List of works - Paul Karplus

(φ,ψ)2 Motifs: A Purely Conformation-Based Fine-Grained Enumeration of Protein Parts at the Two-Residue Level ⬇️

scientific article published on December 16, 2011

A Diiron Protein Autogenerates a Valine-Phenylalanine Cross-Link

scientific article

A Putative Fe 2+ -Bound Persulfenate Intermediate in Cysteine Dioxygenase † ‡

scientific article

A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

scientific article

A crystallographic study of the glutathione binding site of glutathione reductase at 0.3-nm resolution

scientific article published on 01 January 1989

A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions.

scientific article published on 20 February 2008

A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins

scientific article

A novel mechanism of chemoprotection by sulforaphane: inhibition of histone deacetylase.

scientific article

A productive NADP+ binding mode of ferredoxin-NADP + reductase revealed by protein engineering and crystallographic studies

scientific article

Amino acid sequence of spinach ferredoxin:NADP+ oxidoreductase

scientific article published on 01 December 1984

Analysis of the link between enzymatic activity and oligomeric state in AhpC, a bacterial peroxiredoxin

scientific article

Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex

scientific article

Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin

scientific article (publication date: 5 January 1993)

Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins.

scientific article

Better models by discarding data?

scientific article

Biochemical and crystallographic characterization of ferredoxin-NADP(+) reductase from nonphotosynthetic tissues

scientific article

C-Terminal truncation of rabbit flavin-containing monooxygenase isoform 2 enhances solubility

scientific article published on 29 March 2006

Catalytic cycle of human glutathione reductase near 1 A resolution

scientific article

Characterization of metal-substituted Klebsiella aerogenes urease

scientific article

Characterization of the mononickel metallocenter in H134A mutant urease

scientific article

Charge is the major discriminating factor for glutathione reductase versus trypanothione reductase inhibitors

scientific article published on 01 August 1996

Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand

scientific article

Competition between C-terminal Tyrosine and Nicotinamide Modulates Pyridine Nucleotide Affinity and Specificity in Plant Ferredoxin-NADP+Reductase

scientific article published in Journal of Biological Chemistry

Conformational studies of the robust 2-Cys peroxiredoxin Salmonella typhimurium AhpC by solution phase hydrogen/deuterium (H/D) exchange monitored by electrospray ionization mass spectrometry ⬇️

scientific article published on April 30, 2011

Consensus preferred hydration sites in six FKBP12-drug complexes.

scientific article published on September 1995

Crystal Structure and Catalytic Properties of Bacillus anthracis CoADR-RHD: Implications for Flavin-Linked Sulfur Trafficking

scientific article

Crystal Structure of the Antioxidant Enzyme Glutathione Reductase Inactivated by Peroxynitrite ⬇️

scientific article published on November 8, 2001

Crystal structure of mammalian cysteine dioxygenase. A novel mononuclear iron center for cysteine thiol oxidation

scientific article published on 11 April 2006

Crystal structures of two mutants that have implications for the folding of bovine pancreatic ribonuclease A ⬇️

scientific article published on May 1, 1998

Crystallization and preliminary crystallographic analysis of the soluble alpha-glycerophosphate oxidase from Streptococcus sp.

scientific article published on 21 December 2001

Crystallization of Old Yellow Enzyme illustrates an effective strategy for increasing protein crystal size.

scientific article published in November 1993

Crystallographic analysis of the binding of NADPH, NADPH fragments, and NADPH analogues to glutathione reductase

scientific article published on 01 June 1988

Cysteine Dioxygenase Structures from pH4 to 9: Consistent Cys-Persulfenate Formation at Intermediate pH and a Cys-Bound Enzyme at Higher pH ⬇️

scientific article published on June 7, 2013

Cysteine p K a Values for the Bacterial Peroxiredoxin AhpC † ‡

scientific article

Cysteine-Based Redox Switches in Enzymes ⬇️

scientific article published on September 17, 2010

Engineering of fluorescent reporters into redox domains to monitor electron transfers.

