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Papers by Edward Eisenstein

Research paper thumbnail of Local and Global Control Mechanisms in Allosteric Threonine Deaminase

Methods in Enzymology, 2004

Research paper thumbnail of Assisting Functional Assignment for Hypothetical Heamophilus influenzae Gene Products through Structural Genomics

Current Drug Target -Infectious Disorders, 2002

Research paper thumbnail of Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase

Research paper thumbnail of Structure of the YibK methyltransferase fromHaemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot

Proteins: Structure, Function, and Genetics, 2003

Research paper thumbnail of Crystal structure of the YjeE protein fromHaemophilus influenzae: A putative Atpase involved in cell wall synthesis

Proteins: Structure, Function, and Genetics, 2002

Research paper thumbnail of Crystal structure of Yeco fromHaemophilus influenzae (HI0319) reveals a methyltransferase fold and a boundS-adenosylhomocysteine

Proteins: Structure, Function, and Genetics, 2001

Research paper thumbnail of From structure to function: YrbI fromHaemophilus influenzae (HI1679) is a phosphatase

Proteins: Structure, Function, and Genetics, 2002

Research paper thumbnail of Structure of 2C-methyl-D-erythrol-2,4-cyclodiphosphate synthase fromHaemophilus influenzae: Activation by conformational transition

Proteins: Structure, Function, and Genetics, 2002

Research paper thumbnail of Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR

Proteins: Structure, Function, and Bioinformatics, 2002

Research paper thumbnail of Crystal Structure of Dephospho-Coenzyme A Kinase from Haemophilus influenzae

Journal of Structural Biology, 2001

Dephospho-coenzyme A kinase catalyzes the final step in CoA biosynthesis, the phosphorylation of ... more Dephospho-coenzyme A kinase catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The protein from Haemophilus influenzae was cloned and expressed, and its crystal structure was determined at 2.0-A resolution in complex with ATP. The protein molecule consists of three domains: the canonical nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices. The overall topology of the protein resembles the structures of nucleotide kinases. ATP binds in the P-loop in a manner observed in other kinases. The CoA-binding site is located at the interface of all three domains. The double-pocket structure of the substrate-binding site is unusual for nucleotide kinases. Amino acid residues implicated in substrate binding and catalysis have been identified. The structure analysis suggests large domain movements during the catalytic cycle.

Research paper thumbnail of Structural and physicochemical analysis of the reaction between the anti-lysozyme antibody D1.3 and the anti-idiotopic antibodies E225 and E5.2

Journal of Molecular Recognition, 1994

Research paper thumbnail of The Effect of Water Activity on the Association Constant and the Enthalpy of Reaction Between Lysozyme and the Specific Antibodies D1.3 and D44.1

Journal of Molecular Recognition, 1996

Research paper thumbnail of Crystal Structure of the YchF Protein Reveals Binding Sites for GTP and Nucleic Acid

Journal of Bacteriology, 2003

Research paper thumbnail of Biological function made crystal clear — annotation of hypothetical proteins via structural genomics

Current Opinion in Biotechnology, 2000

Research paper thumbnail of Engineering the Independent Folding of the Subtilisin BPN‘ Pro-Domain:  Correlation of Pro-Domain Stability with the Rate of Subtilisin Folding †

Biochemistry, 1998

The 77-amino acid pro-domain greatly accelerates the in vitro folding of subtilisin in a bimolecu... more The 77-amino acid pro-domain greatly accelerates the in vitro folding of subtilisin in a bimolecular reaction whose product is a tight complex between folded subtilisin and folded pro-domain. In this complex the pro-domain has a compact structure with a four-stranded antiparallel beta-sheet and two three-turn alpha-helixes. When isolated from subtilisin, however, the pro-domain is 97% unfolded even under optimal folding conditions. The instability of the isolated pro-domain suggests that there may be a thermodynamic linkage between the stability of the pro-domain and its ability to facilitate subtilisin folding. On the basis of the X-ray crystal structure of the pro-domain subtilisin complex, we have designed stabilizing mutations in three areas of the pro-domain: alpha-helix 23-32 (E32Q), beta-strands 35-51 (Q40L), and alpha-helix 53-61 (K57E). These amino acid positions were selected because they do not contact subtilisin in the complex and because they appear to be in regions of the structure which are not well packed in the wild type pro-domain. Since none of the mutations directly contact subtilisin, their effects on the folding of subtilisin are linked to whether or not they stabilize a conformation of the pro-domain which promotes subtilisin folding. By sequentially introducing the three stabilizing mutations, the equilibrium for folding the pro-domain was shifted from 97% unfolded to 65% folded. By measuring the ability of these mutants to fold subtilisin, we are able to establish a correlation between the stability of the pro-domain and its ability to accelerate subtilisin folding. As the pro-domain is stabilized, the folding reaction becomes faster and distinctly biphasic. A detailed mechanism was determined for the double mutant, Q40L-K57E, which is 50% folded: P + Su if (30 800 M-1 s-1, 0.04 s-1) PSI if (0.07 s-1, <0.005 s-1) PS. PSI is an intermediate complex which accumulates in the course of the reaction, and PS is the fully folded complex. The more stable the pro-domain, the faster the folding reaction up to the point at which the isomerization of the intermediate into the fully folded complex becomes the rate-limiting step in the folding process.

