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Articles 1 - 24 of 24

Full-Text Articles in Organic Chemistry

Molecular Recognition Of Ketamine By A Subset Of Olfactory G Protein–Coupled Receptors, Jianghai Ho, Jose Manuel Perez Aguilar, Lu Gao, Jeffery G. Saven, Hiroaki Matsunami, Roderic G. Eckenhoff Mar 2015

Molecular Recognition Of Ketamine By A Subset Of Olfactory G Protein–Coupled Receptors, Jianghai Ho, Jose Manuel Perez Aguilar, Lu Gao, Jeffery G. Saven, Hiroaki Matsunami, Roderic G. Eckenhoff

Departmental Papers (Chemistry)

Ketamine elicits various neuropharmacological effects, including sedation, analgesia, general anesthesia, and antidepressant activity. Through an in vitro screen, we identified four mouse olfactory receptors (ORs) that responded to ketamine. In addition to their presence in the olfactory epithelium, these G protein (heterotrimeric guanine nucleotide–binding protein)–coupled receptors (GPCRs) are distributed throughout the central nervous system. To better understand the molecular basis of the interactions between ketamine and ORs, we used sequence comparison and molecular modeling to design mutations that (i) increased, reduced, or abolished ketamine responsiveness in responding receptors, and (ii) rendered non-responding receptors responsive to ketamine. We showed ...


Characterization Of A Computationally Designed Water-Soluble Human Μ Opioid Receptor Variant Using X-Ray Structural Information, Xuelian Zhao, Jose Manuel Perez Aguilar, Felipe Matsunaga, Mitchell Bryant Lerner, Jin Xi, Bernard Selling, A. T. Charlie Johnson, Jeffery G. Saven, Renyu Liu Oct 2014

Characterization Of A Computationally Designed Water-Soluble Human Μ Opioid Receptor Variant Using X-Ray Structural Information, Xuelian Zhao, Jose Manuel Perez Aguilar, Felipe Matsunaga, Mitchell Bryant Lerner, Jin Xi, Bernard Selling, A. T. Charlie Johnson, Jeffery G. Saven, Renyu Liu

Departmental Papers (Chemistry)

Background

The recent X-ray crystal structure of the murine μ opioid receptor (MUR) allowed us to reengineer a previously designed water-soluble variant of the transmembrane portion of the human MUR (wsMUR-TM).

Methods

The new variant of water soluble MUR (wsMUR-TM_v2) was engineered based upon the murine MUR crystal structure. This novel variant was expressed in E. coliand purified. The properties of the receptor were characterized and compared with those of wsMUR-TM.

Results

Seven residues originally included for mutation in the design of the wsMUR-TM, were reverted to their native identities. wsMUR-TM_v2 contains 16% mutations of the total sequence. It ...


Scalable Production Of Highly Sensitive Nanosensors Based On Graphene Functionalized With A Designed G Protein-Coupled Receptor, Mitchell Bryant Lerner, Felipe Matsunaga, Gang Hee Han, Sung Ju Hong, Jin Xi, Alexander Crook, Jose Manuel Perez Aguilar, Yung Woo Park, Jeffery G. Saven, Renyu Liu, A. T. Charlie Johnson Apr 2014

Scalable Production Of Highly Sensitive Nanosensors Based On Graphene Functionalized With A Designed G Protein-Coupled Receptor, Mitchell Bryant Lerner, Felipe Matsunaga, Gang Hee Han, Sung Ju Hong, Jin Xi, Alexander Crook, Jose Manuel Perez Aguilar, Yung Woo Park, Jeffery G. Saven, Renyu Liu, A. T. Charlie Johnson

Departmental Papers (Chemistry)

We have developed a novel, all-electronic biosensor for opioids that consists of an engineered μ-opioid receptor protein, with high binding affinity for opioids, chemically bonded to a graphene field-effect transistor to read out ligand binding. A variant of the receptor protein that provided chemical recognition was computationally redesigned to enhance its solubility and stability in an aqueous environment. A shadow mask process was developed to fabricate arrays of hundreds of graphene transistors with average mobility of ∼1500 cm2 V–1 s–1 and yield exceeding 98%. The biosensor exhibits high sensitivity and selectivity for the target naltrexone, an opioid receptor ...


