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Xu C, Chen Y, Zhao S, Li D, Tang X, Zhang H, Huang J, Guo Z, Liu W. Mechanical Regulation of Polymer Gels. Chem Rev 2024; 124:10435-10508. [PMID: 39284130 DOI: 10.1021/acs.chemrev.3c00498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
The mechanical properties of polymer gels devote to emerging devices and machines in fields such as biomedical engineering, flexible bioelectronics, biomimetic actuators, and energy harvesters. Coupling network architectures and interactions has been explored to regulate supportive mechanical characteristics of polymer gels; however, systematic reviews correlating mechanics to interaction forces at the molecular and structural levels remain absent in the field. This review highlights the molecular engineering and structural engineering of polymer gel mechanics and a comprehensive mechanistic understanding of mechanical regulation. Molecular engineering alters molecular architecture and manipulates functional groups/moieties at the molecular level, introducing various interactions and permanent or reversible dynamic bonds as the dissipative energy. Molecular engineering usually uses monomers, cross-linkers, chains, and other additives. Structural engineering utilizes casting methods, solvent phase regulation, mechanochemistry, macromolecule chemical reactions, and biomanufacturing technology to construct and tailor the topological network structures, or heterogeneous modulus compositions. We envision that the perfect combination of molecular and structural engineering may provide a fresh view to extend exciting new perspectives of this burgeoning field. This review also summarizes recent representative applications of polymer gels with excellent mechanical properties. Conclusions and perspectives are also provided from five aspects of concise summary, mechanical mechanism, biofabrication methods, upgraded applications, and synergistic methodology.
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Affiliation(s)
- Chenggong Xu
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Chen
- Key Laboratory of Instrumentation Science and Dynamic Measurement, Ministry of Education, North University of China, Taiyuan 030051, China
| | - Siyang Zhao
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deke Li
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- School of materials engineering, Lanzhou Institute of Technology, Lanzhou 730000, China
| | - Xing Tang
- Hubei Collaborative Innovation Centre for Advanced Organic Chemical Materials and Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubeu University, Wuhan 430062, China
| | - Haili Zhang
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- Hubei Collaborative Innovation Centre for Advanced Organic Chemical Materials and Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubeu University, Wuhan 430062, China
| | - Jinxia Huang
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Zhiguang Guo
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- Hubei Collaborative Innovation Centre for Advanced Organic Chemical Materials and Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Hubeu University, Wuhan 430062, China
| | - Weimin Liu
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
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2
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Goodarzi MM, Jalalirad R. Clear insight into complex multimodal resins and impurities to overcome recombinant protein purification challenges: A review. Biotechnol Bioeng 2024. [PMID: 39290077 DOI: 10.1002/bit.28846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/19/2024] [Accepted: 09/04/2024] [Indexed: 09/19/2024]
Abstract
Increasing attention has been paid to the purity of therapeutic proteins imposing extensive costs and challenges to the downstream processing of biopharmaceuticals. One of the efforts, that has been exerted to overcome such limitations, was developing multimodal or mixed-mode chromatography (MMC) resins for launching selective, orthogonal, non-affinity purification platforms. Despite relatively extensive usage of MMC resins, their real potential and fulfillment have not been extensively reviewed yet. In this work, the explanation of practical and key aspects of downstream processing of recombinant proteins with or without MMC resins was debated, as being useful for further purification process development. This review has been written as a step-by-step guide to deconvolute both inherent protein purification and MMC complexities. Here, after complete elucidation of the potential of MMC resins, the effects of frequently used additives (mobile phase modifiers) and their possible interactions during the purification process, the critical characteristics of common product-related impurities (e.g., aggregates, charge variants, fragments), host-related impurities (e.g., host cell protein and DNA) and process related impurities (e.g., endotoxin, and viruses) with solved or unsolved challenges of traditional and MMC resins have been discussed. Such collective experiences which are reported in this study could be considered as an applied guide for developing successful downstream processing in challenging conditions by providing a clear insight into complex MMC resins and impurities.
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Affiliation(s)
- Maryam Moazami Goodarzi
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, Karaj, Iran
| | - Reza Jalalirad
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, Karaj, Iran
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3
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Vicars Z, Choi J, Marks SM, Remsing RC, Patel AJ. Interfacial Ice Density Fluctuations Inform Surface Ice-Philicity. J Phys Chem B 2024; 128:8512-8521. [PMID: 39171456 DOI: 10.1021/acs.jpcb.4c03783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The propensity of a surface to nucleate ice or bind to ice is governed by its ice-philicity─its relative preference for ice over liquid water. However, the relationship between the features of a surface and its ice-philicity is not well understood, and for surfaces with chemical or topographical heterogeneity, such as proteins, their ice-philicity is not even well-defined. In the analogous problem of surface hydrophobicity, it has been shown that hydrophobic surfaces display enhanced low water-density (vapor-like) fluctuations in their vicinity. To interrogate whether enhanced ice-like fluctuations are similarly observed near ice-philic surfaces, here we use molecular simulations and enhanced sampling techniques. Using a family of model surfaces for which the wetting coefficient, k, has previously been characterized, we show that the free energy of observing rare interfacial ice-density fluctuations decreases monotonically with increasing k. By utilizing this connection, we investigate a set of fcc systems and find that the (110) surface is more ice-philic than the (111) or (100) surfaces. By additionally analyzing the structure of interfacial ice, we find that all surfaces prefer to bind to the basal plane of ice, and the topographical complementarity of the (110) surface to the basal plane explains its higher ice-philicity. Using enhanced interfacial ice-like fluctuations as a measure of surface ice-philicity, we then characterize the ice-philicity of chemically heterogeneous and topologically complex systems. In particular, we study the spruce budworm antifreeze protein (sbwAFP), which binds to ice using a known ice-binding site (IBS) and resists engulfment using nonbinding sites of the protein (NBSs). We find that the IBS displays enhanced interfacial ice-density fluctuations and is therefore more ice-philic than the two NBSs studied. We also find the two NBSs are similarly ice-phobic. By establishing a connection between interfacial ice-like fluctuations and surface ice-philicity, our findings thus provide a way to characterize the ice-philicity of heterogeneous surfaces.
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Affiliation(s)
- Zachariah Vicars
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jeongmoon Choi
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sean M Marks
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Amish J Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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4
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Wang H, Huse DA, Torquato S. Hole statistics of equilibrium 2D and 3D hard-sphere crystals. J Chem Phys 2024; 161:074106. [PMID: 39145547 DOI: 10.1063/5.0228208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024] Open
Abstract
The probability of finding a spherical "hole" of a given radius r contains crucial structural information about many-body systems. Such hole statistics, including the void conditional nearest-neighbor probability functions GV(r), have been well studied for hard-sphere fluids in d-dimensional Euclidean space Rd. However, little is known about these functions for hard-sphere crystals for values of r beyond the hard-sphere diameter, as large holes are extremely rare in crystal phases. To overcome these computational challenges, we introduce a biased-sampling scheme that accurately determines hole statistics for equilibrium hard spheres on ranges of r that far extend those that could be previously explored. We discover that GV(r) in crystal and hexatic states exhibits oscillations whose amplitudes increase rapidly with the packing fraction, which stands in contrast to GV(r) that monotonically increases with r for fluid states. The oscillations in GV(r) for 2D crystals are strongly correlated with the local orientational order metric in the vicinity of the holes, and variations in GV(r) for 3D states indicate a transition between tetrahedral and octahedral holes, demonstrating the power of GV(r) as a probe of local coordination geometry. To further study the statistics of interparticle spacing in hard-sphere systems, we compute the local packing fraction distribution f(ϕl) of Delaunay cells and find that, for d ≤ 3, the excess kurtosis of f(ϕl) switches sign at a certain transitional global packing fraction. Our accurate methods to access hole statistics in hard-sphere crystals at the challenging intermediate length scales reported here can be applied to understand the important problem of solvation and hydrophobicity in water at such length scales.
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Affiliation(s)
- Haina Wang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - David A Huse
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Salvatore Torquato
- Department of Chemistry, Department of Physics, Princeton Institute of Materials, and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
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5
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Joshi A, Avni A, Walimbe A, Rai SK, Sarkar S, Mukhopadhyay S. Hydrogen-Bonded Network of Water in Phase-Separated Biomolecular Condensates. J Phys Chem Lett 2024; 15:7724-7734. [PMID: 39042834 DOI: 10.1021/acs.jpclett.4c01153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Biomolecular condensates formed via phase separation of intrinsically disordered proteins/regions (IDPs/IDRs) and nucleic acids are associated with cell physiology and disease. Water makes up for ∼60-70% of the condensate volume and is thought to influence the complex interplay of chain-chain and chain-solvent interactions, modulating the mesoscale properties of condensates. The behavior of water in condensates and the key roles of protein hydration water in driving the phase separation remain elusive. Here, we employ single-droplet vibrational Raman spectroscopy to illuminate the structural redistribution within protein hydration water during the phase separation of neuronal IDPs. Our Raman measurements reveal the changes in the water hydrogen bonding network during homotypic and heterotypic phase separation governed by various molecular drivers. Such single-droplet water Raman measurements offer a potent generic tool to unmask the intriguing interplay of sequence-encoded chain-chain and chain-solvent interactions governing macromolecular phase separation into membraneless organelles, synthetic condensates, and protocells.
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6
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Lang X, Shi L, Zhao Z, Min W. Probing the structure of water in individual living cells. Nat Commun 2024; 15:5271. [PMID: 38902250 PMCID: PMC11190263 DOI: 10.1038/s41467-024-49404-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
Water regulates or even governs a wide range of biological processes. Despite its fundamental importance, surprisingly little is known about the structure of intracellular water. Herein we employ a Raman micro-spectroscopy technique to uncover the composition, abundance and vibrational spectra of intracellular water in individual living cells. In three different cell types, we show a small but consistent population (~3%) of non-bulk-like water. It exhibits a weakened hydrogen-bonded network and a more disordered tetrahedral structure. We attribute this population to biointerfacial water located in the vicinity of biomolecules. Moreover, our whole-cell modeling suggests that all soluble (globular) proteins inside cells are surrounded by, on average, one full molecular layer (about 2.6 Angstrom) of biointerfacial water. Furthermore, relative invariance of biointerfacial water is observed among different single cells. Overall, our study not only opens up experimental possibilities of interrogating water structure in vivo but also provides insights into water in life.
