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Articles 1 - 30 of 64

Full-Text Articles in Medicinal-Pharmaceutical Chemistry

Rapid Characterization Of Formulated Pharmaceuticals Using Fast Mas 1h Solid-State Nmr Spectroscopy, David A. Hirsh, Anuradha V. Wijesekara, Scott L. Carnahan, Ivan Hung, Joseph W. Lubach, Karthik Nagapudi, Aaron J. Rossini May 2019

Rapid Characterization Of Formulated Pharmaceuticals Using Fast Mas 1h Solid-State Nmr Spectroscopy, David A. Hirsh, Anuradha V. Wijesekara, Scott L. Carnahan, Ivan Hung, Joseph W. Lubach, Karthik Nagapudi, Aaron J. Rossini

Chemistry Publications

Active pharmaceutical ingredients (APIs) can be prepared in many different solid forms and phases that affect their physicochemical properties and suitability for oral dosage forms. The development and commercialization of dosage forms require analytical techniques that can determine and quantify the API phase in the final drug product. 13C solid-state NMR (SSNMR) spectroscopy is widely employed to characterize pure and formulated solid APIs; however, 13C SSNMR experiments on dosage forms with low API loading are often challenging due to low sensitivity and interference from excipients. Here, fast MAS 1H SSNMR experiments are shown to be applicable for the rapid characterization ...


Defining Cell Cluster Size By Dielectrophoretic Capture At An Array Of Wireless Electrodes Of Several Distinct Lengths, Joseph T. Banovetz, Min Li, Darshna Pagariya, Sungu Kim, Baskar Ganapathysubramanian, Robbyn Anand Apr 2019

Defining Cell Cluster Size By Dielectrophoretic Capture At An Array Of Wireless Electrodes Of Several Distinct Lengths, Joseph T. Banovetz, Min Li, Darshna Pagariya, Sungu Kim, Baskar Ganapathysubramanian, Robbyn Anand

Chemistry Publications

Clusters of biological cells play an important role in normal and disease states, such as in the release of insulin from pancreatic islets and in the enhanced spread of cancer by clusters of circulating tumor cells. We report a method to pattern cells into clusters having sizes correlated to the dimensions of each electrode in an array of wireless bipolar electrodes (BPEs). The cells are captured by dielectrophoresis (DEP), which confers selectivity, and patterns cells without the need for physical barriers or adhesive interactions that can alter cell function. Our findings demonstrate that this approach readily achieves fine control of ...


Design And Synthesis Of Multivalent Α-1,2-Trimannose-Linked Bioerodible Microparticles For Applications In Immune Response Studies Of Leishmania Major Infection, Chelsea L. Rintelmann, Tara Grinnage-Pulley, Kathleen Ross, Daniel E. K. Kabotso, Angela Toepp, Anne Cowell, Christine Petersen, Balaji Narasimhan, Nicola Pohl Jan 2019

Design And Synthesis Of Multivalent Α-1,2-Trimannose-Linked Bioerodible Microparticles For Applications In Immune Response Studies Of Leishmania Major Infection, Chelsea L. Rintelmann, Tara Grinnage-Pulley, Kathleen Ross, Daniel E. K. Kabotso, Angela Toepp, Anne Cowell, Christine Petersen, Balaji Narasimhan, Nicola Pohl

Chemical and Biological Engineering Publications

Leishmaniasis, a neglected tropical disease, currently infects approximately 12 million people worldwide with 1 to 2 million new cases each year in predominantly underdeveloped countries. The treatment of the disease is severely underdeveloped due to the ability of the Leishmania pathogen to evade and abate immune responses. In an effort to develop anti-leishmaniasis vaccines and adjuvants, novel carbohydrate-based probes were made to study the mechanisms of immune modulation. In this study, a new bioerodible polyanhydride microparticle was designed and conjugated with a glycodendrimer molecular probe. This molecular probe incorporates a pathogen-like multivalent display of α-1,2-trimannose, for which a more ...


