CMM publications

Recent CMM Publications
Reviews, Commentaries, and Book Chapters indicated by asterisks

Probes for Narcotic Receptor Mediated Phenomena. 39.1 Enantiomeric N-substituted Benzofurol[2,3-c]pyridin-6-ols: Synthesis and Topological Relationship to Oxide-bridged Phenylmorphans
Y. Zhang, Y. S. Lee, R. Rothman, C. Dersch, J. Deschamps, A. Jacobson, and K. Rice; J. Med. Chem. (in press)

Transglutaminase-1 (TGM1) Gene Mutations in Autosomal Recessive Congenital Ichthyosis: Summary of Mutations (Including 23 Novel) and Modeling of TGase-1
M. L. Herman, S. Farasat, P. J. Steinbach, M. H. Wei, O. Toure, P. Fleckman, P. Blake, S. J. Bale, J. R. Toro; Human Mutation (in press)

Modeling Aqueous Solvent Effects through Local Properties of Water
S. A. Hassan and E. L. Mehler; in Modeling Solvent Environments, Ed. M. Feig, Wiley-VCH (in press)*

Intramolecular Disulfide Bridges of the Prolactin Receptor Short Form are required for its Inhibitory Action on the Function of the Long Form of the Receptor
Y. L. Xie, S. A. Hassan, A. M. Qazi, C. H. Tsai-Morris, and M. L. Dufau; Mol. Cell. Biol. 29, 2546 (2009)

Morphology of Ion Clusters in Aqueous Electrolytes
S. A. Hassan; Phys. Rev. E 77, 031501 (2008)

Evidence that Proline Focuses Movement of the Floppy Loop of Arylalkylamine N-Acetyltransferase
J. Pavlicek, S. L. Coon, S. Ganguly, J. Weller, S. A. Hassan, D. L. Sackett, and D. C. Klein; J. Biol. Chem. 283, 14552 (2008)

Computer Simulation of Ion Cluster Speciation in Concentrated Aqueous Solutions at Ambient Conditions
S. A. Hassan; J. Phys. Chem. B 112, 10573 (2008)

Design of Drug-Resistant Alleles of Type-III Phosphatidylinositol 4-Kinases using Mutagenesis and Molecular Modeling
A. Balla, G. Tuymetova, B. Toth, Z. Szentpetery, X. Zhao, Z. A. Knight, K. Shokat, P. J. Steinbach, and T. Balla; Biochemistry 47, 1599 (2008)

Identification of the Transition States in the Inversion of 1,4-Benzodiazepines with the Ab-Initio Replica Path Method
Y. S. Lee, V. W. Pike, M. Hodoscek; J. Phys. Chem. A 112, 1604 (2008)

Synthesis and Pharmacological Effects of the Enantiomers of the N-phenethyl Analogues of the Ortho and Para e- and f-oxide-bridged Phenylmorphans
J. Zezula, L. B. Singer, A. K. Przybyl, A. Hashimoto, C. M. Dersch, R. B. Rothman, J. R. Deschamps, Y. S. Lee, A. E. Jacobson, K. C. Rice; Org. Biomol. Chem. 6, 2868 (2008)

Probes for Narcotic Receptor Mediated Phenomena. 37. Synthesis and Opioid Binding Affinity of the Final Pair of Oxide-bridged Phenylmorphans, rac-(4R,6aS,11bR)-3-Methyl-2,3,4,5,6,6a-hexahydro-1H-4,11b-methanobenzofuro[3,2-d]azocine-8-ol and -10-ol, the ortho-b and para-b Isomers and their N-Phenethyl Analogs
M. Kurimura, H. Liu, A. Sulima, A. Hashimoto, A. K. Przybyl, J. R. Deschamps, C. M. Dersch, R. B. Rothman, Y. S. Lee, A. E. Jacobson, K. C Rice; J. Med. Chem. 51, 7866 (2008)

Targeted Deletion in the beta20-beta21 Loop of HIV Envelope Glycoprotein gp120 Exposes the CD4 Binding Site for Antibody Binding
I. Berkower, C. Patel, Y. Ni, K. Virnik, Z. Xiang, and A. Spadacini; Virology 377, 330 (2008)

Liquid-Structure Forces and Electrostatic Modulation of Biomolecular Interactions in Solution
S. A. Hassan; J. Phys. Chem. B 111, 227 (2007)

