TY  - JOUR
A1  - Otrelo-Cardoso, Ana Rita
A1  - Schwuchow, Viola
A1  - Rodrigues, David
A1  - Cabrita, Eurico J.
A1  - Leimkühler, Silke
A1  - Romao, Maria Joao
A1  - Santos-Silva, Teresa
T1  - Biochemical, stabilization and crystallization studies on a molecular chaperone (PaoD) involved in the maturation of molybdoenzymes
JF  - PLoS one
N2  - Molybdenum and tungsten enzymes require specific chaperones for folding and cofactor insertion. PaoD is the chaperone of the periplasmic aldehyde oxidoreductase PaoABC. It is the last gene in the paoABCD operon in Escherichia coli and its presence is crucial for obtaining mature enzyme. PaoD is an unstable, 35 kDa, protein. Our biochemical studies showed that it is a dimer in solution with a tendency to form large aggregates, especially after freezing/thawing cycles. In order to improve stability, PaoD was thawed in the presence of two ionic liquids [C(4)mim]Cl and [C(2)OHmim]PF6 and no protein precipitation was observed. This allowed protein concentration and crystallization using polyethylene glycol or ammonium sulfate as precipitating agents. Saturation transfer difference - nuclear magnetic resonance (STD-NMR) experiments have also been performed in order to investigate the effect of the ionic liquids in the stabilization process, showing a clear interaction between the acidic ring protons of the cation and, most likely, negatively charged residues at the protein surface. DLS assays also show a reduction of the overall size of the protein aggregates in presence of ionic liquids. Furthermore, cofactor binding studies on PaoD showed that the protein is able to discriminate between molybdenum and tungsten bound to the molybdenum cofactor, since only a Mo-MPT form of the cofactor remained bound to PaoD.
Y1  - 2014
U6  - https://doi.org/10.1371/journal.pone.0087295
SN  - 1932-6203
VL  - 9
IS  - 1
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Mahro, Martin
A1  - Coelho, Catarina
A1  - Trincao, Jose
A1  - Rodrigues, David
A1  - Terao, Mineko
A1  - Garattini, Enrico
A1  - Saggu, Miguel
A1  - Lendzian, Friedhelm
A1  - Hildebrandt, Peter
A1  - Romao, Maria Joao
A1  - Leimkühler, Silke
T1  - Characterization and crystallization of mouse aldehyde oxidase 3 - from mouse liver to escherichia coli heterologous protein expression
JF  - Drug metabolism and disposition : the biological fate of chemicals
N2  - Aldehyde oxidase (AOX) is characterized by a broad substrate specificity, oxidizing aromatic azaheterocycles, such as N(1)-methylnicotinamide and N-methylphthalazinium, or aldehydes, such as benzaldehyde, retinal, and vanillin. In the past decade, AOX has been recognized increasingly to play an important role in the metabolism of drugs through its complex cofactor content, tissue distribution, and substrate recognition. In humans, only one AOX gene (AOX1) is present, but in mouse and other mammals different AOX homologs were identified. The multiple AOX isoforms are expressed tissue-specifically in different organisms, and it is believed that they recognize distinct substrates and carry out different physiological tasks. AOX is a dimer with a molecular mass of approximately 300 kDa, and each subunit of the homodimeric enzyme contains four different cofactors: the molybdenum cofactor, two distinct [2Fe-2S] clusters, and one FAD. We purified the AOX homolog from mouse liver (mAOX3) and established a system for the heterologous expression of mAOX3 in Escherichia coli. The purified enzymes were compared. Both proteins show the same characteristics and catalytic properties, with the difference that the recombinant protein was expressed and purified in a 30% active form, whereas the native protein is 100% active. Spectroscopic characterization showed that FeSII is not assembled completely in mAOX3. In addition, both proteins were crystallized. The best crystals were from native mAOX3 and diffracted beyond 2.9 angstrom. The crystals belong to space group P1, and two dimers are present in the unit cell.
