1
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Nanavare P, Sarkar S, Jena AB, Chakrabarti R. Osmolyte-induced conformational stabilization of a hydrophobic polymer. Phys Chem Chem Phys 2024; 26:24021-24040. [PMID: 39247939 DOI: 10.1039/d4cp01694g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Elucidating the mechanistic role of osmolytes on conformations of hydrophobic prototypical macromolecules in principle is the stepping stone towards understanding the effect of osmolytes on proteins. Motivated by this, we use equilibrium simulations and umbrella sampling techniques to dissect the underlying mechanism of osmolyte-induced conformational stability of a hydrophobic polymer. Our results unveil a remarkable osmolyte-dependent conformational stabilization of the polymer. In an aqueous solution of 4 M choline chloride (ChCl), the polymer has an even more compact structure than in water. On the other hand, an aqueous solution of 8 M urea stabilizes the extended state of the polymer. Interestingly, the polymer adopts an intermediate hairpin conformation in a mixed osmolyte solution of 4 M ChCl and 8 M urea in water due to the interplay of ChCl and urea. Our simulations identify the relative accumulation of water and the hydrophilic part of choline or preferential binding of urea near the collapsed and the extended states, respectively. Analyses split out the enthalpic and entropic contributions to the overall free energy. This decides the stabilization of the preferred conformation in the chosen osmolyte solution. Our simulations show that in an aqueous solution of ChCl, the hairpin state is stabilized by entropy gain. In contrast, the enthalpic contribution stabilizes the hairpin state in mixed environments. However, a collapsed state is energetically not favored in the presence of urea. In brief, via employing an in silico approach, the current findings indicate the importance of osmolytes in stabilizing the conformational states of hydrophobic polymers.
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Affiliation(s)
- Pooja Nanavare
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Soham Sarkar
- Eduard-Zintl-Institute für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Abhijit Bijay Jena
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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2
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Dhibar S, Jana B. Optimized Collective Variable for Collapse Transition in Linear Hydrophobic Polymers: Importance of Hydration Water and End-to-End Distance. J Chem Theory Comput 2024; 20:7404-7415. [PMID: 39252562 DOI: 10.1021/acs.jctc.4c00753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Choosing an appropriate collective variable (CV) for any biomolecular process is a challenging task. Researchers are developing methods to solve this issue using a variety of methodologies, most recently using machine learning (ML) methods. In this work, we investigate the mechanism of collapse transition across various lengths of polymer systems through adaptively sampled multiple short trajectories utilizing the Time Lagged Independent Component Analysis (TICA) framework. From TICA analysis, it is revealed that the radius of gyration (Rg) and end-to-end distance serve as good order parameters (OPs) for these systems describing overall energy landscapes. Markov state model (MSM) and mean first passage time (MFPT) analysis suggest that hydration water (Nw) plays a determining role in dictating the time scale and barrier for the collapsed transition for the C40 system. P-fold analysis on identifying transition state ensembles (TSE) identified by committor analysis also strengthens the role of Nw in such a transition. TICA, MSM, and committor analyses on the collapse transition for C45 reveal similarities with C40 systems in different aspects. Furthermore, we propose a pipeline integrating XGBoost regression along with an interpretable ML model, Shapley Additive exPlanation (SHAP) to precisely elucidate the contribution of each OP locally at the TSE. Through this approach, we observe that the collapse transition is primarily driven by Nw for both polymer systems. A carefully designed protocol for the collapsed transition of C60 systems indirectly reiterates the above result. Overall, our results suggest that while the end-to-end distance should be considered for better resolution of metastable states in the landscape, Nw is the crucial coordinate to be used in enhanced sampling for the exploration of actual collapse transitions for linear hydrophobic polymer systems. The Python code for analyzing the contribution of different OPs in the TSE using an ML-aided protocol is available on GitHub (https://github.com/saikat-ai/linear_polymer_project).
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Affiliation(s)
- Saikat Dhibar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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3
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Ashbaugh HS. Gaussian and Non-Gaussian Solvent Density Fluctuations within Solute Cavities in a Water-like Solvent. J Chem Theory Comput 2024; 20:1505-1518. [PMID: 37437298 PMCID: PMC10902835 DOI: 10.1021/acs.jctc.3c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
We report a Monte Carlo simulation study of length-scale-dependent density fluctuations in cavities in the coarse-grained mW representation of water at ambient conditions. Specifically, we use a combination of test particle insertion and umbrella sampling techniques to examine the full range of water occupation states in spherical cavities up to 6.3 Å radius in water. As has previously been observed, water density fluctuations are found to be effectively Gaussian in nature for atomic-scale cavities, but as the cavities get larger, they exhibit a non-Gaussian "fat-tail" distribution for lower occupancy states. We introduce a new statistical thermodynamic approach to analyze non-Gaussian fluctuations based on the radial distribution of waters about cavities with varying numbers of waters within its boundaries. It is shown that the onset of these non-Gaussian fluctuations is a result of the formation of a bubble within the cavity as it is emptied, which is accompanied by the adsorption of waters onto its interior surface. We revisit a theoretical framework we previously introduced to describe Gaussian fluctuations within cavities to incorporate bubble formation by including surface tension contributions. This modified theory accurately describes density fluctuations within both atomic and meso-scale cavities. Moreover, the theory predicts the transition from Gaussian to non-Gaussian fluctuations at a specific cavity occupancy, in excellent agreement with simulation observations.
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Affiliation(s)
- Henry S Ashbaugh
- Tulane University, Chemical and Biomolecular Engineering, New Orleans, Louisiana 70118, United States
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4
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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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5
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Zhang J, Liang Y, Deng Z, Xu H, Zhang H, Guo B, Zhang J. Adhesive Ion-Conducting Hydrogel Strain Sensor with High Sensitivity, Long-Term Stability, and Extreme Temperature Tolerance. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37319345 DOI: 10.1021/acsami.3c03624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Ion-conducting hydrogels with excellent flexibility and ductility have great potential in human movements monitoring. However, some obstacles, including a small detection range, low sensitivity, low electrical conductivity, and poor stability under extreme conditions, impede their use as sensors. Herein, an ion-conducting hydrogel comprising acrylamide (AM), lauryl methacrylate (LMA), 2-acrylamido-2-methylpropanesulfonic acid (AMPS), and a water/glycerol binary solvent (named the AM-LMA-AMPS-LiCl (water/glycerol) hydrogel) is designed, which exhibits an enlarged detection range of 0%-1823% and improved transparency. Notably, the ion channel constructed using AMPS and LiCl significantly improves the sensitivity (gauge factor = 22.15 ± 2.86) of the hydrogel. The water/glycerol binary solvent endows the hydrogel with electrical and mechanical stability under extreme conditions (70 and -80 °C). Furthermore, the AM-LMA-AMPS-LiCl (water/glycerol) hydrogel exhibits antifatigue properties for 10 cycles (0%-1000%) because of noncovalent interactions such as hydrophobic interactions and hydrogen bonding. The hydrogel can be used to monitor human movements such as joint bending and perceive subtle discrepancies such as different joint bending speeds and angles, showing its great potential application in human movement monitoring, electronic skin, and wearable devices.
