1
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Zheng Y, Wei Q, Han X, Tao X, Cao T, Chen T, Cao P, Zhan Q. Homologous polydopamine ameliorates haemolysis of melittin for enhancing its anticancer efficacy. J Mater Chem B 2024; 12:5431-5438. [PMID: 38726737 DOI: 10.1039/d4tb00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Despite exhibiting potent anticancer activity, the strong hemolytic properties of melittin (MEL) significantly restrict its delivery efficiency and clinical applications. To address this issue, we have devised a strategy wherein homologous dopamine (DA), an essential component of bee venom, is harnessed as a vehicle for the synthesis of MEL-polydopamine (PDA) nanoparticles (MP NPs). The ingenious approach lies in the fact that MEL is a basic polypeptide, and the polymerization of DA is also conducted under alkaline conditions, indicating the distinctive advantages of PDA in MEL encapsulation. Furthermore, MP NPs are modified with folic acid to fabricate tumor-targeted nanomedicine (MPF NPs). MPF NPs can ameliorate the hemolysis of MEL in drug delivery and undergo degradation triggered by high levels of reactive oxygen species (ROS) within solid tumors, thereby facilitating MEL release and subsequent restoration of anticancer activity. After cellular uptake, MPF NPs induce cell apoptosis through the PI3K/Akt-mediated p53 signaling pathway. The tumor growth inhibitory rate of MPF NPs in FA receptor-positive 4T1 and CT26 xenograft mice reached 78.04% and 81.66%, which was significantly higher compared to that in FA receptor-negative HepG2 xenograft mice (45.79%). Homologous vehicles provide a new perspective for nanomedicine design.
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Affiliation(s)
- Yuhan Zheng
- Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Qingyun Wei
- Jiangsu Provincial Medicinal Innovation Centre, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210028, China
| | - Xuan Han
- Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Xiangmin Tao
- Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Tao Cao
- Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Tianbao Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Peng Cao
- Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
- Jiangsu Provincial Medicinal Innovation Centre, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210028, China
- Shandong Academy of Chinese Medicine, Jinan 250014, China
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou Peoples Hospital, Quzhou 324000, China
| | - Qichen Zhan
- Animal-Derived Chinese Medicine and Functional Peptides International Collaboration Joint Laboratory, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
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2
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Jiao S, Shell MS. Inverse design of pore wall chemistry and topology through active learning of surface group interactions. J Chem Phys 2024; 160:124705. [PMID: 38526115 DOI: 10.1063/5.0200900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024] Open
Abstract
Design of next-generation membranes requires a nanoscopic understanding of the effect of biologically inspired heterogeneous surface chemistries and topologies (roughness) on local water and solute behavior. In particular, the rejection of small, neutral solutes, such as boric acid, poses a heretofore unsolved challenge. In prior work, a computational inverse design technique using an evolutionary optimization successfully uncovered new surface design strategies for optimized transport of water over solutes in smooth, model pores consisting of two surface chemistries. However, extending such an approach to more complex (and realistic) scenarios involving many surface chemistries as well as surface roughness is challenging due to the expanded design space. In this work, we develop a new approach that uses active learning to optimize in a reduced feature space of surface group interactions, finding parameters that lead to their assembly into ordered, optimal patterns. This approach rapidly identifies novel surface functionalizations that maximize the difference in water and boric acid transport through the nanopore. Moreover, we find that the roughness of the nanopore wall, independent of its chemistry, can be leveraged to enhance transport selectivity: oscillations in the pore wall diameter optimally inhibit boric acid transport by creating energetic wells from which the solute must escape to transport down the pore. This proof-of-concept demonstrates the potential for active learning strategies, in concert with molecular simulations, to rapidly navigate complex design spaces of aqueous interfaces and is promising as a tool for engineering water-mediated surface interactions for a broad range of applications.
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Affiliation(s)
- Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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3
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Ji J, Carpentier B, Chakraborty A, Nangia S. An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale. J Chem Theory Comput 2024; 20:1656-1672. [PMID: 37018141 PMCID: PMC10902853 DOI: 10.1021/acs.jctc.3c00106] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Indexed: 04/06/2023]
Abstract
The hydropathy of proteins or quantitative assessment of protein-water interactions has been a topic of interest for decades. Most hydropathy scales use a residue-based or atom-based approach to assign fixed numerical values to the 20 amino acids and categorize them as hydrophilic, hydroneutral, or hydrophobic. These scales overlook the protein's nanoscale topography, such as bumps, crevices, cavities, clefts, pockets, and channels, in calculating the hydropathy of the residues. Some recent studies have included protein topography in determining hydrophobic patches on protein surfaces, but these methods do not provide a hydropathy scale. To overcome the limitations in the existing methods, we have developed a Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale that adopts a holistic approach to assigning the hydropathy of a residue. The parch scale evaluates the collective response of the water molecules in the protein's first hydration shell to increasing temperatures. We performed the parch analysis of a set of well-studied proteins that include the following─enzymes, immune proteins, and integral membrane proteins, as well as fungal and virus capsid proteins. Since the parch scale evaluates every residue based on its location, a residue may have very different parch values inside a crevice versus a surface bump. Thus, a residue can have a range of parch values (or hydropathies) dictated by the local geometry. The parch scale calculations are computationally inexpensive and can compare hydropathies of different proteins. The parch analysis can affordably and reliably aid in designing nanostructured surfaces, identifying hydrophilic and hydrophobic patches, and drug discovery.
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Affiliation(s)
- Jingjing Ji
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Britnie Carpentier
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Arindam Chakraborty
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
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4
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Jiao S, Robinson Brown DC, Shell MS. Relationships between Water's Structure and Solute Affinity at Polypeptoid Brush Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:761-771. [PMID: 38118078 DOI: 10.1021/acs.langmuir.3c02971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Excellent antifouling surfaces are generally thought to create a tightly bound layer of water that resists solute adsorption, and highly hydrophilic surfaces such as those with zwitterionic functionalities are of significant current interest as antifoulant strategies. However, despite significant proofs-of-concept, we still lack a fundamental understanding of how the nanoscopic structure of this hydration layer translates to reduced fouling, how surface chemistry can be tuned to achieve antifouling through hydration water, and why, in particular, zwitterionic surfaces seem so promising. Here, we use molecular dynamics simulations and free energy calculations to investigate the molecular relationships among surface chemistry, hydration water structure, and surface-solute affinity across a variety of surface-decorated chemistries. Specifically, we consider polypeptoid-decorated surfaces that display well-known experimental antifouling capabilities and that can be synthesized sequence specifically, with precise backbone positioning of, e.g., charged groups. Through simulations, we calculate the affinities of a range of small solutes to polypeptoid brush surfaces of varied side-chain chemistries. We then demonstrate that measures of the structure of surface hydration water in response to a particular surface chemistry signal solute-surface affinity; specifically, we find that zwitterionic chemistries produce solute-surface repulsion through highly coordinated hydration water while suppressing tetrahedral structuring around the solute, in contrast to uncharged surfaces that show solute-surface affinity. Based on the relationship of this structural perturbation to the affinity of small-molecule solutes, we propose a molecular mechanism by which zwitterionic surface chemistries enhance solute repulsion, with broader implications for the design of antifouling surfaces.
