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1.
Proc Natl Acad Sci U S A ; 121(20): e2322853121, 2024 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-38709921

RESUMO

Mounting experimental evidence supports the existence of a liquid-liquid transition (LLT) in high-pressure supercooled water. However, fast crystallization of supercooled water has impeded identification of the LLT line TLL(p) in experiments. While the most accurate all-atom (AA) water models display a LLT, their computational cost limits investigations of its interplay with ice formation. Coarse-grained (CG) models provide over 100-fold computational efficiency gain over AA models, enabling the study of water crystallization, but have not yet shown to have a LLT. Here, we demonstrate that the CG machine-learned water model Machine-Learned Bond-Order Potential (ML-BOP) has a LLT that ends in a critical point at pc = 170 ± 10 MPa and Tc = 181 ± 3 K. The TLL(p) of ML-BOP is almost identical to the one of TIP4P/2005, adding to the similarity in the equation of state of liquid water in both models. Cooling simulations reveal that ice crystallization is fastest at the LLT and its supercritical continuation of maximum heat capacity, supporting a mechanistic relationship between the structural transformation of water to a low-density liquid (LDL) and ice formation. We find no signature of liquid-liquid criticality in the ice crystallization temperatures. ML-BOP replicates the competition between formation of LDL and ice observed in ultrafast experiments of decompression of the high-density liquid (HDL) into the region of stability of LDL. The simulations reveal that crystallization occurs prior to the coarsening of the HDL and LDL domains, obscuring the distinction between the highly metastable first-order LLT and pronounced structural fluctuations along its supercritical continuation.

2.
Proc Natl Acad Sci U S A ; 120(46): e2303243120, 2023 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-37943838

RESUMO

Biological ice nucleation plays a key role in the survival of cold-adapted organisms. Several species of bacteria, fungi, and insects produce ice nucleators (INs) that enable ice formation at temperatures above -10 °C. Bacteria and fungi produce particularly potent INs that can promote water crystallization above -5 °C. Bacterial INs consist of extended protein units that aggregate to achieve superior functionality. Despite decades of research, the nature and identity of fungal INs remain elusive. Here, we combine ice nucleation measurements, physicochemical characterization, numerical modeling, and nucleation theory to shed light on the size and nature of the INs from the fungus Fusarium acuminatum. We find ice-binding and ice-shaping activity of Fusarium IN, suggesting a potential connection between ice growth promotion and inhibition. We demonstrate that fungal INs are composed of small 5.3 kDa protein subunits that assemble into ice-nucleating complexes that can contain more than 100 subunits. Fusarium INs retain high ice-nucleation activity even when only the ~12 kDa fraction of size-excluded proteins are initially present, suggesting robust pathways for their functional aggregation in cell-free aqueous environments. We conclude that the use of small proteins to build large assemblies is a common strategy among organisms to create potent biological INs.


Assuntos
Gelo , Água , Congelamento , Temperatura , Proteínas da Membrana Bacteriana Externa/metabolismo
3.
Nano Lett ; 23(15): 7206-7212, 2023 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-37490518

RESUMO

Are surface nanobubbles transient or thermodynamically stable structures? This question remained controversial until recently, when the stability of gas nanobubbles at solid-liquid interfaces was demonstrated from thermodynamic arguments in closed systems, establishing that bubbles with radii of hundreds of nanometers can be stable at modest supersaturations if the gas amount is finite. Here we develop a grand-canonical description of bubble formation that predicts that nanobubbles can nucleate and remain thermodynamically stable in open boundaries at high supersaturations when pinned to hydrophobic supports as small as a few nanometers. While larger bubbles can also be stable at lower supersaturations, the corresponding barriers are orders of magnitude above kT, meaning that their formation cannot proceed via heterogeneous nucleation on a uniform solid interface but must follow some alternative path. Moreover, we conclude that a source of growth-limiting mechanism, such as pinning or gas availability, is necessary for the thermodynamic stabilization of surface bubbles.