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Affiliation(s)
- Jiaodi Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710049, China
- State Key Laboratory for Mechanical Behavior of Materials, and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yuqing Liang
- State Key Laboratory for Mechanical Behavior of Materials, and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zexing Deng
- College of Materials Science and Engineering, Xi'an University of Science and Technology, Xi'an 710054, China
| | - Huiru Xu
- State Key Laboratory for Mechanical Behavior of Materials, and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Hualei Zhang
- State Key Laboratory for Mechanical Behavior of Materials, and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Baolin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710049, China
- State Key Laboratory for Mechanical Behavior of Materials, and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jie Zhang
- Institute of Preventive Medicine, Fourth Military Medical University, Xi'an 710032, China
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6
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Di W, Xue K, Cai J, Zhu Z, Li Z, Fu H, Lei H, Hu W, Tang C, Wang W, Cao Y. Single-Molecule Force Spectroscopy Reveals Cation-π Interactions in Aqueous Media Are Highly Affected by Cation Dehydration. PHYSICAL REVIEW LETTERS 2023; 130:118101. [PMID: 37001074 DOI: 10.1103/physrevlett.130.118101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/24/2023] [Indexed: 06/19/2023]
Abstract
Cation-π interactions underlie many important processes in biology and materials science. However, experimental investigations of cation-π interactions in aqueous media remain challenging. Here, we studied the cation-π binding strength and mechanism by pulling two hydrophobic polymers with distinct cation binding properties, i.e., poly-pentafluorostyrene and polystyrene, in aqueous media using single-molecule force spectroscopy and nuclear magnetic resonance measurement. We found that the interaction strengths linearly depend on the cation concentrations, following the order of Li^{+}<NH_{4}^{+}<Na^{+}<K^{+}. The binding energies are 0.03-0.23 kJ mol^{-1} M^{-1}. This order is distinct from the strength of cation-π interactions in gas phase and may be caused by the different dehydration ability of the cations. Taken together, our method provides a unique perspective to investigate cation-π interactions under physiologically relevant conditions.
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Affiliation(s)
- Weishuai Di
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Kai Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- School of Physical and Mathematical Science Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Jun Cai
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Zhenshu Zhu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Zihan Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Fu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Wenbing Hu
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210093, China
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7
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Hu G, Yan H, Xi G, Gao Z, Wu Z, Lu Z, Tu J. Nanopore sensors for single molecular protein detection: Research progress based on computer simulations. IET Nanobiotechnol 2023; 17:257-268. [PMID: 36924083 DOI: 10.1049/nbt2.12124] [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: 12/29/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label-free and high-throughput protein sequencing. In recent years, nanopore-based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing.
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Affiliation(s)
- Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Guohao Xi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhuwei Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ziqing Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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8
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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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9
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Cao N, Cai W, Qian L, Nie Z, Mao C, Cui S. Emulating Titin by a Multidomain DNA Structure. ACS Macro Lett 2023; 12:59-64. [PMID: 36573670 DOI: 10.1021/acsmacrolett.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Titin, a giant protein containing multiple tandem domains, is essential in maintaining the superior mechanical performance of muscle. The consecutive and reversible unfolding and refolding of the domains are crucial for titin to serve as a modular spring. Since the discovery of the mechanical features of a single titin molecule, the exploration of biomimetic materials with titin-emulating modular structures has been an active field. However, it remains a challenge to prepare these modular polymers on a large scale due to the complex synthesis process. In this study, we propose modular DNA with multiple hairpins (MH-DNA) as the fundamental block for the bottom-up design of advanced materials. By analyzing the unfolding and refolding dynamics of modular hairpins by atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS), we find that MH-DNA shows comparable stability to those of polyproteins like titin. The unique low hysteresis of modular hairpin makes it an ideal molecular spring with remarkable mechanical efficiency. On the basis of the well-established DNA synthesis techniques, we anticipate that MH-DNA can be used as a promising building block for advanced materials with a combination of superior structural stability, considerable extensibility, and high mechanical efficiency.
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Affiliation(s)
- Nanpu Cao
- College of Chemistry, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Wanhao Cai
- College of Chemistry, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Lu Qian
- College of Chemistry, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Zhou Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Shuxun Cui
- College of Chemistry, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
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10
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Orientational Preferences of GPI-Anchored Ly6/uPAR Proteins. Int J Mol Sci 2022; 24:ijms24010011. [PMID: 36613456 PMCID: PMC9819746 DOI: 10.3390/ijms24010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Ly6/uPAR proteins regulate many essential functions in the nervous and immune systems and epithelium. Most of these proteins contain single β-structural LU domains with three protruding loops and are glycosylphosphatidylinositol (GPI)-anchored to a membrane. The GPI-anchor role is currently poorly studied. Here, we investigated the positional and orientational preferences of six GPI-anchored proteins in the receptor-unbound state by molecular dynamics simulations. Regardless of the linker length between the LU domain and GPI-anchor, the proteins interacted with the membrane by polypeptide parts and N-/O-glycans. Lynx1, Lynx2, Lypd6B, and Ly6H contacted the membrane by the loop regions responsible for interactions with nicotinic acetylcholine receptors, while Lypd6 and CD59 demonstrated unique orientations with accessible receptor-binding sites. Thus, GPI-anchoring does not guarantee an optimal 'pre-orientation' of the LU domain for the receptor interaction.
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11
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Hu G, Xi G, Yan H, Gao Z, Wu Z, Lu Z, Tu J. A molecular dynamics investigation of Taq DNA polymerase and its complex with a DNA substrate using a solid-state nanopore biosensor. Phys Chem Chem Phys 2022; 24:29977-29987. [PMID: 36472131 DOI: 10.1039/d2cp03993a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proteins have a small volume difference by the diversity of amino acids, which make protein detection and identification a great challenge. Solid-state nanopore as label-free biosensors has attracted attention with high sensitivity. In this work, we investigated the Taq DNA polymerase before and after combining it with a DNA substrate on a solid-state nanopore through molecular dynamics. In simulation, we analyzed the contribution source of nanopore current blockage. In addition to considering the traditional physical exclusion volume model, the non-covalent interaction between the protein molecules and the pore wall also showed to affect the current blockage in the nanopore. When choosing pores of comparable size to protein molecules, the two states of Taq DNA polymerase produce differentiated non-covalent interactions with the pore wall, which enhanced the amplitude difference in current blockage. As a result, the two DNA polymerases can be distinguished through the distinct current blockage. However, when applying additional pulling force or increasing the pore size of the nanopore, the differences between the current blockages are not significant enough to distinguish. The introduction of the non-covalent interaction makes it clear to understand the current blockage differences, which guide the mechanism between molecules with similar structures or volumes.
