201
|
Contribution of cryoelectron microscopy of vitreous sections to the understanding of biological membrane structure. Proc Natl Acad Sci U S A 2012; 109:8959-64. [PMID: 22615384 DOI: 10.1073/pnas.1200881109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Using cryoelectron microscopy of vitreous sections, we investigated in situ the ultrastructure of biological membranes, selected from several cell types for their diverse biological functions. Here we describe how to visualize the two membrane leaflets and tightly apposed membranes, lying as close as 1.1 nm apart, by tuning the imaging conditions. We show how defects in membrane stacks may be clues to resolving their structure. Details of membrane proteins are also resolved, as well as protein lattices with correlations between stacked membranes. Imaging the cell in its native hydrated state can now be done in the nanometer resolution range, which should open unique routes for investigating structure-function relationships.
Collapse
|
202
|
Feng J, Slocik JM, Sarikaya M, Naik RR, Farmer BL, Heinz H. Influence of the shape of nanostructured metal surfaces on adsorption of single peptide molecules in aqueous solution. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:1049-1059. [PMID: 22323430 DOI: 10.1002/smll.201102066] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Indexed: 05/31/2023]
Abstract
Self-assembly and function of biologically modified metal nanostructures depend on surface-selective adsorption; however, the influence of the shape of metal surfaces on peptide adsorption mechanisms has been poorly understood. The adsorption of single peptide molecules in aqueous solution (Tyr(12) , Ser(12) , A3, Flg-Na(3) ) is investigated on even {111} surfaces, stepped surfaces, and a 2 nm cuboctahedral nanoparticle of gold using molecular dynamics simulation with the CHARMM-METAL force field. Strong and selective adsorption is found on even surfaces and the inner edges of stepped surfaces (-20 to -60 kcal/mol peptide) in contrast to weaker and less selective adsorption on small nanoparticles (-15 to -25 kcal/mol peptide). Binding and selectivity appear to be controlled by the size of surface features and the extent of co-ordination of epitaxial sites by polarizable atoms (N, O, C) along the peptide chain. The adsorption energy of a single peptide equals a fraction of the sum of the adsorption energies of individual amino acids that is characteristic of surface shape, epitaxial pattern, and conformation constraints (often β-strand and random coil). The proposed adsorption mechanism is supported and critically evaluated by earlier sequence data from phage display, dissociation constants of small proteins as a function of nanoparticle size, and observed shapes of peptide-stabilized nanoparticles. Understanding the interaction of single peptides with shaped metal surfaces is a key step towards control over self-organization of multiple peptides on shaped metal surfaces and the assembly of superstructures from nanostructures.
Collapse
Affiliation(s)
- Jie Feng
- Department of Polymer Engineering, University of Akron, Akron, OH 44325-0301, USA
| | | | | | | | | | | |
Collapse
|
203
|
Patwardhan SV, Emami FS, Berry RJ, Jones SE, Naik RR, Deschaume O, Heinz H, Perry CC. Chemistry of aqueous silica nanoparticle surfaces and the mechanism of selective peptide adsorption. J Am Chem Soc 2012; 134:6244-56. [PMID: 22435500 DOI: 10.1021/ja211307u] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Control over selective recognition of biomolecules on inorganic nanoparticles is a major challenge for the synthesis of new catalysts, functional carriers for therapeutics, and assembly of renewable biobased materials. We found low sequence similarity among sequences of peptides strongly attracted to amorphous silica nanoparticles of various size (15-450 nm) using combinatorial phage display methods. Characterization of the surface by acid base titrations and zeta potential measurements revealed that the acidity of the silica particles increased with larger particle size, corresponding to between 5% and 20% ionization of silanol groups at pH 7. The wide range of surface ionization results in the attraction of increasingly basic peptides to increasingly acidic nanoparticles, along with major changes in the aqueous interfacial layer as seen in molecular dynamics simulation. We identified the mechanism of peptide adsorption using binding assays, zeta potential measurements, IR spectra, and molecular simulations of the purified peptides (without phage) in contact with uniformly sized silica particles. Positively charged peptides are strongly attracted to anionic silica surfaces by ion pairing of protonated N-termini, Lys side chains, and Arg side chains with negatively charged siloxide groups. Further, attraction of the peptides to the surface involves hydrogen bonds between polar groups in the peptide with silanol and siloxide groups on the silica surface, as well as ion-dipole, dipole-dipole, and van-der-Waals interactions. Electrostatic attraction between peptides and particle surfaces is supported by neutralization of zeta potentials, an inverse correlation between the required peptide concentration for measurable adsorption and the peptide pI, and proximity of cationic groups to the surface in the computation. The importance of hydrogen bonds and polar interactions is supported by adsorption of noncationic peptides containing Ser, His, and Asp residues, including the formation of multilayers. We also demonstrate tuning of interfacial interactions using mutant peptides with an excellent correlation between adsorption measurements, zeta potentials, computed adsorption energies, and the proposed binding mechanism. Follow-on questions about the relation between peptide adsorption on silica nanoparticles and mineralization of silica from peptide-stabilized precursors are raised.