4.
Nature ; 551(7679): 218-222, 2017 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-29120424

RESUMO

The freezing of water affects the processes that determine Earth's climate. Therefore, accurate weather and climate forecasts hinge on good predictions of ice nucleation rates. Such rate predictions are based on extrapolations using classical nucleation theory, which assumes that the structure of nanometre-sized ice crystallites corresponds to that of hexagonal ice, the thermodynamically stable form of bulk ice. However, simulations with various water models find that ice nucleated and grown under atmospheric temperatures is at all sizes stacking-disordered, consisting of random sequences of cubic and hexagonal ice layers. This implies that stacking-disordered ice crystallites either are more stable than hexagonal ice crystallites or form because of non-equilibrium dynamical effects. Both scenarios challenge central tenets of classical nucleation theory. Here we use rare-event sampling and free energy calculations with the mW water model to show that the entropy of mixing cubic and hexagonal layers makes stacking-disordered ice the stable phase for crystallites up to a size of at least 100,000 molecules. We find that stacking-disordered critical crystallites at 230 kelvin are about 14 kilojoules per mole of crystallite more stable than hexagonal crystallites, making their ice nucleation rates more than three orders of magnitude higher than predicted by classical nucleation theory. This effect on nucleation rates is temperature dependent, being the most pronounced at the warmest conditions, and should affect the modelling of cloud formation and ice particle numbers, which are very sensitive to the temperature dependence of ice nucleation rates. We conclude that classical nucleation theory needs to be corrected to include the dependence of the crystallization driving force on the size of the ice crystallite when interpreting and extrapolating ice nucleation rates from experimental laboratory conditions to the temperatures that occur in clouds.

5.
Biomacromolecules ; 23(2): 513-519, 2022 02 14.
Artigo em Inglês | MEDLINE | ID: mdl-34928587

RESUMO

Some of the most potent antifreeze proteins (AFPs) are approximately rigid helical structures that bind with one side in contact with the ice surface at specific orientations. These AFPs take random orientations in solution; however, most orientations become sterically inaccessible as the AFP approaches the ice surface. The effect of these inaccessible orientations on the rate of adsorption of AFP to ice has never been explored. Here, we present a diffusion-controlled theory of adsorption kinetics that accounts for these orientational restrictions to predict a rate constant for adsorption (kon, in m/s) as a function of the length and width of the AFP molecules. We find that kon decreases with length and diameter of the AFP and is almost proportional to the inverse of the area of the binding surface. We demonstrate that the restricted orientations create an entropic barrier to AFP adsorption, which we compute to be approximately 7 kBT for most AFPs and up to 9 kBT for Maxi, the largest known AFP. We compare the entropic resistance 1/kon to resistances for diffusion through boundary layers and across typical distances in the extracellular matrix and find that these entropic and diffusion resistances could become comparable in the small confined spaces of biological environments.


Assuntos
Gelo , alfa-Fetoproteínas , Adsorção , Proteínas Anticongelantes/química , Difusão
6.
J Chem Phys ; 157(21): 214113, 2022 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-36511557

RESUMO

The adsorption of large rod-like molecules or crystallites on a flat crystal face, similar to Buffon's needle, requires the rods to "land," with their binding sites in precise orientational alignment with matching sites on the surface. An example is provided by long, helical antifreeze proteins (AFPs), which bind at specific facets and orientations on the ice surface. The alignment constraint for adsorption, in combination with the loss in orientational freedom as the molecule diffuses toward the surface, results in an entropic barrier that hinders the adsorption. Prior kinetic models do not factor in the complete geometry of the molecule, nor explicitly enforce orientational constraints for adsorption. Here, we develop a diffusion-controlled adsorption theory for AFP molecules binding at specific orientations to flat ice surfaces. We formulate the diffusion equation with relevant boundary conditions and present analytical solutions to the attachment rate constant. The resulting rate constant is a function of the length and aspect ratio of the AFP, the distance threshold associated with binding, and solvent conditions such as temperature and viscosity. These results and methods of calculation may also be useful for predicting the kinetics of crystal growth through oriented attachment.