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Affiliation(s)
- Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Guohao Xi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Zhuwei Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Ziqing Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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12
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Direct observation of Hsp90-induced compaction in a protein chain. Cell Rep 2022; 41:111734. [PMID: 36450251 DOI: 10.1016/j.celrep.2022.111734] [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: 12/08/2021] [Revised: 07/28/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022] Open
Abstract
The chaperone heat shock protein 90 (Hsp90) is well known to undergo important conformational changes, which depend on nucleotide and substrate interactions. Conversely, how the conformations of its unstable and disordered substrates are affected by Hsp90 is difficult to address experimentally yet is central to its function. Here, using optical tweezers, we find that Hsp90 promotes local contractions in unfolded chains that drive their global compaction down to dimensions of folded states. This compaction has a gradual nature while showing small steps, is stimulated by ATP, and performs mechanical work against counteracting forces that expand the chain dimensions. The Hsp90 interactions suppress the formation of larger-scale folded, misfolded, and aggregated structures. The observations support a model in which Hsp90 alters client conformations directly by promoting local intra-chain interactions while suppressing distant ones. We conjecture that chain compaction may be central to how Hsp90 protects unstable clients and cooperates with Hsp70.
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13
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Kaur H, Verma M, Kaur S, Rana B, Singh N, Jena KC. Elucidating the Molecular Structure of Hydrophobically Modified Polyethylenimine Nanoparticles and Its Potential Implications for DNA Binding. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13456-13468. [PMID: 36279506 DOI: 10.1021/acs.langmuir.2c01912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The structural properties of the polyethylenimine (PEI) polymer are generally tuned and selectively modified to reinforce its potential in a broad spectrum of applied domains of medicine, healthcare, material design, sensing, and electronic optimization. The selective modification of the polymer brings about changes in its interfacial characteristics and behavior. The current work involves the synthesis of naphthalimide conjugated polyethylenimine organic nanoparticles (NPEI-ONPs). The interfacial molecular structure of NPEI-ONPs is explored in an aqueous medium at pH 7.4 using surface tensiometry and sum-frequency generation vibrational spectroscopy (SFG-VS). The hydrophobic functionalization rendered a concentration-dependent surface coverage of NPEI-ONPs, where the SFG-VS analysis exhibited the molecular rearrangement of its hydrophobic groups at the interface. The interaction of NPEI-ONPs with double-stranded DNA (dsDNA) is carried out to observe the relevance of the synthesized nanocomposites in the biomedical domain. The bulk-specific studies (i.e., thermal denaturation, viscometry, zeta (ζ) potential, and ATR-FTIR) reveal the condensation of dsDNA in the presence of NPEI-ONPs, making its structure more compact. The interface-sensitive SFG-VS showcased the impact of the dsDNA and NPEI-ONP interaction on the interfacial molecular behavior of NPEI-ONPs at the air-aqueous interface. Our results exhibit the potential of such hydrophobically functionalized ONPs as promising candidates for developing biomedical sealants, substrate coatings, and other biomedical domains.
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14
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Liu J, Guo H, Gao Q, Li H, An Z, Zhang W. Coil–Globule Transition of a Water-Soluble Polymer. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianyu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Huazhang Guo
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Qingjie Gao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Zesheng An
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
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15
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Sinha I, Cramer SM, Ashbaugh HS, Garde S. Connecting Non-Gaussian Water Density Fluctuations to the Lengthscale Dependent Crossover in Hydrophobic Hydration. J Phys Chem B 2022; 126:7604-7614. [PMID: 36154059 DOI: 10.1021/acs.jpcb.2c04990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We connect density fluctuations in liquid water to lengthscale dependent crossover in hydrophobic hydration. Specifically, we employ indirect umbrella sampling (INDUS) simulations to characterize density fluctuations in observation volumes of various sizes and shapes in water and as a function of temperature and salt concentration. Consistent with previous observations, density fluctuations are Gaussian in small molecular scale volumes, but they display non-Gaussian "low-density fat tails" in larger volumes. These non-Gaussian tails are indicative of the proximity of water to its liquid to vapor phase transition and have implications on biomolecular interactions and function. We show that the onset of non-Gaussian fluctuations in large volumes is accompanied by the formation of a cavity in the observation volume. We develop a model that uses the physics of cavity-water interface formation as a key ingredient and show that it captures the nature of non-Gaussian density fluctuations over a broad region in water and in salt solutions. We discuss the limitations of this model in the very low density region of the distribution. Our calculations provide new insights into the origins of non-Gaussian density fluctuations in water and their connections to lengthscale dependent crossover in hydrophobic hydration.
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Affiliation(s)
- Imee Sinha
- 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
| | - 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
| | - Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70123, United States
| | - Shekhar Garde
- 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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16
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Chen J, Peng Q, Peng X, Zhang H, Zeng H. Probing and Manipulating Noncovalent Interactions in Functional Polymeric Systems. Chem Rev 2022; 122:14594-14678. [PMID: 36054924 DOI: 10.1021/acs.chemrev.2c00215] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Noncovalent interactions, which usually feature tunable strength, reversibility, and environmental adaptability, have been recognized as driving forces in a variety of biological and chemical processes, contributing to the recognition between molecules, the formation of molecule clusters, and the establishment of complex structures of macromolecules. The marriage of noncovalent interactions and conventional covalent polymers offers the systems novel mechanical, physicochemical, and biological properties, which are highly dependent on the binding mechanisms of the noncovalent interactions that can be illuminated via quantification. This review systematically discusses the nanomechanical characterization of typical noncovalent interactions in polymeric systems, mainly through direct force measurements at microscopic, nanoscopic, and molecular levels, which provide quantitative information (e.g., ranges, strengths, and dynamics) on the binding behaviors. The fundamental understandings of intermolecular and interfacial interactions are then correlated to the macroscopic performances of a series of noncovalently bonded polymers, whose functions (e.g., stimuli-responsiveness, self-healing capacity, universal adhesiveness) can be customized through the manipulation of the noncovalent interactions, providing insights into the rational design of advanced materials with applications in biomedical, energy, environmental, and other engineering fields.
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Affiliation(s)
- Jingsi Chen
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Qiongyao Peng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Xuwen Peng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Hao Zhang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
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17
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Cao N, Zhao Y, Chen H, Huang J, Yu M, Bao Y, Wang D, Cui S. Poly(ethylene glycol) Becomes a Supra-Polyelectrolyte by Capturing Hydronium Ions in Water. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nanpu Cao
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Yuehua Zhao
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Hongbo Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jinying Huang
- School of Optoelectronic Science, Changchun College of Electronic Technology, Changchun 130114, China
| | - Miao Yu
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Yu Bao
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Dapeng Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Shuxun Cui
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
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18
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Yang J, Wang Y, Qian HJ, Lu ZY, Gong Z, Liu H, Cui S. Force-induced hydrogen bonding between single polyformaldehyde chain and water. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Suating P, Ernst NE, Alagbe BD, Skinner HA, Mague JT, Ashbaugh HS, Gibb BC. On the Nature of Guest Complexation in Water: Triggered Wetting-Water-Mediated Binding. J Phys Chem B 2022; 126:3150-3160. [PMID: 35438501 PMCID: PMC9059121 DOI: 10.1021/acs.jpcb.2c00628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/18/2022] [Indexed: 11/30/2022]
Abstract
The complexity of macromolecular surfaces means that there are still many open questions regarding how specific areas are solvated and how this might affect the complexation of guests. Contributing to the identification and classification of the different possible mechanisms of complexation events in aqueous solution, and as part of the recent SAMPL8 exercise, we report here on the synthesis and conformational properties of TEEtOA 2, a cavitand with conformationally flexible ethyl groups at its portal. Using a combination of ITC and NMR spectroscopy, we report the binding affinities of a series of carboxylates to 2 and compare it to a related cavitand TEMOA 1. Additionally, we report MD simulations revealing how the wetting of the pocket of 2 is controlled by the conformation of its rim ethyl groups and, correspondingly, a novel triggered wetting, guest complexation mechanism, whereby the approaching guest opens up the pocket of the host, inducing its wetting and ultimately allows the formation of a hydrated host-guest complex (H·G·H2O). A general classification of complexation mechanisms is also suggested.
