lee pedersen

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George Kaviris

National & Kapodistrian University of Athens

David Seamon

Kansas State University

Giorgio Seano

Institut Curie

Susana Rostagnol

Universidad de la República

Viacheslav Kuleshov

Stockholm University

rudolph bauer

Washington Center for Consciousness Studies

Stefka G Eriksen

University of Oslo

Karina Felitti

Universidad de Buenos Aires

Conrad Rizal, PhD

University of California, San Diego

Oladosu A Ojengbede

University of Ibadan Nigeria

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Papers by lee pedersen

Quantum chemistry and physics

Structural studies of enzymes involved in peroxisomal β-oxidation

Acta Crystallographica Section A Foundations of Crystallography, 2002

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Sulfotransferases

Wiley Encyclopedia of Molecular Medicine, Jan 15, 2002

Geometrical-Flexibile Binding Pocket and Inherent Versatility of P450 Activity

The structure of the triatomic free radicals HCO, HCN—, and FCO

Journal of Molecular Structure, Feb 1, 1970

... Structure, 5 (1970) 2126 26 L. PEDERSEN that the similarity in the bond angles of these three... more

The n .fwdarw. 3s Rydberg transition of jet-cooled tetrahydropyran, 1,4-dioxane, and 1,4-dioxane-d8 studied by 2 + 1 resonance-enhanced multiphoton ionization

The Journal of Physical Chemistry, Aug 1, 1989

... Chem. SOC. 1988, 110, 6287. of the long-lived Rydberg state, allowing the detection of slight... more

A revisit to the one-form kinetic model of prothrombinase: A comment on the rebuttal

Carolina Digital Repository (University of North Carolina at Chapel Hill), 2010

Thrombin is generated enzymatically from prothrombin by two pathways with the intermediates of me... more Thrombin is generated enzymatically from prothrombin by two pathways with the intermediates of meizothrombin and prethrombin-2. Experimental concentration profiles from two independent groups for these two pathways have been re-analyzed. By rationally combining the independent data sets, a simple mechanism can be established and rate constants determined. A structural model is consistent with the data-derived finding that mechanisms that feature channeling or ratcheting are not necessary to describe thrombin production.

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The n .fwdarw. 3s Rydberg transition of jet-cooled tetrahydropyran, 1,4-dioxane, and 1,4-dioxane-d8 studied by 2 + 1 resonance-enhanced multiphoton ionization

The Journal of Physical Chemistry, 1989

... Chem. SOC. 1988, 110, 6287. of the long-lived Rydberg state, allowing the detection of slight... more

The structure of the triatomic free radicals HCO, HCN—, and FCO

Journal of Molecular Structure, 1970

... Structure, 5 (1970) 2126 26 L. PEDERSEN that the similarity in the bond angles of these three... more

Warfarin and vitamin K epoxide reductase: a molecular accounting for observed inhibition

Blood, 2018

Key PointsWarfarin reversibly inhibits VKOR by forming a T-shaped stacking interaction with resid... more

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ChemInform Abstract: Terbium Ion Binding to a Synthetic γ‐Carboxyglutamic Acid Containing Heptapeptide Corresponding to Bovine Prothrombin Residues 17‐23

ChemInform, 1987

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Atomic-level accuracy in simulations of large protein crystals

Carolina Digital Repository (University of North Carolina at Chapel Hill), 1994

Proper treatment of long-range Coulombic forces presents a major obstacle to providing realistic ... more Proper treatment of long-range Coulombic forces presents a major obstacle to providing realistic molecular dynamics simulations of macromolecules. Traditional approximations made to lessen computational cost ultimately lead to unrealistic behavior. The particle mesh Ewald method accommodates long-range Coulombic forces accurately and efficiently by use of fast Fourier transform techniques. We report a 1-ns simulation of bovine pancreatic trypsin inhibitor in a crystal unit cell using the particle mesh Ewald methodology. We find an rms backbone deviation from the x-ray structure (0.33 A) that is lower than that observed between

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A role of Lys614in the sulfotransferase activity of human heparan sulfateN-deacetylase/N-sulfotransferase

