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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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2
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Tewari M, Pareek P, Kumar S. Correlating Amino Acid Interaction with Graphene-Based Materials Regulating Cell Function. J Indian Inst Sci 2022. [DOI: 10.1007/s41745-021-00272-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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3
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Benková Z, Cordeiro MNDS. Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene. MATERIALS TODAY. CHEMISTRY 2021; 22:100572. [PMID: 34485782 PMCID: PMC8405511 DOI: 10.1016/j.mtchem.2021.100572] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 05/14/2023]
Abstract
Spike glycoprotein of the SARS-CoV-2 virus and its structure play a crucial role in the infections of cells containing angiotensin-converting enzyme 2 (ACE2) as well as in the interactions of this virus with surfaces. Protection against viruses and often even their deactivation is one of the great varieties of graphene applications. The structural changes of the non-glycosylated monomer of the spike glycoprotein trimer (denoted as S-protein in this work) triggered by its adsorption onto graphene at the initial stage are investigated by means of atomistic molecular dynamics simulations. The adsorption of the S-protein happens readily during the first 10 ns. The shape of the S-protein becomes more prolate during the adsorption, but this trend, albeit less pronounced, is observed also for the freely relaxing S-protein in water. The receptor-binding domain (RBD) of the free and adsorbed S-protein manifests itself as the most rigid fragment of the whole S-protein. The adsorption even enhances the rigidity of the whole S-protein as well as its subunits. Only one residue of the RBD involved in the specific interactions with ACE2 during the cell infection is involved in the direct contact of the adsorbed S-protein with the graphene. The new intramolecular hydrogen bonds formed during the S-protein adsorption replace the S-protein-water hydrogen bonds; this trend, although less apparent, is observed also during the relaxation of the free S-protein in water. In the initial phase, the secondary structure of the RBD fragment specifically interacting with ACE2 receptor is not affected during the S-protein adsorption onto the graphene.
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Affiliation(s)
- Z Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia
| | - M N D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, University of Porto, Rua Do Campo Alegre 687, 4168-007 Porto, Portugal
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4
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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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5
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Awuah JB, Walsh TR. Side-chain effects on the co-existence of emergent nanopatterns in amino acid adlayers on graphene. NANOSCALE 2020; 12:13662-13673. [PMID: 32568329 DOI: 10.1039/d0nr01333a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The spontaneous tendency of amino acid adlayers to self-assemble into ordered patterns on non-reactive surfaces is thought to be chiefly influenced by amino acid termination state. Experiments have shown that different side chains can produce different patterns, with a distinction drawn between side chains that can support hydrogen bonds or electrostatic interactions, and those that are hydrophobic. However, as is demonstrated in this work, this distinction is not clear cut, implying that there is currently no way to predict in advance what type of pattern will be formed. Here, we use molecular dynamics simulations of amino acid adlayers in neutral, zwitterion, and neutral-zwitterion states for two types of amino acids, either histidine or alanine, adsorbed at the in-vacuo graphene interface. In contrast to earlier studies on adlayers of tryptophan and methionine on graphene that reveal the presence of only a single type of pattern motif, the canonical dimer row, here we find that emergent patterns of histidine and alanine adlayers supported the co-existence of several different types of motifs, influenced by the different side-chain characteristics. For alanine, the compact side-chain does not support hydrogen bonding and engages weakly with the surface, leading to the emergence of a new dimer row configuration in addition to the canonical dimer row motif. On the contrary, for histidine, the side-chain supports hydrogen bonding, leading to the emergence of a dimer row motif different from the canonical dimer row, co-existing with several different monomer row motifs. On this basis, we propose that emergent canonical dimer row patterns are more likely for amino acids with side-chains that are non-compact and that also lack extensive hydrogen bonding capacity, and that engage strongly with the underlying substrate. These findings provide a fundamental basis to rationally guide the design of desired self-assembled nanostructures on planar surfaces.
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Affiliation(s)
- Joel B Awuah
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia.
