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Barria-Urenda M, Ruiz-Fernandez A, Gonzalez C, Oostenbrink C, Garate JA. Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene. J Chem Inf Model 2023; 63:6642-6654. [PMID: 37909535 DOI: 10.1021/acs.jcim.3c00418] [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: 11/03/2023]
Abstract
There is still growing interest in graphene interactions with proteins, both for its possible biological applications and due to concerns over detrimental effects at the cellular level. As with any process involving proteins, an understanding of amino acid composition is desirable. In this work, we systematically studied the adsorption process of amino acids onto pristine graphene via rigorous free-energy calculations. We characterized the free energy, potential energy, and entropy of the adsorption of all proteinogenic amino acids. The energetic components were further separated into pair interaction contributions. A linear correlation was found between the free energy and the solvent accessible surface area change during adsorption (ΔSASAads) over pristine graphene and uncharged amino acids. Free energies over pristine graphene were compared with adsorption onto graphene oxide, finding an almost complete loss of the favorability of amino acid adsorption onto graphene. Finally, the correlation with ΔSASAads was used to successfully predict the free energy of adsorption of several penta-l-peptides in different structural states and sequences. Due to the relative ease of calculating the ΔSASAads compared to free-energy calculations, it could prove to be a cost-effective predictor of the free energy of adsorption for proteins onto nonpolar surfaces.
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Affiliation(s)
- Mateo Barria-Urenda
- Centro Interdisciplinario de Neurociencia de Valparaíso, Pasaje Harrington 287, Playa Ancha, 2381850 Valparaíso, Chile
- Doctorado en Ciencias, Mención Biofísica y Biología Computacional, Facultad de Ciencias, Universidad de Valparaíso, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics (NNBP), Universidad San Sebastian, Bellavista, 7510602 Santiago, Chile
| | - Alvaro Ruiz-Fernandez
- Centro Científico y Tecnológico de Excelencia, Fundacion Ciencia & Vida, Santiago, Santiago 7780272, Chile
| | - Carlos Gonzalez
- Millennium Nucleus in NanoBioPhysics (NNBP), Universidad San Sebastian, Bellavista, 7510602 Santiago, Chile
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Jose Antonio Garate
- Centro Interdisciplinario de Neurociencia de Valparaíso, Pasaje Harrington 287, Playa Ancha, 2381850 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics (NNBP), Universidad San Sebastian, Bellavista, 7510602 Santiago, Chile
- Centro Científico y Tecnológico de Excelencia, Fundacion Ciencia & Vida, Santiago, Santiago 7780272, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista, 7510602 Santiago, Chile
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Thakkar R, Upreti D, Ishiguro S, Tamura M, Comer J. Computational design of a cyclic peptide that inhibits the CTLA4 immune checkpoint. RSC Med Chem 2023; 14:658-670. [PMID: 37122540 PMCID: PMC10131585 DOI: 10.1039/d2md00409g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Proteins involved in immune checkpoint pathways, such as CTLA4, PD1, and PD-L1, have become important targets for cancer immunotherapy; however, development of small molecule drugs targeting these pathways has proven difficult due to the nature of their protein-protein interfaces. Here, using a hierarchy of computational techniques, we design a cyclic peptide that binds CTLA4 and follow this with experimental verification of binding and biological activity, using bio-layer interferometry, cell culture, and a mouse tumor model. Beginning from a template excised from the X-ray structure of the CTLA4:B7-2 complex, we generate several peptide sequences using flexible docking and modeling steps. These peptides are cyclized head-to-tail to improve structural and proteolytic stability and screened using molecular dynamics simulation and MM-GBSA calculation. The standard binding free energies for shortlisted peptides are then calculated in explicit-solvent simulation using a rigorous multistep technique. The most promising peptide, cyc(EIDTVLTPTGWVAKRYS), yields the standard free energy -6.6 ± 3.5 kcal mol-1, which corresponds to a dissociation constant of ∼15 μmol L-1. The binding affinity of this peptide for CTLA4 is measured experimentally (31 ± 4 μmol L-1) using bio-layer interferometry. Treatment with this peptide inhibited tumor growth in a co-culture of Lewis lung carcinoma (LLC) cells and antigen primed T cells, as well as in mice with an orthotropic Lewis lung carcinoma allograft model.