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Affiliation(s)
- Xiaoqi Lang
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Lixue Shi
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhilun Zhao
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
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7
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Robinson Brown DC, Webber TR, Casey TM, Franck J, Shell MS, Han S. Computation of Overhauser dynamic nuclear polarization processes reveals fundamental correlation between water dynamics, structure, and solvent restructuring entropy. Phys Chem Chem Phys 2024; 26:14637-14650. [PMID: 38742831 DOI: 10.1039/d4cp00030g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Hydration water dynamics, structure, and thermodynamics are crucially important to understand and predict water-mediated properties at molecular interfaces. Yet experimentally and directly quantifying water behavior locally near interfaces at the sub-nanometer scale is challenging, especially at interfaces submerged in biological solutions. Overhauser dynamic nuclear polarization (ODNP) experiments measure equilibrium hydration water dynamics within 8-15 angstroms of a nitroxide spin probe on instantaneous timescales (10 picoseconds to nanoseconds), making ODNP a powerful tool for probing local water dynamics in the vicinity of the spin probe. As with other spectroscopic techniques, concurrent computational analysis is necessary to gain access to detailed molecular level information about the dynamic, structural, and thermodynamic properties of water from experimental ODNP data. We chose a model system that can systematically tune the dynamics of water, a water-glycerol mixture with compositions ranging from 0 to 0.3 mole fraction glycerol. We demonstrate the ability of molecular dynamics (MD) simulations to compute ODNP spectroscopic quantities, and show that translational, rotational, and hydrogen bonding dynamics of hydration water align strongly with spectroscopic ODNP parameters. Moreover, MD simulations show tight correlations between the dynamic properties of water that ODNP captures and the structural and thermodynamic behavior of water. Hence, experimental ODNP readouts of varying water dynamics suggest changes in local structural and thermodynamic hydration water properties.
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Affiliation(s)
- Dennis C Robinson Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Thomas R Webber
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Thomas M Casey
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - John Franck
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA.
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8
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Jiao S, Shell MS. Inverse design of pore wall chemistry and topology through active learning of surface group interactions. J Chem Phys 2024; 160:124705. [PMID: 38526115 DOI: 10.1063/5.0200900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024] Open
Abstract
Design of next-generation membranes requires a nanoscopic understanding of the effect of biologically inspired heterogeneous surface chemistries and topologies (roughness) on local water and solute behavior. In particular, the rejection of small, neutral solutes, such as boric acid, poses a heretofore unsolved challenge. In prior work, a computational inverse design technique using an evolutionary optimization successfully uncovered new surface design strategies for optimized transport of water over solutes in smooth, model pores consisting of two surface chemistries. However, extending such an approach to more complex (and realistic) scenarios involving many surface chemistries as well as surface roughness is challenging due to the expanded design space. In this work, we develop a new approach that uses active learning to optimize in a reduced feature space of surface group interactions, finding parameters that lead to their assembly into ordered, optimal patterns. This approach rapidly identifies novel surface functionalizations that maximize the difference in water and boric acid transport through the nanopore. Moreover, we find that the roughness of the nanopore wall, independent of its chemistry, can be leveraged to enhance transport selectivity: oscillations in the pore wall diameter optimally inhibit boric acid transport by creating energetic wells from which the solute must escape to transport down the pore. This proof-of-concept demonstrates the potential for active learning strategies, in concert with molecular simulations, to rapidly navigate complex design spaces of aqueous interfaces and is promising as a tool for engineering water-mediated surface interactions for a broad range of applications.
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Affiliation(s)
- Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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9
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Ji J, Carpentier B, Chakraborty A, Nangia S. An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale. J Chem Theory Comput 2024; 20:1656-1672. [PMID: 37018141 PMCID: PMC10902853 DOI: 10.1021/acs.jctc.3c00106] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Indexed: 04/06/2023]
Abstract
The hydropathy of proteins or quantitative assessment of protein-water interactions has been a topic of interest for decades. Most hydropathy scales use a residue-based or atom-based approach to assign fixed numerical values to the 20 amino acids and categorize them as hydrophilic, hydroneutral, or hydrophobic. These scales overlook the protein's nanoscale topography, such as bumps, crevices, cavities, clefts, pockets, and channels, in calculating the hydropathy of the residues. Some recent studies have included protein topography in determining hydrophobic patches on protein surfaces, but these methods do not provide a hydropathy scale. To overcome the limitations in the existing methods, we have developed a Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale that adopts a holistic approach to assigning the hydropathy of a residue. The parch scale evaluates the collective response of the water molecules in the protein's first hydration shell to increasing temperatures. We performed the parch analysis of a set of well-studied proteins that include the following─enzymes, immune proteins, and integral membrane proteins, as well as fungal and virus capsid proteins. Since the parch scale evaluates every residue based on its location, a residue may have very different parch values inside a crevice versus a surface bump. Thus, a residue can have a range of parch values (or hydropathies) dictated by the local geometry. The parch scale calculations are computationally inexpensive and can compare hydropathies of different proteins. The parch analysis can affordably and reliably aid in designing nanostructured surfaces, identifying hydrophilic and hydrophobic patches, and drug discovery.
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Affiliation(s)
- Jingjing Ji
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Britnie Carpentier
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Arindam Chakraborty
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
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10
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Salas-Tovar JA, Escobedo-García S, Olivas GI, Acosta-Muñiz CH, Harte F, Sepulveda DR. The MATH test. A three-phase assay? FEMS Microbiol Lett 2024; 371:fnae045. [PMID: 38866708 DOI: 10.1093/femsle/fnae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/09/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024] Open
Abstract
This study aimed to investigating the possible interference caused by glass test tubes on the quantification of bacterial adhesion to hydrocarbons by the MATH test. The adhesion of four bacteria to hexadecane and to glass test tubes was evaluated employing different suspending polar phases. The role of the ionic strength of the polar phase regarding adhesion to glassware was investigated. Within the conditions studied, Gram-positive bacteria adhered to both the test tube and the hydrocarbon regardless of the polar phase employed; meanwhile, Escherichia coli ATCC 25922 did not attach to either one. The capacity of the studied microorganisms to adhere to glassware was associated with their electron-donor properties. The ionic strength of the suspending media altered the patterns of adhesion to glass in a strain-specific manner by defining the magnitude of electrostatic repulsion observed between bacteria and the glass surface. This research demonstrated that glass test tubes may interact with suspended bacterial cells during the MATH test under specific conditions, which may lead to overestimating the percentage of adhesion to hydrocarbons and, thus, to erroneous values of cell surface hydrophobicity.
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Affiliation(s)
- Jesús A Salas-Tovar
- Centro de Investigación en Alimentación y Desarrollo, Ave. Río Conchos S/N, Parque Industrial, Cd. Cuauhtémoc, Chihuahua 31570, Mexico
| | - Sarai Escobedo-García
- Centro de Investigación en Alimentación y Desarrollo, Ave. Río Conchos S/N, Parque Industrial, Cd. Cuauhtémoc, Chihuahua 31570, Mexico
| | - Guadalupe I Olivas
- Centro de Investigación en Alimentación y Desarrollo, Ave. Río Conchos S/N, Parque Industrial, Cd. Cuauhtémoc, Chihuahua 31570, Mexico
| | - Carlos H Acosta-Muñiz
- Centro de Investigación en Alimentación y Desarrollo, Ave. Río Conchos S/N, Parque Industrial, Cd. Cuauhtémoc, Chihuahua 31570, Mexico
| | - Federico Harte
- Department of Food Science, The Pennsylvania State University, 331 Rodney A. Erickson Food Science Building University Park, PA 16802, United States
| | - David R Sepulveda
- Centro de Investigación en Alimentación y Desarrollo, Ave. Río Conchos S/N, Parque Industrial, Cd. Cuauhtémoc, Chihuahua 31570, Mexico
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11
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Watson JL, Seinkmane E, Styles CT, Mihut A, Krüger LK, McNally KE, Planelles-Herrero VJ, Dudek M, McCall PM, Barbiero S, Vanden Oever M, Peak-Chew SY, Porebski BT, Zeng A, Rzechorzek NM, Wong DCS, Beale AD, Stangherlin A, Riggi M, Iwasa J, Morf J, Miliotis C, Guna A, Inglis AJ, Brugués J, Voorhees RM, Chambers JE, Meng QJ, O'Neill JS, Edgar RS, Derivery E. Macromolecular condensation buffers intracellular water potential. Nature 2023; 623:842-852. [PMID: 37853127 PMCID: PMC10665201 DOI: 10.1038/s41586-023-06626-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 09/08/2023] [Indexed: 10/20/2023]
Abstract
Optimum protein function and biochemical activity critically depends on water availability because solvent thermodynamics drive protein folding and macromolecular interactions1. Reciprocally, macromolecules restrict the movement of 'structured' water molecules within their hydration layers, reducing the available 'free' bulk solvent and therefore the total thermodynamic potential energy of water, or water potential. Here, within concentrated macromolecular solutions such as the cytosol, we found that modest changes in temperature greatly affect the water potential, and are counteracted by opposing changes in osmotic strength. This duality of temperature and osmotic strength enables simple manipulations of solvent thermodynamics to prevent cell death after extreme cold or heat shock. Physiologically, cells must sustain their activity against fluctuating temperature, pressure and osmotic strength, which impact water availability within seconds. Yet, established mechanisms of water homeostasis act over much slower timescales2,3; we therefore postulated the existence of a rapid compensatory response. We find that this function is performed by water potential-driven changes in macromolecular assembly, particularly biomolecular condensation of intrinsically disordered proteins. The formation and dissolution of biomolecular condensates liberates and captures free water, respectively, quickly counteracting thermal or osmotic perturbations of water potential, which is consequently robustly buffered in the cytoplasm. Our results indicate that biomolecular condensation constitutes an intrinsic biophysical feedback response that rapidly compensates for intracellular osmotic and thermal fluctuations. We suggest that preserving water availability within the concentrated cytosol is an overlooked evolutionary driver of protein (dis)order and function.
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Affiliation(s)
| | | | | | - Andrei Mihut
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | - Michal Dudek
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, UK
| | - Patrick M McCall
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | | | | | | | | | - Aiwei Zeng
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | - Alessandra Stangherlin
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Margot Riggi
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jörg Morf
- Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK
| | | | - Alina Guna
- California Institute of Technology, Pasadena, CA, USA
| | | | - Jan Brugués
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | | | | | - Qing-Jun Meng
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, UK
| | | | - Rachel S Edgar
- Department of Infectious Disease, Imperial College London, London, UK.