scientific article published on 20 June 2010

Enzyme inactivation through sulfhydryl oxidation by physiologic NO-carriers

scientific article

Evaluating peroxiredoxin sensitivity toward inactivation by peroxide substrates.

scientific article published on January 2013

Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality

scientific article

Flavoprotein structure and mechanism. 8. Structure-function relations for old yellow enzyme.

scientific article published on December 1995

Glutathione reductase of the malarial parasite Plasmodium falciparum: crystal structure and inhibitor development

scientific article (publication date: 9 May 2003)

Hematopoietic growth factors: understanding functional diversity in structural terms.

scientific article

High resolution structure and catalytic action of human glutathione reductase

scientific article published on 01 April 1988

Hydrophobicity regained.

scientific article published on June 1997

Identification and characterization of bacterial cysteine dioxygenases: a new route of cysteine degradation for eubacteria.

scientific article

In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs.

scientific article

Inhibition of human glutathione reductase by the nitrosourea drugs 1,3-bis(2-chloroethyl)-1-nitrosourea and 1-(2-chloroethyl)-3-(2-hydroxyethyl)-1-nitrosourea. A crystallographic analysis

scientific article

Insulin antagonism: a novel role for human serum transferrin

scientific article published on 01 March 1998

Involvement of Serine 96 in the Catalytic Mechanism of Ferredoxin-NADP+ Reductase: Structure-Function Relationship As Studied by Site-Directed Mutagenesis and X-ray Crystallography ⬇️

scientific article published on July 4, 1995

Iron-containing urease in a pathogenic bacterium

scientific article

Kinetic and structural characterization of urease active site variants

scientific article

Kinetics and crystallographic analysis of human glutathione reductase in complex with a xanthene inhibitor

scientific article

Kukoamine A and other hydrophobic acylpolyamines: potent and selective inhibitors of Crithidia fasciculata trypanothione reductase.

scientific article published on October 1995

Linking Crystallographic Model and Data Quality ⬇️

scientific article (publication date: 25 May 2012)

Low-resolution structure of recombinant human granulocyte-macrophage colony stimulating factor

scientific article published on 01 September 1991

Mapping the Active Site Helix-to-Strand Conversion of CxxxxC Peroxiredoxin Q Enzymes ⬇️

scientific article published on September 14, 2012

Multivalency in the Assembly of Intrinsically Disordered Dynein Intermediate Chain

scientific article

Novel fold and putative receptor binding site of granulocyte-macrophage colony-stimulating factor.

scientific article published on December 1991

Observed octameric assembly of a Plasmodium yoelii peroxiredoxin can be explained by the replacement of native "ball-and-socket" interacting residues by an affinity tag. ⬇️

scientific article

Old yellow enzyme at 2 A resolution: overall structure, ligand binding, and comparison with related flavoproteins

scientific article

On the active site of Old Yellow Enzyme. Role of histidine 191 and asparagine 194

scientific article

Overexpression of Crithidia fasciculata trypanothione reductase and crystallization using a novel geometry

scientific article published on 01 May 1995

Oxidized and synchrotron cleaved structures of the disulfide redox center in the N-terminal domain of Salmonella typhimurium AhpF.

scientific article

Peroxiredoxins as molecular triage agents, sacrificing themselves to enhance cell survival during a peroxide attack.

scientific article published on February 2012

Peroxiredoxins in parasites.

scientific article

Polysaccharide hydrolase folds diversity of structure and convergence of function.

scientific article published in January 1997

Preliminary crystallographic studies of urease from jack bean and from Klebsiella aerogenes

scientific article published in October 1992

Probing the function of the invariant glutamyl residue 312 in spinach ferredoxin-NADP+ reductase

scientific article

Probing the roles of active site residues in D-xylose isomerase.

scientific article

Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry.

scientific article

Protein sulfenic acids in redox signaling.