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Affiliation(s)
- Ravindra Thakkar
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Deepa Upreti
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Susumu Ishiguro
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Masaaki Tamura
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Jeffrey Comer
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
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H H, Mewada R, Mallajosyula SS. Capturing charge and size effects of ions at the graphene-electrolyte interface using polarizable force field simulations. NANOSCALE ADVANCES 2023; 5:796-804. [PMID: 36756506 PMCID: PMC9891073 DOI: 10.1039/d2na00733a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/27/2022] [Indexed: 06/18/2023]
Abstract
We present a systematic investigation capturing the charge and size effects of ions interacting with a graphene surface using polarizable simulations. Our results utilizing the Drude polarizable force field (FF) for ions, water and graphene surfaces, show that the graphene parameters previously developed by us are able to accurately capture the dynamics at the electrolyte-graphene interface. For monovalent ions, with increasing size, the solvation shell plays a crucial role in controlling the ion-graphene interactions. Smaller monovalent ions directly interact with the graphene surface, while larger ions interact with the graphene surface via a well-formed solvation shell. For divalent ions, both interaction modes are observed. For the anion Cl-, we observe direct interaction between the ions and the graphene surface. The anion-graphene interactions are strongly driven by the polarizability of the graphene surface. These effects are not captured in the absence of polarization by additive FF simulations. The present study underlines the importance of polarizability in capturing the interfacial phenomenon at the solid-solute interface.
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Affiliation(s)
- Hemanth H
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar Palaj Gujarat India-382355
| | - Rohan Mewada
- Discipline of Material Science and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat India-382355
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar Palaj Gujarat India-382355
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Legleiter J, Thakkar R, Velásquez-Silva A, Miranda-Carvajal I, Whitaker S, Tomich J, Comer J. Design of Peptides that Fold and Self-Assemble on Graphite. J Chem Inf Model 2022; 62:4066-4082. [PMID: 35881533 PMCID: PMC9472279 DOI: 10.1021/acs.jcim.2c00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The graphite-water interface provides a unique environment for polypeptides that generally favors ordered structures more than in solution. Therefore, systems consisting of designed peptides and graphitic carbon might serve as a convenient medium for controlled self-assembly of functional materials. Here, we computationally designed cyclic peptides that spontaneously fold into a β-sheet-like conformation at the graphite-water interface and self-assemble, and we subsequently observed evidence of such assembly by atomic force microscopy. Using a novel protocol, we screened nearly 2000 sequences, optimizing for formation of a unique folded conformation while discouraging unfolded or misfolded conformations. A head-to-tail cyclic peptide with the sequence GTGSGTGGPGGGCGTGTGSGPG showed the greatest apparent propensity to fold spontaneously, and this optimized sequence was selected for larger scale molecular dynamics simulations, rigorous free-energy calculations, and experimental validation. In simulations ranging from hundreds of nanoseconds to a few microseconds, we observed spontaneous folding of this peptide at the graphite-water interface under many different conditions, including multiple temperatures (295 and 370 K), with different initial orientations relative to the graphite surface, and using different molecular dynamics force fields (CHARMM and Amber). The thermodynamic stability of the folded conformation on graphite over a range of temperatures was verified by replica-exchange simulations and free-energy calculations. On the other hand, in free solution, the folded conformation was found to be unstable, unfolding in tens of picoseconds. Intermolecular hydrogen bonds promoted self-assembly of the folded peptides into linear arrangements where the peptide backbone exhibited a tendency to align along one of the six zigzag directions of the graphite basal plane. For the optimized peptide, atomic force microscopy revealed growth of single-molecule-thick linear patterns of 6-fold symmetry, consistent with the simulations, while no such patterns were observed for a control peptide with the same amino acid composition but a scrambled sequence.