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Affiliation(s)
- Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Dennis C Robinson Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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5
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Palmer JC, Sarupria S, Truskett TM. Tribute to Pablo G. Debenedetti. J Phys Chem B 2023; 127:8075-8078. [PMID: 37766640 DOI: 10.1021/acs.jpcb.3c06020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Affiliation(s)
- Jeremy C Palmer
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, United States
| | - Sapna Sarupria
- Department of Chemistry, Chemical Theory Center, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Thomas M Truskett
- McKetta Department of Chemical Engineering and Department of Physics, The University of Texas at Austin, Austin, Texas 78712, United States
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6
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Lanrezac A, Baaden M. UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape. MEMBRANES 2023; 13:362. [PMID: 36984749 PMCID: PMC10054542 DOI: 10.3390/membranes13030362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
The insertion of proteins into membranes is crucial for understanding their function in many biological processes. In this work, we present UNILIPID, a universal implicit lipid-protein description as a methodology for dealing with implicit membranes. UNILIPID is independent of the scale of representation and can be applied at the level of all atoms, coarse-grained particles down to the level of a single bead per amino acid. We provide example implementations for these scales and demonstrate the versatility of our approach by accurately reflecting the free energy of transfer for each amino acid. In addition to single membranes, we describe the analytical implementation of double membranes and show that UNILIPID is well suited for modeling at multiple scales. We generalize to membranes of arbitrary shape. With UNILIPID, we provide a methodological framework for a simple and general parameterization tuned to reproduce a selected reference hydrophobicity scale. The software we provide along with the methodological description is optimized for specific user features such as real-time response, live visual analysis, and virtual reality experiences.
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7
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Qiu C, Whittaker GR, Gellman SH, Daniel S, Abbott NL. Interactions of SARS-CoV-2 and MERS-CoV fusion peptides measured using single-molecule force methods. Biophys J 2023; 122:646-660. [PMID: 36650897 PMCID: PMC9841730 DOI: 10.1016/j.bpj.2023.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/07/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
We address the challenge of understanding how hydrophobic interactions are encoded by fusion peptide (FP) sequences within coronavirus (CoV) spike proteins. Within the FPs of severe acute respiratory syndrome CoV 2 and Middle East respiratory syndrome CoV (MERS-CoV), a largely conserved peptide sequence called FP1 (SFIEDLLFNK and SAIEDLLFDK in SARS-2 and MERS, respectively) has been proposed to play a key role in encoding hydrophobic interactions that drive viral-host cell membrane fusion. Although a non-polar triad (Leu-Leu-Phe (LLF)) is common to both FP1 sequences, and thought to dominate the encoding of hydrophobic interactions, FP1 from SARS-2 and MERS differ in two residues (Phe 2 versus Ala 2 and Asn 9 versus Asp 9, respectively). Here we explore whether single-molecule force measurements can quantify hydrophobic interactions encoded by FP1 sequences, and then ask whether sequence variations between FP1 from SARS-2 and MERS lead to significant differences in hydrophobic interactions. We find that both SARS-2 and MERS wild-type FP1 generate measurable hydrophobic interactions at the single-molecule level, but that SARS-2 FP1 encodes a substantially stronger hydrophobic interaction than its MERS counterpart (1.91 ± 0.03 nN versus 0.68 ± 0.03 nN, respectively). By performing force measurements with FP1 sequences with single amino acid substitutions, we determine that a single-residue mutation (Phe 2 versus Ala 2) causes the almost threefold difference in the hydrophobic interaction strength generated by the FP1 of SARS-2 versus MERS, despite the presence of LLF in both sequences. Infrared spectroscopy and circular dichroism measurements support the proposal that the outsized influence of Phe 2 versus Ala 2 on the hydrophobic interaction arises from variation in the secondary structure adopted by FP1. Overall, these insights reveal how single-residue diversity in viral FPs, including FP1 of SARS-CoV-2 and MERS-CoV, can lead to substantial changes in intermolecular interactions proposed to play a key role in viral fusion, and hint at strategies for regulating hydrophobic interactions of peptides in a range of contexts.
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Affiliation(s)
- Cindy Qiu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Susan Daniel
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Nicholas L Abbott
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York.
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8
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Abu Quba AA, Goebel MO, Karagulyan M, Miltner A, Kästner M, Bachmann J, Schaumann GE, Diehl D. Changes in cell surface properties of Pseudomonas fluorescens by adaptation to NaCl induced hypertonic stress. FEMS MICROBES 2022; 4:xtac028. [PMID: 37333443 PMCID: PMC10169395 DOI: 10.1093/femsmc/xtac028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 10/26/2022] [Accepted: 12/05/2022] [Indexed: 10/12/2023] Open
Abstract
Determination of the effect of water stress on the surface properties of bacteria is crucial to study bacterial induced soil water repellency. Changes in the environmental conditions may affect several properties of bacteria such as the cell hydrophobicity and morphology. Here, we study the influence of adaptation to hypertonic stress on cell wettability, shape, adhesion, and surface chemical composition of Pseudomonas fluorescens. From this we aim to discover possible relations between the changes in wettability of bacterial films studied by contact angle and single cells studied by atomic and chemical force microscopy (AFM, CFM), which is still lacking. We show that by stress the adhesion forces of the cell surfaces towards hydrophobic functionalized probes increase while they decrease towards hydrophilic functionalized tips. This is consistent with the contact angle results. Further, cell size shrunk and protein content increased upon stress. The results suggest two possible mechanisms: Cell shrinkage is accompanied by the release of outer membrane vesicles by which the protein to lipid ratio increases. The higher protein content increases the rigidity and the number of hydrophobic nano-domains per surface area.
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Affiliation(s)
- Abd Alaziz Abu Quba
- Institute of Environmental Sciences, Rheinland-pfälzische Technische Universität Kaiserslauter-Landau, RPTU in Landau, Fortstrasse 7, 76829 Landau, Germany
| | - Marc-Oliver Goebel
- Institute of Soil Science, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Mariam Karagulyan
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Anja Miltner
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Matthias Kästner
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Jörg Bachmann
- Institute of Soil Science, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Gabriele E Schaumann
- Institute of Environmental Sciences, Rheinland-pfälzische Technische Universität Kaiserslauter-Landau, RPTU in Landau, Fortstrasse 7, 76829 Landau, Germany
| | - Doerte Diehl
- Institute of Environmental Sciences, Rheinland-pfälzische Technische Universität Kaiserslauter-Landau, RPTU in Landau, Fortstrasse 7, 76829 Landau, Germany
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9
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Learning the relationship between nanoscale chemical patterning and hydrophobicity. Proc Natl Acad Sci U S A 2022; 119:e2200018119. [PMID: 36409904 PMCID: PMC9860318 DOI: 10.1073/pnas.2200018119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The hydrophobicity of proteins and similar surfaces, which display chemical heterogeneity at the nanoscale, drives countless aqueous interactions and assemblies. However, predicting how surface chemical patterning influences hydrophobicity remains a challenge. Here, we address this challenge by using molecular simulations and machine learning to characterize and model the hydrophobicity of a diverse library of patterned surfaces, spanning a wide range of sizes, shapes, and chemical compositions. We find that simple models, based only on polar content, are inaccurate, whereas complex neural network models are accurate but challenging to interpret. However, by systematically incorporating chemical correlations between surface groups into our models, we are able to construct a series of minimal models of hydrophobicity, which are both accurate and interpretable. Our models highlight that the number of proximal polar groups is a key determinant of hydrophobicity and that polar neighbors enhance hydrophobicity. Although our minimal models are trained on particular patch size and shape, their interpretability enables us to generalize them to rectangular patches of all shapes and sizes. We also demonstrate how our models can be used to predict hot-spot locations with the largest marginal contributions to hydrophobicity and to design chemical patterns that have a fixed polar content but vary widely in their hydrophobicity. Our data-driven models and the principles they furnish for modulating hydrophobicity could facilitate the design of novel materials and engineered proteins with stronger interactions or enhanced solubilities.
