Welcome to the Robertson Laboratory Journal Club! In these meetings, we will discuss new and old papers that are related to the research we carry out in the lab. Selected papers will focus on the following topics: experimental and computational studies of membrane protein form and function, membrane protein folding and synthesis, and the physical behavior of lipid bilayers. If you are interested in attending, please email Janice Robertson (janice.robertson@wustl.edu) to get on the email list.
Where: Zoom
When: Tuesdays, 2-3 pm
11.02.2021
Highly accurate protein structure prediction with AlphaFold
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, Alex Bridgland, Clemens Meyer, Simon A. A. Kohl, Andrew J. Ballard, Andrew Cowie, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Jonas Adler, Trevor Back, Stig Petersen, David Reiman, Ellen Clancy, Michal Zielinski, Martin Steinegger, Michalina Pacholska, Tamas Berghammer, Sebastian Bodenstein, David Silver, Oriol Vinyals, Andrew W. Senior, Koray Kavukcuoglu, Pushmeet Kohli & Demis Hassabis
Nature volume 596, pages583–589 (2021)
10.19.2021
Martini 3: a general purpose force field for coarse-grained molecular dynamics
Paulo C. T. Souza, Riccardo Alessandri,Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino, Fabian Grünewald, Ilias Patmanidis, Haleh Abdizadeh, Bart M. H. Bruininks, Tsjerk A. Wassenaar, Peter C. Kroon, Josef Melcr, Vincent Nieto, Valentina Corradi, Hanif M. Khan, Jan Domański, Matti Javanainen, Hector Martinez-Seara, Nathalie Reuter, Robert B. Best, Ilpo Vattulainen, Luca Monticelli, Xavier Periole, D. Peter Tieleman, Alex H. de Vries & Siewert J. Marrink
Nature Methods volume 18, pages382–388 (2021)
10.05.2021
Membrane Exporters of Fluoride Ion
Benjamin C. McIlwain,1 Michal T. Ruprecht,1 and Randy B. Stockbridge
Annual Review of Biochemistry Vol. 90:559-579 (Volume publication date June 2021)
09.14.2021
Mechanism of CFTR correction by type I folding correctors
Karol Fiedorczuk, Jue Chen
bioRxiv preprint, June 18, 2021
https://doi.org/10.1101/2021.06.18.449063
09.07.2021
Structure and dynamics of the drug-bound bacterial transporter EmrE in lipid bilayers
Alexander A. Shcherbakov, Grant Hisao, Venkata S. Mandala, Nathan E. Thomas, Mohammad Soltani, E. A. Salter, James H. Davis Jr., Katherine A. Henzler-Wildman & Mei Hong
Nature Communications volume 12, Article number: 172 (2021)
04.16.2020
Best Practices for Foundations in Molecular Simulations [Article v1.0]
Efrem Braun, Justin Gilmer, Heather B. Mayes, David L. Mobley, Jacob I. Monroe, Samarjeet Prasad, Daniel M. Zuckerman
LivingJ.Comp.Mol.Sci.2019,1(1),5957
04.02.2020
Best Practices for Foundations in Molecular Simulations [Article v1.0]
Efrem Braun, Justin Gilmer, Heather B. Mayes, David L. Mobley, Jacob I. Monroe, Samarjeet Prasad, Daniel M. Zuckerman
LivingJ.Comp.Mol.Sci.2019,1(1),5957
03.03.2020
Structural characterization of an intermediate reveals a unified mechanism for the CLC Cl–/H+ transport cycle
Tanmay S. Chavan, Ricky C. Cheng, Tao Jiang, Irimpan I. Mathews, Richard A. Stein, Antoine Koehl, Hassane S. Mchaourab, Emad Tajkhorshid, Merritt Maduke
bioRxiv preprint, November 27, 2019
02.25.2020
Mitochondrial ATP synthase dimers spontaneously associate due to a long-range membrane-induced force
Claudio Anselmi, Karen M. Davies, & José D. Faraldo-Gómez
J Gen Physiol (2018) 150 (5): 763–770.