Collapse
Affiliation(s)
- Siddharth V Patwardhan
- Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | | | | | | | | | | | | | | |
Collapse
|
204
|
Coppage R, Slocik JM, Briggs BD, Frenkel AI, Naik RR, Knecht MR. Determining peptide sequence effects that control the size, structure, and function of nanoparticles. ACS NANO 2012; 6:1625-1636. [PMID: 22276921 DOI: 10.1021/nn204600d] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The ability to tune the size, shape, and composition of nanomaterials at length scales <10 nm remains a challenging task. Such capabilities are required to fully realize the application of nanotechnology for catalysis, energy storage, and biomedical technologies. Conversely, nature employs biomacromolecules such as proteins and peptides as highly specific nanoparticle ligands that demonstrate exacting precision over the particle morphology through controlling the biotic/abiotic interface. Here we demonstrate the ability to finely tune the size, surface structure, and functionality of single-crystal Pd nanoparticles between 2 and 3 nm using materials directing peptides. This was achieved by selectively altering the peptide sequence to change the binding motif, which in turn modifies the surface structure of the particles. The materials were fully characterized before and after reduction using atomically resolved spectroscopic and microscopic analyses, which indicated that the coordination environment prior to reduction significantly affects the structure of the final nanoparticles. Additionally, changes to the particle surface structure, as a function of peptide sequence, can allow for chloride ion coordination that alters the catalytic abilities of the materials for the C-C coupling Stille reaction. These results suggest that peptide-based approaches may be able to achieve control over the structure/function relationship of nanomaterials where the peptide sequence could be used to selectivity tune such capabilities.
Collapse
Affiliation(s)
- Ryan Coppage
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | | | | | | | | | | |
Collapse
|
205
|
Ding M, Sorescu DC, Kotchey GP, Star A. Welding of Gold Nanoparticles on Graphitic Templates for Chemical Sensing. J Am Chem Soc 2012; 134:3472-9. [DOI: 10.1021/ja210278u] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mengning Ding
- National Energy
Technology Laboratory, U.S. Department of Energy, Pittsburgh, Pennsylvania
15236, United States
- Department
of Chemistry, University of Pittsburgh,
Pittsburgh, Pennsylvania
15260, United States
| | - Dan C. Sorescu
- National Energy
Technology Laboratory, U.S. Department of Energy, Pittsburgh, Pennsylvania
15236, United States
| | - Gregg P. Kotchey
- Department
of Chemistry, University of Pittsburgh,
Pittsburgh, Pennsylvania
15260, United States
| | - Alexander Star
- National Energy
Technology Laboratory, U.S. Department of Energy, Pittsburgh, Pennsylvania
15236, United States
- Department
of Chemistry, University of Pittsburgh,
Pittsburgh, Pennsylvania
15260, United States
| |
Collapse
|
206
|
Kaur K, Forrest JA. Influence of particle size on the binding activity of proteins adsorbed onto gold nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:2736-44. [PMID: 22132998 DOI: 10.1021/la203528u] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We used optical extinction spectroscopy to study the structure of proteins adsorbed onto gold nanoparticles of sizes 5-60 nm and their resulting biological binding activity. For these studies, proteins differing in size and shape, with well-characterized and specific interactions-rabbit immunoglobulin G (IgG), goat anti-rabbit IgG (anti-IgG), Staphylococcal protein A, streptavidin, and biotin-were used as model systems. Protein interaction with gold nanoparticles was probed by optical extinction measurements of localized surface plasmon resonance (LSPR) of the gold nanoparticles. Binding of the ligands in solution to protein molecules already immobilized on the surface of gold causes a small but detectable shift in the LSPR peak of the gold nanoparticles. This shift can be used to probe the binding activity of the adsorbed protein. Within the context of Mie theory calculations, the thickness of the adsorbed protein layer as well as its apparent refractive index is shown to depend on the size of the gold nanoparticle. The results suggest that proteins can adopt different orientations that depend on the size of the gold nanospheres. These different orientations, in turn, can result in different levels of biological activity. For example, we find that IgG adsorbed on spheres with diameter ≥20 nm does not bind to protein A. This study illustrates the principle that the size of nanoparticles can strongly influence the binding activity of adsorbed proteins. In addition to the importance of this in cases of direct exposure of proteins to nanoparticles, the results have implications for proteins adsorbed to materials with nanometer scale surface roughness.
