Genomes and Genes
Summary: Proteins prepared by recombinant DNA technology.
- Qu D, Han J, Du A. Enhancement of protective immune response to recombinant Toxoplasma gondii ROP18 antigen by ginsenoside Re. Exp Parasitol. 2013;135:234-9 pubmed publisher..gondii, and that Re is a promising vaccine adjuvant against toxoplasmosis, deserves further evaluation and development...
- Larsen S, Weaver J, de Sa Campos K, Bulahan R, Nguyen J, Grove H, et al. Mutant strains of Pichia pastoris with enhanced secretion of recombinant proteins. Biotechnol Lett. 2013;35:1925-35 pubmed publisher..in a gene homologous to Saccharomyces cerevisiae protein kinase C (PKC1), gave enhanced secretion of most recombinant proteins that were tested, raising the possibility that it has the universal super-secreter phenotype needed in an ..
- Jacobson I, Dore G, Foster G, Fried M, Radu M, Rafalsky V, et al. Simeprevir with pegylated interferon alfa 2a plus ribavirin in treatment-naive patients with chronic hepatitis C virus genotype 1 infection (QUEST-1): a phase 3, randomised, double-blind, placebo-controlled trial. Lancet. 2014;384:403-13 pubmed publisher..The efficacy and safety of the combination of simeprevir, a one pill, once-daily, oral HCV NS3/4A protease inhibitor, plus peginterferon alfa 2a plus ribavirin were assessed in treatment-naive patients with HCV genotype 1 infection...
- Song F, Chen P, Sun D, Wang M, Dong L, Liang D, et al. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Science. 2014;344:376-80 pubmed publisher..The asymmetric binding and the location of histone H1 in chromatin play a role in the formation of the 30-nanometer fiber. Our results provide mechanistic insights into how nucleosomes compact into higher-order chromatin fibers. ..
- McAlary L, Yerbury J, Aquilina J. Glutathionylation potentiates benign superoxide dismutase 1 variants to the toxic forms associated with amyotrophic lateral sclerosis. Sci Rep. 2013;3:3275 pubmed publisher..This defines a key role for glutathionylation in superoxide dismutase 1 associated familial amyotrophic lateral sclerosis. ..
- Krainer F, Gmeiner C, Neutsch L, Windwarder M, Pletzenauer R, Herwig C, et al. Knockout of an endogenous mannosyltransferase increases the homogeneity of glycoproteins produced in Pichia pastoris. Sci Rep. 2013;3:3279 pubmed publisher....
- Zeuzem S, Berg T, Gane E, Ferenci P, Foster G, Fried M, et al. Simeprevir increases rate of sustained virologic response among treatment-experienced patients with HCV genotype-1 infection: a phase IIb trial. Gastroenterology. 2014;146:430-41.e6 pubmed publisher....
- Julien J, Cupo A, Sok D, Stanfield R, Lyumkis D, Deller M, et al. Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science. 2013;342:1477-83 pubmed publisher..This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design. ..
- Bleicken S, Landeta O, Landajuela A, Basañez G, García Sáez A. Proapoptotic Bax and Bak proteins form stable protein-permeable pores of tunable size. J Biol Chem. 2013;288:33241-52 pubmed publisher....
- Zhang J, Kang Z, Ling Z, Cao W, Liu L, Wang M, et al. High-level extracellular production of alkaline polygalacturonate lyase in Bacillus subtilis with optimized regulatory elements. Bioresour Technol. 2013;146:543-548 pubmed publisher..6 U mL(-1) h(-1), which was the highest secretory production of PGL by the B. subtilis system. The recombinant B. subtilis strain WB43CB constructed in the present work has great potential in production of alkaline PGL. ..
- Wiener R, Dibello A, Lombardi P, Guzzo C, Zhang X, Matunis M, et al. E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1. Nat Struct Mol Biol. 2013;20:1033-9 pubmed publisher..Our results suggest that OTUB1-E2 complexes in the cell are poised to regulate polyubiquitin chain elongation or degradation in response to changing levels of E2 charging and available free ubiquitin. ..
