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Degrado protein

Nathan W Schmidt, Gevorg Grigoryan, William F DeGrado
Coiled-coils are essential components of many protein complexes. First discovered in structural proteins such as keratins, they have since been found to figure largely in the assembly and dynamics required for diverse functions, including membrane fusion, signal transduction and motors. Coiled-coils have a characteristic repeating 7-residue geometric and sequence motif, which is sometimes interrupted by the insertion of one or more residues. Such insertions are often highly conserved and critical to interdomain communication in signaling proteins such as bacterial histidine kinases...
December 15, 2016: Protein Science: a Publication of the Protein Society
Matthew R Elkins, Tuo Wang, Mimi Nick, Hyunil Jo, Thomas Lemmin, Stanley B Prusiner, William F DeGrado, Jan Stöhr, Mei Hong
The amyloid-β (Aβ) peptide of Alzheimer's disease (AD) forms polymorphic fibrils on the micrometer and molecular scales. Various fibril growth conditions have been identified to cause polymorphism, but the intrinsic amino acid sequence basis for this polymorphism has been unclear. Several single-site mutations in the center of the Aβ sequence cause different disease phenotypes and fibrillization properties. The E22G (Arctic) mutant is found in familial AD and forms protofibrils more rapidly than wild-type Aβ...
August 10, 2016: Journal of the American Chemical Society
Tsz-Leung To, Katalin F Medzihradszky, Alma L Burlingame, William F DeGrado, Hyunil Jo, Xiaokun Shu
Protein-protein interactions regulate many biological processes. Identification of interacting proteins is thus an important step toward molecular understanding of cell signaling. The aim of this study was to investigate the use of photo-generated singlet oxygen and a small molecule for proximity labeling of interacting proteins in cellular environment. The protein of interest (POI) was fused with a small singlet oxygen photosensitizer (miniSOG), which generates singlet oxygen ((1)O2) upon irradiation. The locally generated singlet oxygen then activated a biotin-conjugated thiol molecule to form a covalent bond with the proteins nearby...
July 15, 2016: Bioorganic & Medicinal Chemistry Letters
Kook-Han Kim, Dong-Kyun Ko, Yong-Tae Kim, Nam Hyeong Kim, Jaydeep Paul, Shao-Qing Zhang, Christopher B Murray, Rudresh Acharya, William F DeGrado, Yong Ho Kim, Gevorg Grigoryan
Learning to engineer self-assembly would enable the precise organization of molecules by design to create matter with tailored properties. Here we demonstrate that proteins can direct the self-assembly of buckminsterfullerene (C60) into ordered superstructures. A previously engineered tetrameric helical bundle binds C60 in solution, rendering it water soluble. Two tetramers associate with one C60, promoting further organization revealed in a 1.67-Å crystal structure. Fullerene groups occupy periodic lattice sites, sandwiched between two Tyr residues from adjacent tetramers...
2016: Nature Communications
Jessica L Thomaston, William F DeGrado
The M2 protein is a small proton channel found in the influenza A virus that is necessary for viral replication. The M2 channel is the target of a class of drugs called the adamantanes, which block the channel pore and prevent the virus from replicating. In recent decades mutations have arisen in M2 that prevent the adamantanes from binding to the channel pore, with the most prevalent of these mutations being S31N. Here we report the first crystal structure of the S31N mutant crystallized using lipidic cubic phase crystallization techniques and solved to 1...
August 2016: Protein Science: a Publication of the Protein Society
Gözde Ulas, Thomas Lemmin, Yibing Wu, George T Gassner, William F DeGrado
Enzymes use binding energy to stabilize their substrates in high-energy states that are otherwise inaccessible at ambient temperature. Here we show that a de novo designed Zn(II) metalloprotein stabilizes a chemically reactive organic radical that is otherwise unstable in aqueous media. The protein binds tightly to and stabilizes the radical semiquinone form of 3,5-di-tert-butylcatechol. Solution NMR spectroscopy in conjunction with molecular dynamics simulations show that the substrate binds in the active site pocket where it is stabilized by metal-ligand interactions as well as by burial of its hydrophobic groups...
April 2016: Nature Chemistry
Mukesh K Pandey, Timothy R DeGrado
Glycogen synthase kinase-3 (GSK-3) is associated with various key biological processes, including glucose regulation, apoptosis, protein synthesis, cell signaling, cellular transport, gene transcription, proliferation, and intracellular communication. Accordingly, GSK-3 has been implicated in a wide variety of diseases and specifically targeted for both therapeutic and imaging applications by a large number of academic laboratories and pharmaceutical companies. Here, we review the structure, function, expression levels, and ligand-binding properties of GSK-3 and its connection to various diseases...