scientific article published on January 2004

Redox-dependent dynamics of a dual thioredoxin fold protein: evolution of specialized folds.

scientific article published on June 2009

Refined crystal structure and mutagenesis of human granulocyte-macrophage colony-stimulating factor

scientific article

Refined crystal structure of spinach ferredoxin reductase at 1.7 A resolution: oxidized, reduced and 2'-phospho-5'-AMP bound states

scientific article

Refined structure of glutathione reductase at 1.54 A resolution

scientific article

Refined structure of porcine cytosolic adenylate kinase at 2.1 A resolution

scientific article

Relatedness of baculovirus and gypsy retrotransposon envelope proteins

scientific article

Roles of the catalytic domain and two cellulose binding domains of Thermomonospora fusca E4 in cellulose hydrolysis.

scientific article published on April 1998

Site-directed mutagenesis improves catalytic efficiency and thermostability of Escherichia coli pH 2.5 acid phosphatase/phytase expressed in Pichia pastoris

scientific article published on 01 October 2000

Song: Chymotrypsin (to the tune of “eight days a week,” by the beatles)* ⬇️

scientific article published on 01 July 2006

Song: Enzymes speed reactions (to the tune of "we will rock you," by queen)*S

scientific article published on 01 July 2006

Song: Learn about the buffer (generic rap)*

scientific article published on 01 July 2006

Structural Aspects of Plant Ferredoxin : NADP(+) Oxidoreductases

scientific article published on 01 January 2004

Structural Basis of Improved Second-Generation 3-Nitro-tyrosine tRNA Synthetases

scientific article

Structural Changes Common to Catalysis in the Tpx Peroxiredoxin Subfamily

scientific article

Structural Evidence that Peroxiredoxin Catalytic Power Is Based on Transition-State Stabilization

scientific article

Structural comparisons among the short-chain helical cytokines

scientific article published on 01 March 1994

Structural prototypes for an extended family of flavoprotein reductases: comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin

scientific article

Structural survey of the peroxiredoxins.

scientific article published on January 2007

Structure and dynamics of LC8 complexes with KXTQT-motif peptides: swallow and dynein intermediate chain compete for a common site

scientific article

Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca

scientific article

Structure of Ptr ToxA: an RGD-containing host-selective toxin from Pyrenophora tritici-repentis

scientific article published on 07 October 2005

Structure of alpha-glycerophosphate oxidase from Streptococcus sp.: a template for the mitochondrial alpha-glycerophosphate dehydrogenase

scientific article

Structure of coenzyme A-disulfide reductase from Staphylococcus aureus at 1.54 A resolution.

scientific article published on September 2006

Structure of the ERM protein moesin reveals the FERM domain fold masked by an extended actin binding tail domain

scientific article

Structure of the active N-terminal domain of Ezrin. Conformational and mobility changes identify keystone interactions

scientific article

Structure-based Insights into the Catalytic Power and Conformational Dexterity of Peroxiredoxins ⬇️

scientific article published on April 20, 2011

Structure-function relations for ferredoxin reductase.

scientific article

Substrate binding and catalysis by glutathione reductase as derived from refined enzyme: substrate crystal structures at 2 A resolution

scientific article

Substrate specificity and redox potential of AhpC, a bacterial peroxiredoxin

scholarly article

Symerythrin Structures at Atomic Resolution and the Origins of Rubrerythrins and the Ferritin-Like Superfamily

scientific article

Synthesis and characterization of photolabile o-nitrobenzyl derivatives of urea.

scientific article

The Arg-Gly-Asp-containing, solvent-exposed loop of Ptr ToxA is required for internalization.