Assuntos
Proteínas Anticongelantes , Gelo , Proteínas Anticongelantes/química , Cinética , Cristalização , Adsorção
7.
Proc Natl Acad Sci U S A ; 116(49): 24413-24419, 2019 12 03.
Artigo em Inglês | MEDLINE | ID: mdl-31685641

RESUMO

The appearance of ice I in the smallest possible clusters and the nature of its phase coexistence with liquid water could not thus far be unraveled. The experimental and theoretical infrared spectroscopic and free-energy results of this work show the emergence of the characteristic hydrogen-bonding pattern of ice I in clusters containing only around 90 water molecules. The onset of crystallization is accompanied by an increase of surface oscillator intensity with decreasing surface-to-volume ratio, a spectral indicator of nanoscale crystallinity of water. In the size range from 90 to 150 water molecules, we observe mixtures of largely crystalline and purely amorphous clusters. Our analysis suggests that the liquid-ice I transition in clusters loses its sharp 1st-order character at the end of the crystalline-size regime and occurs over a range of temperatures through heterophasic oscillations in time, a process without analog in bulk water.

8.
Proc Natl Acad Sci U S A ; 116(17): 8184-8189, 2019 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-30948638

RESUMO

Ice nucleation in the atmosphere influences cloud properties, altering precipitation and the radiative balance, ultimately regulating Earth's climate. An accepted ice nucleation pathway, known as deposition nucleation, assumes a direct transition of water from the vapor to the ice phase, without an intermediate liquid phase. However, studies have shown that nucleation occurs through a liquid phase in porous particles with narrow cracks or surface imperfections where the condensation of liquid below water saturation can occur, questioning the validity of deposition nucleation. We show that deposition nucleation cannot explain the strongly enhanced ice nucleation efficiency of porous compared with nonporous particles at temperatures below -40 °C and the absence of ice nucleation below water saturation at -35 °C. Using classical nucleation theory (CNT) and molecular dynamics simulations (MDS), we show that a network of closely spaced pores is necessary to overcome the barrier for macroscopic ice-crystal growth from narrow cylindrical pores. In the absence of pores, CNT predicts that the nucleation barrier is insurmountable, consistent with the absence of ice formation in MDS. Our results confirm that pore condensation and freezing (PCF), i.e., a mechanism of ice formation that proceeds via liquid water condensation in pores, is a dominant pathway for atmospheric ice nucleation below water saturation. We conclude that the ice nucleation activity of particles in the cirrus regime is determined by the porosity and wettability of pores. PCF represents a mechanism by which porous particles like dust could impact cloud radiative forcing and, thus, the climate via ice cloud formation.

9.
Angew Chem Int Ed Engl ; 61(29): e202205095, 2022 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-35502460

RESUMO

Zeolites with a few unit cells are promising as catalyst and adsorbents. The quest to synthesize the smallest zeolites has recently resulted in 4 to 8 nm nanozeolites, about 2 to 4 unit cells. These findings pose the question of what is the smallest zeolite that could be obtained by hydrothermal synthesis. Here we address this question using molecular simulations and thermodynamic analysis. The simulations predict that amorphous precursors as small as 4 nm can crystallize zeolites, in agreement with the experiments. We find that interfacial forces dominate the structure of smaller particles, resulting in size-dependent compact isomers that have ring and pore distributions different from open framework zeolites. The instability of zeolites smaller than 3±0.5 nm precludes a classical mechanism of nucleation from solution or through assembly of small nanoslabs.