Nanoparticle Microarray For High-Throughput Microbiome Metabolomics Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry, Rebecca L. Hansen, Maria Emilia Duenas, Torey Looft, Young Jin Lee Oct 2018

Nanoparticle Microarray For High-Throughput Microbiome Metabolomics Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry, Rebecca L. Hansen, Maria Emilia Duenas, Torey Looft, Young Jin Lee

Chemistry Publications

A high-throughput matrix-assisted laser desorption/ionization mass spectrometry (MALDI)-MS-based metabolomics platform was developed using a pre-fabricated microarray of nanoparticles and organic matrices. Selected organic matrices, inorganic nanoparticle (NP) suspensions, and sputter coated metal NPs, as well as various additives, were tested for metabolomics analysis of the turkey gut microbiome. Four NPs and one organic matrix were selected as the optimal matrix set: α-cyano-4-hydroycinnamic acid, Fe3O4 and Au NPs in positive ion mode with 10 mM sodium acetate, and Cu and Ag NPs in negative ion mode with no additive. Using this set of five matrices, over two thousand unique ...


Indole Anion Cycloadditions With Methyl Coumalate, George A. Kraus, Huangchao Yu Feb 2018

Indole Anion Cycloadditions With Methyl Coumalate, George A. Kraus, Huangchao Yu

Chemistry Publications

The reaction of the anion of indoles with methyl coumalate followed by selective opening of the lactone led to the preparation of tricyclic intermediates for indole alkaloid synthesis.


Characterization Of Pharmaceutical Cocrystals And Salts By Dynamic Nuclear Polarization-Enhanced Solid-State Nmr Spectroscopy, Li Zhao, Michael P. Hanrahan, Genetech, Inc., Aaron J. Rossini Feb 2018

Characterization Of Pharmaceutical Cocrystals And Salts By Dynamic Nuclear Polarization-Enhanced Solid-State Nmr Spectroscopy, Li Zhao, Michael P. Hanrahan, Genetech, Inc., Aaron J. Rossini

Ames Laboratory Accepted Manuscripts

Multicomponent solids such as cocrystals have emerged as a way to control and engineer the stability, solubility, and manufacturability of solid active pharmaceutical ingredients (APIs). Cocrystals are typically formed by solution- or solid-phase reactions of APIs with suitable cocrystal coformers, which are often weak acids. One key structural question about a given multicomponent solid is whether it should be classified as a salt, where the basic API is protonated by the acid, or as a cocrystal, where the API and coformer remain neutral and engage in hydrogen bonding interactions. It has previously been demonstrated that solid-state NMR spectroscopy is a ...


The Role Of A Conserved Membrane Proximal Cysteine In Altering Αps2cβps Integrin Diffusion, Aleem Syed, Neha Arora, Thomas A. Bunch, Emily A. Smith Jan 2016

The Role Of A Conserved Membrane Proximal Cysteine In Altering Αps2cβps Integrin Diffusion, Aleem Syed, Neha Arora, Thomas A. Bunch, Emily A. Smith

Chemistry Publications

Cysteine residues (Cys) in the membrane proximal region are common post-translational modification (PTM) sites in transmembrane proteins. Herein, the effects of a highly conserved membrane proximal α-subunit Cys1368 on the diffusion properties of αPS2CβPS integrins are reported. Sequence alignment shows that this cysteine is palmitoylated in human α3 and α6 integrin subunits. Replacing Cys1368 in wild-type integrins with valine (Val1368) putatively blocks a PTM site and alters integrins' ligand binding and diffusion characteristics. Both fluorescence recovery after photobleaching (FRAP) and single particle tracking (SPT) diffusion measurements show Val1368 integrins are more mobile compared to ...


Heterocycles From Wine: Synthesis And Biological Evaluation Of Salidrosides, Tezcan Guney, Stephanie A. Kohles, Victoria L. Thompson, Gregory J. Phillips, George A. Kraus May 2015

Heterocycles From Wine: Synthesis And Biological Evaluation Of Salidrosides, Tezcan Guney, Stephanie A. Kohles, Victoria L. Thompson, Gregory J. Phillips, George A. Kraus

Chemistry Publications

Wine is composed of a variety of tannins, of which a sub-class includes salidrosides, which are largely uninvestigated compounds. The first syntheses of galloylated salidrosides are reported in 7 steps from commercially available starting materials through a platform approach. The antimicrobial activity of the salidrosides against Escherichia coli strains is described.