Collapse
Affiliation(s)
- Kanwarjeet Kaur
- Department of Physics and Astronomy, Guelph-Waterloo Physics Institute, University of Waterloo, 200 University Avenue W, Waterloo, Ontario N2L 3G1, Canada
| | | |
Collapse
|
207
|
Xavier PL, Chaudhari K, Baksi A, Pradeep T. Protein-protected luminescent noble metal quantum clusters: an emerging trend in atomic cluster nanoscience. NANO REVIEWS 2012; 3:NANO-3-14767. [PMID: 22312454 PMCID: PMC3272820 DOI: 10.3402/nano.v3i0.14767] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/26/2011] [Accepted: 12/30/2011] [Indexed: 11/29/2022]
Abstract
Noble metal quantum clusters (NMQCs) are the missing link between isolated noble metal atoms and nanoparticles. NMQCs are sub-nanometer core sized clusters composed of a group of atoms, most often luminescent in the visible region, and possess intriguing photo-physical and chemical properties. A trend is observed in the use of ligands, ranging from phosphines to functional proteins, for the synthesis of NMQCs in the liquid phase. In this review, we briefly overview recent advancements in the synthesis of protein protected NMQCs with special emphasis on their structural and photo-physical properties. In view of the protein protection, coupled with direct synthesis and easy functionalization, this hybrid QC-protein system is expected to have numerous optical and bioimaging applications in the future, pointers in this direction are visible in the literature.
Collapse
|
208
|
Briggs BD, Knecht MR. Nanotechnology Meets Biology: Peptide-based Methods for the Fabrication of Functional Materials. J Phys Chem Lett 2012; 3:405-18. [PMID: 26285859 DOI: 10.1021/jz2016473] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nature exploits sustainable methods for the creation of inorganic materials on the nanoscale for a variety of applications. To achieve such capabilities, biomolecules such as peptides and proteins have been developed that recognize and bind the different compositions of materials. While a diverse set of materials binding sequences are present in the biosphere, biocombinatorial techniques have been used to rapidly identify peptides that facilitate the formation of new materials of technological importance. Interestingly, the binding motif of the peptides at the inorganic surface is likely to control the size, structure, composition, shape, and functionality of the final materials. In order to advance these intriguing new biomimetic approaches, a complete understanding of this biotic/abiotic interface is required. In this Perspective, we highlight recent advances in the biofunctionalization of nanoparticles with potential applications ranging from catalysis and energy storage to plasmonics and biosensing. We specifically focus on the physical characterization of the peptide-based surface from which specificity and activity are likely embedded.