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Affiliation(s)
- Paolo Suating
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Nicholas E. Ernst
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Busayo D. Alagbe
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Hannah A. Skinner
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Joel T. Mague
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Henry S. Ashbaugh
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Bruce C. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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20
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Yang JX, Qian HJ, Gong Z, Lu ZY, Cui SX. Stretching Elasticity and Flexibility of Single Polyformaldehyde Chain. CHINESE JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1007/s10118-022-2679-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Han Z, Hilburg SL, Alexander-Katz A. Forced Unfolding of Protein-Inspired Single-Chain Random Heteropolymers. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Zexiang Han
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shayna L. Hilburg
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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22
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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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23
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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: 53] [Impact Index Per Article: 26.5] [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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24
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Choi YS, Cho H, Choi WG, Lee SS, Huh KM, Shim MS, Park IS, Cho YY, Lee JY, Lee HS, Kang HC. Beyond hydrophilic polymers in amphiphilic polymer-based self-assembled NanoCarriers: Small hydrophilic carboxylate-capped disulfide drug delivery system and its multifunctionality and multispatial targetability. Biomaterials 2021; 280:121307. [PMID: 34894582 DOI: 10.1016/j.biomaterials.2021.121307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/21/2022]
Abstract
Due to increasing safety and intracellular delivery concerns about hydrophilic polymers in amphiphilic polymer-based nanoparticles (NPs), this study investigates small hydrophilic molecule-stabilized NPs for effective intracellular delivery with multiorganelle targetability and dual responsiveness to acidic pH/glutathione (GSH). In the construction of small hydrophilic molecule-stabilized NP (MSPCL-NP), the A-B-A-type amphiphilic polymer (MSPCL-P) is composed of two short hydrophilic carboxylate-capped disulfide derivatives (A) that replace hydrophilic polymers and assist in providing colloidal stability and preventing antibody (e.g., at least anti-PEG antibody)-mediated specific interactions and complement activation in the plasma and a hydrophobic multiple disulfide-containing poly(ε-caprolactone) block (B) that carries hydrophobic drugs. The carboxylates on the surface of MSPCL-NP target the acidic extratumoral/endolysosomal milieu by sensing and buffering acidic pH values, and the hydrophobic carboxylic acids improve adsorptive endocytosis and effective endosomal escape. Multiple disulfide linkages selectively target cytosolic GSH, resulting in rapid drug release from the destroyed MSPCL-NP via the cleavage of disulfide bonds in MSPCL-P. Doxorubicin (DOX)-loaded NP (DOX@MSPCL-NP) exerts strong effects on killing cells in vitro and inhibits tumor growth in HCT116 xenograft tumor-bearing mice. In conclusion, the multifunctionality and multispatial targetability of MSPCL-NP might effectively overcome various sequential drug delivery hurdles, ranging from blood circulation to drug release. Furthermore, the introduction of small hydrophilic molecules represents a potential strategy to make self-assembled NPs without the use of hydrophilic polymers.
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Affiliation(s)
- Yeon Su Choi
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea
| | - Hana Cho
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea
| | - Won-Gu Choi
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea
| | - Sung Su Lee
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea
| | - Kang Moo Huh
- Department of Polymer Science and Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Min Suk Shim
- Division of Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, Republic of Korea
| | - In Suh Park
- Department of Pathology, Inha University Hospital, 27 Inhang-ro, Jung-gu, Incheon, 22332, Republic of Korea
| | - Yong-Yeon Cho
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea
| | - Joo Young Lee
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea
| | - Hye Suk Lee
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea.
| | - Han Chang Kang
- Department of Pharmacy, College of Pharmacy, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea.
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25
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Anashkina AA, Petrushanko IY, Ziganshin RH, Orlov YL, Nekrasov AN. Entropy Analysis of Protein Sequences Reveals a Hierarchical Organization. ENTROPY (BASEL, SWITZERLAND) 2021; 23:1647. [PMID: 34945953 PMCID: PMC8700119 DOI: 10.3390/e23121647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/28/2021] [Accepted: 12/04/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Analyzing the local sequence content in proteins, earlier we found that amino acid residue frequencies differ on various distances between amino acid positions in the sequence, assuming the existence of structural units. METHODS We used informational entropy of protein sequences to find that the structural unit of proteins is a block of adjacent amino acid residues-"information unit". The ANIS (ANalysis of Informational Structure) method uses these information units for revealing hierarchically organized Elements of the Information Structure (ELIS) in amino acid sequences. RESULTS The developed mathematical apparatus gives stable results on the structural unit description even with a significant variation in the parameters. The optimal length of the information unit is five, and the number of allowed substitutions is one. Examples of the application of the method for the design of protein molecules, intermolecular interactions analysis, and the study of the mechanisms of functioning of protein molecular machines are given. CONCLUSIONS ANIS method makes it possible not only to analyze native proteins but also to design artificial polypeptide chains with a given spatial organization and, possibly, function.
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Affiliation(s)
- Anastasia A. Anashkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia;
| | - Irina Yu. Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia;
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia; (R.H.Z.); (A.N.N.)
| | - Yuriy L. Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Trubetskaya 8-2, 119991 Moscow, Russia;
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
| | - Alexei N. Nekrasov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia; (R.H.Z.); (A.N.N.)
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26
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Huang J, Laaser JE. Charge Density and Hydrophobicity-Dominated Regimes in the Phase Behavior of Complex Coacervates. ACS Macro Lett 2021; 10:1029-1034. [PMID: 35549116 DOI: 10.1021/acsmacrolett.1c00382] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The role of hydrophobicity, and particularly of nonionic hydrophobic comonomers, in the phase behavior of polyelectrolyte complex coacervates is not well-understood. Here, we address this problem by synthesizing a library of polymers with a wide range of charge densities and nonionic hydrophobic side chain lengths, and characterizing their phase behavior by optical turbidity. The polymers were prepared by postpolymerization modification of poly(N-acryloxy succinimide), targeting charge densities between 40 and 100% and nonionic aliphatic side chains with lengths from 0 to 12 carbons long. Turbidity measurements on pairs of polycations and polyanions with matched charge densities and nonionic side chain lengths revealed a complex salt response with distinct charge density-dominated and hydrophobicity-dominated regimes. The polymer solubilities were not directly correlated with the phase behavior of the coacervates, indicating the difficulty of understanding the coacervate phase behavior in terms of the polymer-water interaction parameter. This result suggests that there is significant room for further work to understand the mechanisms by which specific molecular-scale interactions moderate the phase behavior of complex coacervates.