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Affiliation(s)
- Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Ravindra Thakkar
- Nanotechnology Innovation Center of Kansas State, Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Astrid Velásquez-Silva
- Facultad de Ciencias de la Salud, Programa de Fisioterapia, Corporación Universitaria Iberoamericana, Calle 67 No. 5-27, 110231 Bogotá, Colombia
| | - Ingrid Miranda-Carvajal
- Centro de Innovación y Tecnología - Instituto Colombiano del Petróleo - Ecopetrol S.A., Km 7 vía Bucaramanga, 681011 Piedecuesta, Colombia
| | - Susan Whitaker
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - John Tomich
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Jeffrey Comer
- Nanotechnology Innovation Center of Kansas State, Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
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Acero PN, Mohr S, Bernabei M, Fernández C, Domínguez B, Ewen JP. Molecular Simulations of Surfactant Adsorption on Iron Oxide from Hydrocarbon Solvents. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:14582-14596. [PMID: 34878282 DOI: 10.1021/acs.langmuir.1c02133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The performance of organic friction modifiers (OFMs) depends on their ability to adsorb onto surfaces and form protective monolayers. Understanding the relationship between OFM concentration in the base oil and the resulting surface coverage is important for improving lubricant formulations. Here, we use molecular dynamics (MD) simulations to study the adsorption of three OFMs─stearic acid (SA), glycerol monoostearate (GMS), and glycerol monooleate (GMO)─onto a hematite surface from two hydrocarbon solvents─n-hexadecane and poly(α-olefin) (PAO). We calculate the potential of mean force of the adsorption process using the adaptive biasing force algorithm, and the adsorption strength increases in the order SA < GMS < GMO. We estimate the minimum area occupied by OFM molecules on the surface using annealing MD simulations and obtained a similar hard-disk area for GMS and GMO but a lower value for SA. Using the MD results, we determine the adsorption isotherms using the molecular thermodynamic theory (MTT), which agree well with one previous experimental data set for SA on hematite. For two other experimental data sets for SA, lateral interactions between surfactant molecules need to be accounted for within the MTT framework. SA forms monolayers with lower surface coverage than GMO and GMS at low concentrations but also has the highest plateau coverage. We validate the adsorption energies from the MD simulations using high-frequency reciprocating rig friction experiments with different concentrations of the OFMs in PAO. For OFMs with saturated tailgroups (SA and GMS), we obtain good agreement between the simulations and the experiments. The results deviate for OFMs containing Z-unsaturated tailgroups (GMO) due to the additional steric hindrance, which is not accounted for in the current simulation framework. This study demonstrates that MD simulations, alongside MTT, are an accurate and efficient tool to predict adsorption isotherms at solid-liquid interfaces.
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Affiliation(s)
- Pablo Navarro Acero
- Nextmol (Bytelab Solutions SL), Carrer de Roc Boronat 117, 08 018 Barcelona, Spain
- Barcelona Supercomputing Center (BSC-CNS), Plaça Eusebi Güell, 1-3, 08 034 Barcelona, Spain
| | - Stephan Mohr
- Nextmol (Bytelab Solutions SL), Carrer de Roc Boronat 117, 08 018 Barcelona, Spain
- Barcelona Supercomputing Center (BSC-CNS), Plaça Eusebi Güell, 1-3, 08 034 Barcelona, Spain
| | - Marco Bernabei
- Repsol Technology Lab, DC Technology & Corporate Venturing, Agustín de Betancourt s/n, 28 935 Mostoles, Madrid, Spain
| | - Carlos Fernández
- Repsol Technology Lab, DC Technology & Corporate Venturing, Agustín de Betancourt s/n, 28 935 Mostoles, Madrid, Spain
| | - Beatriz Domínguez
- Repsol Technology Lab, DC Technology & Corporate Venturing, Agustín de Betancourt s/n, 28 935 Mostoles, Madrid, Spain
| | - James P Ewen
- Department of Mechanical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
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6
