Literature DB >> 29987018

Preordering of water is not needed for ice recognition by hyperactive antifreeze proteins.

Arpa Hudait1, Daniel R Moberg2, Yuqing Qiu1, Nathan Odendahl1, Francesco Paesani3, Valeria Molinero4.   

Abstract

Antifreeze proteins (AFPs) inhibit ice growth in organisms living in cold environments. Hyperactive insect AFPs are particularly effective, binding ice through "anchored clathrate" motifs. It has been hypothesized that the binding of hyperactive AFPs to ice is facilitated by preordering of water at the ice-binding site (IBS) of the protein in solution. The antifreeze protein TmAFP displays the best matching of its binding site to ice, making it the optimal candidate to develop ice-like order in solution. Here we use multiresolution simulations to unravel the mechanism by which TmAFP recognizes and binds ice. We find that water at the IBS of the antifreeze protein in solution does not acquire ice-like or anchored clathrate-like order. Ice recognition occurs by slow diffusion of the protein to achieve the proper orientation with respect to the ice surface, followed by fast collective organization of the hydration water at the IBS to form an anchored clathrate motif that latches the protein to the ice surface. The simulations suggest that anchored clathrate order could develop on the large ice-binding surfaces of aggregates of ice-nucleating proteins (INP). We compute the infrared and Raman spectra of water in the anchored clathrate motif. The signatures of the OH stretch of water in the anchored clathrate motif can be distinguished from those of bulk liquid in the Raman spectra, but not in the infrared spectra. We thus suggest that Raman spectroscopy may be used to probe the anchored clathrate order at the ice-binding surface of INP aggregates.

Entities:  

Keywords:  antifreeze protein; ice; interfacial water; molecular recognition; vibrational spectroscopy

Mesh:

Substances:

Year:  2018        PMID: 29987018      PMCID: PMC6099916          DOI: 10.1073/pnas.1806996115

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  49 in total

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Journal:  Nature       Date:  2001-01-18       Impact factor: 49.962

2.  Investigation of the Ice-Binding Site of an Insect Antifreeze Protein Using Sum-Frequency Generation Spectroscopy.

Authors:  Konrad Meister; Stephan Lotze; Luuk L C Olijve; Arthur L DeVries; John G Duman; Ilja K Voets; Huib J Bakker
Journal:  J Phys Chem Lett       Date:  2015-03-18       Impact factor: 6.475

3.  On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice.

Authors:  Sandeep K Reddy; Shelby C Straight; Pushp Bajaj; C Huy Pham; Marc Riera; Daniel R Moberg; Miguel A Morales; Chris Knight; Andreas W Götz; Francesco Paesani
Journal:  J Chem Phys       Date:  2016-11-21       Impact factor: 3.488

4.  Molecular Origin of the Vibrational Structure of Ice Ih.

Authors:  Daniel R Moberg; Shelby C Straight; Christopher Knight; Francesco Paesani
Journal:  J Phys Chem Lett       Date:  2017-05-26       Impact factor: 6.475

Review 5.  Ice-Binding Proteins and Their Function.

Authors:  Maya Bar Dolev; Ido Braslavsky; Peter L Davies
Journal:  Annu Rev Biochem       Date:  2016-04-25       Impact factor: 23.643

6.  Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context.

Authors:  Erte Xi; Vasudevan Venkateshwaran; Lijuan Li; Nicholas Rego; Amish J Patel; Shekhar Garde
Journal:  Proc Natl Acad Sci U S A       Date:  2017-11-20       Impact factor: 11.205

7.  Water at Interfaces.

Authors:  Olle Björneholm; Martin H Hansen; Andrew Hodgson; Li-Min Liu; David T Limmer; Angelos Michaelides; Philipp Pedevilla; Jan Rossmeisl; Huaze Shen; Gabriele Tocci; Eric Tyrode; Marie-Madeleine Walz; Josephina Werner; Hendrik Bluhm
Journal:  Chem Rev       Date:  2016-05-27       Impact factor: 60.622

8.  Identification of Clathrate Hydrates, Hexagonal Ice, Cubic Ice, and Liquid Water in Simulations: the CHILL+ Algorithm.

Authors:  Andrew H Nguyen; Valeria Molinero
Journal:  J Phys Chem B       Date:  2014-11-25       Impact factor: 2.991

9.  Novel dimeric β-helical model of an ice nucleation protein with bridged active sites.

Authors:  Christopher P Garnham; Robert L Campbell; Virginia K Walker; Peter L Davies
Journal:  BMC Struct Biol       Date:  2011-09-27

10.  Balance between hydration enthalpy and entropy is important for ice binding surfaces in Antifreeze Proteins.

Authors:  Michael Schauperl; Maren Podewitz; Teresa S Ortner; Franz Waibl; Alexander Thoeny; Thomas Loerting; Klaus R Liedl
Journal:  Sci Rep       Date:  2017-09-19       Impact factor: 4.379

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  9 in total

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2.  Combined molecular dynamics and neural network method for predicting protein antifreeze activity.

Authors:  Daniel J Kozuch; Frank H Stillinger; Pablo G Debenedetti
Journal:  Proc Natl Acad Sci U S A       Date:  2018-12-07       Impact factor: 11.205

3.  Antifreeze protein hydration waters: Unstructured unless bound to ice.

Authors:  Sean M Marks; Amish J Patel
Journal:  Proc Natl Acad Sci U S A       Date:  2018-08-06       Impact factor: 11.205

Review 4.  Ice-binding proteins and bioinspired synthetic mimics in non-physiological environments.

Authors:  Elizabeth A Delesky; Wil V Srubar
Journal:  iScience       Date:  2022-04-22

Review 5.  Mimicking the Ice Recrystallization Activity of Biological Antifreezes. When is a New Polymer "Active"?

Authors:  Caroline I Biggs; Christopher Stubbs; Ben Graham; Alice E R Fayter; Muhammad Hasan; Matthew I Gibson
Journal:  Macromol Biosci       Date:  2019-05-14       Impact factor: 4.979

6.  Screening toward the Development of Fingerprints of Atomic Environments Using Bond-Orientational Order Parameters.

Authors:  Hideo Doi; Kazuaki Z Takahashi; Takeshi Aoyagi
Journal:  ACS Omega       Date:  2022-01-24

7.  Water-organizing motif continuity is critical for potent ice nucleation protein activity.

Authors:  Akalabya Bissoyi; Lukas Eickhoff; Naama Reicher; Jordan Forbes; Thomas Hansen; Christopher G Bon; Virginia K Walker; Thomas Koop; Yinon Rudich; Ido Braslavsky; Peter L Davies
Journal:  Nat Commun       Date:  2022-08-26       Impact factor: 17.694

8.  Hydrogen bonding structure of confined water templated by a metal-organic framework with open metal sites.

Authors:  Adam J Rieth; Kelly M Hunter; Mircea Dincă; Francesco Paesani
Journal:  Nat Commun       Date:  2019-10-18       Impact factor: 14.919

9.  Fish-Derived Antifreeze Proteins and Antifreeze Glycoprotein Exhibit a Different Ice-Binding Property with Increasing Concentration.

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  9 in total

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