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12
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Azizi K, Laio A, Hassanali A. Solvation thermodynamics from cavity shapes of amino acids. PNAS NEXUS 2023; 2:pgad239. [PMID: 37545648 PMCID: PMC10400782 DOI: 10.1093/pnasnexus/pgad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
According to common physical chemistry wisdom, the solvent cavities hosting a solute are tightly sewn around it, practically coinciding with its van der Waals surface. Solvation entropy is primarily determined by the surface and the volume of the cavity while enthalpy is determined by the solute-solvent interaction. In this work, we challenge this picture, demonstrating by molecular dynamics simulations that the cavities surrounding the 20 amino acids deviate significantly from the molecular surface. Strikingly, the shape of the cavity alone can be used to predict the solvation free energy, entropy, enthalpy, and hydrophobicity. Solute-solvent interactions involving the different chemical moieties of the amino acid, determine indirectly the cavity shape, and the properties of the branches but do not have to be taken explicitly into account in the prediction model.
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Affiliation(s)
- Khatereh Azizi
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Alessandro Laio
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- SISSA, Via Bonomea 265, I-34136 Trieste, Italy
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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13
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Bañuelos JL, Borguet E, Brown GE, Cygan RT, DeYoreo JJ, Dove PM, Gaigeot MP, Geiger FM, Gibbs JM, Grassian VH, Ilgen AG, Jun YS, Kabengi N, Katz L, Kubicki JD, Lützenkirchen J, Putnis CV, Remsing RC, Rosso KM, Rother G, Sulpizi M, Villalobos M, Zhang H. Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment. Chem Rev 2023; 123:6413-6544. [PMID: 37186959 DOI: 10.1021/acs.chemrev.2c00130] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.
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Affiliation(s)
- José Leobardo Bañuelos
- Department of Physics, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Eric Borguet
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Gordon E Brown
- Department of Earth and Planetary Sciences, The Stanford Doerr School of Sustainability, Stanford University, Stanford, California 94305, United States
| | - Randall T Cygan
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843, United States
| | - James J DeYoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Patricia M Dove
- Department of Geosciences, Department of Chemistry, Department of Materials Science and Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France
| | - Franz M Geiger
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2Canada
| | - Vicki H Grassian
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, United States
| | - Anastasia G Ilgen
- Geochemistry Department, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Young-Shin Jun
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Nadine Kabengi
- Department of Geosciences, Georgia State University, Atlanta, Georgia 30303, United States
| | - Lynn Katz
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Kubicki
- Department of Earth, Environmental & Resource Sciences, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Johannes Lützenkirchen
- Karlsruher Institut für Technologie (KIT), Institut für Nukleare Entsorgung─INE, Eggenstein-Leopoldshafen 76344, Germany
| | - Christine V Putnis
- Institute for Mineralogy, University of Münster, Münster D-48149, Germany
| | - Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Kevin M Rosso
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Gernot Rother
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Marialore Sulpizi
- Department of Physics, Ruhr Universität Bochum, NB6, 65, 44780, Bochum, Germany
| | - Mario Villalobos
- Departamento de Ciencias Ambientales y del Suelo, LANGEM, Instituto De Geología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Huichun Zhang
- Department of Civil and Environmental Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
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14
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Cheddah S, Xia Z, Wang Y, Yan C. Effect of Hydrophobic Moieties on the Assembly of Silica Particles into Colloidal Crystals. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5655-5669. [PMID: 37021773 DOI: 10.1021/acs.langmuir.2c03155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
To boost the implementation of colloidal crystals (CCs) in separation science, the effects of the most common chromatographic reversed phases, that is, butyl and octadecyl, on the assembly of silica particles into CCs and on the optical properties of CCs are investigated. Interestingly, particle surface modification can cause phase separation during sedimentation because the assembly is highly sensitive to minute changes in surface characteristics. Solvent-induced surface charge generation through acid-base interactions of acidic residual silanol groups with the solvent is enough to promote colloidal crystallization of modified silica particles. In addition, solvation forces at small interparticle distances are also involved in colloidal assembly. The characterization of CCs formed during sedimentation or via evaporative assembly revealed that C4 particles can form CCs more easily than C18 particles because of their low hydrophobicity; the latter can only form CCs in tetrahydrofuran when C18 chains with a high bonding density have extra hydroxyl side groups. These groups can only be hydrolyzed from trifunctional octadecyl silane but not from a monofunctional one. Moreover, after evaporative assembly, CCs formed from particles with different surface moieties exhibit different lattice spacings because their surface hydrophobicity and chemical heterogeneity can modulate interparticle interactions during the two main stages of assembly: the wet stage of crystal growth and the late stage of nano dewetting (evaporation of interparticle solvent bridges). Finally, short, alkyl-modified CCs were effectively assembled inside silica capillaries with a 100 μm inner diameter, laying the foundation for future chromatographic separation using capillary columns.
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Affiliation(s)
- Soumia Cheddah
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zihang Xia
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao Yan
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
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15
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Zhang W, Liu M, Wang Y, Wang X, Wang R, Li S, Yu L, Zhang F, Wang C. β-Sheet Assembly Translates Conservative Single-Site Mutation into a Perturbation in Macroscopic Structure. NANO LETTERS 2023; 23:2370-2378. [PMID: 36897606 DOI: 10.1021/acs.nanolett.3c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Transferring structural information from amino acid sequence to macroscale assembly is a challenging approach for designing protein quaternary structure. However, the pathway by which the slight variations in sequence result in a global perturbation effect on the assembled structure is unknown. Herein, we design two synthetic peptides, QNL-His and QNL-Arg, with one amino acid substitution and use scanning tunneling microscopy (STM) to image individual peptides in the assembled state. The submolecular resolution of STM enables us to determine the folding structure and β-sheet supramolecular organization of peptides. QNL-His and QNL-Arg differ in their β-strand length distribution in pleated β-sheet association. These structural variations lead to distinguishable outcomes in their β-sheet assembled fibrils and phase transitions. The comparison of QNL-His versus QNL-Arg structures and macroscopic properties unveils the role of assembly to amplify the structural variations associated with a single-site mutation from a single-molecule scale to a macroscopic scale.
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Affiliation(s)
- Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Mingwei Liu
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Yang Wang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Xin Wang
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Ruonan Wang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Shuyuan Li
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Feiyi Zhang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, P. R. China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
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16
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Ji J, Hossain MS, Krueger EN, Zhang Z, Nangia S, Carpentier B, Martel M, Nangia S, Mozhdehi D. Lipidation Alters the Structure and Hydration of Myristoylated Intrinsically Disordered Proteins. Biomacromolecules 2023; 24:1244-1257. [PMID: 36757021 PMCID: PMC10017028 DOI: 10.1021/acs.biomac.2c01309] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/25/2023] [Indexed: 02/10/2023]
Abstract
Lipidated proteins are an emerging class of hybrid biomaterials that can integrate the functional capabilities of proteins into precisely engineered nano-biomaterials with potential applications in biotechnology, nanoscience, and biomedical engineering. For instance, fatty-acid-modified elastin-like polypeptides (FAMEs) combine the hierarchical assembly of lipids with the thermoresponsive character of elastin-like polypeptides (ELPs) to form nanocarriers with emergent temperature-dependent structural (shape or size) characteristics. Here, we report the biophysical underpinnings of thermoresponsive behavior of FAMEs using computational nanoscopy, spectroscopy, scattering, and microscopy. This integrated approach revealed that temperature and molecular syntax alter the structure, contact, and hydration of lipid, lipidation site, and protein, aligning with the changes in the nanomorphology of FAMEs. These findings enable a better understanding of the biophysical consequence of lipidation in biology and the rational design of the biomaterials and therapeutics that rival the exquisite hierarchy and capabilities of biological systems.
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Affiliation(s)
- Jingjing Ji
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Md Shahadat Hossain
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Emily N. Krueger
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Zhe Zhang
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Shivangi Nangia
- Department
of Chemistry, University of Hartford, West Hartford, Connecticut 06117, United States
| | - Britnie Carpentier
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Mae Martel
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
| | - Davoud Mozhdehi
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
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17
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Pezzotti S, König B, Ramos S, Schwaab G, Havenith M. Liquid-Liquid Phase Separation? Ask the Water! J Phys Chem Lett 2023; 14:1556-1563. [PMID: 36745512 DOI: 10.1021/acs.jpclett.2c02697] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Water is more than an inert spectator during liquid-liquid phase separation (LLPS), the reversible compartmentalization of protein solutions into a protein-rich and a dilute phase. We show that LLPS is driven by changes in hydration entropy and enthalpy. Tuning LLPS by adjusting experimental parameters, e.g., addition of co-solutes, is a major goal for biological and medical applications. This requires a general model to quantify thermodynamic driving forces. Here, we develop such a model based on the measured amplitudes of characteristic THz-features of two hydration populations: "Cavity-wrap" water hydrating hydrophobic patches is released during LLPS leading to an increase in entropy. "Bound" water hydrating hydrophilic patches is retained since it is enthalpically favorable. We introduce a THz-phase diagram mapping these spectroscopic/thermodynamic changes. This provides not only a precise understanding of hydrophobic and hydrophilic hydration driving forces as a function of temperature and concentration but also a rational means to tune LLPS.
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Affiliation(s)
- Simone Pezzotti
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Benedikt König
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Sashary Ramos
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Gerhard Schwaab
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
- Department of Physics, Technische Universität Dortmund, 44227Dortmund, Germany
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18
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Chen W, Sanders SE, Özdamar B, Louaas D, Brigiano FS, Pezzotti S, Petersen PB, Gaigeot MP. On the Trail of Molecular Hydrophilicity and Hydrophobicity at Aqueous Interfaces. J Phys Chem Lett 2023; 14:1301-1309. [PMID: 36724059 DOI: 10.1021/acs.jpclett.2c03300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Uncovering microscopic hydrophilicity and hydrophobicity at heterogeneous aqueous interfaces is essential as it dictates physico/chemical properties such as wetting, the electrical double layer, and reactivity. Several molecular and spectroscopic descriptors were proposed, but a major limitation is the lack of connections between them. Here, we combine density functional theory-based MD simulations (DFT-MD) and SFG spectroscopy to explore how interfacial water responds in contact with self-assembled monolayers (SAM) of tunable hydrophilicity. We introduce a microscopic metric to track the transition from hydrophobic to hydrophilic interfaces. This metric combines the H/V descriptor, a structural descriptor based on the preferential orientation within the water network in the topmost binding interfacial layer (BIL) and spectroscopic fingerprints of H-bonded and dangling OH groups of water carried by BIL-resolved SFG spectra. This metric builds a bridge between molecular descriptors of hydrophilicity/hydrophobicity and spectroscopically measured quantities and provides a recipe to quantitatively or qualitatively interpret experimental SFG signals.