Collapse
Affiliation(s)
- Beverly D Briggs
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Marc R Knecht
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| |
Collapse
|
209
|
Sule SV, Sukumar M, Weiss WF, Marcelino-Cruz AM, Sample T, Tessier PM. High-throughput analysis of concentration-dependent antibody self-association. Biophys J 2012; 101:1749-57. [PMID: 21961601 DOI: 10.1016/j.bpj.2011.08.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 08/18/2011] [Accepted: 08/22/2011] [Indexed: 10/17/2022] Open
Abstract
Monoclonal antibodies are typically monomeric and nonviscous at low concentrations, yet they display highly variable associative and viscous behavior at elevated concentrations. Although measurements of antibody self-association are critical for understanding this complex behavior, traditional biophysical methods are not capable of characterizing such concentration-dependent self-association in a high-throughput manner. Here we describe a nanoparticle-based method, termed self-interaction nanoparticle spectroscopy, that is capable of rapidly measuring concentration-dependent self-interactions for three human monoclonal antibodies with unique solution behaviors. We demonstrate that gold nanoparticles conjugated with antibodies at low protein concentrations (<40 μg/mL) display self-association behavior (as measured by the interparticle distance-dependent plasmon wavelength) that is well correlated with static light-scattering measurements obtained at three orders of magnitude higher antibody concentrations. Using this methodology, we find that the antibodies display a complex pH-dependent self-association behavior that is strongly influenced by the solution ionic strength. Importantly, we find that a polyclonal human antibody is nonassociative for all solution conditions evaluated in this work, suggesting that antibody self-association is more specific than previously realized. We expect that our findings will guide rational manipulation of antibody phase behavior, and enable studies that elucidate sequence and structural determinants of antibody self-association.
Collapse
Affiliation(s)
- Shantanu V Sule
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | | | | | | | | | | |
Collapse
|
210
|
Yu J, Becker ML, Carri GA. The influence of amino acid sequence and functionality on the binding process of peptides onto gold surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:1408-1417. [PMID: 22148960 DOI: 10.1021/la204109r] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a molecular dynamics study of the binding process of peptide A3 (AYSSGAPPMPPF) and other similar peptides onto gold surfaces, and identify the functions of many amino acids. Our results provide a clear picture of the separate regimes present in the binding process: diffusion, anchoring, crawling and binding. Moreover, we explored the roles of individual residues. We found that tyrosine, methionine, and phenylalanine are strong binding residues; serine serves as an effective anchoring residue; proline acts as a dynamic anchoring point, while glycine and alanine give flexibility to the peptide backbone. We then show that our findings apply to unrelated phage-derived sequences that have been reported recently to facilitate AuNP synthesis. This new knowledge may aid in the design of new peptides for the synthesis of gold nanostructures with novel morphologies.
Collapse
Affiliation(s)
- Jing Yu
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325-3909, USA
| | | | | |
Collapse
|
211
|
Chidiebere MA, Ogukwe CE, Oguzie KL, Eneh CN, Oguzie EE. Corrosion Inhibition and Adsorption Behavior of Punica granatum Extract on Mild Steel in Acidic Environments: Experimental and Theoretical Studies. Ind Eng Chem Res 2012. [DOI: 10.1021/ie201941f] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maduabuchi A. Chidiebere
- Electrochemistry and Materials Science Research Laboratory Department of Chemistry and ‡Department of Environmental Technology, Federal University of Technology Owerri, PMB 1526, Owerri, Nigeria
| | - Cynthia E. Ogukwe
- Electrochemistry and Materials Science Research Laboratory Department of Chemistry and ‡Department of Environmental Technology, Federal University of Technology Owerri, PMB 1526, Owerri, Nigeria
| | - Kanayo L. Oguzie
- Electrochemistry and Materials Science Research Laboratory Department of Chemistry and ‡Department of Environmental Technology, Federal University of Technology Owerri, PMB 1526, Owerri, Nigeria
| | - Chukwuemeka N. Eneh
- Electrochemistry and Materials Science Research Laboratory Department of Chemistry and ‡Department of Environmental Technology, Federal University of Technology Owerri, PMB 1526, Owerri, Nigeria
| | - Emeka E. Oguzie
- Electrochemistry and Materials Science Research Laboratory Department of Chemistry and ‡Department of Environmental Technology, Federal University of Technology Owerri, PMB 1526, Owerri, Nigeria