FEBS Letters, Aug 21, 1998

An active sulfotransferase (ST, residues 558-882) domain of the human heparan sulfate N-deacetyla... more An active sulfotransferase (ST, residues 558-882) domain of the human heparan sulfate N-deacetylaseIN-sulfotransferase (hHSNST) has been identified by aligning the amino acid sequence of hHSNST to that of mouse estrogen sulfotransferase (EST). The bacterially expressed ST domain transfers the 5'-sulfuryl group of 3'-phosphoadenosine-5'-phosphosuifate (PAPS) to only deacetylated heparin with an efficiency similar to that previously reported for the purified rat HSNST. Moreover, the Km,PAPS (2.1 pM) of the ST domain is also similar to that of the rat enzyme. Lys 4s is a key residue in mEST catalysis. The residue corresponding to Lys as is conserved in all known beparan sulfate sulfotransferases (Lys °14 in the ST domain of hHSNST). Mutation of Lys 614 to Ala abolishes Nsulfotransferase activity, indicating an important catalytic role of Lys °14 in the ST domain. Crystals of the ST domain have been grown (orthorhombic space group P21212) with diffraction to 2.5 A resolution.

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Chemical field ionization. Effect of chemically bonded surface groups in field ionization mass spectrometry

Journal of the American Chemical Society, Oct 1, 1980

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Quantum chemical study of the mechanism of action of vitamin K carboxylase in solvent

Carolina Digital Repository (University of North Carolina at Chapel Hill), 2010

We investigate the post-translational generation of Gla (γ-carboxy glutamic acid) from Glu (gluta... more We investigate the post-translational generation of Gla (γ-carboxy glutamic acid) from Glu (glutamic acid) by vitamin K carboxylase (VKC) in solvent. VKC is thought to convert vitamin K, in the vitamin K cycle, to an alkoxide-epoxide form, which then reacts with CO 2 to generate an essential ingredient in blood coagulation, γ-carboxyglutamic acid (Gla). The generation of Gla from Glu is found to be exergenic (−15 kcal/mol) in aqueous solution with the SM6 method. We also produced the free energy profile for this model biochemical process with other solvent methods (polarizable continuum model, dielectric polarizable continuum model) and different dielectric constants. The biological implications are discussed.

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Homology Modeling and Molecular Dynamics Simulations of the Gla Domains of Human Coagulation Factor IX and Its G[12]A Mutant

The Journal of Physical Chemistry, 1996

We have tested molecular dynamics as a predictive tool for stability of protein structure. We fir... more We have tested molecular dynamics as a predictive tool for stability of protein structure. We first used the X-ray crystallographic coordinates of bovine prothrombin fragment 1 to model the structure of the Gla domain of human factor IX, an essential coagulation protein. In addition, a mutant protein that differs in only a single amino acid (G[12]A) but is associated with one form of Hemophilia B was also modeled. Simulations performed in an identical fashion for both proteins, with considerable care to accommodate long-range forces in these highly ionic systems, indicated that substantial distortions occur in the mutant structure relative to the wild type factor IX. Surprisingly, the Gla domain (residues 1−34) of the wild type and mutant remain similar. Instead, it is the interaction of the added Ala at position 12 in the mutant that repels the post-Gla region (residues >33, the C-terminal helix) region.

Homology modeling and molecular dynamics simulation of human prothrombin fragment 1

Protein Science, Nov 1, 1995

The crystallographic structure of bovine prothrombin fragment 1 bound with calcium ions was used ... more The crystallographic structure of bovine prothrombin fragment 1 bound with calcium ions was used to construct the corresponding human prothrombin structure (hfl/Ca). The model structure was refined by molecular dynamics to estimate the average solution structure. Accommodation of long-range ionic forces was essential to reach a stable solution structure. The y-carboxyglutamic acid (Gla) domain and the kringle domain of hfl/Ca independently equilibrated. Likewise, the hydrogen bond network and the calcium ion coordinations were well preserved. A discussion of the phospholipid binding of the vitamin K-dependent coagulation proteins in the context of the structure and mutational data of the Gla domain is presented.