scientific article published in March 2008

The EBP50-moesin interaction involves a binding site regulated by direct masking on the FERM domain

scientific article

The Interplay of Ligand Binding and Quaternary Structure in the Diverse Interactions of Dynein Light Chain LC8

scientific article

The Sensitive Balance between the Fully Folded and Locally Unfolded Conformations of a Model Peroxiredoxin

scientific article

The crystal structure of dynein intermediate chain-light chain roadblock complex gives new insights into dynein assembly

scientific article

The flavin environment in old yellow enzyme. An evaluation of insights from spectroscopic and artificial flavin studies

scientific article published on 01 April 1999

The insect immune protein scolexin is a novel serine proteinase homolog

scientific article

The role of glutamine 114 in old yellow enzyme

scientific article

The tumor suppressor merlin controls growth in its open state, and phosphorylation converts it to a less-active more-closed state.

scientific article published on April 2012

Thiol dioxygenases: unique families of cupin proteins.

scientific article

Trypanocidal Bisbenzylisoquinoline Alkaloids are Inhibitors of Trypanothione Reductase

scientific article published on 01 February 1998

Typical 2-Cys peroxiredoxins--structures, mechanisms and functions.

scientific article published on 24 March 2009

Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins

scientific article

List of works by Paul Karplus

(φ,ψ)2 Motifs: A Purely Conformation-Based Fine-Grained Enumeration of Protein Parts at the Two-Residue Level ⬇️

A Diiron Protein Autogenerates a Valine-Phenylalanine Cross-Link

A Putative Fe 2+ -Bound Persulfenate Intermediate in Cysteine Dioxygenase † ‡

A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

A crystallographic study of the glutathione binding site of glutathione reductase at 0.3-nm resolution

A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions.

A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins

A novel mechanism of chemoprotection by sulforaphane: inhibition of histone deacetylase.

A productive NADP+ binding mode of ferredoxin-NADP + reductase revealed by protein engineering and crystallographic studies

Amino acid sequence of spinach ferredoxin:NADP+ oxidoreductase

Analysis of the link between enzymatic activity and oligomeric state in AhpC, a bacterial peroxiredoxin

Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex

Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin

Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins.

Better models by discarding data?

Biochemical and crystallographic characterization of ferredoxin-NADP(+) reductase from nonphotosynthetic tissues

C-Terminal truncation of rabbit flavin-containing monooxygenase isoform 2 enhances solubility

Catalytic cycle of human glutathione reductase near 1 A resolution

Characterization of metal-substituted Klebsiella aerogenes urease

Characterization of the mononickel metallocenter in H134A mutant urease

Charge is the major discriminating factor for glutathione reductase versus trypanothione reductase inhibitors

Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand

Competition between C-terminal Tyrosine and Nicotinamide Modulates Pyridine Nucleotide Affinity and Specificity in Plant Ferredoxin-NADP+Reductase

Conformational studies of the robust 2-Cys peroxiredoxin Salmonella typhimurium AhpC by solution phase hydrogen/deuterium (H/D) exchange monitored by electrospray ionization mass spectrometry ⬇️

Consensus preferred hydration sites in six FKBP12-drug complexes.

Crystal Structure and Catalytic Properties of Bacillus anthracis CoADR-RHD: Implications for Flavin-Linked Sulfur Trafficking

Crystal Structure of the Antioxidant Enzyme Glutathione Reductase Inactivated by Peroxynitrite ⬇️

Crystal structure of mammalian cysteine dioxygenase. A novel mononuclear iron center for cysteine thiol oxidation

Crystal structures of two mutants that have implications for the folding of bovine pancreatic ribonuclease A ⬇️

Crystallization and preliminary crystallographic analysis of the soluble alpha-glycerophosphate oxidase from Streptococcus sp.

Crystallization of Old Yellow Enzyme illustrates an effective strategy for increasing protein crystal size.

Crystallographic analysis of the binding of NADPH, NADPH fragments, and NADPH analogues to glutathione reductase

Cysteine Dioxygenase Structures from pH4 to 9: Consistent Cys-Persulfenate Formation at Intermediate pH and a Cys-Bound Enzyme at Higher pH ⬇️

Cysteine p K a Values for the Bacterial Peroxiredoxin AhpC † ‡

Cysteine-Based Redox Switches in Enzymes ⬇️

Engineering of fluorescent reporters into redox domains to monitor electron transfers.