10.
J Am Chem Soc ; 143(12): 4607-4624, 2021 03 31.
Artigo em Inglês | MEDLINE | ID: mdl-33729789

RESUMO

Potent ice nucleating organic crystals display an increase in nucleation efficiency with pressure and memory effect after pressurization that set them apart from inorganic nucleants. These characteristics were proposed to arise from an ordered water monolayer at the organic-water interface. It was interpreted that ordering of the monolayer is the limiting step for ice nucleation on organic crystals, rendering their mechanism of nucleation nonclassical. Despite the importance of organics in atmospheric ice nucleation, that explanation has never been investigated. Here we elucidate the structure of interfacial water and its role in ice nucleation at ambient pressure on phloroglucinol dihydrate, the paradigmatic example of outstanding ice nucleating organic crystal, using molecular simulations. The simulations confirm the existence of an interfacial monolayer that orders on cooling and becomes fully ordered upon ice formation. The monolayer does not resemble any ice face but seamlessly connects the distinct hydrogen-bonding orders of ice and the organic surface. Although large ordered patches develop in the monolayer before ice nucleates, we find that the critical step is the formation of the ice crystallite, indicating that the mechanism is classical. We predict that the fully ordered, crystalline monolayer nucleates ice above -2 °C and could be responsible for the exceptional ice nucleation by the organic crystal at high pressures. The lifetime of the fully ordered monolayer around 0 °C, however, is too short to account for the memory effect reported in the experiments. The latter could arise from an increase in the melting temperature of ice confined by strongly ice-binding surfaces.

11.
Proc Natl Acad Sci U S A ; 115(33): 8266-8271, 2018 08 14.
Artigo em Inglês | MEDLINE | ID: mdl-29987018

RESUMO

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.


Assuntos
Proteínas Anticongelantes/química , Gelo , Água/química , Sítios de Ligação , Espectrofotometria Infravermelho , Análise Espectral Raman
12.
J Am Chem Soc ; 142(9): 4356-4366, 2020 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-32050760

RESUMO

Ice recrystallization inhibitors (IRI) are of critical importance in biology, cryopreservation of cells and organs, and frozen foods. Antifreeze glycoproteins (AFGPs) are the most potent IRI. Their cost and cytotoxicity drive the design of synthetic flexible polymers that mimic their function. Poly(vinyl alcohol) (PVA) is the most potent biomimetic found to date, although it is orders of magnitude less potent than AFGPs. A lack of molecular understanding of the factors that limit the IRI efficiency of PVA and other flexible ice-binding polymers hinders the design of more potent IRI. Here, we use molecular and numerical simulations to elucidate how the degree of polymerization (DP) and functionalization of PVA impact its IRI. Our simulations indicate that the onset of IRI activity of PVA occurs for 15 < DP < 20, in agreement with experiments. We predict that polymers with stronger binding to ice per monomer attain IRI activity at lower DP and identify this as a contributor to the higher IRI potency of AFGPs. The simulations reveal that the limiting step for binding of flexible molecules to ice is not the alignment of the molecule to the surface or the initiation of the binding but the propagation to reach its full binding potential. This distinguishes AFGPs and PVA from rigid antifreeze proteins and, we argue, is responsible for their different scaling of efficiencies with molecular size. We use the analysis of PVA to identify the factors that control the IRI activity of flexible polymers and assess the molecular characteristics that endow AFGPs with their exceptional IRI potency.

13.
J Chem Phys ; 153(17): 174106, 2020 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-33167647

RESUMO

Recognition and binding of ice by proteins, crystals, and other surfaces is key for their control of the nucleation and growth of ice. Docking is the state-of-the-art computational method to identify ice-binding surfaces (IBS). However, docking methods require a priori knowledge of the ice plane to which the molecules bind and either neglect the competition of ice and water for the IBS or are computationally expensive. Here we present and validate a robust methodology for the identification of the IBS of molecules and crystals that is easy to implement and a hundred times computationally more efficient than the most advanced ice-docking approaches. The methodology is based on biased sampling with an order parameter that drives the formation of ice. We validate the method using all-atom and coarse-grained models of organic crystals and proteins. To our knowledge, this approach is the first to simultaneously identify the ice-binding surface as well as the plane of ice to which it binds, without the use of structure search algorithms. We show that biased simulations even identify surfaces that are too small or too weak to heterogeneously nucleate ice. The biasing simulations can be used to identify of IBS of antifreeze and ice nucleating proteins and to equilibrate ice seeds bound to an IBS for the calculation of heterogeneous ice nucleation rates using classical nucleation theory.