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Affiliation(s)
- Jun Huang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jennifer E. Laaser
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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27
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Bao Y, Huang X, Xu J, Cui S. Effect of Intramolecular Hydrogen Bonds on the Single-Chain Elasticity of Poly(vinyl alcohol): Evidencing the Synergistic Enhancement Effect at the Single-Molecule Level. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yu Bao
- Key Lab of Advanced Technologies of Materials, Ministry of Education of China, Southwest Jiaotong University, Chengdu 610031, China
| | - Xiaobo Huang
- Key Lab of Advanced Technologies of Materials, Ministry of Education of China, Southwest Jiaotong University, Chengdu 610031, China
| | - Jun Xu
- Key Lab of Advanced Technologies of Materials, Ministry of Education of China, Southwest Jiaotong University, Chengdu 610031, China
| | - Shuxun Cui
- Key Lab of Advanced Technologies of Materials, Ministry of Education of China, Southwest Jiaotong University, Chengdu 610031, China
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28
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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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29
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Nandakumar A, Ito Y, Ueda M. Solvent Effects on the Self-Assembly of an Amphiphilic Polypeptide Incorporating α-Helical Hydrophobic Blocks. J Am Chem Soc 2020; 142:20994-21003. [PMID: 33272014 DOI: 10.1021/jacs.0c03425] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The self-assembly of biological molecules is an important pathway to understanding the molecular basis of complex metabolic events. The presence of a cosolvent in an aqueous solution during the self-assembly process can promote the formation of kinetically trapped metastable intermediates. In nature, a category of cosolvents termed osmolytes can work to strengthen the hydrogen-bond network of water such that the native states of certain proteins are favored, thus modulating their function and stability. However, identifying cosolvents that act as osmolytes in biomimetic applications, such as the self-assembly of soft materials, remains challenging. The present work examined the effects of ethanol (EtOH) and acetonitrile (ACN) as cosolvents on the self-assembly of the amphiphilic polypeptide PSar30-(l-Leu-Aib)6 (S30L12), which incorporates α-helical hydrophobic blocks, in aqueous solution. The results provided a direct observation of morphological behavior of S30L12 as a function of solvent composition. Morphological transitions were investigated using transmission electron microscopy, while the packing of peptide molecules was assessed using circular dichroism analyses and evaluations of membrane fluidity. In the EtOH/H2O mixtures, the EtOH strengthened the hydrogen-bond network of the water, thus limiting the hydrophobic hydration of S30L12 assemblies and enhancing hydrophobic interactions between assemblies. In contrast, ACN formed self-associated nanoclusters in water and at the hydrophobic cores of peptide assemblies to stabilize the edges exposed to bulk water and enhance the assembly kinetics. Fourier transform infrared (FT-IR) analysis indicated that both EtOH and ACN can modify the self-assembly of biomaterials in the same manner as osmolyte protectants or denaturants.
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Affiliation(s)
- Avanashiappan Nandakumar
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Motoki Ueda
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Hu G, Fu J, Qiao Y, Meng H, Wang Z, Tu J, Lu Z. Molecular dynamics discrimination of the conformational states of calmodulin through solid-state nanopores. Phys Chem Chem Phys 2020; 22:19188-19194. [PMID: 32812567 DOI: 10.1039/d0cp02500c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As a type of biological macromolecule, the conformation of proteins dynamically changes in a solution, which often results in a change in their function. However, traditional biological assays have significant drawbacks in detecting the conformation properties of proteins. Alternatively, nanopores have potential advantages in this area, which can detect protein in high throughput and without labelling. Herein, we investigated the translocation of calmodulins through silicon nitride nanopores using molecular dynamics (MD) simulation. Initially, the calmodulins were fixed in the nanopore. Distinguished blocked ionic currents were obtained between the two forms of calmodulin. Next, in the translocation simulations, a prominent difference in time resolution was easily found between the two states of calmodulin by using the appropriate voltage and comparable size of pore to protein, rp/rg→ 1, 4.5 nm (where rp is the protein radius and rg is the gyration radius). These simulations on the nanoscale are helpful for developing Ca2+-sensitive ion channels and nanodevices.
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Affiliation(s)
- Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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Bredt AJ, Ben-Amotz D. Influence of crowding on hydrophobic hydration-shell structure. Phys Chem Chem Phys 2020; 22:11724-11730. [PMID: 32409791 DOI: 10.1039/d0cp00702a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of molecular crowding on water structure, and the associated crossover behavior, is quantified using Raman multivariate curve resolution (Raman-MCR) hydration-shell vibrational spectroscopy of aqueous tert-butyl alcohol, 2-butyl alcohol and 2-butoxyethanol solutions of variable concentration and temperature. Changes in the hydration-shell OH stretch band shape and mean frequency are used to identify the temperature at which the hydration-shell crosses over from a more ordered to less ordered structure, relative to pure water. The influence of crowding on the crossover is found to depend on solute size and shape in a way that is correlated with the corresponding infinitely dilute hydration-shell structure (and the corresponding first hydration-shell spectra are invariably very similar to pure water). Analysis of the results using a Muller-like two-state equilibrium between more ordered and less ordered hydration-shell structures implies that crossover temperature changes are dictated primarily by enthalpic stabilization of the more ordered hydration-shell structures.
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Affiliation(s)
- Aria J Bredt
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
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Spontaneous drying of non-polar deep-cavity cavitand pockets in aqueous solution. Nat Chem 2020; 12:589-594. [PMID: 32424255 DOI: 10.1038/s41557-020-0458-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/11/2020] [Indexed: 11/08/2022]
Abstract
There are many open questions regarding the hydration of solvent-exposed non-polar tracts and pockets in proteins. Although water is predicted to de-wet purely repulsive surfaces and evacuate crevices, the extent of de-wetting is unclear when ubiquitous van der Waals interactions are in play. The structural simplicity of synthetic supramolecular hosts imbues them with considerable potential to address this issue. To this end, here we detail a combination of densimetry and molecular dynamics simulations of three cavitands, coupled with calorimetric studies of their complexes with short-chain carboxylates. Our results reveal the range of wettability possible within the ostensibly identical cavitand pockets-which differ only in the presence and/or position of the methyl groups that encircle the portal to their non-polar pockets. The results demonstrate the ability of macrocycles to template water cavitation within their binding sites and show how the orientation of methyl groups can trigger the drying of non-polar pockets in liquid water, which suggests new avenues to control guest complexation.