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6
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Awuah JB, Walsh TR. Predictions of Pattern Formation in Amino Acid Adlayers at the In Vacuo Graphene Interface: Influence of Termination State. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1903403. [PMID: 31663292 DOI: 10.1002/smll.201903403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Controlled self-assembly of biomolecules on graphene offers a pathway for realizing its full potential in biological applications. Microscopy has revealed the self-assembly of amino acid adlayers into dimer rows on nonreactive substrates. However, neither the spontaneous formation of these patterns, nor the influence of amino acid termination state on the formation of patterns has been directly resolved to date. Molecular dynamics simulations, with the ability to reveal atomic level details and exert full control over the termination state, are used here to model initially disordered adlayers of neutral, zwitterionic, and neutral-zwitterionic mixtures for two types of amino acids, tryptophan and methionine, adsorbed on graphene in vacuo. The simulations of the zwitterion-containing adlayers exhibit the spontaneous emergence of dimer row ordering, mediated by charge-driven intermolecular interactions. In contrast, adlayers containing only neutral species do not assemble into ordered patterns. It is also found that the presence of trace amounts of water reduces the interamino acid interactions in the adlayers, but does not induce or disrupt pattern formation. Overall, the findings reveal the balance between the lateral interamino acid interactions and amino acid-graphene interactions, providing foundational insights for ultimately realizing the predictable pattern formation of biomolecules adsorbed on unreactive surfaces.
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Affiliation(s)
- Joel B Awuah
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3216, Australia
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3216, Australia
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7
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Srivastava R. Interactions, electronic and optical properties of nanographene–peptide complexes: a theoretical study. RSC Adv 2020; 10:38654-38662. [PMID: 35517564 PMCID: PMC9057264 DOI: 10.1039/d0ra07961h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022] Open
Abstract
We studied the interaction of planar phenylalanine (phe), tryptophan (try), tyrosine (tyr); amide asparagine (asn) and glutamine (gln); arginine (arg) side-chains, charged histidine (his-c) and charged lysine (lys-c) side-chains on a nanographene (g) surface by Density Functional theory (DFT) and Time Dependent Density Functional Theory (TDDFT). The occupied number of states by the system at each energy level and relative contribution of a particular atom/orbital has been studied by Density of States (DOS) and Partial Density of States (PDOS) respectively. Atom-in Molecules (AIM) analysis and non-covalent interaction (NCI) PLOT are used to study the interactions in these complexes. The absorption spectra and HOMO–LUMO (HL) gaps are quantitatively analysed to study the correlation between the optical properties of the studied complexes. The HL gap of peptides is larger than the HL gap of graphene–peptide complexes, indicating strong interactions. All the peptides interact from the above the nanographene surfaces. garg, glys-c, gtry and gtyr complexes have smaller bond distance as compared to gasn, ggln, ghis-c and gphe complexes. AIM analysis and (NCI) PLOT showed noncovalent interactions for these complexes. TDDFT calculations indicated the applicability of these complexes as biosensors. We studied interactions of planar phenylalanine, tryptophan, tyrosine; amide asparagine and glutamine; arginine side-chains, charged histidine and charged lysine side-chains on a nanographene surface by density functional theory and time dependent density functional theory.![]()
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Affiliation(s)
- Ruby Srivastava
- CSIR-Centre for Cellular and Molecular Biology
- Hyderabad
- India
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8
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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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9
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Tran DP, Lam VT, Tran TL, Nguyen TNS, Thi Tran HT. In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment. Phys Chem Chem Phys 2018; 20:19240-19249. [PMID: 29989136 DOI: 10.1039/c8cp01886c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Bombyx mori fibroin has been widely used since a long time ago and has become a popular material. Here, we carry out a molecular dynamics simulation-based docking simulation of a small fragment of graphene in order to seek the best binding position on the N-termini domain of Bombyx mori fibroin. We report the best binding position, of which binding free energy falls at -54.8 kJ mol-1, indicating the strong binding. The further analysis of the binding pathway shows that this position is selective for single layered graphene rather than multi-layered graphene within our limited simulation times. Via comparing the RAMAN spectra of the corresponding binding pose of atomic clusters, we report the change in the bands compared with free standing graphene fragments, implying the change in molecular orbitals.