Crystal Structure Of The Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology, Jani Reddy Bolla, Chih-Chia Su, Jared A. Delmar, Pattathil Radhakrishnan, Nitin Kumar, Tsung-Han Chou, Feng Long, Kanagalaghatta R. Rajashankar, Edward Yu Jan 2015

Crystal Structure Of The Alcanivorax Borkumensis Ydah Transporter Reveals An Unusual Topology, Jani Reddy Bolla, Chih-Chia Su, Jared A. Delmar, Pattathil Radhakrishnan, Nitin Kumar, Tsung-Han Chou, Feng Long, Kanagalaghatta R. Rajashankar, Edward Yu

Physics and Astronomy Publications

The potential of the folic acid biosynthesis pathway as a target for the development of antibiotics has been clinically validated. However, many pathogens have developed resistance to these antibiotics, prompting a re-evaluation of potential drug targets within the pathway. The ydaH gene of Alcanivorax borkumensis encodes an integral membrane protein of the AbgT family of transporters for which no structural information was available. Here we report the crystal structure of A. borkumensis YdaH, revealing a dimeric molecule with an architecture distinct from other families of transporters. YdaH is a bowl-shaped dimer with a solvent-filled basin extending from the cytoplasm to ...


Structure And Function Of Neisseria Gonorrhoeae Mtrf Illuminates A Class Of Antimetabolite Efflux Pumps, Chih-Chia Su, Jani Reddy Bolla, Nitin Kumar, Pattathil Radhakrishnan, Feng Long, Jared A. Delmar, Tsung-Han Chou, Kanagalaghatta R. Rajashankar, William M. Shafer, Edward Yu Jan 2015

Structure And Function Of Neisseria Gonorrhoeae Mtrf Illuminates A Class Of Antimetabolite Efflux Pumps, Chih-Chia Su, Jani Reddy Bolla, Nitin Kumar, Pattathil Radhakrishnan, Feng Long, Jared A. Delmar, Tsung-Han Chou, Kanagalaghatta R. Rajashankar, William M. Shafer, Edward Yu

Physics and Astronomy Publications

Neisseria gonorrhoeae is an obligate human pathogen and the causative agent of the sexually transmitted disease gonorrhea. The control of this disease has been compromised by the increasing proportion of infections due to antibiotic-resistant strains, which are growing at an alarming rate. N. gonorrhoeae MtrF is an integral membrane protein that belongs to the AbgT family of transporters for which no structural information is available. Here, we describe the crystal structure of MtrF, revealing a dimeric molecule with architecture distinct from all other families of transporters. MtrF is a bowl-shaped dimer with a solvent-filled basin extending from the cytoplasm to ...


Large Interdomain Rearrangement Triggered By Suppression Of Micro- To Millisecond Dynamics In Bacterial ​Enzyme I, Vincenzo Venditti, Vitali Tugarinov, Charles D. Schwieters, Alexander Grishaev, G. Marius Clore Jan 2015

Large Interdomain Rearrangement Triggered By Suppression Of Micro- To Millisecond Dynamics In Bacterial ​Enzyme I, Vincenzo Venditti, Vitali Tugarinov, Charles D. Schwieters, Alexander Grishaev, G. Marius Clore

Vincenzo Venditti

Enzyme I (EI), the first component of the bacterial phosphotransfer signal transduction system, undergoes one of the largest substrate-induced interdomain rearrangements documented to date. Here we characterize the perturbations generated by two small molecules, the natural substrate phosphoenolpyruvate and the inhibitor a-ketoglutarate, on the structure and dynamics of EI using NMR, small-angle X-ray scattering and biochemical techniques. The results indicate unambiguously that the open-to-closed conformational switch of EI is triggered by complete suppression of micro- to millisecond dynamics within the C-terminal domain of EI. Indeed, we show that a ligand-induced transition from a dynamic to a more rigid conformational state ...


