. The...
Gertz, S D, Kurgan, A, Eisenberg, D
Experimental aneurysmatic dilatation of the rabbit common carotid artery was induced by a single, periarterial application of calcium chloride in vivo. Vessels were fixed in situ after 3 d, 1 wk, 3...
Terwilliger, T C, Weissman, L, Eisenberg, D
Melittin from bee venom is water-soluble, yet integrates into membranes and lyses cells. Each melittin chain consists of 26 amino acid residues and in aqueous salt solutions it exists as a tetramer....
Caenorhabditis elegans embryos contain only one major species of Ro RNP.
Van Horn, D J, Eisenberg, D, O'Brien, C A, Wolin, S L
In virtually all vertebrate cells, Ro RNPs consist of the 60-kDa Ro autoantigen bound to one of several small cytoplasmic RNA molecules known as Y RNAs. Because the 60-kDa Ro autoantigen is also...
Risk reversals in predictive testing for Huntington disease.
Almqvist, E, Adam, S, Bloch, M, Fuller, A, Welch, P, Eisenberg, D, ...
The first predictive testing for Huntington disease (HD) was based on analysis of linked polymorphic DNA markers to estimate the likelihood of inheriting the mutation for HD. Limits to accuracy...
Weiss, M S, Anderson, D H, Raffioni, S, Bradshaw, R A, Ortenzi, C, Luporini, P, ...
The crystal structure of the pheromone Er-1 from the unicellular eukaryotic organism Euplotes raikovi was determined at 1.6 A resolution and refined to a crystallographic R factor of 19.9%. In the...
Domain swapping: entangling alliances between proteins.
Bennett, M J, Choe, S, Eisenberg, D
The comparison of monomeric and dimeric diphtheria toxin (DT) reveals a mode for protein association which we call domain swapping. The structure of dimeric DT has been extensively refined against...
Three short protein sequences have been guided by computer to folds resembling their crystal structures. Initially, peptide fragment conformations ranging in size from 9 to 25 residues were selected...
The three-dimensional profile method expresses the three-dimensional structure of a protein as a table, the profile, which represents the local environment of each residue. The score of an amino acid...
Liaw, S H, Pan, C, Eisenberg, D
Bacterial glutamine synthetase (GS; EC 6.3.1.2) was previously shown to be inhibited by nine end products of glutamine metabolism. Here we present four crystal structures of GS, complexed with the...
The structure of granulocyte-colony-stimulating factor and its relationship to other growth factors.
Hill, C P, Osslund, T D, Eisenberg, D
We have determined the three-dimensional structure of recombinant human granulocyte-colony-stimulating factor by x-ray crystallography. Phases were initially obtained at 3.0-A resolution by multiple...
Schreuder, H A, Knight, S, Curmi, P M, Andersson, I, Cascio, D, Brändén, C I, ...
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the key first step in photosynthetic CO2 fixation, the reaction that incorporates CO2 into sugar. In this study, refined crystal...
Where metal ions bind in proteins.
Yamashita, M M, Wesson, L, Eisenman, G, Eisenberg, D
The environments of metal ions (Li+, Na+, K+, Ag+, Cs+, Mg2+, Ca2+, Mn2+, Cu2+, Zn2+) in proteins and other metal-host molecules have been examined. Regardless of the metal and its precise pattern of...
B29: a member of the immunoglobulin gene superfamily exclusively expressed on beta-lineage cells.
Hermanson, G G, Eisenberg, D, Kincade, P W, Wall, R
A number of the glycoproteins identified on the surfaces of cells of the immune response belong to the immunoglobulin superfamily. We have isolated and characterized cDNA clones and the complete...
Profile analysis: detection of distantly related proteins.
Gribskov, M, McLachlan, A D, Eisenberg, D
Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the...
The hydrophobic moment detects periodicity in protein hydrophobicity.
Eisenberg, D, Weiss, R M, Terwilliger, T C
Periodicities in the polar/apolar character of the amino acid sequence of a protein can be examined by assigning to each residue a numerical hydrophobicity and searching for periodicity in the...
Fisher, P B, Weinstein, I B, Eisenberg, D, Ginsberg, H S
The tumor-promoting agent 12-O-tetradecanoyl-phorbol-13-acetate (TPA) caused a 2- to 3-fold enhancement of transformation of secondary rat embryo cells that had been injected with a...