Assuntos
Gelo , Modelos Químicos , Simulação por Computador , Floroglucinol/química , Propriedades de Superfície , Temperatura , Água/química
14.
J Am Chem Soc ; 141(18): 7439-7452, 2019 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-30977366

RESUMO

Organisms that thrive at cold temperatures produce ice-binding proteins to manage the nucleation and growth of ice. Bacterial ice-nucleating proteins (INP) are typically large and form aggregates in the cell membrane, while insect hyperactive antifreeze proteins (AFP) are soluble and generally small. Experiments indicate that larger ice-binding proteins and their aggregates nucleate ice at warmer temperatures. Nevertheless, a quantitative understanding of how size and aggregation of ice-binding proteins determine the temperature Thet at which proteins nucleate ice is still lacking. Here, we address this question using molecular simulations and nucleation theory. The simulations indicate that the 2.5 nm long antifreeze protein TmAFP nucleates ice at 2 ± 1 °C above the homogeneous nucleation temperature, in good agreement with recent experiments. We predict that the addition of ice-binding loops to TmAFP increases Thet, but not enough to compete in efficiency with the bacterial INP. We implement an accurate procedure to determine Thet of surfaces of finite size using classical nucleation theory, and, after validating the theory against Thet of the proteins in molecular simulations, we use it to predict Thet of the INP of Ps. syringae as a function of the length and number of proteins in the aggregates. We conclude that assemblies with at most 34 INP already reach the Thet = -2 °C characteristic of this bacterium. Interestingly, we find that Thet is a strongly varying nonmonotonic function of the distance between proteins in the aggregates. This indicates that, to achieve maximum freezing efficiency, bacteria must exert exquisite, subangstrom control of the distance between INP in their membrane.


Assuntos
Proteínas Anticongelantes/química , Proteínas da Membrana Bacteriana Externa/química , Congelamento , Simulação de Dinâmica Molecular , Tamanho da Partícula , Agregados Proteicos
15.
J Am Chem Soc ; 141(19): 7887-7898, 2019 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-31020830

RESUMO

Hyperactive insect antifreeze proteins and bacterial ice-nucleating proteins are arguably the most potent ice-binding molecules in nature. These highly effective proteins bind ice through amphiphilic ice-binding sites based on arrays of threonine residues. It remains poorly understood how hydrophilic and hydrophobic groups of the binding site contribute to the ice affinity of proteins. Here, we use molecular simulations to demonstrate that the hydrogen-bonding and hydrophobic groups at the ice-binding site of the antifreeze protein TmAFP of Tenebrio molitor and extended ice-nucleating protein surfaces contribute distinctively yet almost equally in magnitude to their binding free energy to ice. The methyl groups rigidize the ice-binding site, slow the water dynamics at the ice-binding surface, and stabilize the clathrate-like water in the anchored clathrate motif that binds these proteins to ice. We find that hydrophobic dehydration of the methyl group does not contribute to the binding free energy of the protein to ice. The role of the hydroxyl groups is to anchor the clathrate-like water through direct hydrogen-bonding, positioning and slowing the dynamics of water at the trough of the binding site. We uncover a correlation between slower dynamics of water at the binding site for the protein in solution and stronger free energy of binding of the protein to ice. The synergy between hydrophobic and hydrophilic groups unveiled by this study provides guidance for the design of synthetic ice-binding molecules with enhanced ice nucleation and antifreeze activity.