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Bao Y, Luo Z, Cui S. Environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by atomic force microscopy-based single-molecule force spectroscopy and the implications for advanced polymer materials. Chem Soc Rev 2020; 49:2799-2827. [PMID: 32236171 DOI: 10.1039/c9cs00855a] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
"The Tao begets the One. One begets all things of the world." This quote from Tao Te Ching is still inspiring for scientists in chemistry and materials science: The "One" can refer to a single molecule. A macroscopic material is composed of numerous molecules. Although the relationship between the properties of the single molecule and macroscopic material is not well understood yet, it is expected that a deeper understanding of the single-chain mechanics of macromolecules will certainly facilitate the development of materials science. Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) has been exploited extensively as a powerful tool to study the single-chain behaviors of macromolecules. In this review, we summarize the recent advances in the emerging field of environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by means of AFM-SMFS. First, the single-chain inherent elasticities of several typical linear macromolecules are introduced, which are also confirmed by one of three polymer models with theoretical elasticities of the corresponding macromolecules obtained from quantum mechanical (QM) calculations. Then, the effects of the external environments on the single-chain mechanics of synthetic polymers and biomacromolecules are reviewed. Finally, the impacts of single-chain mechanics of macromolecules on the development of polymer science especially polymer materials are illustrated.
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Affiliation(s)
- Yu Bao
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu 610031, China.
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Liu B, Zhang X, Yan D. The responsive behaviors of bilayer membrane under uniaxial mechanical probe. J Chem Phys 2020; 152:104901. [PMID: 32171195 DOI: 10.1063/5.0001784] [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
In experiments, atomic force microscopy technology was used to measure the modulus of the membrane. However, these studies mainly focus on the linear responsive behavior. In the present work, a theoretical study is performed to show the nonlinear responsive behavior, which includes the stretching induced structural transitions. It demonstrates that the structural transition of the bilayer membrane takes place during the stretching process of the mechanical probe. A vertical cylindrical micelle can be obtained by stretching the membrane under deep compression conditions, and the cylindrical micelle can grow continuously along the axial direction. Moreover, under shallow compression conditions, the probe pulls a spherical micelle from the membrane, and then, the membrane returns to flatness. A comprehensive study is performed to show the mechanism of the responsive behaviors of the structural transition during the compression and stretching processes. When the probe acts on the B-rich layer, it is more likely to pull out a regular micelle. However, when the probe acts on the bottom A-rich layer, complex vesicles are more likely to be pulled out from the bilayer membrane. This study provides a comprehensive diagram of the mechanical responsive behavior of the membrane, which would be a guide for an experiment of biomembranes and the design of new self-assembled structures.
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Affiliation(s)
- Baopi Liu
- Department of Physics, Beijing Normal University, Beijing 100875, China
| | - Xinghua Zhang
- School of Science, Beijing Jiaotong University, Beijing 100044, China
| | - Dadong Yan
- Department of Physics, Beijing Normal University, Beijing 100875, China
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Mechanical Unfolding of Spectrin Repeats Induces Water-Molecule Ordering. Biophys J 2020; 118:1076-1089. [PMID: 32027822 DOI: 10.1016/j.bpj.2020.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023] Open
Abstract
Mechanical processes are involved at many stages of the development of living cells, and often external forces applied to a biomolecule result in its unfolding. Although our knowledge of the unfolding mechanisms and the magnitude of the forces involved has evolved, the role that water molecules play in the mechanical unfolding of biomolecules has not yet been fully elucidated. To this end, we investigated with steered molecular dynamics simulations the mechanical unfolding of dystrophin's spectrin repeat 1 and related the changes in the protein's structure to the ordering of the surrounding water molecules. Our results indicate that upon mechanically induced unfolding of the protein, the solvent molecules become more ordered and increase their average number of hydrogen bonds. In addition, the unfolded structures originating from mechanical pulling expose an increasing amount of the hydrophobic residues to the solvent molecules, and the uncoiled regions adapt a convex surface with a small radius of curvature. As a result, the solvent molecules reorganize around the protein's small protrusions in structurally ordered waters that are characteristic of the so-called "small-molecule regime," which allows water to maintain a high hydrogen bond count at the expense of an increased structural order. We also determined that the response of water to structural changes in the protein is localized to the specific regions of the protein that undergo unfolding. These results indicate that water plays an important role in the mechanically induced unfolding of biomolecules. Our findings may prove relevant to the ever-growing interest in understanding macromolecular crowding in living cells and their effects on protein folding, and suggest that the hydration layer may be exploited as a means for short-range allosteric communication.
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Deng GH, Shen Y, Chen H, Chen Y, Jiang B, Wu G, Yang X, Yuan K, Zheng J. Ordered-to-Disordered Transformation of Enhanced Water Structure on Hydrophobic Surfaces in Concentrated Alcohol-Water Solutions. J Phys Chem Lett 2019; 10:7922-7928. [PMID: 31794227 DOI: 10.1021/acs.jpclett.9b03429] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The effects of hydrophobic solutes on the structure of the surrounding water have been a topic of debate for almost 70 years. However, a consistent description of the physical insight into the causes of the anomalous thermodynamic properties of alcohol-water mixtures is lacking. Here we report experimental results that combined temperature-dependent linear and femtosecond infrared spectroscopy measurements to explore the water structural transformation in concentrated alcohol-water solutions. Experiments show that the enhancement of water structure arises around microhydrophobic interfaces at room temperature in the solutions. As temperature increases, this ordered water structure disappears and a surface topography-dependent new disordered water structure arises at concentrated solutions of large alcohols. The water structural transformation is dependent on not only the length of the alkyl chain but also the clustering of the alcohols. A more-ordered-than-water structure can transform into a less-ordered-than-water structure.
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Affiliation(s)
- Gang-Hua Deng
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Yuneng Shen
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Hailong Chen
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics , Institute of Physics, Chinese Academy of Sciences , Beijing 100190 , China
| | - Yajing Chen
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Bo Jiang
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Guorong Wu
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Kaijun Yuan
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Junrong Zheng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences , Peking University , Beijing 100871 , China
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38
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Liang X, Nakajima K. Investigating the Dynamic Viscoelasticity of Single Polymer Chains using Atomic Force Microscopy. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/polb.24908] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xiaobin Liang
- Department of Chemical Science and EngineeringSchool of Materials and Chemical Technology, Tokyo Institute of Technology, Ookayama 2‐12‐1, Meguro‐ku Tokyo 152‐8552 Japan
| | - Ken Nakajima
- Department of Chemical Science and EngineeringSchool of Materials and Chemical Technology, Tokyo Institute of Technology, Ookayama 2‐12‐1, Meguro‐ku Tokyo 152‐8552 Japan
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Li Y, Cao Y. The molecular mechanisms underlying mussel adhesion. NANOSCALE ADVANCES 2019; 1:4246-4257. [PMID: 36134404 PMCID: PMC9418609 DOI: 10.1039/c9na00582j] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 10/09/2019] [Indexed: 06/12/2023]
Abstract
Marine mussels are able to firmly affix on various wet surfaces by the overproduction of special mussel foot proteins (mfps). Abundant fundamental studies have been conducted to understand the molecular basis of mussel adhesion, where the catecholic amino acid, l-3,4-dihydroxyphenylalanine (DOPA) has been found to play the major role. These studies continue to inspire the engineering of novel adhesives and coatings with improved underwater performances. Despite the fact that the recent advances of adhesives and coatings inspired by mussel adhesive proteins have been intensively reviewed in literature, the fundamental biochemical and biophysical studies on the origin of the strong and versatile wet adhesion have not been fully covered. In this review, we show how the force measurements at the molecular level by surface force apparatus (SFA) and single molecule atomic force microscopy (AFM) can be used to reveal the direct link between DOPA and the wet adhesion strength of mussel proteins. We highlight a few important technical details that are critical to the successful experimental design. We also summarize many new insights going beyond DOPA adhesion, such as the surface environment and protein sequence dependent synergistic and cooperative binding. We also provide a perspective on a few uncharted but outstanding questions for future studies. A comprehensive understanding on mussel adhesion will be beneficial to the design of novel synthetic wet adhesives for various biomedical applications.
