Atomistic insight on structure and dynamics of spinach acyl carrier protein with substrate length

Baer, Marcel D.; Shanklin, John; Raugei, Simone

doi:10.1016/j.bpj.2020.12.036

Title: Atomistic insight on structure and dynamics of spinach acyl carrier protein with substrate length

Journal Article · 31 August 2021 · Biophysical Journal

DOI: https://doi.org/10.1016/j.bpj.2020.12.036 · OSTI ID:1812551

Baer, Marcel D.; Shanklin, John; Raugei, Simone

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1812551

Report Number(s):: PNNL-SA--155027; S0006349521001612; PII: S0006349521001612

Journal Information:: Biophysical Journal, Journal Name: Biophysical Journal Journal Issue: 17 Vol. 120; ISSN 0006-3495

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (32)

Peptide Folding: When Simulation Meets Experiment Daura, Xavier; Gademann, Karl; Jaun, Bernhard Angewandte Chemie International Edition, Vol. 38, Issue 1-2 https://doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M	journal	January 1999
Modifying the Thioester Linkage Affects the Structure of the Acyl Carrier Protein Sztain, Terra; Patel, Ashay; Lee, D. John Angewandte Chemie International Edition, Vol. 58, Issue 32 https://doi.org/10.1002/anie.201903815	journal	August 2019
Using Modern Tools To Probe the Structure-Function Relationship of Fatty Acid Synthases Finzel, Kara; Lee, D. John; Burkart, Michael D. ChemBioChem, Vol. 16, Issue 4 https://doi.org/10.1002/cbic.201402578	journal	February 2015
Umbrella sampling: Umbrella sampling Kästner, Johannes Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 6 https://doi.org/10.1002/wcms.66	journal	May 2011
Principal Component Analysis: A Method for Determining the Essential Dynamics of Proteins David, Charles C.; Jacobs, Donald J. Protein Dynamics https://doi.org/10.1007/978-1-62703-658-0_11	book	January 2013
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M. Computer Methods, Part C https://doi.org/10.1016/B978-0-12-381270-4.00019-6	book	January 2011
PLUMED 2: New feathers for an old bird Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide Computer Physics Communications, Vol. 185, Issue 2 https://doi.org/10.1016/j.cpc.2013.09.018	journal	February 2014
Structural Studies of Fatty Acyl-(Acyl Carrier Protein) Thioesters Reveal a Hydrophobic Binding Cavity that Can Expand to Fit Longer Substrates Roujeinikova, Anna; Simon, William J.; Gilroy, John Journal of Molecular Biology, Vol. 365, Issue 1 https://doi.org/10.1016/j.jmb.2006.09.049	journal	January 2007
RosettaLigand Docking with Full Ligand and Receptor Flexibility Davis, Ian W.; Baker, David Journal of Molecular Biology, Vol. 385, Issue 2 https://doi.org/10.1016/j.jmb.2008.11.010	journal	January 2009
Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field Robertson, Michael J.; Tirado-Rives, Julian; Jorgensen, William L. Journal of Chemical Theory and Computation, Vol. 11, Issue 7 https://doi.org/10.1021/acs.jctc.5b00356	journal	June 2015
Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate ^† ^, ^‡ Zornetzer, Gregory A.; Fox, Brian G.; Markley, John L. Biochemistry, Vol. 45, Issue 16 https://doi.org/10.1021/bi052062d	journal	April 2006
The Length of the Bound Fatty Acid Influences the Dynamics of the Acyl Carrier Protein and the Stability of the Thioester Bond Zornetzer, Gregory A.; Tanem, Justinn; Fox, Brian G. Biochemistry, Vol. 49, Issue 3 https://doi.org/10.1021/bi9014659	journal	January 2010
g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates Hub, Jochen S.; de Groot, Bert L.; van der Spoel, David Journal of Chemical Theory and Computation, Vol. 6, Issue 12 https://doi.org/10.1021/ct100494z	journal	November 2010
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation Hess, Berk; Kutzner, Carsten; van der Spoel, David Journal of Chemical Theory and Computation, Vol. 4, Issue 3 https://doi.org/10.1021/ct700301q	journal	February 2008
Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I. Journal of the American Chemical Society, Vol. 115, Issue 21 https://doi.org/10.1021/ja00074a030	journal	October 1993