- Wagley Y, Choi J, Wickramanayake D, Choi G, Kim C, Kim T, et al. A monoclonal antibody against human MUDENG protein. Monoclon Antib Immunodiagn Immunother. 2013;32:277-82 pubmed publisher..These results indicate that the MuD MAb M3H9 could be useful as a new biomarker of hereditary spastic paraplegia and other related diseases. ..
- Fried M, Buti M, Dore G, Flisiak R, Ferenci P, Jacobson I, et al. Once-daily simeprevir (TMC435) with pegylated interferon and ribavirin in treatment-naïve genotype 1 hepatitis C: the randomized PILLAR study. Hepatology. 2013;58:1918-29 pubmed publisher..The adverse event profile was generally similar across the SMV and placebo control groups, with the exception of mild reversible hyperbilirubinemia, without serum aminotransferase abnormalities, associated with higher doses of SMV...
- Edros R, McDonnell S, Al Rubeai M. Using molecular markers to characterize productivity in Chinese hamster ovary cell lines. PLoS ONE. 2013;8:e75935 pubmed publisher..Since the correlation varied from day to day during batch cultivation, single-point measurement was of limited use in making a reliable prediction. ..
- Khan S, Islam A, Hassan M, Sharma S, Singh T, Ahmad F. Effect of conservative mutations (L94V and L94I) on the structure and stability of horse cytochrome c. Arch Biochem Biophys. 2017;633:40-49 pubmed publisher..All these measurements led us to conclude that both mutants exist as molten globule and are less stable than the wild-type protein. These observations are supported well by examining the structure of horse cyt c (PDB ID, 1HRC). ..
- Matoba Y, Kihara S, Muraki Y, Bando N, Yoshitsu H, Kuroda T, et al. Activation Mechanism of the Streptomyces Tyrosinase Assisted by the Caddie Protein. Biochemistry. 2017;56:5593-5603 pubmed publisher..Aggregation of the caddie protein, which is triggered by the conversion of the Tyr98 residue to dopaquinone, may ensure the generation of fully activated tyrosinase...
- Doijen J, Van Loy T, De Haes W, Landuyt B, Luyten W, Schoofs L, et al. Signaling properties of the human chemokine receptors CXCR4 and CXCR7 by cellular electric impedance measurements. PLoS ONE. 2017;12:e0185354 pubmed publisher..Taken together, cellular electric impedance spectroscopy can represent a valuable alternative pharmacological cell-based assay for the identification of molecules targeting CXCR4, but not for CXCR7 in the absence of CXCR4. ..
- Mastrangeli R, Satwekar A, Cutillo F, Ciampolillo C, Palinsky W, Longobardi S. In-vivo biological activity and glycosylation analysis of a biosimilar recombinant human follicle-stimulating hormone product (Bemfola) compared with its reference medicinal product (GONAL-f). PLoS ONE. 2017;12:e0184139 pubmed publisher..The clinical relevance of the differences observed between GONAL-f and Bemfola should be further investigated. ..
- Abil Z, Ellefson J, Gollihar J, Watkins E, Ellington A. Compartmentalized partnered replication for the directed evolution of genetic parts and circuits. Nat Protoc. 2017;12:2493-2512 pubmed publisher..A single round of CPR should take ∼3-5 d, whereas a whole directed evolution can be performed in 3-10 rounds, depending on selection efficiency...
- Sarangi P, Lee H, Lerman Y, Trzeciak A, Harrower E, Rezaie A, et al. Activated Protein C Attenuates Severe Inflammation by Targeting VLA-3high Neutrophil Subpopulation in Mice. J Immunol. 2017;199:2930-2936 pubmed publisher..These data indicate that variants of activated PC have a stronger affinity for integrin VLA-3, which reveals novel therapeutic possibilities. ..
- Hassett M, Riegel B, Callaghan P, Roepe P. Analysis of Plasmodium vivax Chloroquine Resistance Transporter Mutant Isoforms. Biochemistry. 2017;56:5615-5622 pubmed publisher..vivax CQR and other examples of quinoline antimalarial drug resistance. ..