02.11.2020
De novo design of a transmembrane Zn2+-transporting four-helix bundle
Nathan H. Joh, Tuo Wang, Manasi P. Bhate, Rudresh Acharya, Yibing Wu, Michael Grabe, Mei Hong, Gevorg Grigoryan, William F. DeGrado
Science 346 (6216), 1520-1524.
01.28.2020
Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins
Hao Yu, Matthew G. W. Siewny, Devin T. Edwards, Aric W. Sanders, Thomas T. Perkins
Science 355 (6328), 945-950.
01.22.2020
Quantifying secondary transport at single-molecule resolution
Gabriel A. Fitzgerald, Daniel S. Terry, Audrey L. Warren, Matthias Quick, Jpnathan A. Javitch & Scott C. Blanchard
Nature volume 575, pages528–534(2019).
11.21.2019
Packing of apolar side chains enables accurate design of highly stable membrane proteins
Marco Mravic, Jessica L. Thomaston, Maxwell Tucker, Paige E. Solomon, Lijun Liu, William F. DeGrado
Science 363 (6434), 1418-1423.
11.07.2019
Correlation between the Abundance of Escherichia coli Transfer RNAs and the Occurrence of the Respective Codons in its Protein Genes
Toshimichi Ikemura
J. Mol. Biol. (1981) 146, 1-21.
10.24.2019
TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action
Yuan Gao, Erhu Cao, David Julius & Yifan Cheng
Nature volume 534, pages347–351(2016).
08.29.2019
Allostery revealed within lipid binding events to membrane proteins
John W. Patrick, Christopher D. Boone, Wen Liu, Gloria M, Conover, Yang Liu, Xiao Cong, & Arthur Laganowsky
PNAS March 20, 2018 115 (12) 2976-2981.
08.22.2019
Expression, purification, and contaminant detection for structural studies of Ralstonia metallidurance ClC protein rm1
Priyanka D. Abeyrathne, Nikolaus Grigorieff
PLoS ONE 12(7): e0180163.
08.15.2019
Dynamic tunable G protein-coupled receptor monomer-dimer populations
Patricia M. Dijkman, Oliver K. Castell, Alan D. Goddard, Juan C. Munoz-Garcia, Chris de Graaf, Mark I. Wallace & Anthony Watts
Nature Communications 9, Article number:1710 (2018).
08.01.2019
Membrane Proteins Can Hive High Kinetic Stability
Robert E. Jefferson, Tracy M. Blois, & James U. Bowie
J. Am. Chem. Soc. 2013, 135, 40, 15183-15190.
07.25.2019
Structural and mechanistic basis of proton-coupled metal ion transport in the SLC11/NRAMP family
Ines A. Ehrnstorfer, Cristina Manatscha, Fabian M. Arnold, Juerg Laederach & Raimund Dutzler
Nature Communications 8, Article number:14033 (2017).
06.06.2019
Direct protein-lipid interactions shape the conformational landscape of secondary transporters
Chloe Martens, Mrinal Shekhar, Antoni J. Borysik, Andy M. Lau, Eamonn Reading, Emad Tajkhorshid, Paula J. Booth & Argyris Politis.
Nature Communications 9, Article number:4151 (2018).
05.30.2019
Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporter
X. Yu, G. Yang, C. Yan, J.L. Baylon, J. Jiang, H. Fan, G. Lu, K. Hasegawa, H. Okumura, T. Wang, E. Tajkhorshid, S. Li & N. Yan.
Cell Res. 2017 Aug; 27(8): 1020-1033
doi: 10.1038/cr.2017.83
05.23.2019
Diblock copolymers enhance folding of a mechanosensitive membrane protein during cell-free expression.
M.L. Jacobs, M.A. Boyd & N.P. Kamat.
PNAS March 5, 2019 116 (10) 4031-4036
05.16.2019
Dual-topology insertion of a dual-topology membrane protein
N. Woodall, Y. Yin and James U. Bowie.
Nature Communications 6, Article number:8099 (2015).
05.09.2019
Confronting Fusion Protein-Based Membrane Protein Topology Mapping with Reality: The Escherichia coli ClcA H+/Cl- Exchange Transporter.
M. Cassel, S. Seppälä and Gunnar von Heijne.
J. Mol. Biol. (2008) 381, 860-866.