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Affiliation(s)
- Yiran Li
- Shenzhen Research Institute of Nanjing University Shenzhen 518057 China
- Department of Physics, Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Soli State Microstructure, Nanjing University Nanjing 210093 China
| | - Yi Cao
- Shenzhen Research Institute of Nanjing University Shenzhen 518057 China
- Department of Physics, Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Soli State Microstructure, Nanjing University Nanjing 210093 China
- Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210093 China
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40
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Cai W, Lu S, Wei J, Cui S. Single-Chain Polymer Models Incorporating the Effects of Side Groups: An Approach to General Polymer Models. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01542] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Wanhao Cai
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu 610031, China
| | - Song Lu
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu 610031, China
| | - Junhao Wei
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu 610031, China
| | - Shuxun Cui
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu 610031, China
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Robalo JR, Streacker LM, Mendes de Oliveira D, Imhof P, Ben-Amotz D, Verde AV. Hydrophobic but Water-Friendly: Favorable Water–Perfluoromethyl Interactions Promote Hydration Shell Defects. J Am Chem Soc 2019; 141:15856-15868. [DOI: 10.1021/jacs.9b06862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- João R. Robalo
- Department of Theory & Bio-systems, Max Planck Institute for Colloids and Interfaces, Science Park, Potsdam 14476, Germany
| | - Louis M. Streacker
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Petra Imhof
- Institute for Theoretical Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ana Vila Verde
- Department of Theory & Bio-systems, Max Planck Institute for Colloids and Interfaces, Science Park, Potsdam 14476, Germany
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42
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Shao W, Burkert SC, White DL, Scott VL, Ding J, Li Z, Ouyang J, Lapointe F, Malenfant PRL, Islam K, Star A. Probing Ca 2+-induced conformational change of calmodulin with gold nanoparticle-decorated single-walled carbon nanotube field-effect transistors. NANOSCALE 2019; 11:13397-13406. [PMID: 31276143 DOI: 10.1039/c9nr03132d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanomaterials are ideal for electrochemical biosensors, with their nanoscale dimensions enabling the sensitive probing of biomolecular interactions. In this study, we compare field-effect transistors (FET) comprised of unsorted (un-) and semiconducting-enriched (sc-) single-walled carbon nanotubes (SWCNTs). un-SWCNTs have both metallic and semiconducting SWCNTs in the ensemble, while sc-SWCNTs have a >99.9% purity of semiconducting nanotubes. Both SWCNT FET devices were decorated with gold nanoparticles (AuNPs) and were then employed in investigating the Ca2+-induced conformational change of calmodulin (CaM) - a vital process in calcium signal transduction in the human body. Different biosensing behavior was observed from FET characteristics of the two types of SWCNTs, with sc-SWCNT FET devices displaying better sensing performance with a dynamic range from 10-15 M to 10-13 M Ca2+, and a lower limit of detection at 10-15 M Ca2+.
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Affiliation(s)
- Wenting Shao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
| | - Seth C Burkert
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
| | - David L White
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
| | - Valerie L Scott
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
| | - Jianfu Ding
- Security and Disruptive Technologies Portfolio, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
| | - Zhao Li
- Security and Disruptive Technologies Portfolio, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
| | - Jianying Ouyang
- Security and Disruptive Technologies Portfolio, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
| | - François Lapointe
- Security and Disruptive Technologies Portfolio, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
| | - Patrick R L Malenfant
- Security and Disruptive Technologies Portfolio, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
| | - Alexander Star
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
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Kolberg A, Wenzel C, Hackenstrass K, Schwarzl R, Rüttiger C, Hugel T, Gallei M, Netz RR, Balzer BN. Opposing Temperature Dependence of the Stretching Response of Single PEG and PNiPAM Polymers. J Am Chem Soc 2019; 141:11603-11613. [DOI: 10.1021/jacs.9b04383] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Adrianna Kolberg
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 23a, 79104 Freiburg, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 23a, 79104 Freiburg, Germany
| | - Klara Hackenstrass
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 23a, 79104 Freiburg, Germany
| | - Richard Schwarzl
- Department Institute of Theoretical Bio- and Soft Matter Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Christian Rüttiger
- Ernst-Berl-Institute of Technical and Macromolecular Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 23a, 79104 Freiburg, Germany
- Cluster of Excellence livMatS@FIT, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Markus Gallei
- Ernst-Berl-Institute of Technical and Macromolecular Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
- Organic Macromolecular Chemistry, Saarland University, Campus Saarbrücken C4 2, 66123 Saarbrücken, Germany
| | - Roland R. Netz
- Department Institute of Theoretical Bio- and Soft Matter Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Bizan N. Balzer
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 23a, 79104 Freiburg, Germany
- Cluster of Excellence livMatS@FIT, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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44
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Jiang Z, Remsing RC, Rego NB, Patel AJ. Characterizing Solvent Density Fluctuations in Dynamical Observation Volumes. J Phys Chem B 2019; 123:1650-1661. [PMID: 30682885 DOI: 10.1021/acs.jpcb.8b11423] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hydrophobic effects drive diverse aqueous assemblies, such as micelle formation or protein folding, wherein the solvent plays an important role. Consequently, characterizing the free energetics of solvent density fluctuations can lead to important insights into these processes. Although techniques such as the indirect umbrella sampling (INDUS) method can be used to characterize solvent fluctuations in static observation volumes of various sizes and shapes, characterizing how the solvent mediates inherently dynamic processes, such as self-assembly or conformational change, remains a challenge. In this work, we generalize the INDUS method to facilitate the enhanced sampling of solvent fluctuations in dynamical observation volumes, whose positions and shapes can evolve. We illustrate the usefulness of this generalization by characterizing water density fluctuations in dynamical volumes pertaining to the hydration of flexible solutes, the assembly of small hydrophobes, and conformational transitions in a model peptide. We also use the method to probe the dynamics of hard spheres.