O'Keefe, D O, Cabiaux, V, Choe, S, Eisenberg, D, Collier, R J
To investigate how diphtheria toxin (DT) undergoes pH-dependent membrane translocation in mammalian cells, we have isolated and characterized mutants of the toxin that are defective in...
Glutamine synthetase forms three- and seven-stranded helical cables.
Frey, T G, Eisenberg, D, Eiserling, F A
When cobaltous ion is bound to glutamine synthetase [L-glutamate:ammonia ligase (ADP-forming), EC 6.3.1.2], the two-layered hexagonal molecules polymerize face-to-face, to form long strands. The...
Gertz, S D, Kurgan, A, Eisenberg, D
Experimental aneurysmatic dilatation of the rabbit common carotid artery was induced by a single, periarterial application of calcium chloride in vivo. Vessels were fixed in situ after 3 d, 1 wk, 3...
Terwilliger, T C, Weissman, L, Eisenberg, D
Melittin from bee venom is water-soluble, yet integrates into membranes and lyses cells. Each melittin chain consists of 26 amino acid residues and in aqueous salt solutions it exists as a tetramer....
Caenorhabditis elegans embryos contain only one major species of Ro RNP.
Van Horn, D J, Eisenberg, D, O'Brien, C A, Wolin, S L
In virtually all vertebrate cells, Ro RNPs consist of the 60-kDa Ro autoantigen bound to one of several small cytoplasmic RNA molecules known as Y RNAs. Because the 60-kDa Ro autoantigen is also...
Risk reversals in predictive testing for Huntington disease.
Almqvist, E, Adam, S, Bloch, M, Fuller, A, Welch, P, Eisenberg, D, ...
The first predictive testing for Huntington disease (HD) was based on analysis of linked polymorphic DNA markers to estimate the likelihood of inheriting the mutation for HD. Limits to accuracy...
Proceed with Care: Direct Predictive Testing for Huntington Disease
Benjamin, C. M., Adam, S., Wiggins, S., Theilmann, J. L., Copley, T. T., Bloch, M., ...
The cloning of the Huntington disease (HD) gene allows highly accurate predictive testing using direct analysis of the CAG repeat. This new test provides results with almost complete certainty but...
Fujii, G., Horvath, S., Woodward, S., Eiserling, F., Eisenberg, D.
The mechanism of protein-mediated membrane fusion and lysis has been investigated by solution-state studies of the effects of peptides on liposomes. A peptide (SI) corresponding to a highly...
X-ray grade crystals of a designed alpha-helical coiled coil.
Lovejoy, B., Le, T. C., Lüthy, R., Cascio, D., O'Neil, K. T., DeGrado, W. F., ...
Crystallization of proton channel peptides.
Lovejoy, B., Akerfeldt, K. S., DeGrado, W. F., Eisenberg, D.
Crystals have been grown of two similar peptides that form ion-conducting channels in diphytanoyl phosphatidylcholine bilayers. These crystals were grown by slow evaporation of the organic solvent,...
Atomic solvation parameters applied to molecular dynamics of proteins in solution.
A solvation energy function for use in the molecular simulation of proteins is proposed. It is based on the accessible surface areas of atoms in the protein and on atomic solvation parameters derived...
The tetramerization of melittin, a 26-amino acid peptide from Apis mellifera bee venom, has been studied as a model for protein folding. Melittin converts from a monomeric random coil to an...
Schreuder, H. A., Knight, S., Curmi, P. M., Andersson, I., Cascio, D., Sweet, R. M., ...
The crystal structure of activated tobacco rubisco, complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate (CABP) has been determined by molecular replacement, using...
Defensins promote fusion and lysis of negatively charged membranes.
Fujii, G., Selsted, M. E., Eisenberg, D.
Defensins, a family of cationic peptides isolated from mammalian granulocytes and believed to permeabilize membranes, were tested for their ability to cause fusion and lysis of liposomes. Unlike...
Zhang, K. Y., Cascio, D., Eisenberg, D.
The crystal structure of unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate, was...
In the 3-dimensional profile method, the compatibility of an amino acid sequence for a given protein structure is scored as the sum of the preferences of the residues for their environments in the 3D...
Refined structure of dimeric diphtheria toxin at 2.0 A resolution.