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10
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Qu Y, Davey K, Sun Y, Middelberg A, Bi J. Engineered Design of the E-Helix Structure on Ferritin Nanoparticles. ACS APPLIED BIO MATERIALS 2022; 5:3167-3179. [PMID: 35770389 DOI: 10.1021/acsabm.2c00154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Insertion of an immunogenic epitope at the C-terminus of ferritin has shown the potential to produce a stable and efficacious vaccine. There is however limited understanding of how C-terminus insertion affects ferritin protein stability. The E-helix at the C-terminus has attracted interest because there are contradictory reports as to whether it has a role in protein stabilization. Here, we report, for the first time, combining molecular dynamics simulation (MDS) with experiment to engineer the design of the E-helix at the C-terminus of engineered human ferritin heavy chain (F1) inserted with Epstein-Barr nuclear antigen 1 (EBNA1, E1) and flexible linker (L3) residues (to afford F1L3E1). Hot spots on the E-helix of the C-terminus were predicted by MDS at aa 167 (Glu) and aa 171 (Asp). Five (5) variants of F1L3E1 were constructed by considering hot spots and alteration of electrostatic or hydrophobic interfaces, namely, (1) C1, hot spots substituted with noncharged residue Gln; (2) C2, hot spots substituted with positively charged residue Arg; (3) C3, hydrophobic residues substituted with the most hydrophobic residues Val and Ile; (4) C4, hydrophobic residues substituted with the most hydrophilic residues Gln and Asn; and (5) C5, a heptad repeat structure in the E-helix disrupted by substituting "a" and "d" heptad residues with noncharged polar residue Gln. It was found that the E-helix is essential to maintain integrated protein stability and that changing the hydrophobic interface (C3 and C4) had more significant effects on protein folding and stability than changing the electrostatic interface (C1 and C2). It was confirmed by both MDS and experiment that variants C1, C2, and C5 were able to fold to form stable conformational structures with protein surface hydrophobicity similar to that of F1L3E1. However, they are less thermally stable than F1L3E1. Significant changes in hydrophobicity drove significant protein aggregation for variants C3 and C4. It is concluded that the molecular design of the C-terminus in engineered ferritin, especially the E-helix, is important to ensure the epitope-based chimeric vaccine is safe (aggregate free) and efficacious.
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Affiliation(s)
- Yiran Qu
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Kenneth Davey
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Anton Middelberg
- Division of Research and Innovation, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jingxiu Bi
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
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11
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Rajkhowa S, Pathak U, Patgiri H. Elucidating the Interaction and Stability of Withanone and Withaferin‐A with Human Serum Albumin, Lysozyme and Hemoglobin Using Computational Biophysical Modeling. ChemistrySelect 2022. [DOI: 10.1002/slct.202103938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sanchaita Rajkhowa
- Centre for Biotechnology and Bioinformatics Dibrugarh University Dibrugarh 786004 Assam India
| | - Upasana Pathak
- Centre for Biotechnology and Bioinformatics Dibrugarh University Dibrugarh 786004 Assam India
| | - Himangshu Patgiri
- Centre for Biotechnology and Bioinformatics Dibrugarh University Dibrugarh 786004 Assam India
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12
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Jiao S, Rivera Mirabal DM, DeStefano AJ, Segalman RA, Han S, Shell MS. Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics. Biomacromolecules 2022; 23:1745-1756. [PMID: 35274944 DOI: 10.1021/acs.biomac.1c01687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use molecular dynamics simulations to investigate the effect of polypeptoid sequence on the structure and dynamics of its hydration waters. Polypeptoids provide an excellent platform to study small-molecule hydration in disordered polymers, as they can be precisely synthesized with a variety of sidechain chemistries. We examine water behavior near a set of peptoid oligomers in which the number and placement of nonpolar versus polar sidechains are systematically varied. To do this, we leverage a new computational workflow enabling accurate sampling of polypeptoid conformations. We find that the hydration waters are less dense, are more tetrahedral, and have slower dynamics compared to bulk water. The magnitude of these shifts increases with the number of nonpolar groups. We also find that shifts in the water structure and dynamics are strongly correlated, suggesting that experimental insight into the dynamics of hydration water obtained by Overhauser dynamic nuclear polarization (ODNP) also contains information about water structural properties. We then demonstrate the ability of ODNP to probe site-specific dynamics of hydration water near these model peptoid systems.
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Affiliation(s)
- Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Daniela M Rivera Mirabal
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Chemical Engineering, University of Puerto Rico, Mayagüez, Puerto Rico 00681, United States
| | - Audra J DeStefano
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Rachel A Segalman
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Materials, University of California, Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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13
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Identifying hydrophobic protein patches to inform protein interaction interfaces. Proc Natl Acad Sci U S A 2021; 118:2018234118. [PMID: 33526682 DOI: 10.1073/pnas.2018234118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.
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14
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Bilodeau CL, Lau EY, Roush DJ, Snyder MA, Cramer SM. Behavior of Water Near Multimodal Chromatography Ligands and Its Consequences for Modulating Protein-Ligand Interactions. J Phys Chem B 2021; 125:6112-6120. [PMID: 34097423 DOI: 10.1021/acs.jpcb.1c01549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multimodal chromatography is a powerful approach for purifying proteins that uses ligands containing multiple modes of interaction. Recent studies have shown that selectivity in multimodal chromatographic separations is a function of the ligand structure and geometry. Here, we performed molecular dynamics simulations to explore how the ligand structure and geometry affect ligand-water interactions and how these differences in solution affect the nature of protein-ligand interactions. Our investigation focused on three chromatography ligands: Capto MMC, Nuvia cPrime, and Prototype 4, a structural variant of Nuvia cPrime. First, the solvation characteristics of each ligand were quantified via three metrics: average water density, fluctuations, and residence time. We then explored how solvation was perturbed when the ligand was bound to the protein surface and found that the probability of the phenyl ring dewetting followed the order: Capto MMC > Prototype 4 > Nuvia cPrime. To explore how these differences in dewetting affect protein-ligand interactions, we calculated the probability of each ligand binding to different types of residues on the protein surface and found that the probability of binding to a hydrophobic residue followed the same order as the dewetting behavior. This study illustrates the role that wetting and dewetting play in modulating protein-ligand interactions.
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Affiliation(s)
- Camille L Bilodeau
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Edmond Y Lau
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - David J Roush
- Biologics Process R&D, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Mark A Snyder
- Process Chromatography Division, Bio-Rad Laboratories, 6000 James Watson Drive, Hercules, California 94547, United States
| | - Steven M Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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15
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Size dependence of hydrophobic hydration at electrified gold/water interfaces. Proc Natl Acad Sci U S A 2021; 118:2023867118. [PMID: 33876767 DOI: 10.1073/pnas.2023867118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Hydrophobic hydration at metal/water interfaces actively contributes to the energetics of electrochemical reactions, e.g. [Formula: see text] and [Formula: see text] reduction, where small hydrophobic molecules are involved. In this work, constant applied potential molecular dynamics is employed to study hydrophobic hydration at a gold/water interface. We propose an adaptation of the Lum-Chandler-Weeks (LCW) theory to describe the free energy of hydrophobic hydration at the interface as a function of solute size and applied voltage. Based on this model we are able to predict the free energy cost of cavity formation at the interface directly from the free energy cost in the bulk plus an interface-dependent correction term. The interfacial water network contributes significantly to the free energy, yielding a preference for outer-sphere adsorption at the gold surface for ideal hydrophobes. We predict an accumulation of small hydrophobic solutes of sizes comparable to CO or [Formula: see text], while the free energy cost to hydrate larger hydrophobes, above 2.5-Å radius, is shown to be greater at the interface than in the bulk. Interestingly, the transition from the volume dominated to the surface dominated regimes predicted by the LCW theory in the bulk is also found to take place for hydrophobes at the Au/water interface but occurs at smaller cavity radii. By applying the adapted LCW theory to a simple model addition reaction, we illustrate some implications of our findings for electrochemical reactions.