Research paper thumbnail of Equilibrium Folding Studies of Tetrameric R67 Dihydrofolate Reductase

Research paper thumbnail of Nucleoside Diphosphate Kinase from Bovine Retina:  Purification, Subcellular Localization, Molecular Cloning, and Three-Dimensional Structure †

Biochemistry, 1998

The biochemical and structural properties of bovine retinal nucleoside diphosphate kinase were in... more The biochemical and structural properties of bovine retinal nucleoside diphosphate kinase were investigated. The enzyme showed two polypeptides of approximately 17.5 and 18.5 kDa on SDS-PAGE, while isoelectric focusing revealed seven to eight proteins with a pI range of 7.4-8.2. Sedimentation equilibrium yielded a molecular mass of 96 +/- 2 kDa for the enzyme. Carbohydrate analysis revealed that both polypeptides contained Gal, Man, GlcNAc, Fuc, and GalNac saccharides. Like other nucleoside diphosphate kinases, the retinal enzyme showed substantial differences in the Km values for various di- and triphosphate nucleotides. Immunogold labeling of bovine retina revealed that the enzyme is localized on both the membranes and in the cytoplasm. Screening of a retinal cDNA library yielded full-length clones encoding two distinct isoforms (NBR-A and NBR-B). Both isoforms were overexpressed in Escherichia coli and their biochemical properties compared with retinal NDP-kinase. The structures of NBR-A and NBR-B were determined by X-ray crystallography in the presence of guanine nucleotide(s). Both isoforms are hexameric, and the fold of the monomer is similar to other nucleoside diphosphate kinase structures. The NBR-A active site contained both a cGMP and a GDP molecule each bound at half occupancy while the NBR-B active site contained only cGMP.

Research paper thumbnail of Divergence of Function in the Hot Dog Fold Enzyme Superfamily: The Bacterial Thioesterase YciA †

Research paper thumbnail of Solution Structure and Functional Ligand Screening of HI0719, a Highly Conserved Protein from Bacteria to Humans in the YjgF/YER057c/UK114 Family † , ‡

Research paper thumbnail of An Expanded Two-State Model Accounts for Homotropic Cooperativity in Biosynthetic Threonine Deaminase from Escherichia coli

Research paper thumbnail of Local and Global Control Mechanisms in Allosteric Threonine Deaminase

Methods in Enzymology, 2004

Research paper thumbnail of Assisting Functional Assignment for Hypothetical Heamophilus influenzae Gene Products through Structural Genomics

Current Drug Target -Infectious Disorders, 2002

Research paper thumbnail of Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase

Research paper thumbnail of Structure of the YibK methyltransferase fromHaemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot

Proteins: Structure, Function, and Genetics, 2003

Research paper thumbnail of Crystal structure of the YjeE protein fromHaemophilus influenzae: A putative Atpase involved in cell wall synthesis

Proteins: Structure, Function, and Genetics, 2002

Research paper thumbnail of Crystal structure of Yeco fromHaemophilus influenzae (HI0319) reveals a methyltransferase fold and a boundS-adenosylhomocysteine

Proteins: Structure, Function, and Genetics, 2001

Research paper thumbnail of From structure to function: YrbI fromHaemophilus influenzae (HI1679) is a phosphatase

Proteins: Structure, Function, and Genetics, 2002

Research paper thumbnail of Structure of 2C-methyl-D-erythrol-2,4-cyclodiphosphate synthase fromHaemophilus influenzae: Activation by conformational transition

Proteins: Structure, Function, and Genetics, 2002

Research paper thumbnail of Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR

Proteins: Structure, Function, and Bioinformatics, 2002

Research paper thumbnail of Crystal Structure of Dephospho-Coenzyme A Kinase from Haemophilus influenzae

Journal of Structural Biology, 2001

Dephospho-coenzyme A kinase catalyzes the final step in CoA biosynthesis, the phosphorylation of ... more Dephospho-coenzyme A kinase catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The protein from Haemophilus influenzae was cloned and expressed, and its crystal structure was determined at 2.0-A resolution in complex with ATP. The protein molecule consists of three domains: the canonical nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices. The overall topology of the protein resembles the structures of nucleotide kinases. ATP binds in the P-loop in a manner observed in other kinases. The CoA-binding site is located at the interface of all three domains. The double-pocket structure of the substrate-binding site is unusual for nucleotide kinases. Amino acid residues implicated in substrate binding and catalysis have been identified. The structure analysis suggests large domain movements during the catalytic cycle.