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Extraction of Chlorobenzenes and PCBs from Water by ZnO Nanoparticles. Processes (Basel) 2021. [DOI: 10.3390/pr9101764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Metal oxide nanoparticles have great potential for selective adsorption and catalytic degradation of contaminants from aqueous solutions. In this study, we employ mass spectrometry and molecular dynamics simulations to better understand the chemical and physical mechanisms determining the affinity of chlorobenzenes and polychlorinated biphenyls (PCBs) for zinc oxide nanoparticles (ZnO NPs). The experiments and simulations both demonstrate that the adsorption coefficients for chlorobenzenes increase steadily with the number of chlorine atoms, while, for PCBs, the relation is more complex. The simulations link this complexity to chlorine atoms at ortho positions hindering coplanar conformations. For a given number of chlorine atoms, the simulations predict decreasing adsorption affinity with increasing numbers of ortho substitutions. Consequently, the simulations predict that some of the highest adsorption affinities for ZnO NPs are exhibited by dioxin-like PCBs, suggesting the possibility of selective sequestration of these most acutely toxic PCBs. Remarkably, the experiments show that the PCB adsorption coefficients of ZnO NPs with diameters ≤ 80 nm exceed those of a soil sample by 5–7 orders of magnitude, meaning that a single gram of ZnO NPs could sequester low levels of PCB contamination from as much as a ton of soil.
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Comer J, Bassette M, Burghart R, Loyd M, Ishiguro S, Azhagiya Singam ER, Vergara-Jaque A, Nakashima A, Suzuki K, Geisbrecht BV, Tamura M. Beta-1,3 Oligoglucans Specifically Bind to Immune Receptor CD28 and May Enhance T Cell Activation. Int J Mol Sci 2021; 22:ijms22063124. [PMID: 33803858 PMCID: PMC8003162 DOI: 10.3390/ijms22063124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022] Open
Abstract
Beta glucans are known to have immunomodulatory effects that mediated by a variety of mechanisms. In this article, we describe experiments and simulations suggesting that beta-1,3 glucans may promote activation of T cells by a previously unknown mechanism. First, we find that treatment of a T lymphoblast cell line with beta-1,3 oligoglucan significantly increases mRNA levels of T cell activation-associated cytokines, especially in the presence of the agonistic anti-CD3 antibody. This immunostimulatory activity was observed in the absence of dectin-1, a known receptor for beta-1,3 glucans. To clarify the molecular mechanism underlying this activity, we performed a series of molecular dynamics simulations and free-energy calculations to explore the interaction of beta-1,3 oligoglucans with potential immune receptors. While the simulations reveal little association between beta-1,3 oligoglucan and the immune receptor CD3, we find that beta-1,3 oligoglucans bind to CD28 near the region identified as the binding site for its natural ligands CD80 and CD86. Using a rigorous absolute binding free-energy technique, we calculate a dissociation constant in the low millimolar range for binding of 8-mer beta-1,3 oligoglucan to this site on CD28. The simulations show this binding to be specific, as no such association is computed for alpha-1,4 oligoglucan. This study suggests that beta-1,3 glucans bind to CD28 and may stimulate T cell activation collaboratively with T cell receptor activation, thereby stimulating immune function.
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Affiliation(s)
- Jeffrey Comer
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
- Correspondence: (J.C.); (M.T.)
| | - Molly Bassette
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
| | - Riley Burghart
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
| | - Mayme Loyd
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
| | - Susumu Ishiguro
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
| | - Ettayapuram Ramaprasad Azhagiya Singam
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
- Molecular Graphics and Computation Facility, College of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Ariela Vergara-Jaque
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, Talca 3460000, Chile
| | | | - Kengo Suzuki
- Euglena Co., Ltd., Tokyo 108-0014, Japan; (A.N.); (K.S.)
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA;
| | - Masaaki Tamura
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
- Correspondence: (J.C.); (M.T.)