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16
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Verde AR, de Oca JMM, Accordino SR, Alarcón LM, Appignanesi GA. Structural aspects of an energy-based water classification index and the structure-dynamics link in glassy relaxation. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:47. [PMID: 33783648 DOI: 10.1140/epje/s10189-021-00057-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
An energy-based structural indicator for water, [Formula: see text], has been recently introduced by our group. In turn, in this work we aim at: (1) demonstrating that [Formula: see text] is indeed able to correctly classify water molecules between locally structured tetrahedral (T) and locally distorted (D) ones, circumventing the usual problem of certain previous indicators of overestimating the distorted state; (2) correlating [Formula: see text] with dynamic propensity, a measure of the molecular mobility tendency, in order to seek for the existence of a connection between structure and dynamics within the supercooled regime. More specifically, in the first part of this work we will show that [Formula: see text] accurately discriminates between merely thermally deformed local molecular arrangements and truly distorted molecules (defects). This fact will be made evident not only from radial distribution function results but also from the dynamic propensity distributions of the different kinds of molecules. In turn, we shall devote the second part of this work to finding correlations between T and D molecules with low- and high-dynamic-propensity molecules, respectively, thus revealing the existence of a link between local structure and dynamics, while also making evident the dominant role of the D molecules (defects) in the structural relaxation. Moreover, the availability of a proper molecular classification technique will enable us to study the timescale of such influence of structure on dynamics by defining a modified dynamic propensity measure and by applying it to the structured and unstructured water molecular states.
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Affiliation(s)
- Alejandro R Verde
- Departamento de Química, INQUISUR, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Joan Manuel Montes de Oca
- Departamento de Química, INQUISUR, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Sebastián R Accordino
- Departamento de Química, INQUISUR, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Laureano M Alarcón
- Departamento de Química, INQUISUR, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Gustavo A Appignanesi
- Departamento de Química, INQUISUR, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina.
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17
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Wang C, Biok NA, Nayani K, Wang X, Yeon H, Derek Ma CK, Gellman SH, Abbott NL. Cationic Side Chain Identity Directs the Hydrophobically Driven Self-Assembly of Amphiphilic β-Peptides in Aqueous Solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3288-3298. [PMID: 33683138 DOI: 10.1021/acs.langmuir.0c03255] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Hydrophobic interactions mediated by nonpolar molecular fragments in water are influenced by local chemical and physical contexts in ways that are not yet fully understood. Here, we use globally amphiphilic (GA) β-peptides (GA-Lys and GA-Arg) with stable conformations to explore if replacement of β3-homolysine (βLys) with β3-homoarginine (βArg) influences the hydrophobically driven assembly of these peptides in bulk aqueous solution. The studies were conducted in 10 mM triethanolamine buffer at pH 7, where both βLys (ammonium) and βArg (guanidinium) side chains are substantially protonated. Comparisons of light scattering measurements and cryo-electron micrographs before and after the addition of 60 vol% MeOH indicate very different outcomes of the hydrophobically driven assembly of AcY-GA-Lys versus AcY-GA-Arg (AcY denotes an N-acetylated-β3-homotyrosine (βTyr) at each N-terminus). Nuclear magnetic resonance and analytical ultracentrifugation confirm that AcY-GA-Lys assembles into large aggregates in aqueous buffer, whereas AcY-GA-Arg at comparable concentrations forms only small oligomers. Titration of AcY-GA-Arg into aqueous solutions of AcY-GA-Lys reveals that the driving force for AcY-GA-Lys association is far stronger than that for AcY-GA-Arg association. We discuss these results in the light of past experimental observations involving single molecule force measurements with GA β-peptides and hydrophobically driven dimerization of conventional peptides that form a GA α-helix upon dimerization (but do not display the Lys versus Arg trend predicted by extrapolating from the earlier AFM studies with β-peptides). Overall, our results establish that the identity of proximal cationic groups, ammonium versus guanidinium, profoundly modulates the hydrophobically driven self-assembly of conformationally stable β-peptides in bulk aqueous solution.
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Affiliation(s)
- Chenxuan Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
- Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Naomi A Biok
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
| | - Karthik Nayani
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca14853, New York, United States
| | - Xiaoguang Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Hongseung Yeon
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Chi-Kuen Derek Ma
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
| | - Nicholas L Abbott
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca14853, New York, United States
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18
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Utiramerur S, Paulaitis M. Analysis of Cooperativity and Group Additivity in the Hydration of 1,2-Dimethoxyethane. J Phys Chem B 2021; 125:1660-1666. [DOI: 10.1021/acs.jpcb.0c10729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sowmi Utiramerur
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210, United States
| | - Michael Paulaitis
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210, United States
- The Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
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19
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Monroe JI, Jiao S, Davis RJ, Robinson Brown D, Katz LE, Shell MS. Affinity of small-molecule solutes to hydrophobic, hydrophilic, and chemically patterned interfaces in aqueous solution. Proc Natl Acad Sci U S A 2021; 118:e2020205118. [PMID: 33372161 PMCID: PMC7821046 DOI: 10.1073/pnas.2020205118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Performance of membranes for water purification is highly influenced by the interactions of solvated species with membrane surfaces, including surface adsorption of solutes upon fouling. Current efforts toward fouling-resistant membranes often pursue surface hydrophilization, frequently motivated by macroscopic measures of hydrophilicity, because hydrophobicity is thought to increase solute-surface affinity. While this heuristic has driven diverse membrane functionalization strategies, here we build on advances in the theory of hydrophobicity to critically examine the relevance of macroscopic characterizations of solute-surface affinity. Specifically, we use molecular simulations to quantify the affinities to model hydroxyl- and methyl-functionalized surfaces of small, chemically diverse, charge-neutral solutes represented in produced water. We show that surface affinities correlate poorly with two conventional measures of solute hydrophobicity, gas-phase water solubility and oil-water partitioning. Moreover, we find that all solutes show attraction to the hydrophobic surface and most to the hydrophilic one, in contrast to macroscopically based hydrophobicity heuristics. We explain these results by decomposing affinities into direct solute interaction energies (which dominate on hydroxyl surfaces) and water restructuring penalties (which dominate on methyl surfaces). Finally, we use an inverse design algorithm to show how heterogeneous surfaces, with multiple functional groups, can be patterned to manipulate solute affinity and selectivity. These findings, importantly based on a range of solute and surface chemistries, illustrate that conventional macroscopic hydrophobicity metrics can fail to predict solute-surface affinity, and that molecular-scale surface chemical patterning significantly influences affinity-suggesting design opportunities for water purification membranes and other engineered interfaces involving aqueous solute-surface interactions.
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Affiliation(s)
- Jacob I Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
| | - Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
| | - R Justin Davis
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712
| | - Dennis Robinson Brown
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
| | - Lynn E Katz
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106;
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20
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Zhang F, Yu L, Zhang W, Liu L, Wang C. A minireview on the perturbation effects of polar groups to direct nanoscale hydrophobic interaction and amphiphilic peptide assembly. RSC Adv 2021; 11:28667-28673. [PMID: 35478591 PMCID: PMC9038178 DOI: 10.1039/d1ra05463e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/23/2021] [Indexed: 12/29/2022] Open
Abstract
Hydrophobic interaction provides the essential driving force for creating diverse native and artificial supramolecular architectures. Accumulating evidence leads to a hypothesis that the hydrophobicity of a nonpolar patch of a molecule is non-additive and susceptible to the chemical context of a judicious polar patch. However, the quantification of the hydrophobic interaction at the nanoscale remains a central challenge to validate the hypothesis. In this review, we aim to outline the recent efforts made to determine the hydrophobic interaction at a nanoscopic length scale. The advances achieved in the understanding of proximal polar groups perturbing the magnitude of hydrophobic interaction generated by the nonpolar patch are introduced. We will also discuss the influence of chemical heterogeneity on the modulation of amphiphilic peptide/protein assembly and molecular recognition. Hydrophobic interaction provides the essential driving force for creating diverse native and artificial supramolecular architectures.![]()
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Affiliation(s)
- Feiyi Zhang
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Lei Liu
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
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21
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Tian R, Hu G, Ou X, Luo M, Li J. Dynamic behaviors of interfacial water on the self-assembly monolayer (SAM) heterogeneous surface. J Chem Phys 2020; 153:124705. [PMID: 33003729 DOI: 10.1063/5.0019135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dynamic behaviors of water molecules near the surface with mixed hydrophobic and hydrophilic areas are studied by molecular dynamics simulation. More specifically, the diffusion coefficient and hydrogen bond lifetime of interfacial water on the self-assembly monolayer composed of hydrophobic and hydrophilic groups and their dependence on the mixing ratio are studied. The diffusion dramatically slows down, and the hydrogen bond lifetime considerably increases when a few hydrophilic groups are added to the hydrophobic surface. When the percentage of hydrophilic groups increases to 25%, the behavior of interfacial water is similar to the case of the pure hydrophilic surface. The sensitivity to the hydrophilic group can be attributed to the fact that the grafted hydrophilic groups can not only retard the directly bound water molecules but also affect indirectly bound water by stabilizing hydrogen bonds among interfacial water molecules.