Enzyme inactivation through sulfhydryl oxidation by physiologic NO-carriers

Evaluating peroxiredoxin sensitivity toward inactivation by peroxide substrates.

Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality

Flavoprotein structure and mechanism. 8. Structure-function relations for old yellow enzyme.

Glutathione reductase of the malarial parasite Plasmodium falciparum: crystal structure and inhibitor development

Hematopoietic growth factors: understanding functional diversity in structural terms.

High resolution structure and catalytic action of human glutathione reductase

Hydrophobicity regained.

Identification and characterization of bacterial cysteine dioxygenases: a new route of cysteine degradation for eubacteria.

In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs.

Inhibition of human glutathione reductase by the nitrosourea drugs 1,3-bis(2-chloroethyl)-1-nitrosourea and 1-(2-chloroethyl)-3-(2-hydroxyethyl)-1-nitrosourea. A crystallographic analysis

Insulin antagonism: a novel role for human serum transferrin

Involvement of Serine 96 in the Catalytic Mechanism of Ferredoxin-NADP+ Reductase: Structure-Function Relationship As Studied by Site-Directed Mutagenesis and X-ray Crystallography ⬇️

Iron-containing urease in a pathogenic bacterium

Kinetic and structural characterization of urease active site variants

Kinetics and crystallographic analysis of human glutathione reductase in complex with a xanthene inhibitor

Kukoamine A and other hydrophobic acylpolyamines: potent and selective inhibitors of Crithidia fasciculata trypanothione reductase.

Linking Crystallographic Model and Data Quality ⬇️

Low-resolution structure of recombinant human granulocyte-macrophage colony stimulating factor

Mapping the Active Site Helix-to-Strand Conversion of CxxxxC Peroxiredoxin Q Enzymes ⬇️

Multivalency in the Assembly of Intrinsically Disordered Dynein Intermediate Chain

Novel fold and putative receptor binding site of granulocyte-macrophage colony-stimulating factor.

Observed octameric assembly of a Plasmodium yoelii peroxiredoxin can be explained by the replacement of native "ball-and-socket" interacting residues by an affinity tag. ⬇️

Old yellow enzyme at 2 A resolution: overall structure, ligand binding, and comparison with related flavoproteins

On the active site of Old Yellow Enzyme. Role of histidine 191 and asparagine 194

Overexpression of Crithidia fasciculata trypanothione reductase and crystallization using a novel geometry

Oxidized and synchrotron cleaved structures of the disulfide redox center in the N-terminal domain of Salmonella typhimurium AhpF.

Peroxiredoxins as molecular triage agents, sacrificing themselves to enhance cell survival during a peroxide attack.

Peroxiredoxins in parasites.

Polysaccharide hydrolase folds diversity of structure and convergence of function.

Preliminary crystallographic studies of urease from jack bean and from Klebsiella aerogenes

Probing the function of the invariant glutamyl residue 312 in spinach ferredoxin-NADP+ reductase

Probing the roles of active site residues in D-xylose isomerase.

Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry.

Protein sulfenic acids in redox signaling.

Redox-dependent dynamics of a dual thioredoxin fold protein: evolution of specialized folds.

Refined crystal structure and mutagenesis of human granulocyte-macrophage colony-stimulating factor

Refined crystal structure of spinach ferredoxin reductase at 1.7 A resolution: oxidized, reduced and 2'-phospho-5'-AMP bound states

Refined structure of glutathione reductase at 1.54 A resolution

Refined structure of porcine cytosolic adenylate kinase at 2.1 A resolution

Relatedness of baculovirus and gypsy retrotransposon envelope proteins

Roles of the catalytic domain and two cellulose binding domains of Thermomonospora fusca E4 in cellulose hydrolysis.

Site-directed mutagenesis improves catalytic efficiency and thermostability of Escherichia coli pH 2.5 acid phosphatase/phytase expressed in Pichia pastoris