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Affiliation(s)
- Duy Phuoc Tran
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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10
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Hughes ZE, Walsh TR. Probing nano-patterned peptide self-organisation at the aqueous graphene interface. NANOSCALE 2017; 10:302-311. [PMID: 29210426 DOI: 10.1039/c7nr06441a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The peptide sequence GrBP5, IMVTESSDYSSY, is found experimentally to bind to graphene, and ex situ atomic force microscopy indicates the formation of an ordered over-layer on graphite. However, under aqueous conditions neither the molecular conformations of the adsorbed peptide chains, nor the molecular-level spatial ordering of the over-layer, has been directly resolved. Here, we use advanced molecular dynamics simulations of GrBP5, and related mutant sequences, to elucidate the adsorbed structures of both the peptide and the adsorbed peptide over-layer at the aqueous graphene interface. In agreement with a previous hypothesis, we find GrBP5 binds at the aqueous graphene interface chiefly via the tyrosine-rich C-terminal region. Our simulations of the adsorbed peptide over-layers reveal that the peptide chains form an aggregate that does not evolve further into ordered patterns. Instead, we find that the inter-chain interactions are driven by hydrogen bonding and charge-charge interactions that are not sufficiently specific to support pattern formation. Overall, we suggest that the experimentally-observed over-layer pattern may be due to the drying of the sample, and may not be prevalent at the solvated interface. However, our simulations indicate sequence modifications of GrBP5 to promote over-layer ordering under aqueous conditions.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia.
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11
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Adsorption patterns of aromatic amino acids on monolayer MoS 2 and Au-modified MoS 2 surfaces: A first-principles study. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Zou X, Wei S, Jasensky J, Xiao M, Wang Q, Brooks Iii CL, Chen Z. Molecular Interactions between Graphene and Biological Molecules. J Am Chem Soc 2017; 139:1928-1936. [PMID: 28092440 DOI: 10.1021/jacs.6b11226] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e.g., to detect analytes in solution). To control and characterize peptide behavior on a graphene surface in solution is difficult. Here we successfully probed the molecular interactions between two peptides (cecropin P1 and MSI-78(C1)) and graphene in situ and in real-time using sum frequency generation (SFG) vibrational spectroscopy and molecular dynamics (MD) simulation. We demonstrated that the distribution of various planar (including aromatic (Phe, Trp, Tyr, and His)/amide (Asn and Gln)/Guanidine (Arg)) side-chains and charged hydrophilic (such as Lys) side-chains in a peptide sequence determines the orientation of the peptide adsorbed on a graphene surface. It was found that peptide interactions with graphene depend on the competition between both planar and hydrophilic residues in the peptide. Our results indicated that part of cecropin P1 stands up on graphene due to an unbalanced distribution of planar and hydrophilic residues, whereas MSI-78(C1) lies down on graphene due to an even distribution of Phe residues and hydrophilic residues. With such knowledge, we could rationally design peptides with desired residues to manipulate peptide-graphene interactions, which allows peptides to adopt optimized structure and exhibit excellent activity for nanobio-technological applications. This research again demonstrates the power to combine SFG vibrational spectroscopy and MD simulation in studying interfacial biological molecules.
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Affiliation(s)
- Xingquan Zou
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Shuai Wei
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Joshua Jasensky
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Minyu Xiao
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Qiuming Wang
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Charles L Brooks Iii
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Zhan Chen
- Department of Chemistry, and ‡Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
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13
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Soleymani E, Alinezhad H, Darvish Ganji M, Tajbakhsh M. Enantioseparation performance of CNTs as chiral selectors for the separation of ibuprofen isomers: a dispersion corrected DFT study. J Mater Chem B 2017; 5:6920-6929. [PMID: 32264341 DOI: 10.1039/c7tb00755h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The enantioseparation of chiral drugs has been of great interest in the modern pharmaceutical industry since the majority of bioorganic compounds are chiral.