2016: Theranostics
Binxia Yang, Akshaar Brahmbhatt, Evelyn Nieves Torres, Brian Thielen, Deborah L McCall, Sean Engel, Aditya Bansal, Mukesh K Pandey, Allan B Dietz, Edward B Leof, Timothy R DeGrado, Debabrata Mukhopadhyay, Sanjay Misra
PURPOSE: To determine if adventitial transplantation of human adipose tissue-derived mesenchymal stem cells (MSCs) to the outflow vein of B6.Cg-Foxn1(nu)/J mice with arteriovenous fistula (AVF) at the time of creation would reduce monocyte chemoattractant protein-1 (Mcp-1) gene expression and venous neointimal hyperplasia. The second aim was to track transplanted zirconium 89 ((89)Zr)-labeled MSCs serially with positron emission tomography (PET) for 21 days. MATERIALS AND METHODS: All animal experiments were performed according to protocols approved by the institutional animal care and use committee...
May 2016: Radiology
Rae Ana Snyder, Justine Betzu, Susan E Butch, Amanda J Reig, William F DeGrado, Edward I Solomon
DFsc (single-chain due ferri) proteins allow for modeling binuclear non-heme iron enzymes with a similar fold. Three 4A → 4G variants of DFsc were studied to investigate the effects of (1) increasing the size of the substrate/solvent access channel (G4DFsc), (2) including an additional His residue in the first coordination sphere along with three additional helix-stabilizing mutations [3His-G4DFsc(Mut3)], and (3) the three helix-stabilizing mutations alone [G4DFsc(Mut3)] on the biferrous structures and their O2 reactivities...
August 4, 2015: Biochemistry
Rae Ana Snyder, Susan E Butch, Amanda J Reig, William F DeGrado, Edward I Solomon
Using the single-chain due ferri (DFsc) peptide scaffold, the differential oxidase and oxygenase reactivities of two 4A→4G variants, one with two histidines at the diiron center (G4DFsc) and the other with three histidines (3His-G4DFsc(Mut3)), are explored. By controlling the reaction conditions, the active form responsible for 4-aminophenol (4-AP) oxidase activity in both G4DFsc and 3His-G4DFsc(Mut3) is determined to be the substrate-bound biferrous site. Using circular dichroism (CD), magnetic CD (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies, 4-AP is found to bind directly to the biferrous sites of the DF proteins...
July 29, 2015: Journal of the American Chemical Society
Manasi P Bhate, Kathleen S Molnar, Mark Goulian, William F DeGrado
Histidine kinases (HKs) are major players in bacterial signaling. There has been an explosion of new HK crystal structures in the last 5 years. We globally analyze the structures of HKs to yield insights into the mechanisms by which signals are transmitted to and across protein structures in this family. We interpret known enzymological data in the context of new structural data to show how asymmetry across the dimer interface is a key feature of signal transduction in HKs, and discuss how different HK domains undergo asymmetric to symmetric transitions during signal transduction and catalysis...
June 2, 2015: Structure
Aditya Bansal, Mukesh K Pandey, Yunus E Demirhan, Jonathan J Nesbitt, Ruben J Crespo-Diaz, Andre Terzic, Atta Behfar, Timothy R DeGrado
BACKGROUND: With the recent growth of interest in cell-based therapies and radiolabeled cell products, there is a need to develop more robust cell labeling and imaging methods for in vivo tracking of living cells. This study describes evaluation of a novel cell labeling approach with the positron emission tomography (PET) isotope (89)Zr (T 1/2 = 78.4 h). (89)Zr may allow PET imaging measurements for several weeks and take advantage of the high sensitivity of PET imaging. METHODS: A novel cell labeling agent, (89)Zr-desferrioxamine-NCS ((89)Zr-DBN), was synthesized...
2015: EJNMMI Research
Lynne Regan, Diego Caballero, Michael R Hinrichsen, Alejandro Virrueta, Danielle M Williams, Corey S O'Hern
Building on the pioneering work of Ho and DeGrado (J Am Chem Soc 1987, 109, 6751-6758) in the late 1980s, protein design approaches have revealed many fundamental features of protein structure and stability. We are now in the era that the early work presaged - the design of new proteins with practical applications and uses. Here we briefly survey some past milestones in protein design, in addition to highlighting recent progress and future aspirations.