Computational De Novo Design And Characterization Of A Protein That Selectively Binds A Highly Hyperpolarizable Abiological Chromophore, H Christopher Fry, Andreas Lehmann, Louise E. Sinks, Inge Asselberghs, Andrey Tronin, Venkata Krishnan, J Kent Blasie, Koen Clays, William F. Degrado, Jeffery G. Saven, Michael J. Therien Sep 2013

Computational De Novo Design And Characterization Of A Protein That Selectively Binds A Highly Hyperpolarizable Abiological Chromophore, H Christopher Fry, Andreas Lehmann, Louise E. Sinks, Inge Asselberghs, Andrey Tronin, Venkata Krishnan, J Kent Blasie, Koen Clays, William F. Degrado, Jeffery G. Saven, Michael J. Therien

Departmental Papers (Chemistry)

This work reports the first example of a single-chain protein computationally designed to contain four α-helical segments and fold to form a four-helix bundle encapsulating a supramolecular abiological chromophore that possesses exceptional nonlinear optical properties. The 109-residue protein, designated SCRPZ-1, binds and disperses an insoluble hyperpolarizable chromophore, ruthenium(II) [5-(4'-ethynyl-(2,2';6',2″-terpyridinyl))-10,20-bis(phenyl)porphinato]zinc(II)-(2,2';6',2″-terpyridine)(2+) (RuPZn) in aqueous buffer solution at a 1:1 stoichiometry. A 1:1 binding stoichiometry of the holoprotein is supported by electronic absorption and circular dichroism spectra, as well as equilibrium ...


A Computationally Designed Water-Soluble Variant Of A G-Protein-Coupled Receptor: The Human Mu Opioid Receptor, Jose Manuel Perez Aguilar, Jin Xi, Felipe Matsunaga, Xu Cui, Bernard Selling, Jeffery G. Saven, Renyu Liu Jun 2013

A Computationally Designed Water-Soluble Variant Of A G-Protein-Coupled Receptor: The Human Mu Opioid Receptor, Jose Manuel Perez Aguilar, Jin Xi, Felipe Matsunaga, Xu Cui, Bernard Selling, Jeffery G. Saven, Renyu Liu

Departmental Papers (Chemistry)

G-protein-coupled receptors (GPCRs) play essential roles in various physiological processes, and are widely targeted by pharmaceutical drugs. Despite their importance, studying GPCRs has been problematic due to difficulties in isolating large quantities of these membrane proteins in forms that retain their ligand binding capabilities. Creating water-soluble variants of GPCRs by mutating the exterior, transmembrane residues provides a potential method to overcome these difficulties. Here we present the first study involving the computational design, expression and characterization of water-soluble variant of a human GPCR, the human mu opioid receptor (MUR), which is involved in pain and addiction. An atomistic structure of ...


Human Μ Opioid Receptor Models With Evaluation Of The Accuracy Using The Crystal Structure Of The Murine Μ Opioid Receptor, Jose Manuel Perez Aguilar, Jeffery G. Saven, Renyu Liu Jul 2012

Human Μ Opioid Receptor Models With Evaluation Of The Accuracy Using The Crystal Structure Of The Murine Μ Opioid Receptor, Jose Manuel Perez Aguilar, Jeffery G. Saven, Renyu Liu

Departmental Papers (Chemistry)

Models of the human μ opioid receptor were constructed using available G-protein-coupled receptor (GPCR) structures using homology (comparative) modeling techniques. The recent publication of a high-resolution crystal structure of a construct based on the murine μ opioid receptor offers a unique opportunity to evaluate the reliability of the homology models and test the relevance of introducing more templates (known structures) to increase the accuracy of the comparative models. In the first model two templates were used: the β2 adrenergic and bovine rhodopsin receptors. For the second model, four templates were utilized: the β2adrenergic, bovine rhodopsin, β1 adrenergic, and A2A adenosine ...


