Literature DB >> 32424255

Spontaneous drying of non-polar deep-cavity cavitand pockets in aqueous solution.

J Wesley Barnett1, Matthew R Sullivan2, Joshua A Long3, Du Tang1, Thong Nguyen2, Dor Ben-Amotz3, Bruce C Gibb2, Henry S Ashbaugh4.   

Abstract

There are many open questions regarding the hydration of solvent-exposed non-polar tracts and pockets in proteins. Although water is predicted to de-wet purely repulsive surfaces and evacuate crevices, the extent of de-wetting is unclear when ubiquitous van der Waals interactions are in play. The structural simplicity of synthetic supramolecular hosts imbues them with considerable potential to address this issue. To this end, here we detail a combination of densimetry and molecular dynamics simulations of three cavitands, coupled with calorimetric studies of their complexes with short-chain carboxylates. Our results reveal the range of wettability possible within the ostensibly identical cavitand pockets-which differ only in the presence and/or position of the methyl groups that encircle the portal to their non-polar pockets. The results demonstrate the ability of macrocycles to template water cavitation within their binding sites and show how the orientation of methyl groups can trigger the drying of non-polar pockets in liquid water, which suggests new avenues to control guest complexation.

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Year:  2020        PMID: 32424255     DOI: 10.1038/s41557-020-0458-8

Source DB:  PubMed          Journal:  Nat Chem        ISSN: 1755-4330            Impact factor:   24.427


  31 in total

1.  Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation.

Authors:  Marcus D Collins; Gerhard Hummer; Michael L Quillin; Brian W Matthews; Sol M Gruner
Journal:  Proc Natl Acad Sci U S A       Date:  2005-11-03       Impact factor: 11.205

Review 2.  Interfaces and the driving force of hydrophobic assembly.

Authors:  David Chandler
Journal:  Nature       Date:  2005-09-29       Impact factor: 49.962

3.  Water in the polar and nonpolar cavities of the protein interleukin-1β.

Authors:  Hao Yin; Guogang Feng; G Marius Clore; Gerhard Hummer; Jayendran C Rasaiah
Journal:  J Phys Chem B       Date:  2010-11-03       Impact factor: 2.991

4.  A dry ligand-binding cavity in a solvated protein.

Authors:  Johan Qvist; Monika Davidovic; Donald Hamelberg; Bertil Halle
Journal:  Proc Natl Acad Sci U S A       Date:  2008-04-21       Impact factor: 11.205

5.  Temperature-Dependent Hydrophobic Crossover Length Scale and Water Tetrahedral Order.

Authors:  Xiangen Wu; Wanjun Lu; Louis M Streacker; Henry S Ashbaugh; Dor Ben-Amotz
Journal:  J Phys Chem Lett       Date:  2018-02-13       Impact factor: 6.475

6.  Signature of hydrophobic hydration in a single polymer.

Authors:  Isaac T S Li; Gilbert C Walker
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-12       Impact factor: 11.205

7.  Sitting at the edge: how biomolecules use hydrophobicity to tune their interactions and function.

Authors:  Amish J Patel; Patrick Varilly; Sumanth N Jamadagni; Michael F Hagan; David Chandler; Shekhar Garde
Journal:  J Phys Chem B       Date:  2012-02-16       Impact factor: 2.991

8.  Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography.

Authors:  Marcus D Collins; Michael L Quillin; Gerhard Hummer; Brian W Matthews; Sol M Gruner
Journal:  J Mol Biol       Date:  2006-12-15       Impact factor: 5.469

9.  Water conduction through the hydrophobic channel of a carbon nanotube.

Authors:  G Hummer; J C Rasaiah; J P Noworyta
Journal:  Nature       Date:  2001-11-08       Impact factor: 49.962

10.  Water structural transformation at molecular hydrophobic interfaces.

Authors:  Joel G Davis; Kamil P Gierszal; Ping Wang; Dor Ben-Amotz
Journal:  Nature       Date:  2012-11-22       Impact factor: 49.962

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  12 in total

1.  Sticky when dry.

Authors:  Shekhar Garde
Journal:  Nat Chem       Date:  2020-07       Impact factor: 24.427

2.  Navigating the waters of membrane design.

Authors:  Henry S Ashbaugh
Journal:  Proc Natl Acad Sci U S A       Date:  2021-01-05       Impact factor: 11.205

3.  Identifying hydrophobic protein patches to inform protein interaction interfaces.

Authors:  Nicholas B Rego; Erte Xi; Amish J Patel
Journal:  Proc Natl Acad Sci U S A       Date:  2021-02-09       Impact factor: 11.205

Review 4.  Purely Covalent Molecular Cages and Containers for Guest Encapsulation.

Authors:  Giovanni Montà-González; Félix Sancenón; Ramón Martínez-Máñez; Vicente Martí-Centelles
Journal:  Chem Rev       Date:  2022-07-22       Impact factor: 72.087

5.  Microporous water with high gas solubilities.

Authors:  Daniel P Erdosy; Malia B Wenny; Joy Cho; Christopher DelRe; Miranda V Walter; Felipe Jiménez-Ángeles; Baofu Qiao; Ricardo Sanchez; Yifeng Peng; Brian D Polizzotti; Monica Olvera de la Cruz; Jarad A Mason
Journal:  Nature       Date:  2022-08-24       Impact factor: 69.504

6.  Cavitand Complexes in Aqueous Solution: Collaborative Experimental and Computational Studies of the Wetting, Assembly, and Function of Nanoscopic Bowls in Water.

Authors:  Henry S Ashbaugh; Bruce C Gibb; Paolo Suating
Journal:  J Phys Chem B       Date:  2021-03-02       Impact factor: 2.991

7.  The role of water in host-guest interaction.

Authors:  Valerio Rizzi; Luigi Bonati; Narjes Ansari; Michele Parrinello
Journal:  Nat Commun       Date:  2021-01-04       Impact factor: 14.919

8.  Buffer and Salt Effects in Aqueous Host-Guest Systems: Screening, Competitive Binding, or Both?

Authors:  Jacobs H Jordan; Henry S Ashbaugh; Joel T Mague; Bruce C Gibb
Journal:  J Am Chem Soc       Date:  2021-10-27       Impact factor: 15.419

Review 9.  When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water.

Authors:  Stefan Kubik
Journal:  ChemistryOpen       Date:  2022-04       Impact factor: 2.630

10.  SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations.

Authors:  Martin Amezcua; Léa El Khoury; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2021-01-04       Impact factor: 3.686

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