- Roy G, Zhang S, Li L, Higham E, Wu H, Marelli M, et al. Development of a fluorescent reporter system for monitoring ER stress in Chinese hamster ovary cells and its application for therapeutic protein production. PLoS ONE. 2017;12:e0183694 pubmed publisher..This reporter system, with its ability to monitor the stress involved in recombinant protein expression, has utility to assist in devising engineering strategies for improved production of biotherapeutic drugs. ..
- Faburay B, McGill J, Jongejan F. A glycosylated recombinant subunit candidate vaccine consisting of Ehrlichia ruminantium major antigenic protein1 induces specific humoral and Th1 type cell responses in sheep. PLoS ONE. 2017;12:e0185495 pubmed publisher..ruminantium, in infected hosts. These results provide an important basis for development of a subunit vaccine as a novel strategy to protect susceptible livestock against heartwater in non-endemic and endemic areas. ..
- Wan S, Chen P, Chen C, Lai Y, Chu Y, Hung C, et al. Therapeutic Effects of Monoclonal Antibody against Dengue Virus NS1 in a STAT1 Knockout Mouse Model of Dengue Infection. J Immunol. 2017;199:2834-2844 pubmed publisher..Therefore, administration with a single dose of mAb 2E8 can protect mice against DENV infection and pathological effects, suggesting that NS1-specific mAb may be a therapeutic option against dengue disease. ..
- Michel M, Swatek K, Hospenthal M, Komander D. Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling. Mol Cell. 2017;68:233-246.e5 pubmed publisher..A protocol to enrich K6-ubiquitinated proteins from cells identifies HUWE1 as a main E3 ligase for this chain type, and we show that mitofusin-2 is modified with K6-linked polyubiquitin in a HUWE1-dependent manner. ..
- Kalabova D, Smidova A, Petrvalska O, Alblova M, Kosek D, Man P, et al. Human procaspase-2 phosphorylation at both S139 and S164 is required for 14-3-3 binding. Biochem Biophys Res Commun. 2017;493:940-945 pubmed publisher..Furthermore, our data indicate that other regions of procaspase-2, in addition to phosphorylation motifs, may be involved in the interaction with 14-3-3. ..
- Dai H, He R, Zhang Y, Wu R, Xiao Y. Adenoviral vector mediated ferritin over-expression in mesenchymal stem cells detected by 7T MRI in vitro. PLoS ONE. 2017;12:e0185260 pubmed publisher..The correlation between δR2, OD and ferritin concentration suggests that MRI can detect ferritin signal change accurately. ..
- Passarelli P, Pasquantonio G, D addona A. Management of Surgical Third Lower Molar Extraction and Postoperative Progress in Patients With Factor VII Deficiency: A Clinical Protocol and Focus on This Rare Pathologic Entity. J Oral Maxillofac Surg. 2017;75:2070.e1-2070.e4 pubmed publisher..The extraction of the third lower molar appears to be a safe procedure for patients with factor VII deficiency when appropriate prophylaxis with rFVIIa is used. ..
- Subramanian L, Khan A, Allu P, Kiranmayi M, Sahu B, Sharma S, et al. A haplotype variant of the human chromogranin A gene (CHGA) promoter increases CHGA expression and the risk for cardiometabolic disorders. J Biol Chem. 2017;292:13970-13985 pubmed publisher....
- Hirakis S, Malmstrom R, Amaro R. Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism. Biochemistry. 2017;56:3885-3888 pubmed publisher..Brownian dynamics simulations suggest that the Flipback conformation plays a role in cAMP association to the A domain of the R subunit. ..
- Vitali J, Singh A, COLANERI M. Characterization of the Dihydroorotase from Methanococcus jannaschii. Protein J. 2017;36:361-373 pubmed publisher..Additional and better insight into the thermostabilization strategies adopted by this enzyme will be provided when its crystal structure is determined. ..