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Affiliation(s)
- Wanlin Chen
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
| | - Stephanie E Sanders
- Department of Chemistry and Biochemistry, Ruhr University Bochum, 44801Bochum, Germany
| | - Burak Özdamar
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
| | - Dorian Louaas
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
| | - Flavio Siro Brigiano
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 4 Place Jussieu, 75005Paris, France
| | - Simone Pezzotti
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
- Department of Physical Chemistry II, Ruhr University Bochum, D-44801Bochum, Germany
| | - Poul B Petersen
- Department of Chemistry and Biochemistry, Ruhr University Bochum, 44801Bochum, Germany
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, Université Evry, CNRS, LAMBE UMR8587, 91025Evry-Courcouronnes, France
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19
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Dallin BC, Kelkar AS, Van Lehn RC. Structural features of interfacial water predict the hydrophobicity of chemically heterogeneous surfaces. Chem Sci 2023; 14:1308-1319. [PMID: 36756335 PMCID: PMC9891380 DOI: 10.1039/d2sc02856e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
The hydrophobicity of an interface determines the magnitude of hydrophobic interactions that drive numerous biological and industrial processes. Chemically heterogeneous interfaces are abundant in these contexts; examples include the surfaces of proteins, functionalized nanomaterials, and polymeric materials. While the hydrophobicity of nonpolar solutes can be predicted and related to the structure of interfacial water molecules, predicting the hydrophobicity of chemically heterogeneous interfaces remains a challenge because of the complex, non-additive contributions to hydrophobicity that depend on the chemical identity and nanoscale spatial arrangements of polar and nonpolar groups. In this work, we utilize atomistic molecular dynamics simulations in conjunction with enhanced sampling and data-centric analysis techniques to quantitatively relate changes in interfacial water structure to the hydration free energy (a thermodynamically well-defined descriptor of hydrophobicity) of chemically heterogeneous interfaces. We analyze a large data set of 58 self-assembled monolayers (SAMs) composed of ligands with nonpolar and polar end groups of different chemical identity (amine, amide, and hydroxyl) in five mole fractions, two spatial patterns, and with scaled partial charges. We find that only five features of interfacial water structure are required to accurately predict hydration free energies. Examination of these features reveals mechanistic insights into the interfacial hydrogen bonding behaviors that distinguish different surface compositions and patterns. This analysis also identifies the probability of highly coordinated water structures as a unique signature of hydrophobicity. These insights provide a physical basis to understand the hydrophobicity of chemically heterogeneous interfaces and connect hydrophobicity to experimentally accessible perturbations of interfacial water structure.
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Affiliation(s)
- Bradley C. Dallin
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison1415 Engineering DriveMadisonWI53706USA+1-608-263-9487
| | - Atharva S. Kelkar
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison1415 Engineering DriveMadisonWI53706USA+1-608-263-9487
| | - Reid C. Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison1415 Engineering DriveMadisonWI53706USA+1-608-263-9487
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20
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Hohenschutz M, Bauduin P, Lopez CG, Förster B, Richtering W. Superchaotropic Nano-ion Binding as a Gelation Motif in Cellulose Ether Solutions. Angew Chem Int Ed Engl 2023; 62:e202210208. [PMID: 36346946 PMCID: PMC10107358 DOI: 10.1002/anie.202210208] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 11/10/2022]
Abstract
Nanometer-sized anions (nano-ions) like polyoxometalates and boron clusters exhibit so-called superchaotropic behavior, which describes their strong binding to hydrated non-ionic matter in water. We show here that nano-ions, at millimolar concentrations, dramatically enhance the viscosity and induce gelation of aqueous solutions of non-ionic cellulose ethers (CEs), a class of widely utilized polymers known for their thickening and gel-forming ability. These phenomena arise from an interplay of attractive forces and repulsive electrostatic forces between CE-chains upon nano-ion binding. The attractive forces manifest themselves as aggregation of CE-chains into a physically crosslinked polymer network (gel). In turn, the electrostatic repulsions hamper the viscosity increase and gelation. Superchaotropic nano-ion binding emerges as a novel and general physical crosslinking motif for CE-solutions and exceeds by far the conventional thickening effects of classical salts and ionic surfactants.
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Affiliation(s)
- Max Hohenschutz
- RWTH Aachen University, Institute of Physical Chemistry, Landoltweg 2, 52074, Aachen, Germany
| | - Pierre Bauduin
- Institut de Chimie Séparative de Marcoule, ICSM, CEA, CNRS, ENSCM, Univ Montpellier, Marcoule, France
| | - Carlos G Lopez
- RWTH Aachen University, Institute of Physical Chemistry, Landoltweg 2, 52074, Aachen, Germany
| | - Beate Förster
- Forschungszentrum Jülich GmbH, Ernst Ruska-Centrum für Mikroskopie und Spektroskopie mit Elektronen (ER-C-1), 52425, Jülich, Germany
| | - Walter Richtering
- RWTH Aachen University, Institute of Physical Chemistry, Landoltweg 2, 52074, Aachen, Germany.,DWI-Leibniz-Institute for Interactive Materials e.V., RWTH-Aachen University, Forckenbeckstraße 50, 52074, Aachen, Germany
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21
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Jiao S, Katz LE, Shell MS. Inverse Design of Pore Wall Chemistry To Control Solute Transport and Selectivity. ACS CENTRAL SCIENCE 2022; 8:1609-1617. [PMID: 36589891 PMCID: PMC9801506 DOI: 10.1021/acscentsci.2c01011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Indexed: 05/08/2023]
Abstract
Next-generation membranes for purification and reuse of highly contaminated water require materials with precisely tuned functionality to address key challenges, including the removal of small, charge-neutral solutes. Bioinspired multifunctional membrane surfaces enhance transport properties, but the combinatorically large chemical space is difficult to navigate through trial and error. Here, we demonstrate a computational inverse design approach to efficiently identify promising materials and elucidate design rules. We develop a combined evolutionary optimization, machine learning, and molecular simulation workflow to spatially design chemical functional group patterning in a model nanopore that enhances transport of water relative to solutes. The genetic optimization discovers nonintuitive functionalization strategies that hinder the transport of solutes through the pore, simply by patterning hydrophobic methyl and hydrophilic hydroxyl functional groups. Examining these patterns, we demonstrate that they exploit an unexpected diffusive solute hopping mechanism. This inverse design procedure and the identification of novel molecular mechanisms for pore chemical heterogeneity to impact solute selectivity demonstrate new routes to the design of membrane materials with novel functionalities. More broadly, this work illustrates how chemical design is a powerful strategy to modulate water-mediated surface-solute interactions in complex, soft material systems that are relevant to diverse technologies.
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Affiliation(s)
- Sally Jiao
- Department
of Chemical Engineering, University of California, Santa Barbara, California93106, United States
| | - Lynn E. Katz
- Department
of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - M. Scott Shell
- Department
of Chemical Engineering, University of California, Santa Barbara, California93106, United States
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22
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Wang R, Zou Y, Remsing RC, Ross NO, Klein ML, Carnevale V, Borguet E. Superhydrophilicity of α-alumina surfaces results from tight binding of interfacial waters to specific aluminols. J Colloid Interface Sci 2022; 628:943-954. [PMID: 35964442 PMCID: PMC9683471 DOI: 10.1016/j.jcis.2022.07.164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/21/2022]
Abstract
HYPOTHESIS Understanding the microscopic driving force of water wetting is challenging and important for design of materials. The relations between structure, dynamics and hydrogen bonds of interfacial water can be investigated using molecular dynamics simulations. EXPERIMENTS AND SIMULATIONS Contact angles at the alumina (0001) and (112‾0) surfaces are studied using both classical molecular dynamics simulations and experiments. To test the superhydrophilicity, the free energy cost of removing waters near the interfaces are calculated using the density fluctuations method. The strength of hydrogen bonds is determined by their lifetime and geometry. FINDINGS Both surfaces are superhydrophilic and the (0001) surface is more hydrophilic. Interactions between surfaces and interfacial waters promote a templating effect whereby the latter are aligned in a pattern that follows the underlying lattice of the surfaces. Translational and rotational dynamics of interfacial water molecules are slower than in bulk water. Hydrogen bonds between water and both surfaces are asymmetric, water-to-aluminol ones are stronger than aluminol-to-water ones. Molecular dynamics simulations eliminate the impacts of surface contamination when measuring contact angles and the results reveal the microscopic origin of the macroscopic superhydrophilicity of alumina surfaces: strong water-to-aluminol hydrogen bonds.
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Affiliation(s)
- Ruiyu Wang
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States; Center for Complex Materials from First Principles (CCM), Temple University, 1925 North 12th Street, Philadelphia, PA 19122, United States.
| | - Yunqian Zou
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States
| | - Naomi O Ross
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Michael L Klein
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States; Center for Complex Materials from First Principles (CCM), Temple University, 1925 North 12th Street, Philadelphia, PA 19122, United States; Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122, United States
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122, United States; Department of Biology, Temple University, Philadelphia, PA 19122, United States.
| | - Eric Borguet
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States; Center for Complex Materials from First Principles (CCM), Temple University, 1925 North 12th Street, Philadelphia, PA 19122, United States.
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23
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Learning the relationship between nanoscale chemical patterning and hydrophobicity. Proc Natl Acad Sci U S A 2022; 119:e2200018119. [PMID: 36409904 PMCID: PMC9860318 DOI: 10.1073/pnas.2200018119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The hydrophobicity of proteins and similar surfaces, which display chemical heterogeneity at the nanoscale, drives countless aqueous interactions and assemblies. However, predicting how surface chemical patterning influences hydrophobicity remains a challenge. Here, we address this challenge by using molecular simulations and machine learning to characterize and model the hydrophobicity of a diverse library of patterned surfaces, spanning a wide range of sizes, shapes, and chemical compositions. We find that simple models, based only on polar content, are inaccurate, whereas complex neural network models are accurate but challenging to interpret. However, by systematically incorporating chemical correlations between surface groups into our models, we are able to construct a series of minimal models of hydrophobicity, which are both accurate and interpretable. Our models highlight that the number of proximal polar groups is a key determinant of hydrophobicity and that polar neighbors enhance hydrophobicity. Although our minimal models are trained on particular patch size and shape, their interpretability enables us to generalize them to rectangular patches of all shapes and sizes. We also demonstrate how our models can be used to predict hot-spot locations with the largest marginal contributions to hydrophobicity and to design chemical patterns that have a fixed polar content but vary widely in their hydrophobicity. Our data-driven models and the principles they furnish for modulating hydrophobicity could facilitate the design of novel materials and engineered proteins with stronger interactions or enhanced solubilities.