Prediction of Side-Chain Conformations on Protein Surfaces
Z. Xiang, P. J. Steinbach, M. P. Jacobson, R. A. Friesner, and B. Honig; Proteins 66, 814 (2007)

Probes for Narcotic Receptor Mediated Phenomena. 34. Synthesis and Structure-Activity Relationships of a Potent mu-Agonist gamma-Antagonist and an Exceedingly Potent Antinociceptive in the Enantiomeric C9-Substituted 5-(3-Hydroxyphenyl)-N-phenylethylmorphan Series
A. C. Hiebel, Y. S. Lee, E. Bilsky, D. Giuvelis, J. R. Deschamps, D. A. Parrish, M. D. Aceto, E. L. May, L. S. Harris, A. Coop, A. E. Jacobson, K. C. Rice; J. Med. Chem. 50, 3765 (2007)

Loss of Hsp90 Association up-Regulates Src-dependent ErbB2 Activity
W. Xu, X. Yuan, K. Beebe, Z. Xiang, and L. Neckers; Mol. Cell. Biol. 27, 220 (2007)

Ab initio Computer Modeling of Loops in G-protein Coupled Receptors: Lessons from the Crystal Structure of Rhodopsin
E. L. Mehler, S. A. Hassan, S. Kortagere, and H. Weinstein; Proteins 64, 673 (2006)

Effects of Electric Fields on Proton Transport through Water Chains
S. A. Hassan, G. Hummer, and Y. S. Lee; J. Chem. Phys. 124, 204510 (2006)

Biological Effect of a Novel Mutation in the Third Leucine-Rich Repeat of Human Luteinizing Hormone Receptor
M. Y. K. Leung, P. J. Steinbach, D. Bear, V. Baxendale, P.Y. Fechner, O. M. Rennert, and W. Y. Chan; Mol. Endocrinol. 20, 2493 (2006)

Fumarate Hydratase Enzyme Activity in Lymphoblastoid Cells and Fibroblasts of Individuals in Families with Hereditary Leiomyomatosis and Renal Cell Cancer
M. Pithukpakorn, M. H. Wei, O. Toure, P. J. Steinbach, G. M. Glenn, B. Zbar, W. M. Linehan, and J. R. Toro; J. Med. Genet. 43, 755 (2006)

Advances in Homology Protein Structure Modeling
Z. Xiang; Curr. Prot. Pept. Sci. 7, 217 (2006)*

Computer Simulations of Protein-Ligand Interaction: Challenges and Applications
S. A. Hassan, L. Gracia, G. Vasudevan, and P. J. Steinbach; in Methods in Molecular Biology, Ed. U. Nienhaus, Humana Press (2005)*

Long Dynamics Simulations of Proteins using Atomistic Force fields and a Continuum Representation of Solvent Effects: Calculation of Structural and Dynamic Properties
X. Li, S. A. Hassan and E. L. Mehler; Proteins 60, 464 (2005)

From Quantum Chemistry and the Classical Theory of Polar Liquids to Continuum Approximations in Molecular Mechanics Calculations
S. A. Hassan and E. L. Mehler; Int. J. Quantum Chem. 102, 986 (2005)

Amino Acid Side Chain Interactions in the Presence of Salts
S. A. Hassan; J. Phys. Chem. B 109, 21989 (2005)

Eucharyotic Ribonucleases H1 Act Processively by Interactions through the Duplex RNA-binding Domain
S. A. Gaidamakov, I. I. Gorshkova, P. Schuck, P. J. Steinbach, H. Yamada, S. M. Cerritelli, and R. J. Crouch; Nucl. Acids Res. 33, 2166 (2005)

Polyproline and the Spectroscopic Ruler Revisited with Single-Molecule Fluorescence
B. Schuler, E.A. Lipman, P.J. Steinbach, M. Kumke, & W.A. Eaton; Proc. Natl. Acad. Sci. USA 102, 2754 (2005)

Surface Charge and Hydrophobicity determine ErbB2 binding to the HSP90 Chaperone Complex
W. Xu, X. Yuan, Z. Xiang, E. Mimmaugh, M. Marcu, and L. Neckers; Nature Struct. Mol. Biol. 12, 120 (2005)

Mechanistic Hypotheses of Structure-Function Relations of Integrin aIIb3 based on a Refined Three-Dimensional Model
M. Filizola, S. A. Hassan, A. Artoni, B. S. Coller, and H. Weinstein; J. Biol. Chem. 279, 24624 (2004)

Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium
S. A. Hassan; J. Phys. Chem. B 108, 19501 (2004)

Exploring Peptide Energy Landscapes: A Test of Force Fields and Implicit Solvent Models
P. J. Steinbach; Proteins 57, 665 (2004)

Mutation in the Leucine-rich Repeat C-flanking Region of Platelet Glycoprotein Ib-beta Impairs Assembly of von Willebrand Factor Receptor
J. Tang, S. Stern-Nezer, P. C. Liu, L. Matyakhina, M. Riordan, N. L. C. Luban, P. J. Steinbach and S. G. Kaler; Thromb. Haemost. 92, 75 (2004)

Dynamics of Proton Transfer in Bacteriorhodopsin
Y. S. Lee and M. Krauss; J. Am. Chem. Soc. 126, 2225 (2004)

Quantum Chemical Calculations and Mutational Analysis Suggest Heat Shock Protein 90 Catalyzes Trans-Cis Isomerization of Geldanamycin
Y. S. Lee, M. G. Marcu and L. Neckers; Chem. Biol. 11, 991 (2004)

Structure and Reaction in the Active Site of Mammalian Adenylyl Cyclase
Y. S. Lee and M. Krauss; J. Phys. Chem. B 108, 4508 (2004)

Reversible Proton Transfer Dynamics in Bacteriorhodopsin
Y. S. Lee and M. Krauss; J. Mol. Struct. 700, 243 (2004)

The Rules of Attraction
L. Neckers and Y. S. Lee; Nature 106, 357 (2003)*

Exploring the QM/MM Replica Method: A Pathway Optimization of the Chorismate to Prephenate Claisen Rearrangement Catalyzed by
Chorismate Mutase
H. L. Woodcock, M. Hodoscek, P. Sherwood, Y. S. Lee, H. F. Schafer III, and B. R. Brooks; Theor. Chem. Acc. 109, 140 (2003)

Hydrogen Bonding Interactions between Aldose Reductase Complexed with NADP(H) and Inhibitor Tolrestat Studied by Molecular Dynamics Simulations and Binding Assay
Y. S. Lee, M. Hodoscek, P. F. Kador, and K. Sugiyama; Chem-Biol Interact. 143, 307 (2003)