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Affiliation(s)
- Elham Soleymani
- Department of Organic Chemistry
- Faculty of Chemistry
- University of Mazandran
- Babolsar
- Iran
| | | | - Masoud Darvish Ganji
- Department of Nanochemistry
- Faculty of Pharmaceutical Chemistry
- Islamic Azad University
- Pharmaceutical Sciences Branch (IAUPS)
- Tehran
| | - Mahmood Tajbakhsh
- Department of Organic Chemistry
- Faculty of Chemistry
- University of Mazandran
- Babolsar
- Iran
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14
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Larijani HT, Jahanshahi M, Ganji MD, Kiani MH. Computational studies on the interactions of glycine amino acid with graphene, h-BN and h-SiC monolayers. Phys Chem Chem Phys 2017; 19:1896-1908. [DOI: 10.1039/c6cp06672k] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In the present work, the adsorption of glycine amino acid and its zwitterionic form onto three different hexagonal sheets, namely graphene, boron-nitride (h-BN) and silicon carbide (h-SiC), has been investigated within the framework of density functional theory (DFT) calculations.
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Affiliation(s)
- H. Tavassoli Larijani
- Nanotechnology Research Institute
- School of Chemical Engineering
- Babol University of Technology
- Babol
- Iran
| | - M. Jahanshahi
- Nanotechnology Research Institute
- School of Chemical Engineering
- Babol University of Technology
- Babol
- Iran
| | - M. Darvish Ganji
- Department of Nanochemistry
- Faculty of Pharmaceutical Chemistry
- Pharmaceutical Sciences Branch
- Islamic Azad University
- (IAUPS)
| | - M. H. Kiani
- Department of Electrical Engineering
- Faculty of Engineering
- University of Guilan
- Rasht
- Iran
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15
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DeBenedictis EP, Liu J, Keten S. Adhesion mechanisms of curli subunit CsgA to abiotic surfaces. SCIENCE ADVANCES 2016; 2:e1600998. [PMID: 28138525 PMCID: PMC5262458 DOI: 10.1126/sciadv.1600998] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 10/13/2016] [Indexed: 05/24/2023]
Abstract
Curli fibers are functional amyloids that play a key role in biofilm structure and adhesion to various surfaces. Strong bioinspired adhesives comprising curli fibers have recently been created; however, the mechanisms curli uses to attach onto abiotic surfaces are still uncharacterized. Toward a materials-by-design approach for curli-based adhesives and multifunctional materials, we examine curli subunit adsorption onto graphene and silica surfaces through atomistic simulation. We find that both structural features and sequence influence adhesive strength, enabling the CsgA subunit to adhere strongly to both polar and nonpolar surfaces. Specifically, flexible regions facilitate adhesion to both surfaces, charged and polar residues (Arg, Lys, and Gln) enable strong interactions with silica, and six-carbon aromatic rings (Tyr and Phe) adsorb strongly to graphene. We find that adsorption not only lowers molecular mobility but also leads to loss of secondary structure, factors that must be well balanced for effective surface attachment. Both events appear to propagate through the CsgA structure as correlated motion between clusters of residues, often H-bonded between rows on adjacent β strands. To quantify this, we present a correlation analysis approach to detecting collective motion between residue groups. We find that certain clusters of residues have a higher impact on the stability of the rest of the protein structure, often polar and bulky groups within the helix core. These findings lend insight into bacterial adhesion mechanisms and reveal strategies for theory-driven design of engineered curli fibers that harness point mutations and conjugates for stronger adhesion.
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Affiliation(s)
- Elizabeth P. DeBenedictis
- Departments of Civil and Environmental Engineering and Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Jenny Liu
- Northwestern University Medical Scientist Training Program, Northwestern University, Evanston, IL 60208, USA
| | - Sinan Keten
- Departments of Civil and Environmental Engineering and Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA
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16
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Paredes JI, Villar-Rodil S. Biomolecule-assisted exfoliation and dispersion of graphene and other two-dimensional materials: a review of recent progress and applications. NANOSCALE 2016; 8:15389-413. [PMID: 27518874 DOI: 10.1039/c6nr02039a] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Direct liquid-phase exfoliation of layered materials by means of ultrasound, shear forces or electrochemical intercalation holds enormous promise as a convenient, cost-effective approach to the mass production of two-dimensional (2D) materials, particularly in the form of colloidal suspensions of high quality and micrometer- and submicrometer-sized flakes. Of special relevance due to environmental and practical reasons is the production of 2D materials in aqueous medium, which generally requires the use of certain additives (surfactants and other types of dispersants) to assist in the exfoliation and colloidal stabilization processes. In this context, biomolecules have received, in recent years, increasing attention as dispersants for 2D materials, as they provide a number of advantages over more conventional, synthetic surfactants. Here, we review research progress in the use of biomolecules as exfoliating and dispersing agents for the production of 2D materials. Although most efforts in this area have focused on graphene, significant advances have also been reported with transition metal dichalcogenides (MoS2, WS2, etc.) or hexagonal boron nitride. Particular emphasis is placed on the specific merits of different types of biomolecules, including proteins and peptides, nucleotides and nucleic acids (RNA, DNA), polysaccharides, plant extracts and bile salts, on their role as efficient colloidal dispersants of 2D materials, as well as on the potential applications that have been explored for such biomolecule-exfoliated materials. These applications are wide-ranging and encompass the fields of biomedicine (photothermal and photodynamic therapy, bioimaging, biosensing, etc.), energy storage (Li- and Na-ion batteries), catalysis (e.g., catalyst supports for the oxygen reduction reaction or electrocatalysts for the hydrogen evolution reaction), or composite materials. As an incipient area of research, a number of knowledge gaps, unresolved issues and novel future directions remain to be addressed for biomolecule-exfoliated 2D materials, which will be discussed in the last part of this review.