Y1  - 2011
U6  - https://doi.org/10.1124/dmd.111.040873
SN  - 0090-9556
VL  - 39
IS  - 10
SP  - 1939
EP  - 1945
PB  - American Society for Pharmacology and Experimental Therapeutics
CY  - Bethesda
ER  - 
TY  - RPRT
A1  - Brodeur, Abel
A1  - Mikola, Derek
A1  - Cook, Nikolai
A1  - Brailey, Thomas
A1  - Briggs, Ryan
A1  - Gendre, Alexandra de
A1  - Dupraz, Yannick
A1  - Fiala, Lenka
A1  - Gabani, Jacopo
A1  - Gauriot, Romain
A1  - Haddad, Joanne
A1  - Lima, Goncalo
A1  - Ankel-Peters, Jörg
A1  - Dreber, Anna
A1  - Campbell, Douglas
A1  - Kattan, Lamis
A1  - Fages, Diego Marino
A1  - Mierisch, Fabian
A1  - Sun, Pu
A1  - Wright, Taylor
A1  - Connolly, Marie
A1  - Hoces de la Guardia, Fernando
A1  - Johannesson, Magnus
A1  - Miguel, Edward
A1  - Vilhuber, Lars
A1  - Abarca, Alejandro
A1  - Acharya, Mahesh
A1  - Adjisse, Sossou Simplice
A1  - Akhtar, Ahwaz
A1  - Lizardi, Eduardo Alberto Ramirez
A1  - Albrecht, Sabina
A1  - Andersen, Synve Nygaard
A1  - Andlib, Zubaria
A1  - Arrora, Falak
A1  - Ash, Thomas
A1  - Bacher, Etienne
A1  - Bachler, Sebastian
A1  - Bacon, Félix
A1  - Bagues, Manuel
A1  - Balogh, Timea
A1  - Batmanov, Alisher
A1  - Barschkett, Mara
A1  - Basdil, B. Kaan
A1  - Dower, Jaromneda
A1  - Castek, Ondrej
A1  - Caviglia-Harris, Jill
A1  - Strand, Gabriella Chauca
A1  - Chen, Shi
A1  - Chzhen, Asya
A1  - Chung, Jong
A1  - Collins, Jason
A1  - Coppock, Alexander
A1  - Cordeau, Hugo
A1  - Couillard, Ben
A1  - Crechet, Jonathan
A1  - Crippa, Lorenzo
A1  - Cui, Jeanne
A1  - Czymara, Christian
A1  - Daarstad, Haley
A1  - Dao, Danh Chi
A1  - Dao, Dong
A1  - Schmandt, Marco David
A1  - Linde, Astrid de
A1  - Melo, Lucas De
A1  - Deer, Lachlan
A1  - Vera, Micole De
A1  - Dimitrova, Velichka
A1  - Dollbaum, Jan Fabian
A1  - Dollbaum, Jan Matti
A1  - Donnelly, Michael
A1  - Huynh, Luu Duc Toan
A1  - Dumbalska, Tsvetomira
A1  - Duncan, Jamie
A1  - Duong, Kiet Tuan
A1  - Duprey, Thibaut
A1  - Dworschak, Christoph
A1  - Ellingsrud, Sigmund
A1  - Elminejad, Ali
A1  - Eissa, Yasmine
A1  - Erhart, Andrea
A1  - Etingin-Frati, Giulian
A1  - Fatemi-Pour, Elaheh
A1  - Federice, Alexa
A1  - Feld, Jan
A1  - Fenig, Guidon
A1  - Firouzjaeiangalougah, Mojtaba
A1  - Fleisje, Erlend
A1  - Fortier-Chouinard, Alexandre
A1  - Engel, Julia Francesca
A1  - Fries, Tilman
A1  - Fortier, Reid
A1  - Fréchet, Nadjim
A1  - Galipeau, Thomas
A1  - Gallegos, Sebastián
A1  - Gangji, Areez
A1  - Gao, Xiaoying
A1  - Garnache, Cloé
A1  - Gáspár, Attila
A1  - Gavrilova, Evelina
A1  - Ghosh, Arijit
A1  - Gibney, Garreth
A1  - Gibson, Grant
A1  - Godager, Geir
A1  - Goff, Leonard
A1  - Gong, Da
A1  - González, Javier
A1  - Gretton, Jeremy
A1  - Griffa, Cristina
A1  - Grigoryeva, Idaliya
A1  - Grtting, Maja
A1  - Guntermann, Eric
A1  - Guo, Jiaqi
A1  - Gugushvili, Alexi
A1  - Habibnia, Hooman
A1  - Häffner, Sonja
A1  - Hall, Jonathan D.
A1  - Hammar, Olle
A1  - Kordt, Amund Hanson
A1  - Hashimoto, Barry
A1  - Hartley, Jonathan S.