Knowledge-Based Potential For Positioning Membrane-Associated Structures And Assessing Residue-Specific Energetic Contributions, Chaim A Schramm, Brett Thomas Hannigan, Jason E. Donald, Chen Keasar, Jeffery G. Saven, William F. Degrado, Ilan Samish May 2012

Knowledge-Based Potential For Positioning Membrane-Associated Structures And Assessing Residue-Specific Energetic Contributions, Chaim A Schramm, Brett Thomas Hannigan, Jason E. Donald, Chen Keasar, Jeffery G. Saven, William F. Degrado, Ilan Samish

Departmental Papers (Chemistry)

The complex hydrophobic and hydrophilic milieus of membrane-associated proteins pose experimental and theoretical challenges to their understanding. Here we produce a non-redundant database to compute knowledge-based asymmetric cross-membrane potentials from the per-residue distributions of Cβ, Cγ and functional group atoms. We predict transmembrane and peripherally associated regions from genomic sequence and position peptides and protein structures relative to the bilayer (available at http://www.degradolab.org/ez). The pseudo-energy topological landscapes underscore positional stability and functional mechanisms demonstrated here for antimicrobial peptides, transmembrane proteins, and viral fusion proteins. Moreover, experimental effects of point mutations on the relative ratio changes of ...


Computational Design Of A Protein Crystal, Christopher J Lanci, Christopher M Macdermaid, Seung-Gu Keng, Rudresh Acharya, Benjamin North, Xi Yang, X Jade Qiu, William F. Degrado, Jeffery G. Saven May 2012

Computational Design Of A Protein Crystal, Christopher J Lanci, Christopher M Macdermaid, Seung-Gu Keng, Rudresh Acharya, Benjamin North, Xi Yang, X Jade Qiu, William F. Degrado, Jeffery G. Saven

Departmental Papers (Chemistry)

Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the ...


Binding Site And Affinity Prediction Of General Anesthetics To Protein Targets Using Docking, Renyu Liu, Jose Manuel Perez Aguilar, David Liang, Jeffery G. Saven May 2012

Binding Site And Affinity Prediction Of General Anesthetics To Protein Targets Using Docking, Renyu Liu, Jose Manuel Perez Aguilar, David Liang, Jeffery G. Saven

Departmental Papers (Chemistry)

BACKGROUND: The protein targets for general anesthetics remain unclear. A tool to predict anesthetic binding for potential binding targets is needed. In this study, we explored whether a computational method, AutoDock, could serve as such a tool.

METHODS: High-resolution crystal data of water-soluble proteins (cytochrome C, apoferritin, and human serum albumin), and a membrane protein (a pentameric ligand-gated ion channel from Gloeobacter violaceus [GLIC]) were used. Isothermal titration calorimetry (ITC) experiments were performed to determine anesthetic affinity in solution conditions for apoferritin. Docking calculations were performed using DockingServer with the Lamarckian genetic algorithm and the Solis and Wets local search ...


Nmr Structure And Dynamics Of A Designed Water-Soluble Transmembrane Domain Of Nicotinic Acetylcholine Receptor, Tanxing Cui, David Mowrey, Vasyl Bondarenko, Tommy Tillman, Dejian Ma, Elizabeth Landrum, Jose Manuel Perez Aguilar, Jing He, Wei Wang, Jeffery G. Saven, Roderic G. Eckenhoff, Pei Tang, Yan Xu Mar 2012

Nmr Structure And Dynamics Of A Designed Water-Soluble Transmembrane Domain Of Nicotinic Acetylcholine Receptor, Tanxing Cui, David Mowrey, Vasyl Bondarenko, Tommy Tillman, Dejian Ma, Elizabeth Landrum, Jose Manuel Perez Aguilar, Jing He, Wei Wang, Jeffery G. Saven, Roderic G. Eckenhoff, Pei Tang, Yan Xu

Departmental Papers (Chemistry)

The nicotinic acetylcholine receptor (nAChR) is an important therapeutic target for a wide range of pathophysiological conditions, for which rational drug designs often require receptor structures at atomic resolution. Recent proof-of-concept studies demonstrated a water-solubilization approach to structure determination of membrane proteins by NMR (Slovic et al., PNAS, 101: 1828–1833, 2004; Ma et al., PNAS, 105: 16537–42, 2008). We report here the computational design and experimental characterization of WSA, a water-soluble protein with ~ 83% sequence identity to the transmembrane (TM) domain of the nAChR α1 subunit. Although the design was based on a low-resolution structural template, the resulting ...