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Abstract
Understanding peptide-surface interactions is crucial for programming self-assembly of peptides at surfaces and in realizing their applications, such as biosensors and biomimetic materials. In this study, we developed insights into the dependence of a residue's interaction with a surface on its neighboring residue in a tripeptide using molecular dynamics simulations. This knowledge is integral for designing rational mutations to control peptide-surface complexes. Using graphene as our model surface, we estimated the free energy of adsorption (ΔAads) and extracted predominant conformations of 26 tripeptides with the motif LNR-CR-Gly, where LNR and CR are variable left-neighboring and central residues, respectively. We considered a combination of strongly adsorbing (Phe, Trp, and Arg) and weakly adsorbing (Ala, Val, Leu, Ser, and Thr) amino acids on graphene identified in a prior study to form the tripeptides. Our results indicate that ΔAads of a tripeptide cannot be estimated as the sum of ΔAads of each residue indicating that the residues in a tripeptide do not behave as independent entities. We observed that the contributions from the strongly adsorbing amino acids were dominant, which suggests that such residues could be used for strengthening peptide-graphene interactions irrespective of their neighboring residues. In contrast, the adsorption of weakly adsorbing central residues is dependent on their neighboring residues. Our structural analysis revealed that the dihedral angles of LNR are more correlated with that of CR in the adsorbed state than in bulk state. Together with ΔAads trends, this implies that different backbone structures of a given CR can be accessed for a similar ΔAads by varying the LNR. Therefore, incorporation of context effects in designing mutations can lead to desired peptide structure at surfaces. Our results also emphasize that these cooperative effects in ΔAads and structure are not easily predicted a priori. The collective results have applications in guiding rational mutagenesis techniques to control orientation of peptides at surfaces and in developing peptide structure prediction algorithms in adsorbed state from its sequence.
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Affiliation(s)
- Siva Dasetty
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Sapna Sarupria
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
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Bavi O, Ghadak F. Possibility of making aerophobic surfaces by nanoprotrusions: an investigation of atomic-scale friction of the air-solid interfaces. Phys Chem Chem Phys 2021; 23:4711-4717. [PMID: 33595567 DOI: 10.1039/d0cp06404a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Emerging, new atomic-scale fabrication methods have enabled scientists to design and manufacture nanostructured devices for the investigation and application of nanoscale regimes in fluid mechanics. One of the most significant goals in designing these devices is finding an efficient way to reduce the friction of the fluid flow in/on the nanochannels and surfaces. Herein, a set of surfaces with various engineered nanoscale roughnesses (nanoprotrusions) was designed. In addition, a triple point charge/mass model of air molecules was developed based on realistic physicochemical characteristics. All-atom, non-equilibrium molecular dynamics simulations were employed to evaluate the atomic interaction of airflow/solid surfaces for various conditions, such as different fluid velocity, surface material, and geometry of nanoscale roughness. Our results show that there is a significant difference (more than six times) between the fluid/surface interaction energy for graphene and silicone surfaces. However, the interaction energy of the fluid/solid interface does not vary for atomic-scale roughnesses (<10 nm). Our results indicate that for solid surfaces coated by few-layer graphene in high Reynolds (supersonic) regimes, the outer graphene layers are confronted with delamination due to the high shear stress of airflow, which is a serious problem for the structure's strength and durability. We suggest that our computational findings shed light on designing aerophobic surface coatings in a wide range of applications, from nanodevices to conventional aircraft.
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Affiliation(s)
- Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876, Iran.