- Finkelstein D, Billings J, Adlard P, Ayton S, Sedjahtera A, Masters C, et al. The novel compound PBT434 prevents iron mediated neurodegeneration and alpha-synuclein toxicity in multiple models of Parkinson's disease. Acta Neuropathol Commun. 2017;5:53 pubmed publisher..We conclude that compounds designed to target a pool of pathological iron that is not held in high-affinity complexes in the tissue can maintain the survival of SNpc neurons and could be disease-modifying in PD. ..
- Vernon R, Chong P, Lin H, Yang Z, Zhou Q, Aleksandrov A, et al. Stabilization of a nucleotide-binding domain of the cystic fibrosis transmembrane conductance regulator yields insight into disease-causing mutations. J Biol Chem. 2017;292:14147-14164 pubmed publisher....
- McVey A, Medarametla P, Chee X, Bartlett S, Poso A, Spring D, et al. Structural and Functional Characterization of Malate Synthase G from Opportunistic Pathogen Pseudomonas aeruginosa. Biochemistry. 2017;56:5539-5549 pubmed publisher..Our data reveal two promising binding pockets in malate synthase G that may be exploited for drug design...
- Guevara G, Heras L, Perera J, Lloréns J. Functional characterization of 3-ketosteroid 9α-hydroxylases in Rhodococcus ruber strain chol-4. J Steroid Biochem Mol Biol. 2017;172:176-187 pubmed publisher..Accordingly to what it is described for other Rhodococcus strains, our results also suggest that the side chain degradation is KshAB-independent. ..
- Lee J, Lee C, Lee S. Interferon alpha-2a treatment for refractory Behcet uveitis in Korean patients. BMC Ophthalmol. 2018;18:52 pubmed publisher..44 ± 0.38 at baseline to 1.02 ± 0.58 at the final follow up. IFNα2a is an effective therapy for Behcet uveitis refractory to conventional immunosuppressants in Korean patients. ..
- Wilbers R, van Raaij D, Westerhof L, Bakker J, Smant G, Schots A. Re-evaluation of IL-10 signaling reveals novel insights on the contribution of the intracellular domain of the IL-10R2 chain. PLoS ONE. 2017;12:e0186317 pubmed publisher..This observation highlights a novel role for the intracellular domain of IL-10R2 in the molecular mechanisms of IL-10R activation. ..
- Nemergut M, Zoldak G, Schaefer J, Kast F, Miskovsky P, Plückthun A, et al. Analysis of IgG kinetic stability by differential scanning calorimetry, probe fluorescence and light scattering. Protein Sci. 2017;26:2229-2239 pubmed publisher....
- Shete P, Ravindran R, Chang E, Worodria W, Chaisson L, Andama A, et al. Evaluation of antibody responses to panels of M. tuberculosis antigens as a screening tool for active tuberculosis in Uganda. PLoS ONE. 2017;12:e0180122 pubmed publisher..Measuring antibody responses to combinations of antigens could facilitate TB screening and should be further evaluated in populations being targeted for systematic screening. ..
- Gangula N, Maddika S. Interplay between the phosphatase PHLPP1 and E3 ligase RNF41 stimulates proper kinetochore assembly via the outer-kinetochore protein SGT1. J Biol Chem. 2017;292:13947-13958 pubmed publisher..Taken together, our results suggest that PHLPP1 plays an important role in the assembly of kinetochores by counteracting RNF41-mediated SGT1 degradation. ..
- Shimizu H, Toma Fukai S, Saijo S, Shimizu N, Kontani K, Katada T, et al. Structure-based analysis of the guanine nucleotide exchange factor SmgGDS reveals armadillo-repeat motifs and key regions for activity and GTPase binding. J Biol Chem. 2017;292:13441-13448 pubmed publisher..Our findings indicate that the two SmgGDS isoforms differ in GTPase binding and GEF activity, depending on the lipidation state, thus providing useful information about the cellular functions of SmgGDS in cells. ..