Computational Design Of Membrane Proteins, Jose Manuel Perez Aguilar, Jeffery G. Saven Jan 2012

Computational Design Of Membrane Proteins, Jose Manuel Perez Aguilar, Jeffery G. Saven

Departmental Papers (Chemistry)

Membrane proteins are involved in a wide variety of cellular processes, and are typically part of the first interaction a cell has with extracellular molecules. As a result, these proteins comprise a majority of known drug targets. Membrane proteins are among the most difficult proteins to obtain and characterize, and a structure-based understanding of their properties can be difficult to elucidate. Notwithstanding, the design of membrane proteins can provide stringent tests of our understanding of these crucial biological systems, as well as introduce novel or targeted functionalities. Computational design methods have been particularly helpful in addressing these issues and this ...


Computational Protein Design To Re-Engineer Stromal Cell-Derived Factor-1Α (Sdf) Generates An Effective And Translatable Angiogenic Polypeptide Analog, William Hiesinger, Jose Manuel Perez Aguilar, Pavan Atluri, Nicole A. Marotta, John R. Frederick, J Raymond Fitzpatrick, Ryan C. Mccormick, Jeffrey R. Muenzer, Elaine C. Yang, Rebecca D. Levit, Li-Jun Yuan, John W. Macarthur, Jeffery G. Saven, Y Joseph Woo Sep 2011

Computational Protein Design To Re-Engineer Stromal Cell-Derived Factor-1Α (Sdf) Generates An Effective And Translatable Angiogenic Polypeptide Analog, William Hiesinger, Jose Manuel Perez Aguilar, Pavan Atluri, Nicole A. Marotta, John R. Frederick, J Raymond Fitzpatrick, Ryan C. Mccormick, Jeffrey R. Muenzer, Elaine C. Yang, Rebecca D. Levit, Li-Jun Yuan, John W. Macarthur, Jeffery G. Saven, Y Joseph Woo

Departmental Papers (Chemistry)

BACKGROUND: Experimentally, exogenous administration of recombinant stromal cell-derived factor-1α (SDF) enhances neovasculogenesis and cardiac function after myocardial infarction. Smaller analogs of SDF may provide translational advantages including enhanced stability and function, ease of synthesis, lower cost, and potential modulated delivery via engineered biomaterials. In this study, computational protein design was used to create a more efficient evolution of the native SDF protein.

METHODS AND RESULTS: Protein structure modeling was used to engineer an SDF polypeptide analog (engineered SDF analog [ESA]) that splices the N-terminus (activation and binding) and C-terminus (extracellular stabilization) with a diproline segment designed to limit the conformational ...


Computational Protein Design: Engineering Molecular Diversity, Nonnatural Enzymes, Nonbiological Cofactor Complexes, And Membrane Proteins, Jeffery G. Saven Jun 2011

Computational Protein Design: Engineering Molecular Diversity, Nonnatural Enzymes, Nonbiological Cofactor Complexes, And Membrane Proteins, Jeffery G. Saven

Departmental Papers (Chemistry)

Computational and theoretical methods are advancing protein design as a means to create and investigate proteins. Such efforts further our capacity to control, design and understand biomolecular structure, sequence and function. Herein, the focus is on some recent applications that involve using theoretical and computational methods to guide the design of protein sequence ensembles, new enzymes, proteins with novel cofactors, and membrane proteins.