Hydrophobicity Scaling of Aqueous Interfaces by an Electrostatic Mapping Remsing, Richard C.; Weeks, John D. The Journal of Physical Chemistry B, Vol. 119, Issue 29 https://doi.org/10.1021/jp509903n	journal	September 2014
The ubiquitous carrier protein—a window to metabolite biosynthesis Mercer, Andrew C.; Burkart, Michael D. Natural Product Reports, Vol. 24, Issue 4 https://doi.org/10.1039/b603921a	journal	January 2007
The structural role of the carrier protein – active controller or passive carrier Crosby, John; Crump, Matthew P. Natural Product Reports, Vol. 29, Issue 10 https://doi.org/10.1039/c2np20062g	journal	January 2012
Comparative structure, dynamics and evolution of acyl-carrier proteins from Borrelia burgdorferi, Brucella melitensis and Rickettsia prowazekii Barnwal, Ravi P.; Kaur, Mandeep; Heckert, Alec Biochemical Journal, Vol. 477, Issue 2 https://doi.org/10.1042/BCJ20190797	journal	January 2020
Isoforms of acyl carrier protein involved in seed‐specific fatty acid synthesis Suh, Mi Chung; Schultz, David J.; Ohlrogge, John B. The Plant Journal, Vol. 17, Issue 6 https://doi.org/10.1046/j.1365-313X.1999.00418.x	journal	March 1999
Perspective: How good is DFT for water? Gillan, Michael J.; Alfè, Dario; Michaelides, Angelos The Journal of Chemical Physics, Vol. 144, Issue 13 https://doi.org/10.1063/1.4944633	journal	April 2016
Remote control of regioselectivity in acyl-acyl carrier protein-desaturases Guy, J. E.; Whittle, E.; Moche, M. Proceedings of the National Academy of Sciences, Vol. 108, Issue 40 https://doi.org/10.1073/pnas.1110221108	journal	September 2011
Redesign of soluble fatty acid desaturases from plants for altered substrate specificity and double bond position Cahoon, E. B.; Lindqvist, Y.; Schneider, G. Proceedings of the National Academy of Sciences, Vol. 94, Issue 10 https://doi.org/10.1073/pnas.94.10.4872	journal	May 1997
The Crystal Structure of the Ivy Δ ⁴ -16:0-ACP Desaturase Reveals Structural Details of the Oxidized Active Site and Potential Determinants of Regioselectivity Guy, Jodie E.; Whittle, Edward; Kumaran, Desigan Journal of Biological Chemistry, Vol. 282, Issue 27 https://doi.org/10.1074/jbc.M702520200	journal	April 2007
Molecular Dynamics Simulations of the Apo-, Holo-, and Acyl-forms of Escherichia coli Acyl Carrier Protein Chan, David I.; Stockner, Thomas; Tieleman, D. Peter Journal of Biological Chemistry, Vol. 283, Issue 48 https://doi.org/10.1074/jbc.M805323200	journal	September 2008
Desaturases: Emerging Models for Understanding Functional Diversification of Diiron-containing Enzymes Shanklin, John; Guy, Jodie E.; Mishra, Girish Journal of Biological Chemistry, Vol. 284, Issue 28 https://doi.org/10.1074/jbc.R900009200	journal	April 2009
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Pronk, Sander; Páll, Szilárd; Schulz, Roland Bioinformatics, Vol. 29, Issue 7 https://doi.org/10.1093/bioinformatics/btt055	journal	February 2013
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
Desaturation and Related Modifications of Fatty Acids Shanklin, John; Cahoon, Edgar B. Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 49, Issue 1 https://doi.org/10.1146/annurev.arplant.49.1.611	journal	June 1998
The application of computational methods to explore the diversity and structure of bacterial fatty acid synthase Zhang, Yong-Mei; Marrakchi, Hedia; White, Stephen W. Journal of Lipid Research, Vol. 44, Issue 1 https://doi.org/10.1194/jlr.R200016-JLR200	journal	November 2002
Structure, function and dynamics in acyl carrier proteins Farmer, Rohit; Thomas, Christopher Morton; Winn, Peter James PLOS ONE, Vol. 14, Issue 7 https://doi.org/10.1371/journal.pone.0219435	journal	July 2019
Structural Characterization of an ACP from Thermotoga maritima: Insights into Hyperthermal Adaptation Lee, Yeongjoon; Jang, Ahjin; Jeong, Min-Cheol International Journal of Molecular Sciences, Vol. 21, Issue 7 https://doi.org/10.3390/ijms21072600	journal	April 2020

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