- HIRBAWI J, Bialkowska K, Bledzka K, Liu J, Fukuda K, Qin J, et al. The extreme C-terminal region of kindlin-2 is critical to its regulation of integrin activation. J Biol Chem. 2017;292:14258-14269 pubmed publisher..Our findings indicate that the extreme C terminus of K2 is essential for integrin co-activation and highlight the importance of an atypical architecture of the K2 FERM domain in regulating integrin activation. ..
- Acciani M, Alston J, Zhao G, Reynolds H, Ali A, Xu B, et al. Mutational Analysis of Lassa Virus Glycoprotein Highlights Regions Required for Alpha-Dystroglycan Utilization. J Virol. 2017;91: pubmed publisher..Our results highlight a region within the Lassa virus GP1 protein that interacts with the cellular receptor alpha-dystroglycan. This information may be used for future development of new Lassa virus antivirals. ..
- Shay A, Diwakar B, Guan B, Narayan V, Urban J, Prabhu K. IL-4 up-regulates cyclooxygenase-1 expression in macrophages. J Biol Chem. 2017;292:14544-14555 pubmed publisher..In summary, these findings suggest a new paradigm where IL-4-dependent up-regulation of Cox-1 expression may play a key role in tissue homeostasis and wound healing during Th2-mediated immune responses, such as parasitic infections. ..
- Gerodimos C, Chang H, Watanabe G, Lieber M. Effects of DNA end configuration on XRCC4-DNA ligase IV and its stimulation of Artemis activity. J Biol Chem. 2017;292:13914-13924 pubmed publisher..These data suggest specific functional and positional relationships among these components that explain genetic and molecular features of NHEJ and V(D)J recombination within cells. ..
- Wang Y, Chen F, Zhao M, Yang Z, Li J, Zhang S, et al. The long noncoding RNA HULC promotes liver cancer by increasing the expression of the HMGA2 oncogene via sequestration of the microRNA-186. J Biol Chem. 2017;292:15395-15407 pubmed publisher....
- Galan A, Lozano G, Piñeiro D, Martinez Salas E. G3BP1 interacts directly with the FMDV IRES and negatively regulates translation. FEBS J. 2017;284:3202-3217 pubmed publisher..Our results highlight the IRES-binding capacity of G3BP1 and illustrate its function as a translation inhibitor. ..
- Chaton C, Herr A. Defining the metal specificity of a multifunctional biofilm adhesion protein. Protein Sci. 2017;26:1964-1973 pubmed publisher..These characteristics allow Aap to function as an environmental sensor that regulates biofilm formation in response to local concentrations of Zn2+ and Cu2+ , both of which are implicated in immune cell activity. ..
- Kroh H, Chandrasekaran R, Rosenthal K, Woods R, Jin X, Ohi M, et al. Use of a neutralizing antibody helps identify structural features critical for binding of Clostridium difficile toxin TcdA to the host cell surface. J Biol Chem. 2017;292:14401-14412 pubmed publisher..We conclude that PA50 protects host cells by blocking the binding of TcdA to cell surfaces. ..
- Magaña Vergara C, Kallenberg C, Rogasch M, Hübner C, Song Y. A versatile vector for mycobacterial protein production with a functional minimized acetamidase regulon. Protein Sci. 2017;26:2302-2311 pubmed publisher..Additionally, our results propose a new understanding of the regulation mechanism of the acetamidase regulon with the potential to construct more optimized vectors in the future. ..
- Rasquinha J, Bej A, Dutta S, Mukherjee S. Intrinsic Differences in Backbone Dynamics between Wild Type and DNA-Contact Mutants of the p53 DNA Binding Domain Revealed by Nuclear Magnetic Resonance Spectroscopy. Biochemistry. 2017;56:4962-4971 pubmed publisher....
- Gaytan Cervantes J, Gonzalez Torres C, Maldonado V, Zampedri C, Ceballos Cancino G, Melendez Zajgla J. Protein Sam68 regulates the alternative splicing of survivin DEx3. J Biol Chem. 2017;292:13745-13757 pubmed publisher..This work provides the first clues regarding the regulation of survivin DEx3 mRNA splicing. ..