| |
Collapse
|
212
|
Cui R, Gu YP, Zhang ZL, Xie ZX, Tian ZQ, Pang DW. Controllable synthesis of PbSe nanocubes in aqueous phase using a quasi-biosystem. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm15691a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
213
|
Fuku K, Sakano T, Kamegawa T, Mori K, Yamashita H. Enhanced hydrogenation activity of nano-sized Pd–Ni bimetal particles on Ti-containing mesoporous silica prepared by a photo-assisted deposition method. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm31584j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
214
|
Li T, He X, Wang Z. The Application of Peptide Functionalized Gold Nanoparticles. ACS SYMPOSIUM SERIES 2012. [DOI: 10.1021/bk-2012-1113.ch004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Science and Technology, Changchun University of Science and Technology, Changchun 130022, China
| | - Xiuxia He
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Science and Technology, Changchun University of Science and Technology, Changchun 130022, China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Science and Technology, Changchun University of Science and Technology, Changchun 130022, China
| |
Collapse
|
215
|
Bouchet-Marquis C, Pagratis M, Kirmse R, Hoenger A. Metallothionein as a clonable high-density marker for cryo-electron microscopy. J Struct Biol 2012; 177:119-27. [PMID: 22068155 PMCID: PMC3261350 DOI: 10.1016/j.jsb.2011.10.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/21/2011] [Accepted: 10/24/2011] [Indexed: 11/24/2022]
Abstract
Cryo-electron microscopy is expanding its scope from macromolecules towards much larger and more complex cellular specimens such as organelles, cells and entire tissues. While isolated macromolecular specimens are typically composed of only very few different components that may be recognized by their shape, size or state of polymerization, cellular specimens combine large numbers of proteinaceous structures as well as nucleic acids and lipid arrays. Consequently, an unambiguous identification of these structures within the context of a whole cell may create a very difficult challenge. On plastic-embedded specimens, or Tokuyasu sections (Tokuyasu, 1980), epitopes that are exposed at the surface can be tagged by antibodies. However, vitrified sections have to be kept at strict cryo-conditions (below -140 °C) and therefore do not allow any post-sectioning treatment of the specimens other than data acquisition in the microscope. Hence, the labels have to be placed into the specimen before freezing. Here we report on the application of a small metal-clustering protein, metallothionein (MTH), as a clonable label capable of clustering metal atoms into a high-density particle with high spatial resolution. We tested MTH as a label for kinesin-decorated microtubules (MTs) as well as the building blocks of desmin intermediate filaments (IFs).
Collapse
Affiliation(s)
| | | | | | - Andreas Hoenger
- Dept. of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder CO, 80309-0347, USA
| |
Collapse
|
216
|
Chaudhari K, Xavier PL, Pradeep T. Understanding the evolution of luminescent gold quantum clusters in protein templates. ACS NANO 2011; 5:8816-27. [PMID: 22010989 DOI: 10.1021/nn202901a] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We show that the time-dependent biomineralization of Au(3+) by native lactoferrin (NLf) and bovine serum albumin (BSA) resulting in near-infrared (NIR) luminescent gold quantum clusters (QCs) occurs through a protein-bound Au(1+) intermediate and subsequent emergence of free protein. The evolution was probed by diverse tools, principally, using matrix-assisted laser desorption ionization mass spectrometry (MALDI MS), X-ray photoelectron spectroscopy (XPS), and photoluminescence spectroscopy (PL). The importance of alkaline pH in the formation of clusters was probed. At neutral pH, a Au(1+)-protein complex was formed (starting from Au(3+)) with the binding of 13-14 gold atoms per protein. When the pH was increased above 12, these bound gold ions were further reduced to Au(0) and nucleation and growth of cluster commenced, which was corroborated by the beginning of emission; at this point, the number of gold atoms per protein was ~25, suggesting the formation of Au(25). During the cluster evolution, at certain time intervals, for specific molar ratios of gold and protein, occurrence of free protein was noticed in the mass spectra, suggesting a mixture of products and gold ion redistribution. By providing gold ions at specific time of the reaction, monodispersed clusters with enhanced luminescence could be obtained, and the available quantity of free protein could be utilized efficiently. Monodispersed clusters would be useful in obtaining single crystals of protein-protected noble metal quantum clusters where homogeneity of the system is of primary concern.