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The Preferred Conformation of Noradrenaline

Journal of Pharmacy and Pharmacology, Mar 1, 1971

A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa)

Carolina Digital Repository (University of North Carolina at Chapel Hill), 2009

Protein Z-dependent protease inhibitor (ZPI) and antithrombin III (AT3) are members of the serpin... more Protein Z-dependent protease inhibitor (ZPI) and antithrombin III (AT3) are members of the serpin superfamily of protease inhibitors that inhibit factor Xa (FXa) and other proteases in the coagulation pathway. While experimental structural information is available for the interaction of AT3 with FXa, at present there is no structural data regarding the interaction of ZPI with FXa, and the precise role of this interaction in the blood coagulation pathway is poorly understood. In an effort to gain a structural understanding of this system, we have built a solvent equilibrated three-dimensional structural model of the Michaelis complex of human ZPI/FXa using homology modeling, proteinprotein docking and molecular dynamics simulation methods. Preliminary analysis of interactions at the complex interface from our simulations suggests that the interactions of the reactive center loop (RCL) and the exosite surface of ZPI with FXa are similar to those observed from X-ray crystal structure-based simulations of AT3/FXa. However, detailed comparison of our modeled structure of ZPI/FXa with that of AT3/FXa points to differences in interaction specificity at the reactive center and in the stability of the inhibitory complex, due to the presence of a tyrosine residue at the P1 position in ZPI, instead of the P1 arginine residue in AT3. The modeled structure also shows specific structural differences between AT3 and ZPI in the heparin-binding and flexible N-terminal tail regions. Our structural model of ZPI/FXa is also compatible with available experimental information regarding the importance for the inhibitory action of certain basic residues in FXa.

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Erratum: Molecular orbital studies of the protonation of the methylanisoles (Journal of the American Chemical Society (1976) 98, (4061))

Journal of the American Chemical Society, Dec 1, 1976

Quantum chemistry and physics

Structural studies of enzymes involved in peroxisomal β-oxidation

Acta Crystallographica Section A Foundations of Crystallography, 2002

Download

Sulfotransferases

Wiley Encyclopedia of Molecular Medicine, Jan 15, 2002

Geometrical-Flexibile Binding Pocket and Inherent Versatility of P450 Activity

The structure of the triatomic free radicals HCO, HCN—, and FCO

Journal of Molecular Structure, Feb 1, 1970

... Structure, 5 (1970) 2126 26 L. PEDERSEN that the similarity in the bond angles of these three... more

The n .fwdarw. 3s Rydberg transition of jet-cooled tetrahydropyran, 1,4-dioxane, and 1,4-dioxane-d8 studied by 2 + 1 resonance-enhanced multiphoton ionization

The Journal of Physical Chemistry, Aug 1, 1989

... Chem. SOC. 1988, 110, 6287. of the long-lived Rydberg state, allowing the detection of slight... more

A revisit to the one-form kinetic model of prothrombinase: A comment on the rebuttal

Carolina Digital Repository (University of North Carolina at Chapel Hill), 2010

Download

The n .fwdarw. 3s Rydberg transition of jet-cooled tetrahydropyran, 1,4-dioxane, and 1,4-dioxane-d8 studied by 2 + 1 resonance-enhanced multiphoton ionization

The Journal of Physical Chemistry, 1989

... Chem. SOC. 1988, 110, 6287. of the long-lived Rydberg state, allowing the detection of slight... more

The structure of the triatomic free radicals HCO, HCN—, and FCO

Journal of Molecular Structure, 1970

... Structure, 5 (1970) 2126 26 L. PEDERSEN that the similarity in the bond angles of these three... more

Warfarin and vitamin K epoxide reductase: a molecular accounting for observed inhibition

Blood, 2018

Key PointsWarfarin reversibly inhibits VKOR by forming a T-shaped stacking interaction with resid... more

Download

ChemInform Abstract: Terbium Ion Binding to a Synthetic γ‐Carboxyglutamic Acid Containing Heptapeptide Corresponding to Bovine Prothrombin Residues 17‐23

ChemInform, 1987

Download