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Affiliation(s)
| | - Richard C Remsing
- Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
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Di W, Gao X, Huang W, Sun Y, Lei H, Liu Y, Li W, Li Y, Wang X, Qin M, Zhu Z, Cao Y, Wang W. Direct Measurement of Length Scale Dependence of the Hydrophobic Free Energy of a Single Collapsed Polymer Nanosphere. PHYSICAL REVIEW LETTERS 2019; 122:047801. [PMID: 30768307 DOI: 10.1103/physrevlett.122.047801] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/15/2018] [Indexed: 06/09/2023]
Abstract
The physics underlying hydrophobicity at macroscopic and microscopic levels is fundamentally distinct. However, experimentally quantifying the length scale dependence of hydrophobicity is challenging. Here we show that the size-dependent hydrophobic free energy of a collapsed polymer nanosphere can be continuously monitored from its single-molecule force-extension curve using a novel theoretical framework. The hydrophobic free energy shows a change from cubic to square dependence of the radius of the polymer nanosphere at a radius of ∼1 nm-this is consistent with Lum-Chandler-Weeks theory and simulations. We can also observe a large variation of the hydrophobic free energy of each polymer nanosphere implying the heterogeneity of the self-assembled structures and/or the fluctuation of the water-polymer interface. We expect that our approach can be used to address many fundamental questions about hydrophobic hydration, which are otherwise inaccessible by ensemble measurements.
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Affiliation(s)
- Weishuai Di
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Xiang Gao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Wenmao Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Yang Sun
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Yang Liu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Wenfei Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
- Institute for Brain Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yiran Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Xin Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Zhenshu Zhu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
- Institute for Brain Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
- Institute for Brain Sciences, Nanjing University, Nanjing 210023, People's Republic of China
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46
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Tang Y, Zhang X, Choi P, Xu Z, Liu Q. Contributions of van der Waals Interactions and Hydrophobic Attraction to Molecular Adhesions on a Hydrophobic MoS 2 Surface in Water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14196-14203. [PMID: 30373365 DOI: 10.1021/acs.langmuir.8b02636] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Pushing the boundaries of the investigation of hydrophobic attraction (HA) to the molecular scale readily ensures the collection of experimental results free of secondary effects, thereby facilitating the unraveling of the underlying mechanism by providing clean experimental results that truly reflect the hydrophobic attraction. Regardless of the feasibility of this approach, investigations using this promising method are stagnant due to the difficulties in determining the individual contributions of HA and van der Waals (vdW) interactions at the molecular scale. Here, a novel approach was proposed for the first time to determine the individual contributions of vdW interactions and HA by studying the single-molecule adhesion forces of a neutral oligo ethylene glycol methacrylate copolymer on a MoS2 crystal exposed to different water chemistry. The anisotropic surface properties of MoS2 enabled the partitioning of vdW interactions and hydrophobic attraction in total single-molecule adhesion forces and also enabled determining the contribution of electrostatic interaction (ESI). When the presence of ESI is excluded, the study of single-molecule adhesion forces using single-molecule force spectroscopy (SMFS) revealed that the contribution of vdW interactions to total molecular interactions was smaller than 9 pN. The strong single-molecule adhesion forces of oligo ethylene glycol copolymer on the hydrophobic basal surface of MoS2 demonstrated that HA plays a dominant role with contribution up to 89% to the total single-molecule adhesion force. By utilizing the derived theoretical model, we quantified the individual contribution of each fundamental interaction under a variety of conditions. This study proposed a facile approach to quantitatively clarify the roles of vdW interactions and HA at the molecular scale, which may help assist future experimental and theoretical investigations of hydrophobic (solvophobic) effects and vdW interactions in aqueous solutions.
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Affiliation(s)
- Yuechao Tang
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta T6G 1H9 , Canada
| | - Xurui Zhang
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta T6G 1H9 , Canada
| | - Phillip Choi
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta T6G 1H9 , Canada
| | - Zhenghe Xu
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta T6G 1H9 , Canada
| | - Qingxia Liu
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta T6G 1H9 , Canada
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47
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Ekladious I, Liu R, Varongchayakul N, Mejia Cruz LA, Todd DA, Zhang H, Oberlies NH, Padera RF, Colson YL, Grinstaff MW. Reinforcement of polymeric nanoassemblies for ultra-high drug loadings, modulation of stiffness and release kinetics, and sustained therapeutic efficacy. NANOSCALE 2018; 10:8360-8366. [PMID: 29717728 DOI: 10.1039/c8nr01978a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The optimization of current polymeric nanoparticle therapies is restricted by low drug loadings and limited tunability of core properties. To overcome these shortcomings, a novel self-association approach is utilized to fabricate a dual-loaded poly(1,2-glycerol carbonate)-graft-succinic acid-paclitaxel (PGC-PTX) conjugate nanoparticle (NP) in which the physical entrapment of free paclitaxel (PTX) affords unprecedented ultra-high drug loadings >100 wt%, modulation of mechanical stiffness, and tunable release kinetics. Despite high incorporation of free PTX (up to 50 wt%), the dual-loaded PGC-PTX nanocarriers (i.e., PGC-PTX + PTX NPs) exhibit controlled and sustained drug release over 15 days, without burst release effects. Importantly, optimization of drug/material efficiency concomitantly affords improved in vitro efficacy. In vivo, PGC-PTX + PTX NPs are safely administered at doses exceeding the median lethal dose of standard PTX, while a single high dose significantly extends survival relative to weekly PTX administrations in a murine model of peritoneal carcinomatosis.
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Affiliation(s)
- Iriny Ekladious
- Departments of Biomedical Engineering and Chemistry, Boston University, Boston, MA 02215, USA.
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48
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Das Mahanta D, Rana D, Patra A, Mukherjee B, Mitra RK. Heterogeneous structure and solvation dynamics of DME/water binary mixtures: A combined spectroscopic and simulation investigation. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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49
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Wu X, Lu W, Streacker LM, Ashbaugh HS, Ben-Amotz D. Temperature-Dependent Hydrophobic Crossover Length Scale and Water Tetrahedral Order. J Phys Chem Lett 2018; 9:1012-1017. [PMID: 29420897 DOI: 10.1021/acs.jpclett.7b03431] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Experimental Raman multivariate curve resolution and molecular dynamics simulations are performed to demonstrate that the vibrational frequency and tetrahedrality of water molecules in the hydration-shells of short-chain alcohols differ from those of pure water and undergo a crossover above 100 °C (at 30 MPa) to a structure that is less tetrahedral than pure water. Our results demonstrate that the associated crossover length scale decreases with increasing temperature, suggesting that there is a fundamental connection between the spectroscopically observed crossover and that predicted to take place around idealized purely repulsive solutes dissolved in water, although the water structure changes in the hydration-shells of alcohols are far smaller than those associated with an idealized "dewetting" transition.
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Affiliation(s)
- Xiangen Wu
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences , Wuhan 430074, China
| | - Wanjun Lu
- State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences , Wuhan 430074, China
| | - Louis M Streacker
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University , New Orleans, Louisiana 70118, United States
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
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50
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Abstract
This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins.
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Affiliation(s)
- Matthew B Hillyer
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118;
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118;
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