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Affiliation(s)
- Ranran Tian
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Guorong Hu
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Xinwen Ou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Mengbo Luo
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
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22
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Kelkar AS, Dallin BC, Van Lehn RC. Predicting Hydrophobicity by Learning Spatiotemporal Features of Interfacial Water Structure: Combining Molecular Dynamics Simulations with Convolutional Neural Networks. J Phys Chem B 2020; 124:9103-9114. [DOI: 10.1021/acs.jpcb.0c05977] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Atharva S. Kelkar
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Bradley C. Dallin
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Reid C. Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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23
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Tse C, Wickstrom L, Kvaratskhelia M, Gallicchio E, Levy R, Deng N. Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association. Biophys J 2020; 119:1226-1238. [PMID: 32877664 DOI: 10.1016/j.bpj.2020.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 01/30/2023] Open
Abstract
We report the free-energy landscape and thermodynamics of the protein-protein association responsible for the drug-induced multimerization of HIV-1 integrase (IN). Allosteric HIV-1 integrase inhibitors promote aberrant IN multimerization by bridging IN-IN intermolecular interactions. However, the thermodynamic driving forces and kinetics of the multimerization remain largely unknown. Here, we explore the early steps in the IN multimerization by using umbrella sampling and unbiased molecular dynamics simulations in explicit solvent. In direct simulations, the two initially separated dimers spontaneously associate to form near-native complexes that resemble the crystal structure of the aberrant tetramer. Most strikingly, the effective interaction of the protein-protein association is very short-ranged: the two dimers associate rapidly within tens of nanoseconds when their binding surfaces are separated by d ≤ 4.3 Å (less than two water diameters). Beyond this distance, the oligomerization kinetics appears to be diffusion controlled with a much longer association time. The free-energy profile also captured the crucial role of allosteric IN inhibitors in promoting multimerization and explained why several C-terminal domain mutations are remarkably resistant to the drug-induced multimerization. The results also show that at small separation, the protein-protein binding process contains two consecutive phases with distinct thermodynamic signatures. First, interprotein water molecules are expelled to the bulk, resulting in a small increase in entropy, as the solvent entropy gain from the water release is nearly cancelled by the loss of side-chain entropies as the two proteins approach each other. At shorter distances, the two dry binding surfaces adapt to each other to optimize their interaction energy at the expense of further protein configurational entropy loss. Although the binding interfaces feature clusters of hydrophobic residues, overall, the protein-protein association in this system is driven by enthalpy and opposed by entropy.
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Affiliation(s)
- Celine Tse
- Department of Chemistry and Physical Sciences, Pace University, New York, New York
| | - Lauren Wickstrom
- Borough of Manhattan Community College, the City University of New York, Department of Science, New York, New York
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado
| | - Emilio Gallicchio
- Department of Chemistry, Brooklyn College, the City University of New York, Brooklyn, New York; PhD Program in Biochemistry and PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, New York
| | - Ronald Levy
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, Pennsylvania
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, New York.
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24
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Borgis D, Luukkonen S, Belloni L, Jeanmairet G. Simple Parameter-Free Bridge Functionals for Molecular Density Functional Theory. Application to Hydrophobic Solvation. J Phys Chem B 2020; 124:6885-6893. [DOI: 10.1021/acs.jpcb.0c04496] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Borgis
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
| | - Sohvi Luukkonen
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, 91191, France
| | - Guillaume Jeanmairet
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, Paris, F-75005, France
- Réseau sur le Stockage Électrochimique de l’Énergie, CNRS FR3459, 33 rue Saint Leu, Amiens, Cedex 80039, France
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25
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26
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Dynamical control by water at a molecular level in protein dimer association and dissociation. Proc Natl Acad Sci U S A 2020; 117:2302-2308. [PMID: 31969453 DOI: 10.1073/pnas.1908379117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Water, often termed as the "lubricant of life," is expected to play an active role in navigating protein dissociation-association reactions. In order to unearth the molecular details, we first compute the free-energy surface (FES) of insulin dimer dissociation employing metadynamics simulation, and then carry out analyses of insulin dimerization and dissociation using atomistic molecular-dynamics simulation in explicit water. We select two sets of initial configurations from 1) the dissociated state and 2) the transition state, and follow time evolution using several long trajectories (∼1-2 μs). During the process we not only monitor configuration of protein monomers, but also the properties of water. Although the equilibrium structural properties of water between the two monomers approach bulklike characteristics at a separation distance of ∼5 nm, the dynamics differ considerably. The complex association process is observed to be accompanied by several structural and dynamical changes of the system, such as large-scale correlated water density fluctuations, coupled conformational fluctuation of protein monomers, a dewettinglike transition with the change of intermonomeric distance RMM from ∼4 to ∼2 nm, orientation of monomers and hydrophobic hydration in the monomers. A quasistable, solvent-shared, protein monomer pair (SSPMP) forms at around 2 nm during association process which is a local free-energy minimum having ∼50-60% of native contacts. Simulations starting with arrangements sampled from the transition state (TS) of the dimer dissociation reveal that the final outcome depends on relative orientation of the backbone in the "hotspot" region.
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27
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Determination and evaluation of the nonadditivity in wetting of molecularly heterogeneous surfaces. Proc Natl Acad Sci U S A 2019; 116:25516-25523. [PMID: 31792179 PMCID: PMC6926055 DOI: 10.1073/pnas.1916180116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Every folded protein presents an interface with water that is composed of domains of varying hydrophilicity/-phobicity. Many simulation studies have highlighted the nonadditivity in the wetting of such nanostructured surfaces in contrast with the accepted theoretical formula that is additive. We present here an experimental study on surfaces of identical composition but different organization of hydrophobic and hydrophilic domains. We prove that the interfacial energy of such surfaces differs by ∼20% and that a significant difference in the interfacial water H-bonding structure can be measured. As a result, in combination with molecular-dynamics simulations, we propose a model that captures the wetting of molecularly heterogeneous surfaces, showing the importance of local structure (first-nearest neighbors) in determining the wetting properties. The interface between water and folded proteins is very complex. Proteins have “patchy” solvent-accessible areas composed of domains of varying hydrophobicity. The textbook understanding is that these domains contribute additively to interfacial properties (Cassie’s equation, CE). An ever-growing number of modeling papers question the validity of CE at molecular length scales, but there is no conclusive experiment to support this and no proposed new theoretical framework. Here, we study the wetting of model compounds with patchy surfaces differing solely in patchiness but not in composition. Were CE to be correct, these materials would have had the same solid–liquid work of adhesion (WSL) and time-averaged structure of interfacial water. We find considerable differences in WSL, and sum-frequency generation measurements of the interfacial water structure show distinctively different spectral features. Molecular-dynamics simulations of water on patchy surfaces capture the observed behaviors and point toward significant nonadditivity in water density and average orientation. They show that a description of the molecular arrangement on the surface is needed to predict its wetting properties. We propose a predictive model that considers, for every molecule, the contributions of its first-nearest neighbors as a descriptor to determine the wetting properties of the surface. The model is validated by measurements of WSL in multiple solvents, where large differences are observed for solvents whose effective diameter is smaller than ∼6 Å. The experiments and theoretical model proposed here provide a starting point to develop a comprehensive understanding of complex biological interfaces as well as for the engineering of synthetic ones.