Collapse
Affiliation(s)
- Kamalesh Chaudhari
- Department of Biotechnology, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
| | | | | |
Collapse
|
217
|
Hissam RS, Farmer BL, Pandey RB. Scaffolding of an antimicrobial peptide (KSL) by a scale-down coarse-grained approach. Phys Chem Chem Phys 2011; 13:21262-72. [PMID: 22031450 DOI: 10.1039/c1cp22361e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A coarse-grained approach with enhanced representation of amino acid (involving four components, i.e. a central alpha carbon and its side group along with C and N terminals) is used to study the multi-scale assembly of an antimicrobial peptide (KSL) in an explicit solvent (in a scale-down hierarchy of Eby et al. [Phys. Chem. Chem. Phys., 2011, 13, 1123-1130]). Both local (mobility, solvent-surrounding, energy profiles) and global (variation of the root mean square displacement of peptides and its gyration radius with time steps, radial distribution function, and structure factors) physical quantities are analyzed as a function of the solvent quality (i.e. the solvent-residue interaction strength). We find that the mobility of the interacting side group (lysine) decays as the number of its surrounding solvent constituents grows systematically on increasing the interaction strength. Pinning of lysine directs the underlying segmental conformation that propagates to larger scale scaffolding. The radial distribution function (a measure of the correlated peptide assembly) decays with the distance (faster with stronger solvent interaction). Scaling of the structure factor (S(q)) of peptide assembly with the wave vector q = 2π/λ (λ is the wavelength), S(q) ∝q(-1/ν) provides an insight into its multi-scale mass (N) distribution. The effective dimension D(e) = 1/ν of the peptide assembly over the spatial distribution (R) can be estimated using N∝R(D(e)). On scales larger than the size (i.e. the radius of gyration R(g)) of the peptide, D(e) ≈ 1.303 ± 0.070 to D(e) ≈ 1.430 ± 0.096, a rather fibrous morphology appears perhaps due to directed pinning while the morphology appears like an ideal chain, D(e) ≈ 1.809 ± 0.017 to D(e) ≈ 1.978 ± 0.017, at a smaller scale R≤R(g).
Collapse
Affiliation(s)
- R S Hissam
- Department of Chemical Engineering, West Virginia University, Morgantown, WV 26506-6102, USA
| | | | | |
Collapse
|
218
|
Mirau PA, Naik RR, Gehring P. Structure of Peptides on Metal Oxide Surfaces Probed by NMR. J Am Chem Soc 2011; 133:18243-8. [DOI: 10.1021/ja205454t] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Peter A. Mirau
- Materials and Manufacturing Directorate, Nanostructured and Biological Materials Branch, Air Force Research Laboratories, Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R. Naik
- Materials and Manufacturing Directorate, Nanostructured and Biological Materials Branch, Air Force Research Laboratories, Wright-Patterson AFB, Ohio 45433, United States
| | - Patricia Gehring
- Materials and Manufacturing Directorate, Nanostructured and Biological Materials Branch, Air Force Research Laboratories, Wright-Patterson AFB, Ohio 45433, United States
| |
Collapse
|
219
|
Ignatjev I, Podstawka-Proniewicz E, Niaura G, Lombardi JR, Proniewicz LM. Potential Induced Changes in Neuromedin B Adsorption on Ag, Au, and Cu Electrodes Monitored by Surface-Enhanced Raman Scattering. J Phys Chem B 2011; 115:10525-36. [DOI: 10.1021/jp2026863] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Ilja Ignatjev
- Institute of Chemistry, Center for Physical Sciences and Technology, A. Gostauto 9, LT-01108, Vilnius, Lithuania
| | | | - Gediminas Niaura
- Institute of Chemistry, Center for Physical Sciences and Technology, A. Gostauto 9, LT-01108, Vilnius, Lithuania
| | - John R. Lombardi
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, New York 10031, United States
| | - Leonard M. Proniewicz
- Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| |
Collapse
|
220
|
Coppage R, Slocik JM, Briggs BD, Frenkel AI, Heinz H, Naik RR, Knecht MR. Crystallographic Recognition Controls Peptide Binding for Bio-Based Nanomaterials. J Am Chem Soc 2011; 133:12346-9. [DOI: 10.1021/ja203726n] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryan Coppage
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States
| | - Joseph M. Slocik
- Nanostructured and Biological Materials Branch, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433-7702, United States