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Affiliation(s)
- J I Paredes
- Instituto Nacional del Carbón, INCAR-CSIC, Apartado 73, 33080 Oviedo, Spain.
| | - S Villar-Rodil
- Instituto Nacional del Carbón, INCAR-CSIC, Apartado 73, 33080 Oviedo, Spain.
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17
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Dragneva N, Rubel O, Floriano WB. Molecular Dynamics of Fibrinogen Adsorption onto Graphene, but Not onto Poly(ethylene glycol) Surface, Increases Exposure of Recognition Sites That Trigger Immune Response. J Chem Inf Model 2016; 56:706-20. [DOI: 10.1021/acs.jcim.5b00703] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Nadiya Dragneva
- Thunder Bay Regional Research Institute, 290 Munro Street, Thunder Bay, Ontario P7A 7T1, Canada
- Biotechnology
Ph.D. Program, Faculty of Science and Environment Studies, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada
| | - Oleg Rubel
- Thunder Bay Regional Research Institute, 290 Munro Street, Thunder Bay, Ontario P7A 7T1, Canada
- Department
of Materials Science and Engineering, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Wely B. Floriano
- Thunder Bay Regional Research Institute, 290 Munro Street, Thunder Bay, Ontario P7A 7T1, Canada
- Biotechnology
Ph.D. Program, Faculty of Science and Environment Studies, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada
- Department
of Chemistry, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada
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18
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Mahdavi M, Rahmani F, Nouranian S. Molecular simulation of pH-dependent diffusion, loading, and release of doxorubicin in graphene and graphene oxide drug delivery systems. J Mater Chem B 2016; 4:7441-7451. [DOI: 10.1039/c6tb00746e] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We investigated the pH-dependent energetics and mechanisms of doxorubicin (DOX) drug adsorption on graphene oxide nanocarriers using molecular dynamics simulation.
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Affiliation(s)
- Mina Mahdavi
- Department of Chemical Engineering
- The University of Mississippi, University
- MS 38677
- USA
| | - Farzin Rahmani
- Department of Chemical Engineering
- The University of Mississippi, University
- MS 38677
- USA
| | - Sasan Nouranian
- Department of Chemical Engineering
- The University of Mississippi, University
- MS 38677
- USA
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19
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Timón V, Gálvez Ó, Maté B, Tanarro I, Herrero VJ, Escribano R. Theoretical model of the interaction of glycine with hydrogenated amorphous carbon (HAC). Phys Chem Chem Phys 2015; 17:28966-76. [PMID: 26456640 DOI: 10.1039/c5cp03938j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A theoretical model of hydrogenated amorphous carbon (HAC) is developed and applied to study the interaction of glycine with HAC surfaces at astronomical temperatures. Two models with different H content are tried for the HAC surface. The theory is applied at the Density Functional Theory (DFT) level, including a semiempirical dispersion correlation potential, d-DFT or Grimme DFT-D2. The level of theory is tested on glycine adsorption on a Si(001) surface. Crystalline glycine is also studied in its two stable phases, α and β, and the metastable γ phase. For the adsorption on Si or HAC surfaces, molecular glycine is introduced in the neutral and zwitterionic forms, and the most stable configurations are searched. All theoretical predictions are checked against experimental observations. HAC films are prepared by plasma enhanced vapor deposition at room temperature. Glycine is deposited at 20 K into a high vacuum, cold temperature chamber, to simulate astronomical conditions. Adsorption takes place through the acidic group COO(-) and when several glycine molecules are present, they form H-bond chains among them. Comparison between experiments and predictions suggests that a possible way to improve the theoretical model would require the introduction of aliphatic chains or a polycyclic aromatic core. The lack of previous models to study the interaction of amino-acids with HAC surfaces provides a motivation for this work.