Application Of Scanning Angle Raman Spectroscopy For Determining The Location Of Buried Polymer Interfaces With Tens Of Nanometer Precision, Craig A. Damin, Vy H.T. Nguyen, Auguste S. Niyibizi, Emily A. Smith Jan 2015

Application Of Scanning Angle Raman Spectroscopy For Determining The Location Of Buried Polymer Interfaces With Tens Of Nanometer Precision, Craig A. Damin, Vy H.T. Nguyen, Auguste S. Niyibizi, Emily A. Smith

Chemistry Publications

Near-infrared scanning angle (SA) Raman spectroscopy was utilized to determine the interface location in bilayer films (a stack of two polymer layers) of polystyrene (PS) and polycarbonate (PC). Finite-difference-time-domain (FDTD) calculations of the sum square electric field (SSEF) for films with total bilayer thicknesses of 1200–3600 nm were used to construct models for simultaneously measuring the film thickness and the location of the buried interface between the PS and PC layers. Samples with total thicknesses of 1320, 1890, 2300, and 2750 nm and varying PS/PC interface locations were analyzed using SA Raman spectroscopy. Comparing SA Raman spectroscopy and ...


Upgrading Malic Acid To Bio-Based Benzoates Via A Diels–Alder-Initiated Sequence With The Methyl Coumalate Platform, Jennifer J. Lee, Gerald R. Pollock Iii, Donald Mitchell, Lindsay Kasuga, George A. Kraus Sep 2014

Upgrading Malic Acid To Bio-Based Benzoates Via A Diels–Alder-Initiated Sequence With The Methyl Coumalate Platform, Jennifer J. Lee, Gerald R. Pollock Iii, Donald Mitchell, Lindsay Kasuga, George A. Kraus

Chemistry Publications

The conversion of naturally-occurring malic acid to the 2-pyrone methyl coumalate was optimized using a variety of acid catalysts. Coupling methyl coumalate with electron-rich dienophiles in an inverse electron-demand Diels–Alder (IEDDA)/decarboxylation/elimination domino sequence resulted in an investigation of the scope and limitations of the methodology. The thermal, metal-free, and one-pot procedure allows regioselective access to diverse aromatic compounds including tricyclic, biphenyl, and pyridinyl systems for elaboration. A comparison with analogous pyrones demonstrates the striking efficacy of methyl coumalate as a versatile platform for the generation of biorenewable functionalized benzoates.


Synthesis And Functionalization Of Virus-Mimicking Cationic Block Copolymers With Pathogen-Associated Carbohydrates As Potential Vaccine Adjuvants, J. R. Adams, M. Goswami, N. L.B. Pohl, Surya K. Mallapragada Mar 2014

Synthesis And Functionalization Of Virus-Mimicking Cationic Block Copolymers With Pathogen-Associated Carbohydrates As Potential Vaccine Adjuvants, J. R. Adams, M. Goswami, N. L.B. Pohl, Surya K. Mallapragada

Chemical and Biological Engineering Publications

We report the synthesis of a family of amphiphilic pentablock polymers with different cationic blocks and with controlled architectures as potential vaccine carriers for subunit vaccines. The temperature and pH-dependent micellization and gelation of these pentablock copolymers can provide a depot for sustained protein and gene delivery. The amphiphilic central triblock promotes cellular endocytosis, good gene delivery and has been used effectively as a vaccine adjuvant. The pentablock copolymer outer blocks condense DNA spontaneously as a result of electrostatic interactions for sustained combinational therapy. This family of polymers with different cationic groups was evaluated based on DNA complexation-ability and cytotoxicity ...


Crystal Structure Of The Neisseria Gonorrhoeae Mtrd Inner Membrane Multidrug Efflux Pump, Jani Reddy Bolla, Chih-Chia Su, Sylvia V. Do, Pattathil Radhakrishnan, Nitin Kumar, Feng Long, Tsung-Han Chou, Jared A. Delmar, Hsiang-Ting Lei, Kanagalaghatta R. Rajashankar, William M. Shafer, Edward Yu Jan 2014

Crystal Structure Of The Neisseria Gonorrhoeae Mtrd Inner Membrane Multidrug Efflux Pump, Jani Reddy Bolla, Chih-Chia Su, Sylvia V. Do, Pattathil Radhakrishnan, Nitin Kumar, Feng Long, Tsung-Han Chou, Jared A. Delmar, Hsiang-Ting Lei, Kanagalaghatta R. Rajashankar, William M. Shafer, Edward Yu

Physics and Astronomy Publications

Neisseria gonorrhoeae is an obligate human pathogen and the causative agent of the sexually-transmitted disease gonorrhea. The control of this disease has been compromised by the increasing proportion of infections due to antibiotic-resistant strains, which are growing at an alarming rate. The MtrCDE tripartite multidrug efflux pump, belonging to the hydrophobic and amphiphilic efflux resistance-nodulation-cell division (HAE-RND) family, spans both the inner and outer membranes of N. gonorrhoeae and confers resistance to a variety of antibiotics and toxic compounds. We here report the crystal structure of the inner membrane MtrD multidrug efflux pump, which reveals a novel structural feature that ...