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28
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Giacomello A, Schimmele L, Dietrich S, Tasinkevych M. Recovering superhydrophobicity in nanoscale and macroscale surface textures. SOFT MATTER 2019; 15:7462-7471. [PMID: 31512709 PMCID: PMC8751625 DOI: 10.1039/c9sm01049a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/15/2019] [Indexed: 05/30/2023]
Abstract
Here, we investigate the complete drying of hydrophobic cavities in order to elucidate the dependence of drying on the size, the geometry, and the degree of hydrophobicity of the confinement. Two complementary theoretical approaches are adopted: a macroscopic one based on classical capillarity and a microscopic classical density functional theory. This combination allows us to pinpoint unique drying mechanisms at the nanoscale and to clearly differentiate them from the mechanisms operational at the macroscale. Nanoscale hydrophobic cavities allow the thermodynamic destabilization of the confined liquid phase over an unexpectedly broad range of conditions, including pressures as large as 10 MPa and contact angles close to 90°. On the other hand, for cavities on the micron scale, such destabilization occurs only for much larger contact angles and close to liquid-vapor coexistence. These scale-dependent drying mechanisms are used to propose design criteria for hierarchical superhydrophobic surfaces capable of spontaneous self-recovery over a broad range of operating conditions. In particular, we detail the requirements under which it is possible to realize perpetual superhydrophobicity at positive pressures on surfaces with micron-sized textures by exploiting drying, facilitated by nanoscale coatings. Concerning the issue of superhydrophobicity, these findings indicate a promising direction both for surface fabrication and for the experimental characterization of perpetual surperhydrophobicity. From a more basic perspective, the present results have an echo on a wealth of biological problems in which hydrophobic confinement induces drying, such as in protein folding, molecular recognition, and hydrophobic gating.
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Affiliation(s)
- Alberto Giacomello
- Sapienza Università di Roma, Dipartimento di Ingegneria Meccanica e Aerospaziale, 00184 Rome, Italy. and Max-Planck-Institut für Intelligente Systeme, 70569 Stuttgart, Germany
| | - Lothar Schimmele
- Max-Planck-Institut für Intelligente Systeme, 70569 Stuttgart, Germany
| | - Siegfried Dietrich
- Max-Planck-Institut für Intelligente Systeme, 70569 Stuttgart, Germany and IV. Institut für Theoretische Physik, Universität Stuttgart, 70569 Stuttgart, Germany
| | - Mykola Tasinkevych
- Centro de Física Teórica e Computacional, Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, P-1749-016 Lisboa, Portugal
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29
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Montes de Oca JM, Accordino SR, Verde AR, Alarcón LM, Appignanesi GA. Structural features of high-local-density water molecules: Insights from structure indicators based on the translational order between the first two molecular shells. Phys Rev E 2019; 99:062601. [PMID: 31330696 DOI: 10.1103/physreve.99.062601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Indexed: 11/07/2022]
Abstract
The two-liquids scenario for liquid water assumes the existence of two competing preferential local molecular structural states characterized by either low or high local density. While the former is expected to present good local order thus involving privileged structures, the latter is usually regarded as conforming a high-entropy unstructured state. A main difference in the local arrangement of such "classes" of water molecules can be inferred from the degree of translational order between the first and second molecular shells. This is so, since the low-local-density molecules present a clear gap between the first two shells while in the case of the high-local-density ones, one or more molecules from the second shell have collapsed toward the first one, thus populating the intershell region. Some structural indicators, like the widely employed local structure index and the recently introduced ζ index, have been devised precisely on the basis of this observation, being successful in detecting well-structured low-local-density molecules. However, the nature of the high-local-density state has been mainly disregarded over the years. In this work we employ molecular dynamics simulations for two water models (the extended simple point charge model and the five-site model) at the liquid and supercooled regimes combined with the inherent dynamics approach (energy minimizations of the instantaneous configurations) in order to both rationalize the detailed structural and topological information that these indicators provide and to advance in our understanding of the high-density state.
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Affiliation(s)
- Joan Manuel Montes de Oca
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Sebastián R Accordino
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Alejandro R Verde
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Laureano M Alarcón
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
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Dallin BC, Van Lehn RC. Spatially Heterogeneous Water Properties at Disordered Surfaces Decrease the Hydrophobicity of Nonpolar Self-Assembled Monolayers. J Phys Chem Lett 2019; 10:3991-3997. [PMID: 31265306 DOI: 10.1021/acs.jpclett.9b01707] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding the relationship between hydrophobicity and the properties of functionalized surfaces is vital to the design of materials that interact in aqueous environments. In this Letter, we use atomistic molecular dynamics simulations to investigate the effects of surface order on the hydrophobicity of self-assembled monolayers (SAMs) containing nonpolar ligands. We find that the interfacial hydrophobicity is highly correlated with SAM order and, strikingly, poorly correlated with the solvent-accessible surface area, which typically has been related to interfacial hydrophobicity. Analysis of spatial variations in both SAM and water properties reveals that the SAM-water interface is pinned near regions of disordered SAM surfaces with increased free volume, decreasing the overall interfacial hydrophobicity. Spatial variations in ligand end group positions at disordered SAM surfaces thus translate to spatial variations in hydrophobicity, yielding heterogeneous surface properties. These findings provide new insights into how surface order can alter the hydrophobicity of chemically uniform surfaces.
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Affiliation(s)
- Bradley C Dallin
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 , United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 , United States
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Verde AR, Montes de Oca JM, Accordino SR, Alarcón LM, Appignanesi GA. Comparing the performance of two structural indicators for different water models while seeking for connections between structure and dynamics in the glassy regime. J Chem Phys 2019; 150:244504. [DOI: 10.1063/1.5108796] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Alejandro R. Verde
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Joan Manuel Montes de Oca
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Sebastián R. Accordino
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Laureano M. Alarcón
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Gustavo A. Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
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32
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Montes de Oca JM, Accordino SR, Appignanesi GA, Handle PH, Sciortino F. Size dependence of dynamic fluctuations in liquid and supercooled water. J Chem Phys 2019; 150:144505. [DOI: 10.1063/1.5085886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joan Manuel Montes de Oca
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Sebastián R. Accordino
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Gustavo A. Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000 Bahía Blanca, Argentina
| | - Philip H. Handle
- Department of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Universita’ di Roma, Piazzale A. Moro 5, Roma 00185, Italy
- CNR-ISC, c/o Sapienza, Piazzale A. Moro 5, Roma 00185, Italy
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Dallin BC, Yeon H, Ostwalt AR, Abbott NL, Van Lehn RC. Molecular Order Affects Interfacial Water Structure and Temperature-Dependent Hydrophobic Interactions between Nonpolar Self-Assembled Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:2078-2088. [PMID: 30645942 DOI: 10.1021/acs.langmuir.8b03287] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding how material properties affect hydrophobic interactions-the water-mediated interactions that drive the association of nonpolar materials-is vital to the design of materials in contact with water. Conventionally, the magnitude of the hydrophobic interactions between extended interfaces is attributed to interfacial chemical properties, such as the amount of nonpolar solvent-exposed surface area. However, recent experiments have demonstrated that the hydrophobic interactions between uniformly nonpolar self-assembled monolayers (SAMs) also depend on molecular-level SAM order. In this work, we use atomistic molecular dynamics simulations to investigate the relationship between SAM order, water structure, and hydrophobic interactions to explain these experimental observations. The SAM-SAM hydrophobic interactions calculated from the simulations increase in magnitude as SAM order increases, matching experimental observations. We explain this trend by showing that the molecular-level order of the SAM impacts the nanoscale structure of interfacial water molecules, leading to an increase in water structure near disordered SAMs. These findings are consistent with a decrease in the solvation entropy of disordered SAMs, which is confirmed by measuring the temperature dependence of hydrophobic interactions using both simulations and experiments. This study elucidates how hydrophobic interactions can be influenced by an interfacial physical property, which may guide the design of synthetic materials with fine-tuned interfacial hydrophobicity.