Bennett, M. J., Choe, S., Eisenberg, D.
The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections (F > 1 sigma (F)), yields a final R factor of 19.5% with a model obeying standard...
Refined structure of monomeric diphtheria toxin at 2.3 A resolution.
The structure of toxic monomeric diphtheria toxin (DT) was determined at 2.3 A resolution by molecular replacement based on the domain structures in dimeric DT and refined to an R factor of 20.7%....
Discovery of the ammonium substrate site on glutamine synthetase, a third cation binding site.
Liaw, S. H., Kuo, I., Eisenberg, D.
Glutamine synthetase (GS) catalyzes the ATP-dependent condensation of ammonia and glutamate to yield glutamine, ADP, and inorganic phosphate in the presence of divalent cations. Bacterial GS is an...
3D domain swapping: a mechanism for oligomer assembly.
Bennett, M. J., Schlunegger, M. P., Eisenberg, D.
3D domain swapping is a mechanism for forming oligomeric proteins from their monomers. In 3D domain swapping, one domain of a monomeric protein is replaced by the same domain from an identical...
Crystallization of the chaperone protein SecB.
Vrielink, A., Beamer, L., Le, T., Eisenberg, D.
The secretory protein SecB found in Escherichia coli is a molecular chaperone that binds to precursor forms of a number of proteins targeted for export to the periplasmic space. SecB maintains these...
A missing link in cupredoxins: crystal structure of cucumber stellacyanin at 1.6 A resolution.
Hart, P. J., Nersissian, A. M., Herrmann, R. G., Nalbandyan, R. M., Valentine, J. S., Eisenberg, D.
Stellacyanins are blue (type I) copper glycoproteins that differ from other members of the cupredoxin family in their spectroscopic and electron transfer properties. Until now, stellacyanins have...
Protein fold recognition using sequence-derived predictions.
In protein fold recognition, one assigns a probe amino acid sequence of unknown structure to one of a library of target 3D structures. Correct assignment depends on effective scoring of the probe...
Ogihara, N. L., Weiss, M. S., Degrado, W. F., Eisenberg, D.
The three-dimensional structure of the 29-residue designed coiled coil having the amino acid sequence acetyl-E VEALEKK VAALESK VQALEKK VEALEHG-amide has been determined and refined to a...
Bell, C. E., Yeates, T. O., Eisenberg, D.
The conformation of NAD bound to diphtheria toxin (DT), an ADP-ribosylating enzyme, has been compared to the conformations of NAD(P) bound to 23 distinct NAD(P)-binding oxidoreductase enzymes, whose...
Hart, P. J., Liu, H., Pellegrini, M., Nersissian, A. M., Gralla, E. B., Valentine, J. S., ...
The X-ray crystal structure of a human copper/zinc superoxide dismutase mutant (G37R CuZnSOD) found in some patients with the inherited form of Lou Gehrig's disease (FALS) has been determined to 1.9...
The BPI/LBP family of proteins: a structural analysis of conserved regions.
Beamer, L. J., Carroll, S. F., Eisenberg, D.
Two related mammalian proteins, bactericidal/permeability-increasing protein (BPI) and lipopolysaccharide-binding protein (LBP), share high-affinity binding to lipopolysaccharide (LPS), a glycolipid...
Detecting distant relatives of mammalian LPS-binding and lipid transport proteins.
Beamer, L. J., Fischer, D., Eisenberg, D.
In mammals, a family of four lipid binding proteins has been previously defined that includes two lipopolysaccharide binding proteins and two lipid transfer proteins. The first member of this family...
Patterson, W. R., Anderson, D. H., DeGrado, W. F., Cascio, D., Eisenberg, D.
We report the 0.75 A crystal structure of a racemic mixture of the 12-residue designed peptide "Alpha-1" (Acetyl-ELLKKLLEELKG), the L-enantiomer of which is described in the accompanying paper....
Packed protein bilayers in the 0.90 A resolution structure of a designed alpha helical bundle.
Privé, G. G., Anderson, D. H., Wesson, L., Cascio, D., Eisenberg, D.
A 12-residue peptide designed to form an alpha-helix and self-associate into an antiparallel 4-alpha-helical bundle yields a 0.9 A crystal structure revealing unanticipated features. The structure...