Assuntos
Proteínas Anticongelantes/química , Interações Hidrofóbicas e Hidrofílicas , Gelo , Sítios de Ligação , Ligação de Hidrogênio , Conformação Molecular , Simulação de Dinâmica Molecular , Água/química
16.
J Am Chem Soc ; 141(27): 10801-10811, 2019 07 10.
Artigo em Inglês | MEDLINE | ID: mdl-31190533

RESUMO

Gas evolving reactions are ubiquitous in the operation of electrochemical devices. Recent studies of individual gas bubbles on nanoelectrodes have resulted in unprecedented control and insights on their formation. The experiments, however, lack the spatial resolution to elucidate the molecular pathway of nucleation of nanobubbles and their stationary size and shape. Here we use molecular simulations with an algorithm that mimics the electrochemical formation of gas, to investigate the mechanisms of nucleation of gas bubbles on nanoelectrodes, and characterize their stationary states. The simulations reproduce the experimental currents in the induction and stationary stages, and indicate that surface nanobubbles nucleate through a classical mechanism. We identify three distinct regimes for bubble nucleation, depending on the binding free energy per area of bubble to the electrode, Δγbind. If Δγbind is negative, the nucleation is heterogeneous and the nanobubble remains bound to the electrode, resulting in a low-current stationary state. For very negative Δγ, the bubble fully wets the electrode, forming a one-layer-thick micropancake that nucleates without supersaturation. On the other hand, when Δγbind > 0 the nanobubble nucleates homogeneously close to the electrode, but never attaches to it. We conclude that all surface nanobubbles must nucleate heterogeneously. The simulations reveal that the size and contact angle of stationary nanobubbles increase with the reaction driving force, although their residual current is invariant. The myriad of driven nonequilibrium stationary states with the same rate of production of gas, but distinct bubble properties, suggests that these dissipative systems have attractors that control the stationary current.

17.
J Chem Phys ; 151(11): 114707, 2019 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-31542043

RESUMO

Methane hydrates can be preserved at ambient pressure, beyond their region of thermodynamic stability, by storing them at temperatures from 240 to 270 K. The origin of this anomalous self-preservation is the formation of an ice coating that covers the clathrate particles and prevents further loss of gas. While there have been several studies on self-preservation, the question of what is the mechanism by which ice nucleates on the decomposing clathrate hydrates has not yet been fully explained. Here, we use molecular simulations, thermodynamic analysis, and nucleation theory to investigate possible scenarios for the nucleation of ice: heterogeneous nucleation at the clathrate/vapor or clathrate/liquid interfaces and homogeneous nucleation from supercooled water. Our results indicate that clathrates cannot heterogeneously nucleate ice and that ice nucleation is due to the cooling of water at the decomposing clathrate/liquid interface, which suffices to trigger homogeneous ice nucleation. We find that the (111) face of the sII structure clathrate can bind to the (111) plane of cubic ice or the basal plane of hexagonal ice through domain matching, resulting in a weak binding that-while insufficient to promote heterogeneous ice nucleation-suffices to produce epitaxy and alignment between these crystals. We use thermodynamic relations, theory, and the contact angles of ice at the (111) sII clathrate/liquid interface to determine-for the first time-the interfacial free energy of this most favorable ice-clathrate interface, 59 ± 5 mJ/m2. We discuss the implications of our results for the feasibility of heterogeneous nucleation of gas clathrates at ice/vapor interfaces.

18.
J Chem Phys ; 150(16): 164902, 2019 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-31042878

RESUMO

Mesophases have order intermediate between liquids and crystals and arise in systems with frustration, such as surfactants, block copolymers, and Janus nanoparticles. The gyroid mesophase contains two interpenetrated, nonintersecting chiral networks that give it properties useful for photonics. It is challenging to nucleate a gyroid from the liquid. Elucidating the reaction coordinate for gyroid nucleation could assist in designing additives that facilitate the formation of the mesophase. However, the complexity of the gyroid structure and the extreme weakness of the first-order liquid to gyroid transition make this a challenging quest. Here, we investigate the pathway and transition states for the nucleation of a gyroid from the liquid in molecular simulations with a mesogenic binary mixture. We find that the gyroid nuclei at the transition states have a large degree of positional disorder and are not compact, consistent with the low surface free energy of the liquid-gyroid interface. A combination of bond-order parameters for the minor component is best to describe the passage from liquid to gyroid, among those we consider. The committor analyses, however, show that this best coordinate is not perfect and suggests that accounting for the relative ordering of the two interpenetrated networks in infant nuclei, as well as for signatures of ordering in the major component of the mesophase, would improve the accuracy of the reaction coordinate for gyroid formation and its use to evaluate nucleation barriers. To our knowledge, this study is the first to investigate the reaction coordinate and critical nuclei for the formation of any mesophase from an amorphous phase.