Recent CMM Publications Reviews, Commentaries, and Book Chapters indicated by asterisks
Probes for Narcotic Receptor Mediated Phenomena. 39.1 Enantiomeric N-substituted Benzofurol[2,3-c]pyridin-6-ols: Synthesis and Topological Relationship to Oxide-bridged Phenylmorphans Y. Zhang, Y. S. Lee, R. Rothman, C. Dersch, J. Deschamps, A. Jacobson, and K. Rice; J. Med. Chem. (in press)
Transglutaminase-1 (TGM1) Gene Mutations in Autosomal Recessive Congenital Ichthyosis: Summary of Mutations (Including 23 Novel) and Modeling of TGase-1 M. L. Herman, S. Farasat, P. J. Steinbach, M. H. Wei, O. Toure, P. Fleckman, P. Blake, S. J. Bale, J. R. Toro; Human Mutation (in press)
Modeling Aqueous Solvent Effects through Local Properties of Water S. A. Hassan and E. L. Mehler; in Modeling Solvent Environments, Ed. M. Feig, Wiley-VCH (in press)*
Intramolecular Disulfide Bridges of the Prolactin Receptor Short Form are required for its Inhibitory Action on the Function of the Long Form of the Receptor Y. L. Xie, S. A. Hassan, A. M. Qazi, C. H. Tsai-Morris, and M. L. Dufau; Mol. Cell. Biol. 29, 2546 (2009)
Morphology of Ion Clusters in Aqueous Electrolytes S. A. Hassan; Phys. Rev. E 77, 031501 (2008)
Evidence that Proline Focuses Movement of the Floppy Loop of Arylalkylamine N-Acetyltransferase J. Pavlicek, S. L. Coon, S. Ganguly, J. Weller, S. A. Hassan, D. L. Sackett, and D. C. Klein; J. Biol. Chem. 283, 14552 (2008)
Computer Simulation of Ion Cluster Speciation in Concentrated Aqueous Solutions at Ambient Conditions S. A. Hassan; J. Phys. Chem. B 112, 10573 (2008)
Design of Drug-Resistant Alleles of Type-III Phosphatidylinositol 4-Kinases using Mutagenesis and Molecular Modeling A. Balla, G. Tuymetova, B. Toth, Z. Szentpetery, X. Zhao, Z. A. Knight, K. Shokat, P. J. Steinbach, and T. Balla; Biochemistry 47, 1599 (2008)
Identification of the Transition States in the Inversion of 1,4-Benzodiazepines with the Ab-Initio Replica Path Method Y. S. Lee, V. W. Pike, M. Hodoscek; J. Phys. Chem. A 112, 1604 (2008)
Synthesis and Pharmacological Effects of the Enantiomers of the N-phenethyl Analogues of the Ortho and Para e- and f-oxide-bridged Phenylmorphans J. Zezula, L. B. Singer, A. K. Przybyl, A. Hashimoto, C. M. Dersch, R. B. Rothman, J. R. Deschamps, Y. S. Lee, A. E. Jacobson, K. C. Rice; Org. Biomol. Chem. 6, 2868 (2008)
Probes for Narcotic Receptor Mediated Phenomena. 37. Synthesis and Opioid Binding Affinity of the Final Pair of Oxide-bridged Phenylmorphans, rac-(4R,6aS,11bR)-3-Methyl-2,3,4,5,6,6a-hexahydro-1H-4,11b-methanobenzofuro[3,2-d]azocine-8-ol and -10-ol, the ortho-b and para-b Isomers and their N-Phenethyl Analogs M. Kurimura, H. Liu, A. Sulima, A. Hashimoto, A. K. Przybyl, J. R. Deschamps, C. M. Dersch, R. B. Rothman, Y. S. Lee, A. E. Jacobson, K. C Rice; J. Med. Chem. 51, 7866 (2008)
Targeted Deletion in the beta20-beta21 Loop of HIV Envelope Glycoprotein gp120 Exposes the CD4 Binding Site for Antibody Binding I. Berkower, C. Patel, Y. Ni, K. Virnik, Z. Xiang, and A. Spadacini; Virology 377, 330 (2008)
Liquid-Structure Forces and Electrostatic Modulation of Biomolecular Interactions in Solution S. A. Hassan; J. Phys. Chem. B 111, 227 (2007)
Prediction of Side-Chain Conformations on Protein Surfaces Z. Xiang, P. J. Steinbach, M. P. Jacobson, R. A. Friesner, and B. Honig; Proteins 66, 814 (2007)
Probes for Narcotic Receptor Mediated Phenomena. 34. Synthesis and Structure-Activity Relationships of a Potent mu-Agonist gamma-Antagonist and an Exceedingly Potent Antinociceptive in the Enantiomeric C9-Substituted 5-(3-Hydroxyphenyl)-N-phenylethylmorphan Series A. C. Hiebel, Y. S. Lee, E. Bilsky, D. Giuvelis, J. R. Deschamps, D. A. Parrish, M. D. Aceto, E. L. May, L. S. Harris, A. Coop, A. E. Jacobson, K. C. Rice; J. Med. Chem. 50, 3765 (2007)
Loss of Hsp90 Association up-Regulates Src-dependent ErbB2 Activity W. Xu, X. Yuan, K. Beebe, Z. Xiang, and L. Neckers; Mol. Cell. Biol. 27, 220 (2007)
Ab initio Computer Modeling of Loops in G-protein Coupled Receptors: Lessons from the Crystal Structure of Rhodopsin E. L. Mehler, S. A. Hassan, S. Kortagere, and H. Weinstein; Proteins 64, 673 (2006)