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Affiliation(s)
- Bradley C Dallin
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 United States
| | - Hongseung Yeon
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 United States
| | - Alexis R Ostwalt
- Department of Chemical and Biological Engineering , Montana State University , 306 Cobleigh Hall , Bozeman , Montana 59715 United States
| | - Nicholas L Abbott
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 United States
- Department of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall , Ithaca , New York 14853 , United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 United States
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Jiang H, Fialoke S, Vicars Z, Patel AJ. Characterizing surface wetting and interfacial properties using enhanced sampling (SWIPES). SOFT MATTER 2019; 15:860-869. [PMID: 30644500 DOI: 10.1039/c8sm02317d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We introduce an accurate and efficient method for characterizing surface wetting and interfacial properties, such as the contact angle made by a liquid droplet on a solid surface, and the vapor-liquid surface tension of a fluid. The method makes use of molecular simulations in conjunction with the indirect umbrella sampling technique to systematically wet the surface and estimate the corresponding free energy. To illustrate the method, we study the wetting of a family of Lennard-Jones surfaces by water. For surfaces with a wide range of attractions for water, we estimate contact angles using our method, and compare them with contact angles obtained using droplet shapes. Notably, our method is able to capture the transition from partial to complete wetting as surface-water attractions are increased. Moreover, the method is straightforward to implement and is computationally efficient, providing accurate contact angle estimates in roughly 5 nanoseconds of simulation time.
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Affiliation(s)
- Hao Jiang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Rego NB, Xi E, Patel AJ. Protein Hydration Waters Are Susceptible to Unfavorable Perturbations. J Am Chem Soc 2019; 141:2080-2086. [DOI: 10.1021/jacs.8b11448] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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36
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Ebrahim-Habibi MB, Ghobeh M, Aghakhani Mahyari F, Rafii-Tabar H, Sasanpour P. Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study. J Mol Graph Model 2018; 87:257-267. [PMID: 30594774 DOI: 10.1016/j.jmgm.2018.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure. METHODS Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized. RESULTS Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the first (PGB-CNT1) and the aromatic residues in the second (PGB-CNT2) surface patch. Displacement of amino acids in the PGB-CNT2 complex occurred during the simulation and it caused an increase in its stability at the end of simulation. The amino acids' displacements diminished the PGB α-helix structure by breakage of hydrogen bonds and generated more transient structures. Principal component analysis determined that the interaction of the CNT with the second surface patch of the PGB raised the extent and modes of the PGB motions. In contrast, insignificant structural changes induced in the PGB while the CNT bonded through the first surface patch. CONCLUSION Even though neither of the PGB-CNT complexes could prevent structural changes in the PGB, development of the PGB-CNT1 complex induce slight structural changes in its fragment of crystallizable receptor (FCR). Dissimilar structural changes induced in the PGB-CNT complexes are possibly related to various characteristics of the PGB binding sites.
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Affiliation(s)
- Mohammad-Bagher Ebrahim-Habibi
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Ghobeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Hashem Rafii-Tabar
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Pezhman Sasanpour
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; School of Nanoscience, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
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37
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Limo MJ, Sola-Rabada A, Boix E, Thota V, Westcott ZC, Puddu V, Perry CC. Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications. Chem Rev 2018; 118:11118-11193. [PMID: 30362737 DOI: 10.1021/acs.chemrev.7b00660] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO2, SiO2, and GeO2 has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.
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Affiliation(s)
- Marion J Limo
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Interface and Surface Analysis Centre, School of Pharmacy , University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna Sola-Rabada
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Estefania Boix
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Department of Bioproducts and Biosystems , Aalto University , P.O. Box 16100, FI-00076 Aalto , Finland
| | - Veeranjaneyulu Thota
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Zayd C Westcott
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Valeria Puddu
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Carole C Perry
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
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38
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Zhang BW, Cui D, Matubayasi N, Levy RM. The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations. J Phys Chem B 2018; 122:4700-4707. [PMID: 29634902 DOI: 10.1021/acs.jpcb.8b02666] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We use end point simulations to estimate the excess chemical potential of water in the homogeneous liquid and at the interface with a protein in solution. When the pure liquid is taken as the reference, the excess chemical potential of interfacial water is the difference between the solvation free energy of a water molecule at the interface and in the bulk. Using the homogeneous liquid as an example, we show that the solvation free energy for growing a water molecule can be estimated by applying UWHAM to the simulation data generated from the initial and final states (i.e., "the end points") instead of multistate free energy perturbation simulations because of the possible overlaps of the configurations sampled at the end points. Then end point simulations are used to estimate the solvation free energy of water at the interface with a protein in solution. The estimate of the solvation free energy at the interface from two simulations at the end points agrees with the benchmark using 32 states within a 95% confidence interval for most interfacial locations. The ability to accurately estimate the excess chemical potential of water from end point simulations facilitates the statistical thermodynamic analysis of diverse interfacial phenomena. Our focus is on analyzing the excess chemical potential of water at protein receptor binding sites with the goal of using this information to assist in the design of tight binding ligands.
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Affiliation(s)
- Bin W Zhang
- Center for Biophysics and Computational Biology , Department of Chemistry , and Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Di Cui
- Center for Biophysics and Computational Biology , Department of Chemistry , and Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science , Osaka University , Toyonaka , Osaka 560-8531 , Japan.,Elements Strategy Initiative for Catalysts and Batteries , Kyoto University , Katsura , Kyoto 615-8520 , Japan
| | - Ronald M Levy
- Center for Biophysics and Computational Biology , Department of Chemistry , and Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
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39
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Ding X, Zheng RC, Tang XL, Zheng YG. Engineering of Talaromyces thermophilus lipase by altering its crevice-like binding site for highly efficient biocatalytic synthesis of chiral intermediate of Pregablin. Bioorg Chem 2018; 77:330-338. [DOI: 10.1016/j.bioorg.2018.01.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 02/02/2023]
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40
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Samanta T, Bagchi B. Temperature effects on the hydrophobic force between two graphene-like surfaces in liquid water. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1433-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Remsing RC, Xi E, Patel AJ. Protein Hydration Thermodynamics: The Influence of Flexibility and Salt on Hydrophobin II Hydration. J Phys Chem B 2018; 122:3635-3646. [DOI: 10.1021/acs.jpcb.7b12060] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard C. Remsing
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Erte Xi
- 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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42
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Ho TA, Ilgen A. Density Fluctuation in Aqueous Solutions and Molecular Origin of Salting-Out Effect for CO 2. J Phys Chem B 2017; 121:11485-11491. [PMID: 29072910 DOI: 10.1021/acs.jpcb.7b09215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using molecular dynamics simulation, we studied the density fluctuations and cavity formation probabilities in aqueous solutions and their effect on the hydration of CO2. With increasing salt concentration, we report an increased probability of observing a larger than the average number of species in the probe volume. Our energetic analyses indicate that the van der Waals and electrostatic interactions between CO2 and aqueous solutions become more favorable with increasing salt concentration, favoring the solubility of CO2 (salting in). However, due to the decreasing number of cavities forming when salt concentration is increased, the solubility of CO2 decreases. The formation of cavities was found to be the primary control on the dissolution of gas, and is responsible for the observed CO2 salting-out effect. Our results provide the fundamental understanding of the density fluctuation in aqueous solutions and the molecular origin of the salting-out effect for real gas.