Crystal Structure Of The Open State Of The Neisseria Gonorrhoeae Mtre Outer Membrane Channel, Hsiang-Ting Lei, Tsung-Han Chou, Chih-Chia Su, Jani Reddy Bolla, Nitin Kumar, Pattathil Radhakrishnan, Feng Long, Jared A. Delmar, Sylvia V. Do, Kanagalaghatta R. Rajashankar, William M. Shafer, Edward Yu Jan 2014

Crystal Structure Of The Open State Of The Neisseria Gonorrhoeae Mtre Outer Membrane Channel, Hsiang-Ting Lei, Tsung-Han Chou, Chih-Chia Su, Jani Reddy Bolla, Nitin Kumar, Pattathil Radhakrishnan, Feng Long, Jared A. Delmar, Sylvia V. Do, Kanagalaghatta R. Rajashankar, William M. Shafer, Edward Yu

Physics and Astronomy Publications

Active efflux of antimicrobial agents is one of the most important strategies used by bacteria to defend against antimicrobial factors present in their environment. Mediating many cases of antibiotic resistance are transmembrane efflux pumps, composed of one or more proteins. The Neisseria gonorrhoeae MtrCDE tripartite multidrug efflux pump, belonging to the hydrophobic and amphiphilic efflux resistance-nodulation-cell division (HAE-RND) family, spans both the inner and outer membranes of N. gonorrhoeae and confers resistance to a variety of antibiotics and toxic compounds. We here describe the crystal structure of N. gonorrhoeae MtrE, the outer membrane component of the MtrCDE tripartite multidrug efflux ...


A Nmr Experiment For Simultaneous Correlations Of Valine And Leucine/Isoleucine Methyls With Carbonyl Chemical Shifts In Proteins, Vitali Tugarinov, Vincenzo Venditti, G. Marius Clore Jan 2014

A Nmr Experiment For Simultaneous Correlations Of Valine And Leucine/Isoleucine Methyls With Carbonyl Chemical Shifts In Proteins, Vitali Tugarinov, Vincenzo Venditti, G. Marius Clore

Vincenzo Venditti

A methyl-detected ‘out-and-back’ NMR experiment for obtaining simultaneous correlations of methyl resonances of valine and isoleucine/leucine residues with backbone carbonyl chemical shifts, SIM-HMCM(CGCBCA)CO, is described. The developed pulse-scheme serves the purpose of convenience in recording a single data set for all Ileδ1, Leuδ and Valγ (ILV) methyl positions instead of acquiring two separate spectra selective for valine or leucine/isoleucine residues. The SIM-HMCM(CGCBCA)CO experiment can be used for ILV methyl assignments in moderately sized protein systems (up to ~100 kDa) where the backbone chemical shifts of 13Cα, 13Cβ and 13CO are known from prior NMR ...


Structure, Dynamics And Biophysics Of The Cytoplasmic Protein–Protein Complexes Of The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System, Vincenzo Venditti Jan 2013

Structure, Dynamics And Biophysics Of The Cytoplasmic Protein–Protein Complexes Of The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System, Vincenzo Venditti

Vincenzo Venditti

The bacterial phosphotransferase system (PTS) couples phosphoryl transfer, via a series of bimolecular protein–protein interactions, to sugar transport across the membrane. The multitude of complexes in the PTS provides a paradigm for studying protein interactions, and for understanding how the same binding surface can specifically recognize a diverse array of targets. Fifteen years of work aimed at solving the solution structures of all soluble protein–protein complexes of the PTS has served as a test bed for developing NMR and integrated hybrid approaches to study larger complexes in solution and to probe transient, spectroscopically invisible states, including encounter complexes ...