| | - Farhad Ghadak
- Qadr Aerodynamic Research Center, Imam Hossein University, P.O. Box 14588-89694, Tehran, Iran
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10
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H H, Mallajosyula SS. Polarization influences the evolution of nucleobase-graphene interactions. NANOSCALE 2021; 13:4060-4072. [PMID: 33595570 DOI: 10.1039/d0nr08796c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In recent years, graphene has attracted attention from researchers as an atomistically thin solid state material for the study on the self-assembly of nucleobases. Non-covalent interactions between nucleobases and graphene sheets play a fundamental role in understanding the self-assembly of nucleobases on the graphene sheet. A fundamental understanding of the effect of molecular polarizability on these non-covalent interactions between the nucleobases and the underlying graphene sheet is absent in the literature. In this paper, we present the results from polarizable molecular dynamics simulation studies to understand the effect of polarization on the strength of non-covalent interactions. To this end, we report the development of Drude parameters for describing the polarizable graphene sheet. The developed parameters were used to study the self-aggregation phenomenon of nucleobases on a graphene support. We observe a significant change in the interaction patterns upon the inclusion of polarization into the system, with polarizable simulations yielding results that closely resemble the experimental studies. Two of the key observations were the probability of the formation of stacks in guanine-rich systems, and the spontaneous formation of H-bonded structures over the graphene sheet, which allude to the importance of the DNA sequence and composition. Both these effects were not observed in the additive simulations. The present study sheds light on the effect of polarization on the adsorption of DNA nucleobases on a graphene sheet, but the methodology can be extended to include a variety of small molecules and complete DNA strands.
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Affiliation(s)
- Hemanth H
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India-382355.
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India-382355.
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11
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Dasari S, Mallik BS. Conformational Free-Energy Landscapes of Alanine Dipeptide in Hydrated Ionic Liquids from Enhanced Sampling Methods. J Phys Chem B 2020; 124:6728-6737. [PMID: 32666802 DOI: 10.1021/acs.jpcb.0c05629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Understanding the interaction of the ionic liquid (IL) with protein is vital to find the origin of the conformational changes of proteins in these alternative solvents. Here, we performed biased molecular dynamics simulations of alanine dipeptide (ADP), a widely used model for protein backbone structure, in water and two hydrated ionic liquids (ILs): 80% (w/w) 1-ethyl-3-methylimidazolium acetate ([EMIm][Ac]) and 80% (w/w) choline dihydrogen phosphate ([Cho][DHP]). We employed three different biasing methods, metadynamics (metaD), well-tempered metadynamics (WT-metaD), and adaptive biasing force (ABF), to construct the free-energy landscapes of the ADP conformations using the backbone dihedral angles (ϕ and ψ) as the collective variables. The calculations were also performed in water; the free-energy landscapes of ADP in water obtained from three methods are similar and agree well with the previously reported results. In hydrated [EMIm][Ac], α-planar conformation emerges as a minimum, which is comparable to that of α and β conformations corresponding to α-helix and β-sheet-like conformations of proteins. Investigation of corresponding conformations suggests that the imidazolium ring of [EMIm] cation is stacked with the amide bonds of ADP. Acetate anion makes hydrogen bonds with the amide hydrogens of the ADP. The amide-π stacking interaction is the driving force for α-planar conformation to become one of the minimum energy conformations in this IL, which destabilizes the protein conformation. However, α and β conformations are more stable in hydrated [Cho][DHP] compared to α-planar and β-planar conformations; therefore, this IL stabilizes the protein conformation. These findings are in good correlation with the previous study of proteins in these ILs. Our study helps to understand the interaction of proteins with the ionic entities and their stability in ILs.
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Affiliation(s)
- Sathish Dasari
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, Telangana, India
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12
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Denatured lysozyme-coated carbon nanotubes: a versatile biohybrid material. Sci Rep 2019; 9:16643. [PMID: 31719550 PMCID: PMC6851173 DOI: 10.1038/s41598-019-52701-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022] Open
Abstract
Carbon nanotubes (CNTs) are among the most versatile nanomaterials, but their exploitation is hindered by limited dispersibility, especially in aqueous solvents. Here, we show that AP-LYS, a highly cationic soluble derivative of denatured hen egg lysozyme, is a very effective tool for the unbundling and solubilisation of CNTs. AP-LYS proved to mediate the complete and stable dispersion of CNTs at protein: CNT ratios ≥1: 3 (w:w) in very mild conditions (10–20 minutes sonication in ammonium acetate buffer, pH 5.0). Electrophoretic mobility and ζ-potential measurements confirmed that dispersed CNTs were coated by the protein, whereas molecular docking was used to study the interactions between AP-LYS and CNTs. AP-LYS-coated CNTs proved to be a very effective microbial cell-flocculating agent with an efficiency similar to that of chitosan, one of the best available flocculating agents, thus suggesting that this hybrid could find industrial applications in the treatment of wastewaters contaminated by microbial cells, or to remove microbial cells after fermentation processes. Moreover, we exploited the low stability of AP-LYS-coated CNT dispersions in eukaryotic cell culture media to prepare scaffolds with an extracellular matrix-like rough surface for the cultivation of eukaryotic cells.
