boat conformation - PMC

Wenxin Fu, Todd M. Alam, Jiachen Li, Jacqueline Bustamante, Thanh Lien, Ralph W. Adams, Simon J. Teat, Benjamin J. Stokes, Weitao Yang, Yi Liu, Jennifer Q. Lu

J Am Chem Soc. Author manuscript; available in PMC 2021 Sep 30.

Published in final edited form as: J Am Chem Soc. 2020 Sep 30; 142(39): 16651–16660. Published online 2020 Sep 17. doi: 10.1021/jacs.0c06579

PMCID:: PMC8341137

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How Accurate Can Crystal Structure Predictions Be for High-Energy Molecular Crystals?

Xavier Bidault, Santanu Chaudhuri

Molecules. 2023 Jun; 28(11): 4471. Published online 2023 May 31. doi: 10.3390/molecules28114471

PMCID:: PMC10254755

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Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy

Göran Widmalm

JACS Au. 2024 Jan 22; 4(1): 20–39. Published online 2024 Jan 3. doi: 10.1021/jacsau.3c00639

PMCID:: PMC10807006

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Controlling opioid receptor functional selectivity by targeting distinct subpockets of the orthosteric site

Rajendra Uprety, Tao Che, Saheem A Zaidi, Steven G Grinnell, Balázs R Varga, Abdelfattah Faouzi, Samuel T Slocum, Abdullah Allaoa, András Varadi, Melissa Nelson, Sarah M Bernhard, Elizaveta Kulko, Valerie Le Rouzic, Shainnel O Eans, Chloe A Simons, Amanda Hunkele, Joan Subrath, Ying Xian Pan, Jonathan A Javitch, Jay P McLaughlin, Bryan L Roth, Gavril W Pasternak, Vsevolod Katritch, Susruta Majumdar

eLife. 2021; 10: e56519. Published online 2021 Feb 8. doi: 10.7554/eLife.56519

PMCID:: PMC7909954

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Self-Assembly of Mesoscale Isomers: The Role of Pathways and Degrees of Freedom

Shivendra Pandey, Daniel Johnson, Ryan Kaplan, Joseph Klobusicky, Govind Menon, David H. Gracias

PLoS One. 2014; 9(10): e108960. Published online 2014 Oct 9. doi: 10.1371/journal.pone.0108960

PMCID:: PMC4191966

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Squaraine Rotaxanes with Boat Conformation Macrocycles

Na Fu, Jeffrey M. Baumes, Easwaran Arunkumar, Bruce C. Noll, Bradley D. Smith

J Org Chem. Author manuscript; available in PMC 2010 Mar 31.

Published in final edited form as: J Org Chem. 2009 Sep 4; 74(17): 6462–6468. doi: 10.1021/jo901298n

PMCID:: PMC2847772

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A Twist on Facial Selectivity of Hydride Reductions of Cyclic Ketones: Twist-Boat Conformers in Cyclohexanone, Piperidone, and Tropinone Reactions

Sharon R. Neufeldt, Gonzalo Jiménez-Osés, Daniel L. Comins, K. N. Houk

J Org Chem. 2014 Dec 5; 79(23): 11609–11618. Published online 2014 Nov 5. doi: 10.1021/jo5022635

PMCID:: PMC4260662

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Glycosyl Oxocarbenium Ions: Structure, Conformation, Reactivity, and Interactions

Antonio Franconetti, Ana Ardá, Juan Luis Asensio, Yves Blériot, Sébastien Thibaudeau, Jesús Jiménez-Barbero

Acc Chem Res. 2021 Jun 1; 54(11): 2552–2564. Published online 2021 Apr 30. doi: 10.1021/acs.accounts.1c00021

PMCID:: PMC8173606

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Glycoside Hydrolases Restrict the Side Chain Conformation of their Substrates to Gain Additional Transition State Stabilization

Jonathan C. K. Quirke, David Crich

J Am Chem Soc. Author manuscript; available in PMC 2021 Oct 7.

Published in final edited form as: J Am Chem Soc. 2020 Oct 7; 142(40): 16965–16973. Published online 2020 Sep 24. doi: 10.1021/jacs.0c05592

PMCID:: PMC7544649

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BoatNet: automated small boat composition detection using deep learning on satellite imagery

Guo Jialeng, Santiago Suárez de la Fuente, Tristan Smith

UCL Open Environ. 2023; 5: e058. Published online 2023 May 24. doi: 10.14324/111.444/ucloe.000058

PMCID:: PMC10208328

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RmlC, a C3′ and C3′ carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation.

Changjiang Dong, Louise L. Major, Velupillai Srikannathasan, James C. Errey, Marie-France Giraud, Joseph S. Lam, Michael Graninger, Paul Messner, Michael R. McNeil, Robert A. Field, Chris Whitfield, James H. Naismith

J Mol Biol. Author manuscript; available in PMC 2008 Jan 5.

Published in final edited form as: J Mol Biol. 2007 Jan 5; 365(1): 146–159. Published online 2006 Sep 29. doi: 10.1016/j.jmb.2006.09.063

PMCID:: PMC1805628

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Conformation-Activity Relationships of Polyketide Natural Products

Erik M. Larsen, Matthew R. Wilson, Richard E. Taylor

Nat Prod Rep. Author manuscript; available in PMC 2016 Aug 1.