Research paper thumbnail of Structural and physicochemical analysis of the reaction between the anti-lysozyme antibody D1.3 and the anti-idiotopic antibodies E225 and E5.2

Journal of Molecular Recognition, 1994

Research paper thumbnail of The Effect of Water Activity on the Association Constant and the Enthalpy of Reaction Between Lysozyme and the Specific Antibodies D1.3 and D44.1

Journal of Molecular Recognition, 1996

Research paper thumbnail of Crystal Structure of the YchF Protein Reveals Binding Sites for GTP and Nucleic Acid

Journal of Bacteriology, 2003

Research paper thumbnail of Biological function made crystal clear — annotation of hypothetical proteins via structural genomics

Current Opinion in Biotechnology, 2000

Research paper thumbnail of Engineering the Independent Folding of the Subtilisin BPN‘ Pro-Domain:  Correlation of Pro-Domain Stability with the Rate of Subtilisin Folding †

Biochemistry, 1998

The 77-amino acid pro-domain greatly accelerates the in vitro folding of subtilisin in a bimolecu... more The 77-amino acid pro-domain greatly accelerates the in vitro folding of subtilisin in a bimolecular reaction whose product is a tight complex between folded subtilisin and folded pro-domain. In this complex the pro-domain has a compact structure with a four-stranded antiparallel beta-sheet and two three-turn alpha-helixes. When isolated from subtilisin, however, the pro-domain is 97% unfolded even under optimal folding conditions. The instability of the isolated pro-domain suggests that there may be a thermodynamic linkage between the stability of the pro-domain and its ability to facilitate subtilisin folding. On the basis of the X-ray crystal structure of the pro-domain subtilisin complex, we have designed stabilizing mutations in three areas of the pro-domain: alpha-helix 23-32 (E32Q), beta-strands 35-51 (Q40L), and alpha-helix 53-61 (K57E). These amino acid positions were selected because they do not contact subtilisin in the complex and because they appear to be in regions of the structure which are not well packed in the wild type pro-domain. Since none of the mutations directly contact subtilisin, their effects on the folding of subtilisin are linked to whether or not they stabilize a conformation of the pro-domain which promotes subtilisin folding. By sequentially introducing the three stabilizing mutations, the equilibrium for folding the pro-domain was shifted from 97% unfolded to 65% folded. By measuring the ability of these mutants to fold subtilisin, we are able to establish a correlation between the stability of the pro-domain and its ability to accelerate subtilisin folding. As the pro-domain is stabilized, the folding reaction becomes faster and distinctly biphasic. A detailed mechanism was determined for the double mutant, Q40L-K57E, which is 50% folded: P + Su if (30 800 M-1 s-1, 0.04 s-1) PSI if (0.07 s-1, <0.005 s-1) PS. PSI is an intermediate complex which accumulates in the course of the reaction, and PS is the fully folded complex. The more stable the pro-domain, the faster the folding reaction up to the point at which the isomerization of the intermediate into the fully folded complex becomes the rate-limiting step in the folding process.

Research paper thumbnail of Equilibrium Folding Studies of Tetrameric R67 Dihydrofolate Reductase

Research paper thumbnail of Nucleoside Diphosphate Kinase from Bovine Retina:  Purification, Subcellular Localization, Molecular Cloning, and Three-Dimensional Structure †

Biochemistry, 1998

The biochemical and structural properties of bovine retinal nucleoside diphosphate kinase were in... more The biochemical and structural properties of bovine retinal nucleoside diphosphate kinase were investigated. The enzyme showed two polypeptides of approximately 17.5 and 18.5 kDa on SDS-PAGE, while isoelectric focusing revealed seven to eight proteins with a pI range of 7.4-8.2. Sedimentation equilibrium yielded a molecular mass of 96 +/- 2 kDa for the enzyme. Carbohydrate analysis revealed that both polypeptides contained Gal, Man, GlcNAc, Fuc, and GalNac saccharides. Like other nucleoside diphosphate kinases, the retinal enzyme showed substantial differences in the Km values for various di- and triphosphate nucleotides. Immunogold labeling of bovine retina revealed that the enzyme is localized on both the membranes and in the cytoplasm. Screening of a retinal cDNA library yielded full-length clones encoding two distinct isoforms (NBR-A and NBR-B). Both isoforms were overexpressed in Escherichia coli and their biochemical properties compared with retinal NDP-kinase. The structures of NBR-A and NBR-B were determined by X-ray crystallography in the presence of guanine nucleotide(s). Both isoforms are hexameric, and the fold of the monomer is similar to other nucleoside diphosphate kinase structures. The NBR-A active site contained both a cGMP and a GDP molecule each bound at half occupancy while the NBR-B active site contained only cGMP.

Research paper thumbnail of Divergence of Function in the Hot Dog Fold Enzyme Superfamily: The Bacterial Thioesterase YciA †

Research paper thumbnail of Solution Structure and Functional Ligand Screening of HI0719, a Highly Conserved Protein from Bacteria to Humans in the YjgF/YER057c/UK114 Family † , ‡

Research paper thumbnail of An Expanded Two-State Model Accounts for Homotropic Cooperativity in Biosynthetic Threonine Deaminase from Escherichia coli