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24
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Pezzotti S, Sebastiani F, van Dam EP, Ramos S, Conti Nibali V, Schwaab G, Havenith M. Spectroscopic Fingerprints of Cavity Formation and Solute Insertion as a Measure of Hydration Entropic Loss and Enthalpic Gain. Angew Chem Int Ed Engl 2022; 61:e202203893. [PMID: 35500074 PMCID: PMC9401576 DOI: 10.1002/anie.202203893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Indexed: 11/09/2022]
Abstract
Hydration free energies are dictated by a subtle balance of hydrophobic and hydrophilic interactions. We present here a spectroscopic approach, which gives direct access to the two main contributions: Using THz-spectroscopy to probe the frequency range of the intermolecular stretch (150-200 cm-1 ) and the hindered rotations (450-600 cm-1 ), the local contributions due to cavity formation and hydrophilic interactions can be traced back. We show that via THz calorimetry these fingerprints can be correlated 1 : 1 with the group specific solvation entropy and enthalpy. This allows to deduce separately the hydrophobic (i.e. cavity formation) and hydrophilic contributions to thermodynamics, as shown for hydrated alcohols as a case study. Accompanying molecular dynamics simulations quantitatively support our experimental results. In the future our approach will allow to dissect hydration contributions in inhomogeneous mixtures and under non-equilibrium conditions.
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Affiliation(s)
- Simone Pezzotti
- Department of Physical Chemistry IIRuhr University BochumBochumGermany
| | - Federico Sebastiani
- Department of Physical Chemistry IIRuhr University BochumBochumGermany
- Current affiliation: Department of Chemistry “U. Schiff”University of FlorenceI-50019Sesto FiorentinoFIItaly
| | - Eliane P. van Dam
- Department of Physical Chemistry IIRuhr University BochumBochumGermany
| | - Sashary Ramos
- Department of Physical Chemistry IIRuhr University BochumBochumGermany
| | - Valeria Conti Nibali
- Department of Physical Chemistry IIRuhr University BochumBochumGermany
- Current affiliation: Dipartimento di Scienze Matematiche e InformaticheScienze Fisiche e Scienze della Terra (MIFT)Università di Messina98166MessinaItaly
| | - Gerhard Schwaab
- Department of Physical Chemistry IIRuhr University BochumBochumGermany
| | - Martina Havenith
- Department of Physical Chemistry IIRuhr University BochumBochumGermany
- Department of PhysicsTechnische Universität Dortmund44227DortmundGermany
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25
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Engstler J, Giovambattista N. Different Temperature- and Pressure-Effects on the Water-Mediated Interactions between Hydrophobic, Hydrophilic, and Hydrophobic-Hydrophilic Nanoscale Surfaces. J Chem Phys 2022; 157:064701. [DOI: 10.1063/5.0097908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water-mediated interactions (WMI) are responsible for diverse processes in aqueous solutions, including protein folding and nanoparticle aggregation. WMI may be affected by changes in temperature and pressure and hence, they can alter chemical/physical processes that occur in aqueous environments. Traditionally, attention has been focused on hydrophobic interactions while, in comparison, the role of hydrophilic and hybrid (hydrophobic-hydrophilic) interactions have been mostly overlooked. Here we study the role of T and P of the WMI between nanoscale (i) hydrophobic-hydrophobic, (ii) hydrophilic-hydrophilic, and (iii) hydrophilic-hydrophobic pairs of (hydroxylated/non-hydroxylated) graphene-based surfaces. We find that hydrophobic, hydrophilic and hybrid interactions are all sensitive to P. However, while hydrophobic interactions [case (i)] are sensitive to T-variations, hydrophilic [case (ii)] and hybrid interactions [case (iii)] are practically T-independent. An analysis of the entropic and enthalpic contributions to the PMF for cases (i)-(iii) is also presented. Our results are important in understanding T- and P-induced protein denaturation, and the interactions of biomolecules in solution, including protein aggregation andphase separation processes. From the computational point of view, the results presented here are relevant in the design of implicit water models for the study of molecular and colloidal/nanoparticle systems at different thermodynamic conditions.
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26
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Boutonnet C, Lyonnais S, Alpha-Bazin B, Armengaud J, Château A, Duport C. Dynamic Profile of S-Layer Proteins Controls Surface Properties of Emetic Bacillus cereus AH187 Strain. Front Microbiol 2022; 13:937862. [PMID: 35847057 PMCID: PMC9277125 DOI: 10.3389/fmicb.2022.937862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Many prokaryotes are covered by a two-dimensional array of proteinaceous subunits. This surface layers (S-layer) is incompletely characterized for many microorganisms. Here, we studied Bacillus cereus AH187. A genome analysis identified two genes encoding the S-layer proteins SL2 and EA1, which we experimentally confirmed to encode the two protein components of the S-layer covering the surface of B. cereus. Shotgun proteomics analysis indicated that SL2 is the major component of the B. cereus S-layer at the beginning of exponential growth, whereas EA1 becomes more abundant than SL2 during later stages of stationary growth. Microscopy analysis revealed the spatial organization of SL2 and EA1 at the surface of B. cereus to depend on their temporal-dynamics during growth. Our results also show that a mutant strain lacking functional SL2 and EA1 proteins has distinct surface properties compared to its parental strain, in terms of stiffness and hydrophilicity during the stationary growth phase. Surface properties, self-aggregation capacity, and bacterial adhesion were observed to correlate. We conclude that the dynamics of SL2 and EA1 expression is a key determinant of the surface properties of B. cereus AH187, and that the S-layer could contribute to B. cereus survival in starvation conditions.
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Affiliation(s)
| | | | - Beatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Alice Château
- Avignon Université, INRAE, UMR SQPOV, Avignon, France
| | - Catherine Duport
- Avignon Université, INRAE, UMR SQPOV, Avignon, France
- *Correspondence: Catherine Duport,
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27
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Ryerson WG, Schwenk K. The kinematics and functional significance of chemosensory tongue-flicking in northern water snakes (Nerodia sipedon) on land, in water, and in between. Integr Comp Biol 2022; 62:852-864. [PMID: 35657730 DOI: 10.1093/icb/icac077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/29/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
As organisms transition between different environments, they must do more than simply move through that transition and those environments. Changes in the environment must be detected via the senses. The types of sensory information and the mechanisms of collecting that information may also change as an individual moves through different environments. We use tongue-flicking in northern water snakes, Nerodia sipedon, to examine the mechanics of sensory behavior as snakes move from terrestrial to aquatic habitats. A combination of high-speed video and mesocosm experiment revealed that water snakes will alter the mechanics of tongue-flicking in the context of their environment. Tongue-flicks on land are distinctive, with multiple oscillations, large protrusion distance, and high velocities. Comparatively, tongue-flicks under water are much shorter events, with reduced protrusion and fewer oscillations. At the surface of the water, in the presence of potential anuran prey, water snakes will tap the tips of the tongue on the surface of the water, without undergoing the full oscillations observed on land or underwater. We attribute the differences in the aerial and underwater tongue-flicks to trade-offs in the physical and chemical properties of the environment. The surface tapping behavior we observed is likely snakes altering their behavior to maximize the encounter and collection of frog-specific chemical cues, which are known to travel on the water's surface. Given the ecological transitions and distinctive biogeographical patterns rooted in water snake ecology, there are likely more examples of changing sensory mechanics to be discovered upon further investigation. All our knowledge begins with the senses. (Immanuel Kant, Critique of Pure Reason, 1781).
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Affiliation(s)
- William G Ryerson
- Biology Department, Saint Anselm College. 100 Saint Anselm Drive, Manchester, NH 03102.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043
| | - Kurt Schwenk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043
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28
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Singh H, Sharma S. Hydration of Linear Alkanes is Governed by the Small Length-Scale Hydrophobic Effect. J Chem Theory Comput 2022; 18:3805-3813. [PMID: 35648114 DOI: 10.1021/acs.jctc.2c00219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Length-scale dependence of the hydrophobic effect is well understood for apolar spherical solutes: for small solutes (diameter, d ≲ 0.8 nm), the hydration free energy is entropically driven, while for larger solutes (d ≳ 2 nm), it is enthalpically driven. The nature of the hydrophobic effect in the case of anisotropic molecules such as linear alkanes is not understood yet. In this work, we have calculated the hydration free energy of linear alkanes going from methane to octadecane and of a spherical decane droplet of d ≈ 3 nm using molecular simulations. We show that the hydration free energies of alkanes, irrespective of their size, are governed by the small length-scale hydrophobic effect. That is, unlike the case of large spherical solutes, the hydration free energies of linear alkanes are entropically driven.
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Affiliation(s)
- Himanshu Singh
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, Ohio 45701, United States
| | - Sumit Sharma
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, Ohio 45701, United States
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29
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Li H, Song R, Wang Y, Zhong R, Wang T, Jia H, Zhu L. Environmental free radicals efficiently inhibit the conjugative transfer of antibiotic resistance by altering cellular metabolism and plasmid transfer. WATER RESEARCH 2022; 209:117946. [PMID: 34923439 DOI: 10.1016/j.watres.2021.117946] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/07/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Spread of antibiotic-resistant genes (ARGs) is a global public safety issue and inhibition their transfer is imperative. In this study, a novel strategy using environmental free radical exposure was developed to inhibit conjugative transfer of ARGs (RP4 plasmid) in aqueous solutions. Long-time free radical (·OH, 1O2, and O2·-) exposure significantly suppressed the conjugative transfer frequency of ARGs between Escherichia coli (E. coli) strains, and ·OH was more likely to attack ARG, thereby inhibiting the conjugate transfer frequency, compared to 1O2 and O2·-. Compared with the control, the conjugative transfer frequency significantly decreased from 4.08 × 10-5 to 1.2 × 10-8 after 10 min free radical exposure, confirming that the transfer and proliferation of ARGs were well inhibited. Correspondingly, the number of transconjugant significantly decreased by 61.7% after 10 min free radical exposure. Significant reductions in reactive oxygen species levels (ROS content and enzyme levels) and DNA damage-induced responses in the donor strains were observed after 10 min free radical exposure. Concurrently, intercellular contact was also weakened via inhibiting the synthesis of polysaccharides in extracellular polymeric substances. Moreover, the expressions of plasmid transfer genes were down-regulated after 10 min exposure due to the shortage of adenosine-triphosphate supply. This study firstly disclosed the underneath mechanisms for depressing ARGs transfer and dissemination via environmental free radical exposure.