Structural Basis For Enzyme I Inhibition By Α-Ketoglutarate, Vincenzo Venditti, Rodolfo Ghirlando, G. Marius Clore Jan 2013

Structural Basis For Enzyme I Inhibition By Α-Ketoglutarate, Vincenzo Venditti, Rodolfo Ghirlando, G. Marius Clore

Vincenzo Venditti

Creating new bacterial strains in which carbon and nitrogen metabolism are uncoupled is potentially very useful for optimizing yields of microbial produced chemicals from renewable carbon sources. However, the mechanisms that balance carbon and nitrogen consumption in bacteria are poorly understood. Recently, α-ketoglutarate (αKG), the carbon substrate for ammonia assimilation, has been observed to inhibit Escherichia coli enzyme I (EI), the first component of the bacterial phosphotransferase system (PTS), thereby providing a direct biochemical link between central carbon and nitrogen metabolism. Here we investigate the EI-αKG interaction by NMR and enzymatic assays. We show that αKG binds with a KD ...


Near Ir Scanning Angle Total Internal Reflection Raman Spectroscopy At Smooth Gold Films, Kristopher J. Mckee, Matthew W. Meyer, Emily A. Smith Apr 2012

Near Ir Scanning Angle Total Internal Reflection Raman Spectroscopy At Smooth Gold Films, Kristopher J. Mckee, Matthew W. Meyer, Emily A. Smith

Chemistry Publications

Total internal reflection (TIR) Raman and reflectivity spectra were collected for nonresonant analytes as a function of incident angle at sapphire or sapphire/smooth 50 nm gold interfaces using 785 nm excitation. For both interfaces, the Raman signal as a function of incident angle is well-modeled by the calculated interfacial mean square electric field (MSEF) relative to the incident field times the thickness of the layer being probed in the Raman measurement (DRS). The Raman scatter was reproducibly enhanced at the interface containing a gold film relative to the sapphire interface by a factor of 4.3−4.6 for ...


Materials For Diabetes Therapeutics, Kaitlin M. Bratlie, Roger L. York, Michael A. Invernale, Robert Langer, Daniel G. Anderson Jan 2012

Materials For Diabetes Therapeutics, Kaitlin M. Bratlie, Roger L. York, Michael A. Invernale, Robert Langer, Daniel G. Anderson

Kaitlin M. Bratlie

This review is focused on the materials and methods used to fabricate closedloop systems for type 1 diabetes therapy. Herein, we give a brief overview of current methods used for patient care and discuss two types of possible treatments and the materials used for these therapies-(i) artificial pancreases, comprised of insulin producing cells embedded in a polymeric biomaterial, and (ii) totally synthetic pancreases formulated by integrating continuous glucose monitors with controlled insulin release through degradable polymers and glucose-responsive polymer systems. Both the artificial and the completely synthetic pancreas have two major design requirements: the device must be both biocompatible ...


The Use Of A Ditopic Gd(Iii) Paramagnetic Probe For Investigating Α-Bungarotoxin Surface Accessibility, Andrea Bernini, Ottavia Spiga, Vincenzo Venditti, Filippo Prischi, Mauro Botta, Gianluca Croce, Angela Pui-Ling Tong, Wing-Talk Wong, Neri Niccolai Jan 2012

The Use Of A Ditopic Gd(Iii) Paramagnetic Probe For Investigating Α-Bungarotoxin Surface Accessibility, Andrea Bernini, Ottavia Spiga, Vincenzo Venditti, Filippo Prischi, Mauro Botta, Gianluca Croce, Angela Pui-Ling Tong, Wing-Talk Wong, Neri Niccolai

Vincenzo Venditti

Protein surface accessibility is a critical parameter which drives all intermolecular interaction processes. In this respect a big deal of information has been derived by analyzing paramagnetic perturbation profiles obtained from NMR protein spectra, particularly in the case that the effects due to different soluble paramagnets can be compared. Here Gd2L7, a neutral ditopic paramagnetic NMR probe, has been characterized in terms of structure and relaxivity and its paramagnetic perturbations on α-bungarotoxin CαH signals in 1H–13C HSQC (heteronuclear single quantum coherence) spectra have been analyzed. Then, these signal attenuations have been compared with the ones previously obtained in the ...