Published in final edited form as: Nat Prod Rep. 2015 Aug; 32(8): 1183–1206. doi: 10.1039/c5np00014a

PMCID:: PMC4443481

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Mechanisms of Stereodirecting Participation and Ester Migration from Near and Far in Glycosylation and Related Reactions

Asiri A. Hettikankanamalage, Robert Lassfolk, Filip S. Ekholm, Reko Leino, David Crich

Chem Rev. Author manuscript; available in PMC 2021 Aug 12.

Published in final edited form as: Chem Rev. 2020 Aug 12; 120(15): 7104–7151. Published online 2020 Jul 5. doi: 10.1021/acs.chemrev.0c00243

PMCID:: PMC7429366

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Human O-GlcNAcase Uses a Preactivated Boat-skew Substrate Conformation for Catalysis. Evidence from X-ray Crystallography and QM/MM Metadynamics

Martín Calvelo, Alexandra Males, Matthew G. Alteen, Lianne I. Willems, David J. Vocadlo, Gideon J. Davies, Carme Rovira

ACS Catal. 2023 Oct 20; 13(20): 13672–13678. Published online 2023 Oct 10. doi: 10.1021/acscatal.3c02378

PMCID:: PMC10636738

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Sub-Angstrom Conformational Changes of a Single Molecule Captured by AFM Variance Analysis

Kirstin A. Walther, Jasna Brujić, Hongbin Li, Julio M. Fernández

Biophys J. 2006 May 15; 90(10): 3806–3812. Published online 2006 Feb 24. doi: 10.1529/biophysj.105.076224

PMCID:: PMC1440761

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Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM

Piotr E. Marszalek, Hongbin Li, Andres F. Oberhauser, Julio M. Fernandez

Proc Natl Acad Sci U S A. 2002 Apr 2; 99(7): 4278–4283. Published online 2002 Mar 26. doi: 10.1073/pnas.072435699

PMCID:: PMC123639

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PMC Images search for boat conformation

Fig. 7(a). Key NOESY correlations of the selected norditerpenoid alkaloids in depiction B1 (B1′). Depiction B1 shows the A-ring in chair conformation and depiction B1′ shows the A-ring in boat conformation. (b) Key NOESY correlations of the selected norditerpenoid alkaloids in depiction C2 (C2′). Depiction C2 shows the A-ring in chair conformation and depiction C2′ shows the A-ring in boat conformation. (c). Key NOESY correlations of the selected norditerpenoid alkaloids in depiction B4 (B4′). Depiction B4 shows the A-ring in chair conformation and depiction B4′ shows the A-ring in boat conformation.

The 1α-hydroxy-A-rings of norditerpenoid alkaloids are twisted-boat conformers

RSC Adv. 2020 May 14;10(32):18797-18805.
Figure 8OOP ring conformations and validation of mm_std score function on side chain dihedrals in different ring conformations.

A) Overlay of half-chair (blue) and boat (green) OOP ring conformations. B) Structure of half-chair OOP ring conformation. C) Structure of boat OOP ring conformation. D) QM energy calculations (Kcal/mol) of different side chain dihedral angles. Blue represents half-chair conformation. Green represents boat conformation. The half-chair conformation is lower in energy in two out of the three dihedral energy wells ( and ) but nearly isoenergetic with the boat conformation in the third (). E) QM energy (solid) and ROSETTA mm_std (dash, ROSETTA Energy Units) energy calculations for dihedral angles with OOP ring in half-chair conformation. Red X's show values of oxopiperazine side chains (labeled with Cambridge Structural Database code). F) QM energy (solid) and ROSETTA mm_std (dash, ROSETTA Energy Units) energy calculations for dihedral angles with OOP ring in boat conformation. For both (E) and (F), ROSETTA mm_std score function recapitulates the low energy minima.

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

PLoS One. 2013;8(7):e67051.
Figure 6

Dipeptide low-energy conformation: (a) boat conformation with natural amino acid isomers, (b) boat conformation with unnatural amino acid isomers, and (c) chair conformation with balanced dipoles.

Design, Synthesis, and Evaluation of Lung-Retentive Prodrugs for Extending the Lung Tissue Retention of Inhaled Drugs

J Med Chem. 2022 Jul 28;65(14):9802-9818.
FIGURE 6

Conformations of dextran monomer during extension. (A) chair (⁴C₁), (B) inverted chair (¹C₄), (C) boat, and (D) inverted boat. Boat conformations extracted from simulation are actually a mixture of boat and twisted boat conformations. (E,F) Population of glucopyranose ring conformation states: chair (⁴C₁) (circles), inverted chair (¹C₄) (triangles), boatlike (squares), and inverted boatlike (diamonds) conformations for inner dextran monomers in 10-mer: (E) AMBER94 and (F) AMBER-GLYCAM04 force fields at T = 300 K.

Molecular Dynamics Simulation of Dextran Extension by Constant Force in Single Molecule AFM

Biophys J. 2006 Nov 15;91(10):3579-3588.