Effects of Electric Fields on Proton Transport through Water Chains S. A. Hassan, G. Hummer, and Y. S. Lee; J. Chem. Phys. 124, 204510 (2006)
Biological Effect of a Novel Mutation in the Third Leucine-Rich Repeat of Human Luteinizing Hormone Receptor M. Y. K. Leung, P. J. Steinbach, D. Bear, V. Baxendale, P.Y. Fechner, O. M. Rennert, and W. Y. Chan; Mol. Endocrinol. 20, 2493 (2006)
Fumarate Hydratase Enzyme Activity in Lymphoblastoid Cells and Fibroblasts of Individuals in Families with Hereditary Leiomyomatosis and Renal Cell Cancer M. Pithukpakorn, M. H. Wei, O. Toure, P. J. Steinbach, G. M. Glenn, B. Zbar, W. M. Linehan, and J. R. Toro; J. Med. Genet. 43, 755 (2006)
Advances in Homology Protein Structure Modeling Z. Xiang; Curr. Prot. Pept. Sci. 7, 217 (2006)*
Computer Simulations of Protein-Ligand Interaction: Challenges and Applications S. A. Hassan, L. Gracia, G. Vasudevan, and P. J. Steinbach; in Methods in Molecular Biology, Ed. U. Nienhaus, Humana Press (2005)*
Long Dynamics Simulations of Proteins using Atomistic Force fields and a Continuum Representation of Solvent Effects: Calculation of Structural and Dynamic Properties X. Li, S. A. Hassan and E. L. Mehler; Proteins 60, 464 (2005)
From Quantum Chemistry and the Classical Theory of Polar Liquids to Continuum Approximations in Molecular Mechanics Calculations S. A. Hassan and E. L. Mehler; Int. J. Quantum Chem. 102, 986 (2005)
Amino Acid Side Chain Interactions in the Presence of Salts S. A. Hassan; J. Phys. Chem. B 109, 21989 (2005)
Eucharyotic Ribonucleases H1 Act Processively by Interactions through the Duplex RNA-binding Domain S. A. Gaidamakov, I. I. Gorshkova, P. Schuck, P. J. Steinbach, H. Yamada, S. M. Cerritelli, and R. J. Crouch; Nucl. Acids Res. 33, 2166 (2005)
Polyproline and the Spectroscopic Ruler Revisited with Single-Molecule Fluorescence B. Schuler, E.A. Lipman, P.J. Steinbach, M. Kumke, & W.A. Eaton; Proc. Natl. Acad. Sci. USA 102, 2754 (2005)
Surface Charge and Hydrophobicity determine ErbB2 binding to the HSP90 Chaperone Complex W. Xu, X. Yuan, Z. Xiang, E. Mimmaugh, M. Marcu, and L. Neckers; Nature Struct. Mol. Biol. 12, 120 (2005)
Mechanistic Hypotheses of Structure-Function Relations of Integrin aIIb3 based on a Refined Three-Dimensional Model M. Filizola, S. A. Hassan, A. Artoni, B. S. Coller, and H. Weinstein; J. Biol. Chem. 279, 24624 (2004)
Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium S. A. Hassan; J. Phys. Chem. B 108, 19501 (2004)
Exploring Peptide Energy Landscapes: A Test of Force Fields and Implicit Solvent Models P. J. Steinbach; Proteins 57, 665 (2004)
Mutation in the Leucine-rich Repeat C-flanking Region of Platelet Glycoprotein Ib-beta Impairs Assembly of von Willebrand Factor Receptor J. Tang, S. Stern-Nezer, P. C. Liu, L. Matyakhina, M. Riordan, N. L. C. Luban, P. J. Steinbach and S. G. Kaler; Thromb. Haemost. 92, 75 (2004)
Dynamics of Proton Transfer in Bacteriorhodopsin Y. S. Lee and M. Krauss; J. Am. Chem. Soc. 126, 2225 (2004)
Quantum Chemical Calculations and Mutational Analysis Suggest Heat Shock Protein 90 Catalyzes Trans-Cis Isomerization of Geldanamycin Y. S. Lee, M. G. Marcu and L. Neckers; Chem. Biol. 11, 991 (2004)
Structure and Reaction in the Active Site of Mammalian Adenylyl Cyclase Y. S. Lee and M. Krauss; J. Phys. Chem. B 108, 4508 (2004)
Reversible Proton Transfer Dynamics in Bacteriorhodopsin Y. S. Lee and M. Krauss; J. Mol. Struct. 700, 243 (2004)
The Rules of Attraction L. Neckers and Y. S. Lee; Nature 106, 357 (2003)*
Exploring the QM/MM Replica Method: A Pathway Optimization of the Chorismate to Prephenate Claisen Rearrangement Catalyzed by Chorismate Mutase H. L. Woodcock, M. Hodoscek, P. Sherwood, Y. S. Lee, H. F. Schafer III, and B. R. Brooks; Theor. Chem. Acc. 109, 140 (2003)
Hydrogen Bonding Interactions between Aldose Reductase Complexed with NADP(H) and Inhibitor Tolrestat Studied by Molecular Dynamics Simulations and Binding Assay Y. S. Lee, M. Hodoscek, P. F. Kador, and K. Sugiyama; Chem-Biol Interact. 143, 307 (2003)