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Ishii Y, Yamamoto N, Matubayasi N, Zhang BW, Cui D, Levy RM. Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method. J Chem Theory Comput 2019; 15:2896-2912. [PMID: 30990682 DOI: 10.1021/acs.jctc.8b01309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A spatially resolved version of the density-functional method for solvation thermodynamics is presented by extending the free-energy functional previously established in the one-dimensional, energy representation and formulating a new expression in a mixed four-dimensional representation (three dimensions for position and one dimension for energy). The space was further divided into a set of discrete regions with respect to the relative position of a solvent molecule from the solute, and the spatially decomposed energetics of solvation were analyzed for small molecules with a methyl, amine, or hydroxyl group and alanine dipeptide in solvent water. It was observed that the density of the solvation free energy is weakly dependent on the solute site in the excluded-volume region and is distinctively favorable in the first shells of the solute atoms that can readily form hydrogen bonds with water. The solvent-reorganization term reduces faster with the separation from the solute than the direct interaction between the solute and solvent, and the latter governs the energetics in the second shell and outer regions. The sum of the contributions to the free energy from the excluded volume and first shell was found to deviate significantly from the total sum over all the regions, implying that the solvation free energy is not spatially localized near the solute in a quantitative sense. Still, a local description was shown to be valid as confirmed by the correlation of the total value of free energy with the corresponding value obtained by integrating the free-energy density to the second shell. The theoretical framework developed in the present work to spatially decompose the solvation free energy can thus be useful to identify stabilizing or destabilizing regions of solvent proximate to a solute and to analyze the role that the displacement of interfacial water plays in the thermodynamics of molecular association.
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Affiliation(s)
- Yoshiki Ishii
- Division of Chemical Engineering, Graduate School of Engineering Science , Osaka University , Toyonaka , Osaka 560-8531 , Japan
| | - Naoki Yamamoto
- Division of Chemical Engineering, Graduate School of Engineering Science , Osaka University , Toyonaka , Osaka 560-8531 , Japan
| | - 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
| | - 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
| | - 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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Liu S, Comer J, van Duin ACT, van Duin DM, Liu B, Edgar JH. Predicting the preferred morphology of hexagonal boron nitride domain structure on nickel from ReaxFF-based molecular dynamics simulations. NANOSCALE 2019; 11:5607-5616. [PMID: 30860524 DOI: 10.1039/c8nr10291k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
An understanding of the nucleation and growth of hexagonal boron nitride (hBN) on nickel substrates is essential to its development as a functional material. In particular, fundamental insights into the formation of the hexagonal lattices with alternating boron (B) and nitrogen (N) atoms could be exploited to control hBN lattice morphologies for targeted applications. In this study, the preferred shapes and edge configurations of atomically smooth hBN on Ni(111) were investigated using molecular dynamics (MD) simulations, along with reactive force field (ReaxFF) developed to represent the Ni/B/N system and the lattice-building B-N bond formation. The obtained hBN lattices, from different B : N feed ratios, are able to confirm that hBN domain geometries can indeed be tuned by varying thermodynamic parameters (i.e., chemical potentials of N and B) - a finding that has only been predicted using quantum mechanical theories. Here, we also showed that the nitrogen fed to the system plays a more crucial role in dictating the size of hBN lattices. With an increase of the relative N content, the simulated hBN domain shapes also transition from equilateral triangles to hexagons, again, consistent with the anticipation based on Density Functional Theory (DFT) calculations. Hence, a plausible approach to acquire a desired hBN nanostructure depends on careful control over the synthesis conditions, which now can benefit from reliable molecular simulations.