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Affiliation(s)
- Hu Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Ruiying Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Yangyang Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Rongwei Zhong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Lingyan Zhu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
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30
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Moon H, Collanton RP, Monroe JI, Casey TM, Shell MS, Han S, Scott SL. Evidence for Entropically Controlled Interfacial Hydration in Mesoporous Organosilicas. J Am Chem Soc 2022; 144:1766-1777. [PMID: 35041412 DOI: 10.1021/jacs.1c11342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
At aqueous interfaces, the distribution and dynamics of adsorbates are modulated by the behavior of interfacial water. Hydration of a hydrophobic surface can store entropy via the ordering of interfacial water, which contributes to the Gibbs energy of solute binding. However, there is little experimental evidence for the existence of such entropic reservoirs, and virtually no precedent for their rational design in systems involving extended interfaces. In this study, two series of mesoporous silicas were modified in distinct ways: (1) progressively deeper thermal dehydroxylation, via condensation of surface silanols, and (2) increasing incorporation of nonpolar organic linkers into the silica framework. Both approaches result in decreasing average surface polarity, manifested in a blue-shift in the fluorescence of an adsorbed dye. For the inorganic silicas, hydrogen-bonding of water becomes less extensive as the number of surface silanols decreases. Overhauser dynamic nuclear polarization (ODNP) relaxometry indicates enhanced surface water diffusivity, reflecting a loss of enthalpic hydration. In contrast, organosilicas show a monotonic decrease in surface water diffusivity with decreasing polarity, reflecting enhanced hydrophobic hydration. Molecular dynamics simulations predict increased tetrahedrality of interfacial water for the organosilicas, implying increased ordering near the nm-size organic domains (relative to inorganic silicas, which necessarily lack such domains). These findings validate the prediction that hydrophobic hydration at interfaces is controlled by the microscopic length scale of the hydrophobic regions. They further suggest that the hydration thermodynamics of structurally heterogeneous silica surfaces can be tuned to promote adsorption, which in turn tunes the selectivity in catalytic reactions.
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Affiliation(s)
- Hyunjin Moon
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Ryan P Collanton
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Jacob I Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Thomas M Casey
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States.,Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Susannah L Scott
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States.,Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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31
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Kelkar AS, Dallin BC, Van Lehn RC. Identifying nonadditive contributions to the hydrophobicity of chemically heterogeneous surfaces via dual-loop active learning. J Chem Phys 2022; 156:024701. [PMID: 35032988 DOI: 10.1063/5.0072385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Hydrophobic interactions drive numerous biological and synthetic processes. The materials used in these processes often possess chemically heterogeneous surfaces that are characterized by diverse chemical groups positioned in close proximity at the nanoscale; examples include functionalized nanomaterials and biomolecules, such as proteins and peptides. Nonadditive contributions to the hydrophobicity of such surfaces depend on the chemical identities and spatial patterns of polar and nonpolar groups in ways that remain poorly understood. Here, we develop a dual-loop active learning framework that combines a fast reduced-accuracy method (a convolutional neural network) with a slow higher-accuracy method (molecular dynamics simulations with enhanced sampling) to efficiently predict the hydration free energy, a thermodynamic descriptor of hydrophobicity, for nearly 200 000 chemically heterogeneous self-assembled monolayers (SAMs). Analysis of this dataset reveals that SAMs with distinct polar groups exhibit substantial variations in hydrophobicity as a function of their composition and patterning, but the clustering of nonpolar groups is a common signature of highly hydrophobic patterns. Further molecular dynamics analysis relates such clustering to the perturbation of interfacial water structure. These results provide new insight into the influence of chemical heterogeneity on hydrophobicity via quantitative analysis of a large set of surfaces, enabled by the active learning approach.
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Affiliation(s)
- Atharva S Kelkar
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, USA
| | - Bradley C Dallin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, USA
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, USA
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32
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Rogers BA, Okur HI, Yan C, Yang T, Heyda J, Cremer PS. Weakly hydrated anions bind to polymers but not monomers in aqueous solutions. Nat Chem 2022; 14:40-45. [PMID: 34725491 DOI: 10.1038/s41557-021-00805-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023]
Abstract
Weakly hydrated anions help to solubilize hydrophobic macromolecules in aqueous solutions, but small molecules comprising the same chemical constituents precipitate out when exposed to these ions. Here, this apparent contradiction is resolved by systematically investigating the interactions of NaSCN with polyethylene oxide oligomers and polymers of varying molecular weight. A combination of spectroscopic and computational results reveals that SCN- accumulates near the surface of polymers, but is excluded from monomers. This occurs because SCN- preferentially binds to the centre of macromolecular chains, where the local water hydrogen-bonding network is disrupted. These findings suggest a link between ion-specific effects and theories addressing how hydrophobic hydration is modulated by the size and shape of a hydrophobic entity.
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Affiliation(s)
- Bradley A Rogers
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Halil I Okur
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.,Department of Chemistry and National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey
| | - Chuanyu Yan
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Tinglu Yang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Dejvice, Czech Republic
| | - Paul S Cremer
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA. .,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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33
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Mao D, Wang X, Wu Y, Gu Z, Wang C, Tu Y. Unexpected hydrophobicity on self-assembled monolayers terminated with two hydrophilic hydroxyl groups. NANOSCALE 2021; 13:19604-19609. [PMID: 34812817 DOI: 10.1039/d1nr05048f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules onto the surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations show an unexpected hydrophobicity with a contact angle of 82° on a flexible self-assembled monolayer terminated only with two hydrophilic OH groups ((OH)2-SAM). This hydrophobicity, verified by a water slip phenomenon characterizing the friction on the (OH)2-SAM surface, is attributed to the formation of a hexagonal-ice-like H-bonding structure in the OH matrix of (OH)2-SAM, which sharply reduces the hydrogen bonds between the surface and the water molecules above. The unique simple interface presented here offers a significant molecular-level platform for examining the bio-interfacial interactions ranging from biomolecule binding to cell adhesion.
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Affiliation(s)
- Dangxin Mao
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
| | - Xian Wang
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
| | - Yuanyan Wu
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
| | - Zonglin Gu
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
| | - Chunlei Wang
- Zhangjiang Lab, Interdisplinary Research Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yusong Tu
- College of Physics Science and Technology, Yangzhou University, Jiangsu 225009, China.
- Key Laboratory of Polar Materials and Devices Ministry of Education, School of Physics and Electrical Science, East China Normal University, Shanghai 200241, China
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34
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Bharadwaj S, B SJ, van der Vegt NFA. Direct Calculation of Entropic Components in Cohesive Interaction Free Energies. J Phys Chem B 2021; 125:11026-11035. [PMID: 34570491 DOI: 10.1021/acs.jpcb.1c05748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cohesive interaction free energies entail an entropic component related to fluctuations of the energy associated with the attractive portion of the solute-solvent potential. The corresponding "fluctuation entropy" is fundamental in the solvation thermodynamics of macromolecular solutes and is linked to interfacial solvent density fluctuations and hydrophobic effects. Since the direct calculation of fluctuation entropy in molecular simulations is hampered by the poor sampling of high-energy tails in the solute-solvent energy distribution, indirect, and often approximate, routes for the calculation of fluctuation entropy are usually required, involving the modeling of geometrically frozen repulsive solute cavities in thermodynamic integration approaches. Herein, we propose a method to directly compute the fluctuation entropy by employing indirect umbrella sampling (INDUS). To validate the method, we consider model systems consisting of subnanometer oil droplets in water for which the fluctuation entropy can be computed exactly using indirect methods. The fluctuation entropy calculated with the newly proposed direct method agrees with the indirect reference calculations. We also observe that the solvation free energy and the contribution of the fluctuation entropy to it are of comparable magnitudes, particularly for larger oil droplets (∼1 nm). The proposed method can readily be employed for flexible macromolecular solutes and systems with extended hydrophobic surfaces or in the vicinity of a dewetting transition.
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Affiliation(s)
- Swaminath Bharadwaj
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Shadrack Jabes B
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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35
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Adams E, Pezzotti S, Ahlers J, Rüttermann M, Levin M, Goldenzweig A, Peleg Y, Fleishman SJ, Sagi I, Havenith M. Local Mutations Can Serve as a Game Changer for Global Protein Solvent Interaction. JACS AU 2021; 1:1076-1085. [PMID: 34337607 PMCID: PMC8317155 DOI: 10.1021/jacsau.1c00155] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 05/15/2023]
Abstract
Although it is well-known that limited local mutations of enzymes, such as matrix metalloproteinases (MMPs), may change enzyme activity by orders of magnitude as well as its stability, the completely rational design of proteins is still challenging. These local changes alter the electrostatic potential and thus local electrostatic fields, which impacts the dynamics of water molecules close the protein surface. Here we show by a combined computational design, experimental, and molecular dynamics (MD) study that local mutations have not only a local but also a global effect on the solvent: In the specific case of the matrix metalloprotease MMP14, we found that the nature of local mutations, coupled with surface morphology, have the ability to influence large patches of the water hydrogen-bonding network at the protein surface, which is correlated with stability. The solvent contribution can be experimentally probed via terahertz (THz) spectroscopy, thus opening the door to the exciting perspective of rational protein design in which a systematic tuning of hydration water properties allows manipulation of protein stability and enzymatic activity.
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Affiliation(s)
- Ellen
M. Adams
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801 Bochum, Germany
| | - Simone Pezzotti
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801 Bochum, Germany
| | - Jonas Ahlers
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801 Bochum, Germany
| | - Maximilian Rüttermann
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801 Bochum, Germany
| | - Maxim Levin
- Department
of Biological Regulation, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Adi Goldenzweig
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Yoav Peleg
- Structural
Proteomics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J. Fleishman
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Irit Sagi
- Department
of Biological Regulation, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Martina Havenith
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801 Bochum, Germany
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36
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Identifying hydrophobic protein patches to inform protein interaction interfaces. Proc Natl Acad Sci U S A 2021; 118:2018234118. [PMID: 33526682 DOI: 10.1073/pnas.2018234118] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.
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37
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Bilodeau CL, Lau EY, Roush DJ, Snyder MA, Cramer SM. Behavior of Water Near Multimodal Chromatography Ligands and Its Consequences for Modulating Protein-Ligand Interactions. J Phys Chem B 2021; 125:6112-6120. [PMID: 34097423 DOI: 10.1021/acs.jpcb.1c01549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multimodal chromatography is a powerful approach for purifying proteins that uses ligands containing multiple modes of interaction. Recent studies have shown that selectivity in multimodal chromatographic separations is a function of the ligand structure and geometry. Here, we performed molecular dynamics simulations to explore how the ligand structure and geometry affect ligand-water interactions and how these differences in solution affect the nature of protein-ligand interactions. Our investigation focused on three chromatography ligands: Capto MMC, Nuvia cPrime, and Prototype 4, a structural variant of Nuvia cPrime. First, the solvation characteristics of each ligand were quantified via three metrics: average water density, fluctuations, and residence time. We then explored how solvation was perturbed when the ligand was bound to the protein surface and found that the probability of the phenyl ring dewetting followed the order: Capto MMC > Prototype 4 > Nuvia cPrime. To explore how these differences in dewetting affect protein-ligand interactions, we calculated the probability of each ligand binding to different types of residues on the protein surface and found that the probability of binding to a hydrophobic residue followed the same order as the dewetting behavior. This study illustrates the role that wetting and dewetting play in modulating protein-ligand interactions.