Computational Protein Design: Advances In The Design And Redesign Of Biomolecular Nanostructures, Jeffery G. Saven Apr 2010

Computational Protein Design: Advances In The Design And Redesign Of Biomolecular Nanostructures, Jeffery G. Saven

Departmental Papers (Chemistry)

Computational protein design facilitates the continued development of methods for the design of biomolecular structure, sequence and function. Recent applications include the design of novel protein sequences and structures, proteins incorporating nonbiological components, protein assemblies, soluble variants of membrane proteins, and proteins that modulate membrane function.


Computational Design And Elaboration Of A De Novo Heterotetrameric Α-Helical Protein That Selectively Binds An Emissive Abiological (Porphinato)Zinc Chromophore, H Christopher Fry, Andreas Lehmann, Jeffery G. Saven, William F. Degrado, Michael J. Therien Mar 2010

Computational Design And Elaboration Of A De Novo Heterotetrameric Α-Helical Protein That Selectively Binds An Emissive Abiological (Porphinato)Zinc Chromophore, H Christopher Fry, Andreas Lehmann, Jeffery G. Saven, William F. Degrado, Michael J. Therien

Departmental Papers (Chemistry)

The first example of a computationally de novo designed protein that binds an emissive abiological chromophore is presented, in which a sophisticated level of cofactor discrimination is pre-engineered. This heterotetrameric, C(2)-symmetric bundle, A(His):B(Thr), uniquely binds (5,15-di[(4-carboxymethyleneoxy)phenyl]porphinato)zinc [(DPP)Zn] via histidine coordination and complementary noncovalent interactions. The A(2)B(2) heterotetrameric protein reflects ligand-directed elements of both positive and negative design, including hydrogen bonds to second-shell ligands. Experimental support for the appropriate formulation of [(DPP)Zn:A(His):B(Thr)](2) is provided by UV/visible and circular dichroism spectroscopies ...


Identification Of The Active Form Of Endothelial Lipase, A Homodimer In A Head-To-Tail Conformation, Nathalie Griffon, Weijin Jin, Thomas John Petty Ii, John Millar, Karen O. Badellino, Jeffery G. Saven, Dawn H. Marchadier, Ellis S. Kempner, Jeffrey Billheimer, Jane M. Glick, Daniel J. Rader Aug 2009

Identification Of The Active Form Of Endothelial Lipase, A Homodimer In A Head-To-Tail Conformation, Nathalie Griffon, Weijin Jin, Thomas John Petty Ii, John Millar, Karen O. Badellino, Jeffery G. Saven, Dawn H. Marchadier, Ellis S. Kempner, Jeffrey Billheimer, Jane M. Glick, Daniel J. Rader

Departmental Papers (Chemistry)

Endothelial lipase (EL) is a member of a subfamily of lipases that act on triglycerides and phospholipids in plasma lipoproteins, which also includes lipoprotein lipase and hepatic lipase. EL has a tropism for high density lipoprotein, and its level of phospholipase activity is similar to its level of triglyceride lipase activity. Inhibition or loss-of-function of EL in mice results in an increase in high density lipoprotein cholesterol, making it a potential therapeutic target. Although hepatic lipase and lipoprotein lipase have been shown to function as homodimers, the active form of EL is not known. In these studies, the size and ...


Characterization Of Cofactor-Induced Folding Mechanism Of A Zinc Binding Peptide Using Computationally Designed Mutants, Jia Tang, Seung-Gu Kang, Jeffery G. Saven, Feng Gai May 2009

Characterization Of Cofactor-Induced Folding Mechanism Of A Zinc Binding Peptide Using Computationally Designed Mutants, Jia Tang, Seung-Gu Kang, Jeffery G. Saven, Feng Gai

Departmental Papers (Chemistry)

Metals are the most commonly encountered protein cofactors, and they play important structural and functional roles in biology. In many cases, metal binding provides a major driving force for a polypeptide chain to fold. While there are many studies on the structure, stability, and function of metal-binding proteins, there are few studies focusing on understanding the kinetic mechanism of metal-induced folding. Herein, the Zn(2+)-induced folding kinetics of a small zinc-binding protein are studied; the CH1(1) peptide is derived from the first cysteine/histidine-rich region (CH1 domain) of the protein interaction domains of the transcriptional coregulator CREB-binding protein ...