July 2015: Biopolymers
Shao-Qing Zhang, Daniel W Kulp, Chaim A Schramm, Marco Mravic, Ilan Samish, William F DeGrado
α Helices are a basic unit of protein secondary structure and therefore the interaction between helices is crucial to understanding tertiary and higher-order folds. Comparing subtle variations in the structural and sequence motifs between membrane and soluble proteins sheds light on the different constraints faced by each environment and elucidates the complex puzzle of membrane protein folding. Here, we demonstrate that membrane and water-soluble helix pairs share a small number of similar folds with various interhelical distances...
March 3, 2015: Structure
Shenstone Huang, Bryan Green, Megan Thompson, Richard Chen, Jessica Thomaston, William F DeGrado, Kathleen P Howard
The influenza A M2 protein is a 97-residue integral membrane protein involved in viral budding and proton conductance. Although crystal and NMR structures exist of truncated constructs of the protein, there is disagreement between models and only limited structural data are available for the full-length protein. Here, the structure of the C-terminal juxtamembrane region (sites 50-60) is investigated in the full-length M2 protein using site-directed spin-labeling electron paramagnetic resonance (EPR) spectroscopy in lipid bilayers...
March 2015: Protein Science: a Publication of the Protein Society
Nathan H Joh, Tuo Wang, Manasi P Bhate, Rudresh Acharya, Yibing Wu, Michael Grabe, Mei Hong, Gevorg Grigoryan, William F DeGrado
The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn(2+) and Co(2+), but not Ca(2+), across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity. X-ray crystallography and solid-state and solution nuclear magnetic resonance indicate that the overall helical bundle is formed from two tightly interacting pairs of helices, which form individual domains that interact weakly along a more dynamic interface...
December 19, 2014: Science
E Domingo-Musibay, C Allen, C Kurokawa, J J Hardcastle, I Aderca, P Msaouel, A Bansal, H Jiang, T R DeGrado, E Galanis
Osteosarcoma (OS) is the most common primary bone tumor affecting children and young adults, and development of metastatic disease is associated with poor prognosis. The purpose of this study was to evaluate the antitumor efficacy of virotherapy with engineered measles virus (MV) vaccine strains in the treatment of OS. Cell lines derived from pediatric patients with OS (HOS, MG63, 143B, KHOS-312H, U2-OS and SJSA1) were infected with MV expressing green fluorescent protein (MV-GFP) and MV-expressing sodium iodide symporter (MV-NIS) strains...
November 2014: Cancer Gene Therapy
Eleonora Gianti, Vincenzo Carnevale, William F DeGrado, Michael L Klein, Giacomo Fiorin
The tetrameric M2 proton channel of influenza A virus is an integral membrane protein responsible for the acidification of the viral interior. Drugs such as amantadine target the transmembrane region of wild type M2 by acting as pore blockers. However, a number of mutations affecting this domain confer drug resistance, prompting the need for alternative inhibitors. The availability of high-resolution structures of drug-bound M2, paired with computational investigations, revealed that inhibitors can bind at different sites, and provided useful insights in understanding the principles governing proton conduction...
January 22, 2015: Journal of Physical Chemistry. B
Hao Dong, Giacomo Fiorin, William F DeGrado, Michael L Klein
The activity of the M2 proton channel of the influenza A virus is controlled by pH. The tautomeric state and conformation of His37, a key residue in the M2 transmembrane four-helix bundle, controls the gating of the channel. Previously, we compared the energetics and dynamics of two alternative conformations of the doubly protonated state at neutral pH, namely, a 4-fold symmetric "histidine-box" and a 2-fold symmetric "dimer-of-dimers", and proposed a multiconfiguration model for this charge state. Here, we elaborate this model by further studying configurations of the His37 tetrad in the triply protonated state and its subsequent deprotonation via quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, starting with the aforementioned configurations, to gain information about proton release in a viral membrane environment...
November 6, 2014: Journal of Physical Chemistry. B
Katelyn M Seither, Heather A McMahon, Nikita Singh, Hejia Wang, Mimi Cushman-Nick, Geronda L Montalvo, William F DeGrado, James Shorter
Amyloid fibrils are self-propagating entities that spread pathology in several devastating disorders including Alzheimer's disease (AD). In AD, amyloid-β (Aβ) peptides form extracellular plaques that contribute to cognitive decline. One potential therapeutic strategy is to develop inhibitors that prevent Aβ misfolding into proteotoxic conformers. Here, we design specific aromatic foldamers, synthetic polymers with an aromatic salicylamide (Sal) or 3-amino benzoic acid (Benz) backbone, short length (four repetitive units), basic arginine (Arg), lysine (Lys) or citrulline (Cit) side chains, and various N- and C-terminal groups that prevent spontaneous and seeded Aβ fibrillization...
November 15, 2014: Biochemical Journal
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