- Ata Ö, Prielhofer R, Gasser B, Mattanovich D, Calik P. Transcriptional engineering of the glyceraldehyde-3-phosphate dehydrogenase promoter for improved heterologous protein production in Pichia pastoris. Biotechnol Bioeng. 2017;114:2319-2327 pubmed publisher..Biotechnol. Bioeng. 2017;114: 2319-2327. © 2017 Wiley Periodicals, Inc. ..
- Kean K, Carpenter R, Pandini V, Zanetti G, Hall A, Faber R, et al. High-resolution studies of hydride transfer in the ferredoxin:NADP+ reductase superfamily. FEBS J. 2017;284:3302-3319 pubmed publisher..Enzyme Commission number: ferredoxin:NADP+ reductase - E C188.8.131.52. ..
- Fujiwara K, Kobayashi T, Fujimoto H, Nakahara H, D Alessandro Gabazza C, Hinneh J, et al. Inhibition of Cell Apoptosis and Amelioration of Pulmonary Fibrosis by Thrombomodulin. Am J Pathol. 2017;187:2312-2322 pubmed publisher....
- Korasick D, Singh H, Pemberton T, Luo M, Dhatwalia R, Tanner J. Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure. FEBS J. 2017;284:3029-3049 pubmed publisher..3 mg·mL-1 ), SASDCT3 (BjPutA 4.7 mg·mL-1 ), SASDCU3 (BjPutA 7.0 mg·mL-1 ), SASDCZ3 (R51E 2.3 mg·mL-1 ), SASDC24 (R51E 4.7 mg·mL-1 ), SASDC34 (R51E 7.0 mg·mL-1 ). ..
- Vivcharuk V, Baardsnes J, Deprez C, Sulea T, Jaramillo M, Corbeil C, et al. Assisted Design of Antibody and Protein Therapeutics (ADAPT). PLoS ONE. 2017;12:e0181490 pubmed publisher..ADAPT is a very focused search of sequence space and required only 20-30 mutants for each system to be made and tested to achieve the affinity enhancements mentioned above. ..
- Horimizu R, Ogawa R, Watanabe Y, Tatsukawa H, Kinoshita M, Hashimoto H, et al. Biochemical characterization of a medaka (Oryzias latipes) orthologue for mammalian Factor XIII and establishment of a gene-edited mutant. FEBS J. 2017;284:2843-2855 pubmed publisher..The loss of FXIIIA expression was validated in the mutants, and phenotypes, such as absence of fibrin cross-linking, were investigated in the established mutant fish. ..
- Baba M, Kakue R, Leucht C, Rasor P, Walch H, Ladiges D, et al. Further increase in thermostability of Moloney murine leukemia virus reverse transcriptase by mutational combination. Protein Eng Des Sel. 2017;30:551-557 pubmed publisher..The sextuple variant MM3.14 (A32V/L72R/E286R/E302K/W388R/L435R) exhibited higher thermostability than MM3...
- Lisenko K, Baertsch M, Meiser R, Pavel P, Bruckner T, Kriegsmann M, et al. Comparison of biosimilar filgrastim, originator filgrastim, and lenograstim for autologous stem cell mobilization in patients with multiple myeloma. Transfusion. 2017;57:2359-2365 pubmed publisher....
- Hino K, Horigome K, Nishio M, Komura S, Nagata S, Zhao C, et al. Activin-A enhances mTOR signaling to promote aberrant chondrogenesis in fibrodysplasia ossificans progressiva. J Clin Invest. 2017;127:3339-3352 pubmed publisher..These results uncovered the crucial role of the Activin-A/FOP-ACVR1/ENPP2/mTOR axis in FOP pathogenesis. ..
- Kerekes A, Hoffmann O, Iski G, Lipták N, Gócza E, Kues W, et al. Secretion of a recombinant protein without a signal peptide by the exocrine glands of transgenic rabbits. PLoS ONE. 2017;12:e0187214 pubmed publisherTransgenic rabbits carrying mammary gland specific gene constructs are extensively used for excreting recombinant proteins into the milk...