Structural Coupling Between Fkbp12 And Buried Water, Szilvia Szep, Sheldon Park, Eric T Boder, Gregory D Van Duyne, Jeffery G. Saven Feb 2009

Structural Coupling Between Fkbp12 And Buried Water, Szilvia Szep, Sheldon Park, Eric T Boder, Gregory D Van Duyne, Jeffery G. Saven

Departmental Papers (Chemistry)

Globular proteins often contain structurally well-resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that buried water (Wat3) may play a role in modulating the structure of the FK506 binding protein-12 (FKBP12) (Park and Saven, Proteins 2005; 60:450-463). In particular, simulations suggested that disrupting a hydrogen bond to Wat3 by mutating E60 to either A or Q would cause a structural perturbation involving the distant W59 side chain, which rotates to a new conformation in response to the mutation. This effectively remodels the ligand-binding pocket, as the side chain in the new conformation ...


Using Α-Helical Coiled-Coils To Design Nanostructured Metalloporphyrin Arrays, Karen A. Mcallister, Hongling Zou, Frank V. Cochran, Gretchen M Bender, Alessandro Senes, H Christopher Fry, Vikas Nanda, Patricia A. Keenan, James D. Lear, Jeffery G. Saven, Michael J. Therien, J Kent Blasie, William F. Degrado Sep 2008

Using Α-Helical Coiled-Coils To Design Nanostructured Metalloporphyrin Arrays, Karen A. Mcallister, Hongling Zou, Frank V. Cochran, Gretchen M Bender, Alessandro Senes, H Christopher Fry, Vikas Nanda, Patricia A. Keenan, James D. Lear, Jeffery G. Saven, Michael J. Therien, J Kent Blasie, William F. Degrado

Departmental Papers (Chemistry)

We have developed a computational design strategy based on the alpha-helical coiled-coil to generate modular peptide motifs capable of assembling into metalloporphyrin arrays of varying lengths. The current study highlights the extension of a two-metalloporphyrin array to a four-metalloporphyrin array through the incorporation of a coiled-coil repeat unit. Molecular dynamics simulations demonstrate that the initial design evolves rapidly to a stable structure with a small rmsd compared to the original model. Biophysical characterization reveals elongated proteins of the desired length, correct cofactor stoichiometry, and cofactor specificity. The successful extension of the two-porphyrin array demonstrates how this methodology serves as a ...


A Focused Antibody Library For Selecting Scfvs Expressed At High Levels In The Cytoplasm, Pascal Philbert, Audrey Stoessel, Wei Wang, Annie-Paule Sibler, Nicole Bec, Christian Larroque, Jeffery G. Saven, Jérôme Courtête, Etienne Weiss, Pierre Martineau Nov 2007

A Focused Antibody Library For Selecting Scfvs Expressed At High Levels In The Cytoplasm, Pascal Philbert, Audrey Stoessel, Wei Wang, Annie-Paule Sibler, Nicole Bec, Christian Larroque, Jeffery G. Saven, Jérôme Courtête, Etienne Weiss, Pierre Martineau

Departmental Papers (Chemistry)

Background

Intrabodies are defined as antibody molecules which are ectopically expressed inside the cell. Such intrabodies can be used to visualize or inhibit the targeted antigen in living cells. However, most antibody fragments cannot be used as intrabodies because they do not fold under the reducing conditions of the cell cytosol and nucleus.

Results

We describe the construction and validation of a large synthetic human single chain antibody fragment library based on a unique framework and optimized for cytoplasmic expression. Focusing the library by mimicking the natural diversity of CDR3 loops ensured that the scFvs were fully human and functional ...