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Affiliation(s)
- Camille L Bilodeau
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Edmond Y Lau
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - David J Roush
- Biologics Process R&D, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Mark A Snyder
- Process Chromatography Division, Bio-Rad Laboratories, 6000 James Watson Drive, Hercules, California 94547, United States
| | - Steven M Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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38
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Dhabal D, Jiang Z, Pallath A, Patel AJ. Characterizing the Interplay between Polymer Solvation and Conformation. J Phys Chem B 2021; 125:5434-5442. [PMID: 33978411 DOI: 10.1021/acs.jpcb.1c02191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and extended states can be quantified by the strength of the requisite potential. Our results also provide mechanistic insights into the collapse transition, highlighting that the bottleneck to polymer collapse is the formation of a sufficiently large cluster, and the collective dewetting of such a cluster. We also study the collapse of the hydrophobic polymer in octane, a nonpolar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhitong Jiang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Akash Pallath
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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39
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Jakob LA, Beyer B, Janeiro Ferreira C, Lingg N, Jungbauer A, Tscheließnig R. Protein-protein interactions and reduced excluded volume increase dynamic binding capacity of dual salt systems in hydrophobic interaction chromatography. J Chromatogr A 2021; 1649:462231. [PMID: 34038776 DOI: 10.1016/j.chroma.2021.462231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
Deploying two salts in hydrophobic interaction chromatography can significantly increase dynamic binding capacities. Nevertheless, the mechanistic understanding of this phenomenon is lacking. Here, we investigate whether surface tension or ionic strength govern dynamic binding capacities of the chromatographic resin Toyopearl Butyl-650 M in dual salt systems. Small-angle X-ray scattering was employed to analyze the model proteins and the protein-resin adduct in the respective dual salt systems. The dual salt systems incorporate sodium citrate and a secondary sodium salt (acetate, sulfate, or phosphate). As model proteins, we used lysozyme, GFP, and a monoclonal antibody (adalimumab). Moreover, for the protein-resin adduct, we determined the model parameters of a self-avoiding random walk model fitted into the pair density distribution function of the SAXS data. Ionic strength is more predictive for dynamic binding capacities in HIC dual salt systems than surface tension. However, dynamic binding capacities still differ by up to 30 % between the investigated dual salt systems. The proteins exhibit extensive protein-protein interactions in the studied dual salt HIC buffers. We found a correlation of protein-protein interactions with the well-known Hofmeister series. For systems with elevated protein-protein interactions, adsorption isotherms deviate from Langmuirian behavior. This highlights the importance of lateral protein-protein interactions in protein adsorption, where monomolecular protein layers are usually assumed. SAXS analysis of the protein-resin adduct indicates an inverse correlation of the binding capacity and the excluded volume parameter. This is indicative of the deposition of proteins in the cavities of the stationary phase. We hypothesize that increasing protein-protein interactions allow the formation of attractive clusters and multilayers in the cavities, respectively.
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Affiliation(s)
- Leo A Jakob
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190, Austria
| | - Beate Beyer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190, Austria; Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna A-1190, Austria
| | | | - Nico Lingg
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190, Austria; Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna A-1190, Austria
| | - Alois Jungbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190, Austria; Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna A-1190, Austria.
| | - Rupert Tscheließnig
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190, Austria
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40
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Pezzotti S, Serva A, Sebastiani F, Brigiano FS, Galimberti DR, Potier L, Alfarano S, Schwaab G, Havenith M, Gaigeot MP. Molecular Fingerprints of Hydrophobicity at Aqueous Interfaces from Theory and Vibrational Spectroscopies. J Phys Chem Lett 2021; 12:3827-3836. [PMID: 33852317 PMCID: PMC9004482 DOI: 10.1021/acs.jpclett.1c00257] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/09/2021] [Indexed: 05/28/2023]
Abstract
Hydrophobicity/hydrophilicity of aqueous interfaces at the molecular level results from a subtle balance in the water-water and water-surface interactions. This is characterized here via density functional theory-molecular dynamics (DFT-MD) coupled with vibrational sum frequency generation (SFG) and THz-IR absorption spectroscopies. We show that water at the interface with a series of weakly interacting materials is organized into a two-dimensional hydrogen-bonded network (2D-HB-network), which is also found above some macroscopically hydrophilic silica and alumina surfaces. These results are rationalized through a descriptor that measures the number of "vertical" and "horizontal" hydrogen bonds formed by interfacial water, quantifying the competition between water-surface and water-water interactions. The 2D-HB-network is directly revealed by THz-IR absorption spectroscopy, while the competition of water-water and water-surface interactions is quantified from SFG markers. The combination of SFG and THz-IR spectroscopies is thus found to be a compelling tool to characterize the finest details of molecular hydrophobicity at aqueous interfaces.
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Affiliation(s)
- Simone Pezzotti
- Université
Paris-Saclay, Univ Evry, CNRS, LAMBE
UMR8587, 91025 Evry-Courcouronnes, France
| | - Alessandra Serva
- Université
Paris-Saclay, Univ Evry, CNRS, LAMBE
UMR8587, 91025 Evry-Courcouronnes, France
| | - Federico Sebastiani
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44801 Bochum, Germany
| | - Flavio Siro Brigiano
- Université
Paris-Saclay, Univ Evry, CNRS, LAMBE
UMR8587, 91025 Evry-Courcouronnes, France
| | - Daria Ruth Galimberti
- Université
Paris-Saclay, Univ Evry, CNRS, LAMBE
UMR8587, 91025 Evry-Courcouronnes, France
| | - Louis Potier
- Université
Paris-Saclay, Univ Evry, CNRS, LAMBE
UMR8587, 91025 Evry-Courcouronnes, France
| | - Serena Alfarano
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44801 Bochum, Germany
| | - Gerhard Schwaab
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44801 Bochum, Germany
| | - Martina Havenith
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44801 Bochum, Germany
| | - Marie-Pierre Gaigeot
- Université
Paris-Saclay, Univ Evry, CNRS, LAMBE
UMR8587, 91025 Evry-Courcouronnes, France
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41
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Ahlers J, Adams EM, Bader V, Pezzotti S, Winklhofer KF, Tatzelt J, Havenith M. The key role of solvent in condensation: Mapping water in liquid-liquid phase-separated FUS. Biophys J 2021; 120:1266-1275. [PMID: 33515602 PMCID: PMC8059208 DOI: 10.1016/j.bpj.2021.01.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/21/2020] [Accepted: 01/19/2021] [Indexed: 01/09/2023] Open
Abstract
Formation of biomolecular condensates through liquid-liquid phase separation (LLPS) has emerged as a pervasive principle in cell biology, allowing compartmentalization and spatiotemporal regulation of dynamic cellular processes. Proteins that form condensates under physiological conditions often contain intrinsically disordered regions with low-complexity domains. Among them, the RNA-binding proteins FUS and TDP-43 have been a focus of intense investigation because aberrant condensation and aggregation of these proteins is linked to neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. LLPS occurs when protein-rich condensates form surrounded by a dilute aqueous solution. LLPS is per se entropically unfavorable. Energetically favorable multivalent protein-protein interactions are one important aspect to offset entropic costs. Another proposed aspect is the release of entropically unfavorable preordered hydration water into the bulk. We used attenuated total reflection spectroscopy in the terahertz frequency range to characterize the changes in the hydrogen bonding network accompanying the FUS enrichment in liquid-liquid phase-separated droplets to provide experimental evidence for the key role of the solvent as a thermodynamic driving force. The FUS concentration inside LLPS droplets was determined to be increased to 2.0 mM independent of the initial protein concentration (5 or 10 μM solutions) by fluorescence measurements. With terahertz spectroscopy, we revealed a dewetting of hydrophobic side chains in phase-separated FUS. Thus, the release of entropically unfavorable water populations into the bulk goes hand in hand with enthalpically favorable protein-protein interaction. Both changes are energetically favorable, and our study shows that both contribute to the thermodynamic driving force in phase separation.
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Affiliation(s)
- Jonas Ahlers
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany
| | - Ellen M Adams
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Simone Pezzotti
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Martina Havenith
- Department Physical Chemistry, Ruhr-University Bochum, Bochum, Germany.
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42
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Chew AK, Dallin BC, Van Lehn RC. The Interplay of Ligand Properties and Core Size Dictates the Hydrophobicity of Monolayer-Protected Gold Nanoparticles. ACS NANO 2021; 15:4534-4545. [PMID: 33621066 DOI: 10.1021/acsnano.0c08623] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The hydrophobicity of monolayer-protected gold nanoparticles is a crucial design parameter that influences self-assembly, preferential binding to proteins and membranes, and other nano-bio interactions. Predicting the effects of monolayer components on nanoparticle hydrophobicity is challenging due to the nonadditive, cooperative perturbations to interfacial water structure that dictate hydrophobicity at the nanoscale. In this work, we quantify nanoparticle hydrophobicity by using atomistic molecular dynamics simulations to calculate local hydration free energies at the nanoparticle-water interface. The simulations reveal that the hydrophobicity of large gold nanoparticles is determined primarily by ligand end group chemistry, as expected. However, for small gold nanoparticles, long alkanethiol ligands interact to form anisotropic bundles that lead to substantial spatial variations in hydrophobicity even for homogeneous monolayer compositions. We further show that nanoparticle hydrophobicity is modulated by changing the ligand structure, ligand chemistry, and gold core size, emphasizing that single-ligand properties alone are insufficient to characterize hydrophobicity. Finally, we illustrate that hydration free energy measurements correlate with the preferential binding of propane as a representative hydrophobic probe molecule. Together, these results show that both physical and chemical properties influence the hydrophobicity of small nanoparticles and must be considered together when predicting gold nanoparticle interactions with biomolecules.