A1  - Hausladen, Carina I.
A1  - Havránek, Tomáš
A1  - Hazen, Jacob
A1  - He, Harry
A1  - Hepplewhite, Matthew
A1  - Herrera-Rodriguez, Mario
A1  - Heuer, Felix
A1  - Heyes, Anthony
A1  - Ho, Anson T. Y.
A1  - Holmes, Jonathan
A1  - Holzknecht, Armando
A1  - Hsu, Yu-Hsiang Dexter
A1  - Hu, Shiang-Hung
A1  - Huang, Yu-Shiuan
A1  - Huebener, Mathias
A1  - Huber, Christoph
A1  - Huynh, Kim P.
A1  - Irsova, Zuzana
A1  - Isler, Ozan
A1  - Jakobsson, Niklas
A1  - Frith, Michael James
A1  - Jananji, Raphaël
A1  - Jayalath, Tharaka A.
A1  - Jetter, Michael
A1  - John, Jenny
A1  - Forshaw, Rachel Joy
A1  - Juan, Felipe
A1  - Kadriu, Valon
A1  - Karim, Sunny
A1  - Kelly, Edmund
A1  - Dang, Duy Khanh Hoang
A1  - Khushboo, Tazia
A1  - Kim, Jin
A1  - Kjellsson, Gustav
A1  - Kjelsrud, Anders
A1  - Kotsadam, Andreas
A1  - Korpershoek, Jori
A1  - Krashinsky, Lewis
A1  - Kundu, Suranjana
A1  - Kustov, Alexander
A1  - Lalayev, Nurlan
A1  - Langlois, Audrée
A1  - Laufer, Jill
A1  - Lee-Whiting, Blake
A1  - Leibing, Andreas
A1  - Lenz, Gabriel
A1  - Levin, Joel
A1  - Li, Peng
A1  - Li, Tongzhe
A1  - Lin, Yuchen
A1  - Listo, Ariel
A1  - Liu, Dan
A1  - Lu, Xuewen
A1  - Lukmanova, Elvina
A1  - Luscombe, Alex
A1  - Lusher, Lester R.
A1  - Lyu, Ke
A1  - Ma, Hai
A1  - Mäder, Nicolas
A1  - Makate, Clifton
A1  - Malmberg, Alice
A1  - Maitra, Adit
A1  - Mandas, Marco
A1  - Marcus, Jan
A1  - Margaryan, Shushanik
A1  - Márk, Lili
A1  - Martignano, Andres
A1  - Marsh, Abigail
A1  - Masetto, Isabella
A1  - McCanny, Anthony
A1  - McManus, Emma
A1  - McWay, Ryan
A1  - Metson, Lennard
A1  - Kinge, Jonas Minet
A1  - Mishra, Sumit
A1  - Mohnen, Myra
A1  - Möller, Jakob
A1  - Montambeault, Rosalie
A1  - Montpetit, Sébastien
A1  - Morin, Louis-Philippe
A1  - Morris, Todd
A1  - Moser, Scott
A1  - Motoki, Fabio
A1  - Muehlenbachs, Lucija
A1  - Musulan, Andreea
A1  - Musumeci, Marco
A1  - Nabin, Munirul
A1  - Nchare, Karim
A1  - Neubauer, Florian
A1  - Nguyen, Quan M. P.
A1  - Nguyen, Tuan
A1  - Nguyen-Tien, Viet
A1  - Niazi, Ali
A1  - Nikolaishvili, Giorgi
A1  - Nordstrom, Ardyn
A1  - Nü, Patrick
A1  - Odermatt, Angela
A1  - Olson, Matt
A1  - ien, Henning
A1  - Ölkers, Tim
A1  - Vert, Miquel Oliver i.
A1  - Oral, Emre
A1  - Oswald, Christian
A1  - Ousman, Ali
A1  - Özak, Ömer
A1  - Pandey, Shubham
A1  - Pavlov, Alexandre
A1  - Pelli, Martino
A1  - Penheiro, Romeo
A1  - Park, RyuGyung
A1  - Martel, Eva Pérez
A1  - Petrovičová, Tereza
A1  - Phan, Linh
A1  - Prettyman, Alexa
A1  - Procházka, Jakub
A1  - Putri, Aqila
A1  - Quandt, Julian
A1  - Qiu, Kangyu
A1  - Nguyen, Loan Quynh Thi
A1  - Rahman, Andaleeb
A1  - Rea, Carson H.