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Affiliation(s)
- Song Liu
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS 66506, USA.
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Dasetty S, Barrows JK, Sarupria S. Adsorption of amino acids on graphene: assessment of current force fields. SOFT MATTER 2019; 15:2359-2372. [PMID: 30789189 DOI: 10.1039/c8sm02621a] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We compare the free energies of adsorption (ΔAads) and the structural preferences of amino acids on graphene obtained using the non-polarizable force fields-Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid-graphene interactions are favorable irrespective of the force field. While the magnitudes of ΔAads differ between the force fields, the relative free energy of adsorption across amino acids is similar for the studied force fields. ΔAads positively correlates with amino acid-graphene and negatively correlates with graphene-water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that the force fields studied will give qualitatively consistent relative strength of adsorption across proteins but different structural preferences in the graphene adsorbed state.
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Affiliation(s)
- Siva Dasetty
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA.
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Azhagiya Singam ER, Zhang Y, Magnin G, Miranda-Carvajal I, Coates L, Thakkar R, Poblete H, Comer J. Thermodynamics of Adsorption on Graphenic Surfaces from Aqueous Solution. J Chem Theory Comput 2018; 15:1302-1316. [DOI: 10.1021/acs.jctc.8b00830] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. R. Azhagiya Singam
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Yuntao Zhang
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Geraldine Magnin
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Ingrid Miranda-Carvajal
- Universidad Nacional de Colombia, sede Bogotá, Facultad de Ciencias, Departamento de Química, Carrera 30 No. 45-03, Bogotá 111321, Colombia
| | - Logan Coates
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Ravindra Thakkar
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
| | - Horacio Poblete
- Center for Bioinformatics and Molecular Simulation, Facultad de Ingeniería, Nucleo Científico Multidiciplinario-DI, Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Talca, 3460000 Talca, Chile
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802, United States
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Abstract
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Several apical iodide translocation
pathways have been proposed
for iodide efflux out of thyroid follicular cells, including a pathway
mediated by the sodium-coupled monocarboxylate transporter 1 (SMCT1),
which remains controversial. Herein, we evaluate structural and functional
similarities between SMCT1 and the well-studied sodium-iodide symporter
(NIS) that mediates the first step of iodide entry into the thyroid.
Free-energy calculations using a force field with electronic polarizability
verify the presence of a conserved iodide-binding pocket between the
TM2, TM3, and TM7 segments in hNIS, where iodide is coordinated by
Phe67, Gln72, Cys91, and Gln94. We demonstrate the mutation of residue
Gly93 of hNIS to a larger amino acid expels the side chain of a critical
tryptophan residue (Trp255) into the interior of the binding pocket,
partially occluding the iodide binding site and reducing iodide affinity,
which is consistent with previous reports associating mutation of
this residue with iodide uptake deficiency and hypothyroidism. Furthermore,
we find that the position of Trp255 in this hNIS mutant mirrors that
of Trp253 in wild-type hSMCT1, where a threonine (Thr91) occupies
the position homologous to that occupied by glycine in wild-type hNIS
(Gly93). Correspondingly, mutation of Thr91 to glycine in hSMCT1 makes
the pocket structure more like that of wild-type hNIS, increasing
its iodide affinity. These results suggest that wild-type hSMCT1 in
the inward-facing conformation may bind iodide only very weakly, which
may have implications for its ability to transport iodide.
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Affiliation(s)
- Ariela Vergara-Jaque
- Center for Bioinformatics and Molecular Simulation, Universidad de Talca , 2 Norte 685, Talca 3460000, Chile.,Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Kansas State University , Manhattan, Kansas 66506, United States
| | - Peying Fong
- Department of Anatomy and Physiology, Kansas State University College of Veterinary Medicine , Manhattan, Kansas 66506, United States
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Kansas State University , Manhattan, Kansas 66506, United States.,Department of Anatomy and Physiology, Kansas State University College of Veterinary Medicine , Manhattan, Kansas 66506, United States
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