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Affiliation(s)
- Alex K Chew
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Bradley C Dallin
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
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43
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Monroe JI, Jiao S, Davis RJ, Robinson Brown D, Katz LE, Shell MS. Affinity of small-molecule solutes to hydrophobic, hydrophilic, and chemically patterned interfaces in aqueous solution. Proc Natl Acad Sci U S A 2021; 118:e2020205118. [PMID: 33372161 PMCID: PMC7821046 DOI: 10.1073/pnas.2020205118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Performance of membranes for water purification is highly influenced by the interactions of solvated species with membrane surfaces, including surface adsorption of solutes upon fouling. Current efforts toward fouling-resistant membranes often pursue surface hydrophilization, frequently motivated by macroscopic measures of hydrophilicity, because hydrophobicity is thought to increase solute-surface affinity. While this heuristic has driven diverse membrane functionalization strategies, here we build on advances in the theory of hydrophobicity to critically examine the relevance of macroscopic characterizations of solute-surface affinity. Specifically, we use molecular simulations to quantify the affinities to model hydroxyl- and methyl-functionalized surfaces of small, chemically diverse, charge-neutral solutes represented in produced water. We show that surface affinities correlate poorly with two conventional measures of solute hydrophobicity, gas-phase water solubility and oil-water partitioning. Moreover, we find that all solutes show attraction to the hydrophobic surface and most to the hydrophilic one, in contrast to macroscopically based hydrophobicity heuristics. We explain these results by decomposing affinities into direct solute interaction energies (which dominate on hydroxyl surfaces) and water restructuring penalties (which dominate on methyl surfaces). Finally, we use an inverse design algorithm to show how heterogeneous surfaces, with multiple functional groups, can be patterned to manipulate solute affinity and selectivity. These findings, importantly based on a range of solute and surface chemistries, illustrate that conventional macroscopic hydrophobicity metrics can fail to predict solute-surface affinity, and that molecular-scale surface chemical patterning significantly influences affinity-suggesting design opportunities for water purification membranes and other engineered interfaces involving aqueous solute-surface interactions.
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Affiliation(s)
- Jacob I Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
| | - Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
| | - R Justin Davis
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712
| | - Dennis Robinson Brown
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
| | - Lynn E Katz
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106;
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44
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Navigating the waters of membrane design. Proc Natl Acad Sci U S A 2021; 118:2024346118. [PMID: 33384327 DOI: 10.1073/pnas.2024346118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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45
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Zhang F, Yu L, Zhang W, Liu L, Wang C. A minireview on the perturbation effects of polar groups to direct nanoscale hydrophobic interaction and amphiphilic peptide assembly. RSC Adv 2021; 11:28667-28673. [PMID: 35478591 PMCID: PMC9038178 DOI: 10.1039/d1ra05463e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/23/2021] [Indexed: 12/29/2022] Open
Abstract
Hydrophobic interaction provides the essential driving force for creating diverse native and artificial supramolecular architectures. Accumulating evidence leads to a hypothesis that the hydrophobicity of a nonpolar patch of a molecule is non-additive and susceptible to the chemical context of a judicious polar patch. However, the quantification of the hydrophobic interaction at the nanoscale remains a central challenge to validate the hypothesis. In this review, we aim to outline the recent efforts made to determine the hydrophobic interaction at a nanoscopic length scale. The advances achieved in the understanding of proximal polar groups perturbing the magnitude of hydrophobic interaction generated by the nonpolar patch are introduced. We will also discuss the influence of chemical heterogeneity on the modulation of amphiphilic peptide/protein assembly and molecular recognition. Hydrophobic interaction provides the essential driving force for creating diverse native and artificial supramolecular architectures.![]()
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Affiliation(s)
- Feiyi Zhang
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Lei Liu
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
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46
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Büscher TH, Lohar R, Kaul MC, Gorb SN. Multifunctional Adhesives on the Eggs of the Leaf Insect Phyllium philippinicum (Phasmatodea: Phylliidae): Solvent Influence and Biomimetic Implications. Biomimetics (Basel) 2020; 5:biomimetics5040066. [PMID: 33261153 PMCID: PMC7768468 DOI: 10.3390/biomimetics5040066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/14/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Leaf insects (Phylliidae) are well-camouflaged terrestrial herbivores. They imitate leaves of plants almost perfectly and even their eggs resemble seeds—visually and regarding to dispersal mechanisms. The eggs of the leaf insect Phyllium philippinicum utilize an adhesive system with a combination of glue, which can be reversibly activated through water contact and a water-responding framework of reinforcing fibers that facilitates their adjustment to substrate asperities and real contact area enhancement. So far, the chemical composition of this glue remains unknown. To evaluate functional aspects of the glue–solvent interaction, we tested the effects of a broad array of chemical solvents on the glue activation and measured corresponding adhesive forces. Based on these experiments, our results let us assume a proteinaceous nature of the glue with different functional chemical subunits, which enable bonding of the glue to both the surface of the egg and the unpredictable substrate. Some chemicals inhibited adhesion, but the deactivation was always reversible by water-contact and in some cases yielded even higher adhesive forces. The combination of glue and fibers also enables retaining the adhesive on the egg, even if detached from the egg’s surface. The gained insights into this versatile bioadhesive system could hereafter inspire further biomimetic adhesives.
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47
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Shin D, Seo H, Jhe W. Exploring the Hydration Water Character on Atomically Dislocated Surfaces by Surface Enhanced Raman Spectroscopy. ACS CENTRAL SCIENCE 2020; 6:2079-2087. [PMID: 33274284 PMCID: PMC7706083 DOI: 10.1021/acscentsci.0c01009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 06/12/2023]
Abstract
Hydration is ubiquitous in any kind of water-substance interaction such as in various interfacial and biological processes. Despite substantial progress made to date, however, still less explored is the hydration behavior on complex heterogeneous surfaces, such as the water surrounding the protein, which requires a platform that enables systematic investigation at the atomic scale. Here, we realized a heterogeneous self-assembled monolayer system that allows both controllable mixing with hydrophobic or hydrophilic groups and precise distance control of the functional carboxyl groups from the surface by methylene spacer groups. Using surface-enhanced Raman spectroscopy (SERS), we first demonstrated the hydrophobic (or hydrophilic) mixing ratio-dependent pK a variation of the carboxyl group. Interestingly, we observed a counterintuitive, non-monotonic behavior that a fractionally mixed hydrophobic group can induce significant enhancement of dielectric strength of the interfacial water. In particular, such a fractional mixing substantially decreases the amide coupling efficiency at the surface, as manifested by the corresponding pK a decrease. The SERS-based platform we demonstrated can be widely applied for atomically precise control and molecular-level characterization of hydration water on various heterogeneous surfaces of biological and industrial importance.
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Affiliation(s)
- Dongha Shin
- Center
for 0D Nanofluidics, Institute of Applied Physics, Department of Physics
and Astronomy, Seoul National University, Seoul 08826, Republic of Korea
- Division
of Fine Chemistry and Engineering, College of Natural Science, Pai Chai University, Daejeon 35345, Republic of Korea
| | - Hoyoung Seo
- Center
for 0D Nanofluidics, Institute of Applied Physics, Department of Physics
and Astronomy, Seoul National University, Seoul 08826, Republic of Korea
| | - Wonho Jhe
- Center
for 0D Nanofluidics, Institute of Applied Physics, Department of Physics
and Astronomy, Seoul National University, Seoul 08826, Republic of Korea
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48
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Bhattacharya M, Sharma AR, Mallick B, Sharma G, Lee SS, Chakraborty C. Immunoinformatics approach to understand molecular interaction between multi-epitopic regions of SARS-CoV-2 spike-protein with TLR4/MD-2 complex. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104587. [PMID: 33039603 PMCID: PMC7543713 DOI: 10.1016/j.meegid.2020.104587] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The coronavirus (CoV) spike (S) protein is critical for receptor binding, membrane fusion and internalization of the virus into the human cells. We have tried to search the epitopic component of the S-protein that might be served as crucial targets for the vaccine development and also tried to understand the molecular mechanism of epitopes and TLR4/MD-2 complex for adaptive immunity. MATERIAL AND METHODS Here we identified the antigenicity and the epitopic divergence of S-protein via immunoinformatics approach. The study was performed to identify the epitopes, composition of amino acids and its distribution in epitopic regions, composition of amino acid between the identified epitopes, secondary structure architecture of epitopes, physicochemical and biochemical parameters and molecular interaction between the identified epitope and TLR4/MD-2 complex. The SARS-CoV-2 can be possibly recognised by TLR4 of host immune cells that are responsible for the adaptive immune response. RESULTS We identified four SARS-CoV-2 S-protein 9mer antigenic epitopes and observed that they bind with the TLR4/MD-2 complex by varied stable molecular bonding interactions. Molecular interaction between these characterized epitopes with TLR4/MD-2 complex might be indicated the binding affinity and downstream signalling of adaptive immune response. Different physicochemical and biochemical parameters such as O-glycosylation and N-glycosylation, Hydrophobicity, GRAVY were identified within epitopic regions of S-protein. These parameters help to understand the protein-protein interaction between epitopes and TLR4/MD-2 complex. The study also revealed different epitopic binding pockets of TLR4/MD-2 complex. CONCLUSIONS The identified epitopes impart suitable prospects for the development of novel peptide-based epitopic vaccine for the control of COVID-19 infection.
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Affiliation(s)
- Manojit Bhattacharya
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Bidyut Mallick
- Department of Applied Science, Galgotias College of Engineering and Technology I, Knowledge Park-II, Greater Noida, Uttar Pradesh 201306, India
| | - Garima Sharma
- Neuropsychopharmacology and Toxicology Program, College of Pharmacy, Kangwon National University, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea.
| | - Chiranjib Chakraborty
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea; Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal 700126, India.
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Tian R, Hu G, Ou X, Luo M, Li J. Dynamic behaviors of interfacial water on the self-assembly monolayer (SAM) heterogeneous surface. J Chem Phys 2020; 153:124705. [PMID: 33003729 DOI: 10.1063/5.0019135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dynamic behaviors of water molecules near the surface with mixed hydrophobic and hydrophilic areas are studied by molecular dynamics simulation. More specifically, the diffusion coefficient and hydrogen bond lifetime of interfacial water on the self-assembly monolayer composed of hydrophobic and hydrophilic groups and their dependence on the mixing ratio are studied. The diffusion dramatically slows down, and the hydrogen bond lifetime considerably increases when a few hydrophilic groups are added to the hydrophobic surface. When the percentage of hydrophilic groups increases to 25%, the behavior of interfacial water is similar to the case of the pure hydrophilic surface. The sensitivity to the hydrophilic group can be attributed to the fact that the grafted hydrophilic groups can not only retard the directly bound water molecules but also affect indirectly bound water by stabilizing hydrogen bonds among interfacial water molecules.
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Affiliation(s)
- Ranran Tian
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Guorong Hu
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Xinwen Ou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Mengbo Luo
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
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Kelkar AS, Dallin BC, Van Lehn RC. Predicting Hydrophobicity by Learning Spatiotemporal Features of Interfacial Water Structure: Combining Molecular Dynamics Simulations with Convolutional Neural Networks. J Phys Chem B 2020; 124:9103-9114. [DOI: 10.1021/acs.jpcb.0c05977] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Atharva S. Kelkar
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Bradley C. Dallin
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Reid C. Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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