An Efficient Protocol For Incorporation Of An Unnatural Amino Acid In Perdeuterated Recombinant Proteins Using Glucose-Based Media, Vincenzo Venditti, Nicolas L. Fawzi, G. Marius Clore Jan 2012

An Efficient Protocol For Incorporation Of An Unnatural Amino Acid In Perdeuterated Recombinant Proteins Using Glucose-Based Media, Vincenzo Venditti, Nicolas L. Fawzi, G. Marius Clore

Vincenzo Venditti

The in vivo incorporation of unnatural amino acids into proteins is a well-established technique requiring an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is incorporated at a position encoded by a TAG amber codon. Although this technology provides unique opportunities to engineer protein structures, poor protein yields are usually obtained in deuterated media, hampering its application in the protein NMR field. Here, we describe a novel protocol for incorporating unnatural amino acids into fully deuterated proteins using glucose-based media (which are relevant to the production, for example, of amino acid-specific methyl-labeled proteins used in the ...


Conformational Selection And Substrate Binding Regulate The Monomer/Dimer Equilibrium Of The C-Terminal Domain Of Escherichia Coli Enzyme I, Vincenzo Venditti, G. Marius Clore Jan 2012

Conformational Selection And Substrate Binding Regulate The Monomer/Dimer Equilibrium Of The C-Terminal Domain Of Escherichia Coli Enzyme I, Vincenzo Venditti, G. Marius Clore

Vincenzo Venditti

The bacterial phosphotransferase system (PTS) is a signal transduction pathway that couples phosphoryl transfer to active sugar transport across the cell membrane. The PTS is initiated by the binding of phosphoenolpyruvate (PEP) to the C-terminal domain (EIC) of enzyme I (EI), a highly conserved protein that is common to all sugar branches of the PTS. EIC exists in a dynamic monomer/dimer equilibrium that is modulated by ligand binding and is thought to regulate the overall PTS. Isolation of EIC has proven challenging, and conformational dynamics within the EIC domain during the catalytic cycle are still largely unknown. Here, we ...


Membrane-Dependent Effects Of A Cytoplasmic Helix On The Structure And Drug Binding Of The Influenza Virus M2 Protein, Sarah D. Cady, Tuo Wang, Mei Hong Jun 2011

Membrane-Dependent Effects Of A Cytoplasmic Helix On The Structure And Drug Binding Of The Influenza Virus M2 Protein, Sarah D. Cady, Tuo Wang, Mei Hong

Chemistry Publications

The influenza A M2 protein forms a proton channel for virus infection and also mediates virus assembly and budding. The minimum protein length that encodes both functions contains the transmembrane (TM) domain (roughly residues 22–46) for the amantadine-sensitive proton-channel activity and an amphipathic cytoplasmic helix (roughly residues 45–62) for curvature induction and virus budding. However, structural studies involving the TM domain with or without the amphipathic helix differed on the drug-binding site. Here we use solid-state NMR spectroscopy to determine the amantadine binding site in the cytoplasmic-helix-containing M2(21–61). 13C–2H distance measurements of 13C-labeled protein and ...


Specific Binding Of Adamantane Drugs And Direction Of Their Polar Amines In The Pore Of The Influenza M2 Transmembrane Domain In Lipid Bilayers And Dodecylphosphocholine Micelles Determined By Nmr Spectroscopy, Sarah D. Cady, Jun Wang, Yibing Wu, William F. Degrado, Mei Hong Mar 2011

Specific Binding Of Adamantane Drugs And Direction Of Their Polar Amines In The Pore Of The Influenza M2 Transmembrane Domain In Lipid Bilayers And Dodecylphosphocholine Micelles Determined By Nmr Spectroscopy, Sarah D. Cady, Jun Wang, Yibing Wu, William F. Degrado, Mei Hong

Chemistry Publications

The transmembrane domain of the influenza M2 protein (M2TM) forms a tetrameric proton channel important for the virus lifecycle. The proton-channel activity is inhibited by amine-containing adamantyl drugs amantadine and rimantadine, which have been shown to bind specifically to the pore of M2TM near Ser31. However, whether the polar amine points to the N- or C-terminus of the channel has not yet been determined. Elucidating the polar group direction will shed light on the mechanism by which drug binding inhibits this proton channel and will facilitate rational design of new inhibitors. In this study, we determine the polar amine direction ...