De Novo Design Of A Single Chain Diphenylporphyrin Metalloprotein, Gretchen M Bender, Andreas Lehmann, Hongling Zou, Hong Cheng, H Christopher Fry, Don Engel, Michael J. Therien, J Kent Blasie, Heinrich Roder, Jeffery G. Saven, William F. Degrado Sep 2007

De Novo Design Of A Single Chain Diphenylporphyrin Metalloprotein, Gretchen M Bender, Andreas Lehmann, Hongling Zou, Hong Cheng, H Christopher Fry, Don Engel, Michael J. Therien, J Kent Blasie, Heinrich Roder, Jeffery G. Saven, William F. Degrado

Departmental Papers (Chemistry)

We describe the computational design of a single-chain four-helix bundle that noncovalently self-assembles with fully synthetic non-natural porphyrin cofactors. With this strategy, both the electronic structure of the cofactor as well as its protein environment may be varied to explore and modulate the functional and photophysical properties of the assembly. Solution characterization (NMR, UV-vis) of the protein showed that it bound with high specificity to the desired cofactors, suggesting that a uniquely structured protein and well-defined site had indeed been created. This provides a genetically expressed single-chain protein scaffold that will allow highly facile, flexible, and asymmetric variations to enable ...


Fluorescence Correlation Spectroscopic Study Of Serpin Depolymerization By Computationally Designed Peptides, Pramit Chowdhury, Wei Wang, Stacey Lavender, Michelle R Bunagan, Jason W. Klemke, Jia Tang, Jeffery G. Saven, Barry S. Cooperman, Feng Gai Jun 2007

Fluorescence Correlation Spectroscopic Study Of Serpin Depolymerization By Computationally Designed Peptides, Pramit Chowdhury, Wei Wang, Stacey Lavender, Michelle R Bunagan, Jason W. Klemke, Jia Tang, Jeffery G. Saven, Barry S. Cooperman, Feng Gai

Departmental Papers (Chemistry)

Members of the serine proteinase inhibitor (serpin) family play important roles in the inflammatory and coagulation cascades. Interaction of a serpin with its target proteinase induces a large conformational change, resulting in insertion of its reactive center loop (RCL) into the main body of the protein as a new strand within beta-sheet A. Intermolecular insertion of the RCL of one serpin molecule into the beta-sheet A of another leads to polymerization, a widespread phenomenon associated with a general class of diseases known as serpinopathies. Small peptides are known to modulate the polymerization process by binding within beta-sheet A. Here, we ...


Computational Design Of Water-Soluble Analogues Of The Potassium Channel Kcsa, Avram Michael Slovic, Hidetoshi Kono, James D. Lear, Jeffery G. Saven, William F. Degrado Feb 2004

Computational Design Of Water-Soluble Analogues Of The Potassium Channel Kcsa, Avram Michael Slovic, Hidetoshi Kono, James D. Lear, Jeffery G. Saven, William F. Degrado

Departmental Papers (Chemistry)

Although the interiors of membrane and water-soluble proteins are similar in their physicochemical properties, membrane proteins differ in having larger fractions of hydrophobic residues on their exteriors. Thus, it should be possible to water-solubilize membrane proteins by mutating their lipid-contacting side chains to more polar groups. Here, a computational approach was used to generate water-soluble variants of the potassium channel KcsA. As a probe of the correctness of the fold, the proteins contain an agitoxin2 binding site from a mammalian homologue of the channel. The resulting proteins express in high yield inEscherichia coli and share the intended functional and ...


Statistical Theory Of Protein Combinatorial Libraries, Hidetoshi Kono, Jinming Zou, Jeffery G. Saven Jan 2001

Statistical Theory Of Protein Combinatorial Libraries, Hidetoshi Kono, Jinming Zou, Jeffery G. Saven

Departmental Papers (Chemistry)

Combinatorial experiments provide new ways to probe the determinants of protein folding and to identify novel folding amino acid sequences. These types of experiments, however, are complicated both by enormous conformational complexity and by large numbers of possible sequences. Therefore, a quantitative computational theory would be helpful in designing and interpreting these types of experiment. Here, we present and apply a statistically based, computational approach for identifying the properties of sequences compatible with a given main-chain structure. Protein side-chain conformations are included in an atom-based fashion. Calculations are performed for a variety of similar backbone structures to identify sequence properties ...