19.
J Am Chem Soc ; 140(14): 4803-4811, 2018 04 11.
Artigo em Inglês | MEDLINE | ID: mdl-29392937

RESUMO

Antifreeze molecules allow organisms to survive in subzero environments. Antifreeze glycoproteins (AFGPs), produced by polar fish, are the most potent inhibitors of ice recrystallization. To date, the molecular mechanism by which AFGPs bind to ice has not yet been elucidated. Mutation experiments cannot resolve whether the binding occurs through the peptide, the saccharides, or both. Here, we use molecular simulations to determine the mechanism and driving forces for binding of AFGP8 to ice, its selectivity for the primary prismatic plane, and the molecular origin of its exceptional ice recrystallization activity. Consistent with experiments, AFGP8 in simulations preferentially adopts the PPII helix secondary structure in solution. We show that the segregation of hydrophilic and hydrophobic groups in the PPII helix is vital for ice binding. Binding occurs through adsorption of methyl groups of the peptide and disaccharides to ice, driven by the entropy of dehydration of the hydrophobic groups as they nest in the cavities at the ice surface. The selectivity to the primary prismatic plane originates in the deeper cavities it has compared to the basal plane. We estimate the free energy of binding of AFGP8 and the longer AFGPs4-6, and find them to be consistent with the reversible binding demonstrated in experiments. The simulations reveal that AFGP8 binds to ice through a myriad of conformations that it uses to diffuse through the ice surface and find ice steps, to which it strongly adsorbs. We interpret that the existence of multiple, weak binding sites is the key for the exceptional ice recrystallization inhibition activity of AFGPs.


Assuntos
Proteínas Anticongelantes/química , Gelo , Sítios de Ligação , Interações Hidrofóbicas e Hidrofílicas , Simulação de Dinâmica Molecular
20.
J Am Chem Soc ; 140(14): 4905-4912, 2018 04 11.
Artigo em Inglês | MEDLINE | ID: mdl-29564892

RESUMO

Cold-adapted organisms produce antifreeze and ice-nucleating proteins to prevent and promote ice formation. The crystal structure of hyperactive bacterial antifreeze protein (AFP) MpAFP suggests that this protein binds ice through an anchored clathrate motif. It is not known whether other hyperactive AFPs and ice-nucleating proteins (INPs) use the same motif to recognize or nucleate ice. Here we use molecular simulations to elucidate the ice-binding motifs of hyperactive insect AFPs and a model INP of Pseudomonas syringae. We find that insect AFPs recognize ice through anchored clathrate motifs distinct from that of MpAFP. By performing simulations of ice nucleation by PsINP, we identify two distinct ice-binding sites on opposite sides of the ß-helix. The ice-nucleating sequences identified in the simulations agree with those previously proposed for the closely related INP of Pseudomonas borealis based on the structure of the protein. The simulations indicate that these sites have comparable ice-nucleating efficiency, but distinct binding motifs, controlled by the amino acid sequence: one is an anchored clathrate and the other ice-like. We conclude that anchored clathrate and ice-like motifs can be equally effective for binding proteins to ice and promoting ice nucleation.


Assuntos
Proteínas Anticongelantes/química , Proteínas da Membrana Bacteriana Externa/química , Gelo , Simulação de Dinâmica Molecular , Pseudomonas syringae/química
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