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Affiliation(s)
- Tuan Anh Ho
- Geochemistry Department, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| | - Anastasia Ilgen
- Geochemistry Department, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
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43
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Wang C, Ma CKD, Yeon H, Wang X, Gellman SH, Abbott NL. Nonadditive Interactions Mediated by Water at Chemically Heterogeneous Surfaces: Nonionic Polar Groups and Hydrophobic Interactions. J Am Chem Soc 2017; 139:18536-18544. [DOI: 10.1021/jacs.7b08367] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chenxuan Wang
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Chi-Kuen Derek Ma
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Hongseung Yeon
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Xiaoguang Wang
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nicholas L. Abbott
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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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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45
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Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context. Proc Natl Acad Sci U S A 2017; 114:13345-13350. [PMID: 29158409 DOI: 10.1073/pnas.1700092114] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrophobic interactions drive many important biomolecular self-assembly phenomena. However, characterizing hydrophobicity at the nanoscale has remained a challenge due to its nontrivial dependence on the chemistry and topography of biomolecular surfaces. Here we use molecular simulations coupled with enhanced sampling methods to systematically displace water molecules from the hydration shells of nanostructured solutes and calculate the free energetics of interfacial water density fluctuations, which quantify the extent of solute-water adhesion, and therefore solute hydrophobicity. In particular, we characterize the hydrophobicity of curved graphene sheets, self-assembled monolayers (SAMs) with chemical patterns, and mutants of the protein hydrophobin-II. We find that water density fluctuations are enhanced near concave nonpolar surfaces compared with those near flat or convex ones, suggesting that concave surfaces are more hydrophobic. We also find that patterned SAMs and protein mutants, having the same number of nonpolar and polar sites but different geometrical arrangements, can display significantly different strengths of adhesion with water. Specifically, hydroxyl groups reduce the hydrophobicity of methyl-terminated SAMs most effectively not when they are clustered together but when they are separated by one methyl group. Hydrophobin-II mutants show that a charged amino acid reduces the hydrophobicity of a large nonpolar patch when placed at its center, rather than at its edge. Our results highlight the power of water density fluctuations-based measures to characterize the hydrophobicity of nanoscale surfaces and caution against the use of additive approximations, such as the commonly used surface area models or hydropathy scales for characterizing biomolecular hydrophobicity and the associated driving forces of assembly.
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Karzar Jeddi M, Romero-Vargas Castrillón S. Dynamics of Water Monolayers Confined by Chemically Heterogeneous Surfaces: Observation of Surface-Induced Anisotropic Diffusion. J Phys Chem B 2017; 121:9666-9675. [PMID: 28938070 DOI: 10.1021/acs.jpcb.7b07454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water present in confining geometries plays key roles in many systems of scientific and technological relevance. Prominent examples are living cells and nanofluidic devices. Despite its importance, a complete understanding of the dynamics of water in nanoscale confinement remains elusive. In this work, we use molecular dynamics (MD) simulation to investigate the diffusive dynamics of water monolayers confined in chemically heterogeneous silica slit pores. The effect of chemical heterogeneity is systematically investigated through the fraction fSiOH of randomly distributed surface sites that possess hydroxyl functional groups. Partial hydroxylation results in heterogeneous surfaces comprising nanoscale hydrophobic and hydrophilic regions. We find that the in-plane diffusivity of water increases monotonically with fSiOH; at low surface hydroxylation (fSiOH ≤ 50%), slow water dynamics arise due to the formation of icelike structures in the hydrophobic regions, while at fSiOH ≥ 75%, surface-water H-bonds in the hydrophilic regions result in faster dynamics. We show that surface patterning with ordered hydrophobic and hydrophilic "stripes" can be used to induce one-dimensional diffusion, with water diffusing through the slit pore preferentially along the direction of the hydrophilic surface patterns.
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Affiliation(s)
- Mehdi Karzar Jeddi
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Santiago Romero-Vargas Castrillón
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
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Montes de Oca JM, Menéndez CA, Accordino SR, Malaspina DC, Appignanesi GA. Studies on electrostatic interactions within model nano-confined aqueous environments of different chemical nature. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:78. [PMID: 28929428 DOI: 10.1140/epje/i2017-11568-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
We study the potential of mean force for pairs of parallel flat surfaces with attractive electrostatic interactions by employing model systems functionalized with different charged, hydrophobic and hydrophilic groups. We study the way in which the local environment (hydrophobic or hydrophilic moieties) modulates the interaction between the attractive charged groups on the plates by removing or attracting nearby water and thus screening or not the electrostatic interaction. To explicitly account for the role of the solvent and the local hydrophobicity, we also perform studies in vacuo. Additionally, the results are compared to that for non-charged plates in order to single out and rationalize the non-additivity of the different non-covalent interactions. Our simulations demonstrate that the presence of neighboring hydrophobic groups promote water removal in the vicinity of the charged groups, thus enhancing charge attraction upon self-assembly. This role of the local hydrophobicity modulating electrostatic interactions is consistent with recent qualitative descriptions in the protein binding context.
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Affiliation(s)
- Joan Manuel Montes de Oca
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Cintia A Menéndez
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Sebastián R Accordino
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - David C Malaspina
- Biomedical Engineering Department, Northwestern University, 2145 Sheridan Road, 60208, Evanston, IL, USA
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina.
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Martin DR, Matyushov DV. Terahertz absorption of lysozyme in solution. J Chem Phys 2017; 147:084502. [DOI: 10.1063/1.4989641] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel R. Martin
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287,
USA
| | - Dmitry V. Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287,
USA
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Chen CR, Makhatadze GI. Molecular Determinants of Temperature Dependence of Protein Volume Change upon Unfolding. J Phys Chem B 2017; 121:8300-8310. [PMID: 28795561 DOI: 10.1021/acs.jpcb.7b05831] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Pressure is a well-known environmental stressor that can either stabilize or destabilize proteins. The volumetric change upon protein unfolding determines the effect of pressure on protein stability, where negative volume changes destabilized proteins at high pressures. High temperature often accompanies high pressure, for example, in the ocean depths near hydrothermal vents or near faults, so it is important to study the effect of temperature on the volumetric change upon unfolding. We previously detailed the magnitude and sign of the molecular determinants of volumetric change, allowing us to quantitatively predict the volumetric change upon protein unfolding. Here, we present a comprehensive analysis of the temperature dependence of the volumetric components of proteins, showing that hydration volume is the primary component that defines expansivities of the native and unfolded states and void volume only contributes slightly to the folded state expansivity.
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Affiliation(s)
- Calvin R Chen
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , 110 8th Street, Troy, New York 12180, United States
| | - George I Makhatadze
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , 110 8th Street, Troy, New York 12180, United States
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Abstract
Szent-Győrgi called water the "matrix of life" and claimed that there was no life without it. This statement is true, as far as we know, on our planet, but it is not clear whether it must hold throughout the cosmos. To evaluate that question requires a close consideration of the many varied and subtle roles that water plays in living cells-a consideration that must be free of both an assumed essentialism that gives water an almost mystical life-giving agency and a traditional tendency to see it as a merely passive solvent. Water is a participant in the "life of the cell," and here I describe some of the features of that active agency. Water's value for molecular biology comes from both the structural and dynamic characteristics of its status as a complex, structured liquid as well as its nature as a polar, protic, and amphoteric reagent. Any discussion of water as life's matrix must, however, begin with an acknowledgment that our understanding of it as both a liquid and a solvent is still incomplete.
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