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Affiliation(s)
- Vicente Timón
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Óscar Gálvez
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Belén Maté
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Isabel Tanarro
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Víctor J Herrero
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Rafael Escribano
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
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20
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Iwashita K, Shiraki K, Ishii R, Tanaka T, Hirano A. Liquid Chromatographic Analysis of the Interaction between Amino Acids and Aromatic Surfaces Using Single-Wall Carbon Nanotubes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015. [PMID: 26208035 DOI: 10.1021/acs.langmuir.5b02500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins have nonspecific adsorption capacities for solid surfaces. Although the nonspecific adsorption capacities are generally understood to be related to the hydrophobicity or charge density of the surfaces, little is known at the amino acid level about the interaction between proteins and polyaromatic surfaces such as carbon nanotubes, which have recently been used for biotechnology applications. In this study, we investigated the interaction between proteinogenic amino acids and carbon nanotubes using high-performance liquid chromatography on silica matrices coated by single-wall carbon nanotubes (SWCNTs). Among the amino acids used in this study, tryptophan, tyrosine, and phenylalanine showed exceptional affinity for the matrices. The characteristic affinities of these amino acids were ascribed to their unique interactions with the large polyaromatic surfaces of the SWCNTs. These results are useful for understanding and controlling protein adsorption onto aromatic surfaces.
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Affiliation(s)
- Kazuki Iwashita
- †Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kentaro Shiraki
- †Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Rieko Ishii
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Takeshi Tanaka
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Atsushi Hirano
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
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21
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De Leo F, Magistrato A, Bonifazi D. Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies. Chem Soc Rev 2015; 44:6916-53. [DOI: 10.1039/c5cs00190k] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Thiscritical reviewpresents a detailed overview of the chemico-physical principles ruling the non-covalent association between proteins and fullerene, carbon nanotubes and graphene towards the creation of fascinating and innovative hybrid materials for biotechnological applications.
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Affiliation(s)
- Federica De Leo
- Department of Chemistry and Namur Research College (NARC)
- University of Namur (UNamur)
- B-5000 Namur
- Belgium
| | - Alessandra Magistrato
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA)
- Trieste
- Italy
| | - Davide Bonifazi
- Department of Chemistry and Namur Research College (NARC)
- University of Namur (UNamur)
- B-5000 Namur
- Belgium
- Dipartimento di Scienze Chimiche e Farmaceutiche and INSTM UdR Trieste
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22
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Hughes ZE, Walsh TR. What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces. J Mater Chem B 2015; 3:3211-3221. [DOI: 10.1039/c5tb00004a] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Molecular dynamics simulations of the aqueous biomolecule–graphene interface have predicted the free energy of adsorption of amino acids and the structure of peptides.
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Affiliation(s)
- Zak E. Hughes
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Tiffany R. Walsh
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
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23
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Stauffer D, Dragneva N, Floriano WB, Mawhinney RC, Fanchini G, French S, Rubel O. An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water. J Chem Phys 2014; 141:044705. [DOI: 10.1063/1.4890503] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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24
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Sheikholeslami S, Pandey RB, Dragneva N, Floriano W, Rubel O, Barr SA, Kuang Z, Berry R, Naik R, Farmer B. Binding of solvated peptide (EPLQLKM) with a graphene sheet via simulated coarse-grained approach. J Chem Phys 2014; 140:204901. [DOI: 10.1063/1.4876716] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Nawrocki G, Cieplak M. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations. J Chem Phys 2014; 140:095101. [DOI: 10.1063/1.4866763] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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