Automated Sequence- And Stereo-Specific Assignment Of Methyl-Labeled Proteins By Paramagnetic Relaxation And Methyl–Methyl Nuclear Overhauser Enhancement Spectroscopy, Vincenzo Venditti, Nicolas L. Fawzi, G. Marius Clore Jan 2011

Automated Sequence- And Stereo-Specific Assignment Of Methyl-Labeled Proteins By Paramagnetic Relaxation And Methyl–Methyl Nuclear Overhauser Enhancement Spectroscopy, Vincenzo Venditti, Nicolas L. Fawzi, G. Marius Clore

Vincenzo Venditti

Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ~1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the ...


A Structurally Driven Analysis Of Thiol Reactivity In Mammalian Albumins, Ottavia Spiga, Domenico Summa, Simone Cirri, Andrea Bernini, Vincenzo Venditti, Matteo De Chiara, Raffaella Priora, Simona Frosail, Antonios Margaritis, Danila Di Giuseppe, Paolo Di Simplicio, Neri Niccolai Jan 2011

A Structurally Driven Analysis Of Thiol Reactivity In Mammalian Albumins, Ottavia Spiga, Domenico Summa, Simone Cirri, Andrea Bernini, Vincenzo Venditti, Matteo De Chiara, Raffaella Priora, Simona Frosail, Antonios Margaritis, Danila Di Giuseppe, Paolo Di Simplicio, Neri Niccolai

Vincenzo Venditti

Understanding the structural basis of protein redox activity is still an open question. Hence, by using a structural genomics approach, different albumins have been chosen to correlate protein structural features with the corresponding reaction rates of thiol exchange between albumin and disulfide DTNB. Predicted structures of rat, porcine, and bovine albumins have been compared with the experimentally derived human albumin. High structural similarity among these four albumins can be observed, in spite of their markedly different reactivity with DTNB. Sequence alignments offered preliminary hints on the contributions of sequence-specific local environments modulating albumin reactivity. Molecular dynamics simulations performed on experimental ...


Conformational Plasticity Of The Influenza A M2 Transmembrane Helix In Lipid Bilayers Under Varying Ph, Drug Binding, And Membrane Thickness, Fanghao Hu, Wenbin Luo, Sarah D. Cady, Mei Hong Jan 2011

Conformational Plasticity Of The Influenza A M2 Transmembrane Helix In Lipid Bilayers Under Varying Ph, Drug Binding, And Membrane Thickness, Fanghao Hu, Wenbin Luo, Sarah D. Cady, Mei Hong

Chemistry Publications

Membrane proteins change their conformations to respond to environmental cues, thus conformational plasticity is important for function. The influenza A M2 protein forms an acid-activated proton channel important for the virus lifecycle. Here we have used solid-state NMR spectroscopy to examine the conformational plasticity of membrane-bound transmembrane domain of M2 (M2TM). 13C and 15N chemical shifts indicate coupled conformational changes of several pore-facing residues due to changes in bilayer thickness, drug binding, and pH. The structural changes are attributed to the formation of a well-defined helical kink at G34 in the drug-bound state and in thick lipid bilayers, nonideal backbone ...


Development Of A Scanning Angle Total Internal Reflection Raman Spectrometer, Kristopher J. Mckee, Emily A. Smith Apr 2010

Development Of A Scanning Angle Total Internal Reflection Raman Spectrometer, Kristopher J. Mckee, Emily A. Smith

Chemistry Publications

A scanning angle total internal reflection (SATIR) Raman spectrometer has been developed for measuring interfacial phenomena with chemical specificity and high axial resolution perpendicular to the interface. The instrument platform is an inverted optical microscope with added automated variable angle optics to control the angle of an incident laser on a prism/sample interface. These optics include two motorized translation stages, the first containing a focusing lens and the second a variable angle galvanometer mirror. The movement of all instrument components is coordinated to ensure that the same sample location and area are probed at each angle. At angles greater ...