A1  - Reiremo, Adam
A1  - Renée, Laëtitia
A1  - Richardson, Joseph
A1  - Rivers, Nicholas
A1  - Rodrigues, Bruno
A1  - Roelofs, William
A1  - Roemer, Tobias
A1  - Rogeberg, Ole
A1  - Rose, Julian
A1  - Roskos-Ewoldsen, Andrew
A1  - Rosmer, Paul
A1  - Sabada, Barbara
A1  - Saberian, Soodeh
A1  - Salamanca, Nicolas
A1  - Sator, Georg
A1  - Sawyer, Antoine
A1  - Scates, Daniel
A1  - Schlüter, Elmar
A1  - Sells, Cameron
A1  - Sen, Sharmi
A1  - Sethi, Ritika
A1  - Shcherbiak, Anna
A1  - Sogaolu, Moyosore
A1  - Soosalu, Matt
A1  - Srensen, Erik
A1  - Sovani, Manali
A1  - Spencer, Noah
A1  - Staubli, Stefan
A1  - Stans, Renske
A1  - Stewart, Anya
A1  - Stips, Felix
A1  - Stockley, Kieran
A1  - Strobel, Stephenson
A1  - Struby, Ethan
A1  - Tang, John
A1  - Tanrisever, Idil
A1  - Yang, Thomas Tao
A1  - Tastan, Ipek
A1  - Tatić, Dejan
A1  - Tatlow, Benjamin
A1  - Seuyong, Féraud Tchuisseu
A1  - Thériault, Rémi
A1  - Thivierge, Vincent
A1  - Tian, Wenjie
A1  - Toma, Filip-Mihai
A1  - Totarelli, Maddalena
A1  - Tran, Van-Anh
A1  - Truong, Hung
A1  - Tsoy, Nikita
A1  - Tuzcuoglu, Kerem
A1  - Ubfal, Diego
A1  - Villalobos, Laura
A1  - Walterskirchen, Julian
A1  - Wang, Joseph Taoyi
A1  - Wattal, Vasudha
A1  - Webb, Matthew D.
A1  - Weber, Bryan
A1  - Weisser, Reinhard
A1  - Weng, Wei-Chien
A1  - Westheide, Christian
A1  - White, Kimberly
A1  - Winter, Jacob
A1  - Wochner, Timo
A1  - Woerman, Matt
A1  - Wong, Jared
A1  - Woodard, Ritchie
A1  - Wroński, Marcin
A1  - Yazbeck, Myra
A1  - Yang, Gustav Chung
A1  - Yap, Luther
A1  - Yassin, Kareman
A1  - Ye, Hao
A1  - Yoon, Jin Young
A1  - Yurris, Chris
A1  - Zahra, Tahreen
A1  - Zaneva, Mirela
A1  - Zayat, Aline
A1  - Zhang, Jonathan
A1  - Zhao, Ziwei
A1  - Yaolang, Zhong
T1  - Mass reproducibility and replicability
BT  - a new hope
T2  - I4R discussion paper series
N2  - This study pushes our understanding of research reliability by reproducing and replicating claims from 110 papers in leading economic and political science journals. The analysis involves computational reproducibility checks and robustness assessments. It reveals several patterns. First, we uncover a high rate of fully computationally reproducible results (over 85%). Second, excluding minor issues like missing packages or broken pathways, we uncover coding errors for about 25% of studies, with some studies containing multiple errors. Third, we test the robustness of the results to 5,511 re-analyses. We find a robustness reproducibility of about 70%. Robustness reproducibility rates are relatively higher for re-analyses that introduce new data and lower for re-analyses that change the sample or the definition of the dependent variable. Fourth, 52% of re-analysis effect size estimates are smaller than the original published estimates and the average statistical significance of a re-analysis is 77% of the original. Lastly, we rely on six teams of researchers working independently to answer eight additional research questions on the determinants of robustness reproducibility. Most teams find a negative relationship between replicators' experience and reproducibility, while finding no relationship between reproducibility and the provision of intermediate or even raw data combined with the necessary cleaning codes.
KW  - conomics
KW  - open science
KW  - political science
KW  - replication
KW  - reproduction
KW  - research transparency
Y1  - 2024
SN  - 2752-1931
IS  - 107
PB  - Institute for Replication
CY  - Essen
ER  -