| | - Beverly D. Briggs
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States
| | - Anatoly I. Frenkel
- Department of Physics, Yeshiva University, New York, New York 10016, United States
| | - Hendrik Heinz
- Department of Polymer Engineering, University of Akron, Akron, Ohio 44325, United States
| | - Rajesh R. Naik
- Nanostructured and Biological Materials Branch, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433-7702, United States
| | - Marc R. Knecht
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States
| |
Collapse
|
221
|
Vila Verde A, Beltramo PJ, Maranas JK. Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:5918-5926. [PMID: 21488613 DOI: 10.1021/la104814z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala(10), Ser(10), Thr(10), Arg(10), Lys(10), and Gln(10)], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movement and flexibility of the peptide within a given conformation. Low conformational movement indicates stability of a given conformation and leads to less adsorption than homopolypeptides with faster conformational movement. Likewise, low flexibility within a given conformation also leads to less adsorption. Neither amino acid affinities nor dynamic considerations alone predict surface coverage; rather both quantities must be considered in peptide adsorption to gold surfaces.
Collapse
Affiliation(s)
- Ana Vila Verde
- University of Minho, Department of Physics, Braga, Portugal
| | | | | |
Collapse
|
222
|
Xu Z, Yuan SL, Yan H, Liu CB. Adsorption of histidine and histidine-containing peptides on Au(111): A molecular dynamics study. Colloids Surf A Physicochem Eng Asp 2011. [DOI: 10.1016/j.colsurfa.2011.02.046] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
223
|
Platinum nanocrystals selectively shaped using facet-specific peptide sequences. Nat Chem 2011; 3:393-9. [PMID: 21505499 DOI: 10.1038/nchem.1025] [Citation(s) in RCA: 262] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 03/08/2011] [Indexed: 11/08/2022]
Abstract
The properties of a nanocrystal are heavily influenced by its shape. Shape control of a colloidal nanocrystal is believed to be a kinetic process, with high-energy facets growing faster then vanishing, leading to nanocrystals enclosed by low-energy facets. Identifying a surfactant that can specifically bind to a particular crystal facet is critical, but has proved challenging to date. Biomolecules have exquisite specific molecular recognition properties that can be explored for the precise engineering of nanostructured materials. Here, we report the use of facet-specific peptide sequences as regulating agents for the predictable synthesis of platinum nanocrystals with selectively exposed crystal surfaces and particular shapes. The formation of platinum nanocubes and nanotetrahedrons are demonstrated with Pt-{100} and Pt-{111} binding peptides, respectively. Our studies unambiguously demonstrate the abilities of facet-selective binding peptides in determining nanocrystal shape, representing a critical step forward in the use of biomolecules for programmable synthesis of nanostructures.
Collapse
|
224
|
Arai Y, Okabe KI, Sekiguchi H, Hayashi T, Hara M. Nanoscale chemical composition analysis using peptides targeting inorganic materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:2478-2483. [PMID: 21284389 DOI: 10.1021/la104178h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Chemical composition analysis by scanning probe microscopy (SPM) in water is a method whose introduction has been long-awaited. Here we propose a simple method for performing chemical composition analyses of solid surfaces in water using atomic force microscopes (AFMs) with probes functionalized with peptides targeting inorganic materials. In this work, bicompositional surfaces of gold and titanium oxide were scanned with AFM probes modified with the titanium-binding peptide (TBP). We found that surface chemical composition clearly appeared as contrast in the mapping images of adhesion forces with nanometer-scale resolution. In this Article, we further discuss appropriate designs of the AFM probes and appropriate imaging conditions for the chemical composition analysis based on the results of force measurements of the single TBP-titanium bond.
Collapse
Affiliation(s)
- Yuki Arai
- Department of Electronic Chemistry, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | | | | | | | | |
Collapse
|
225
|
Costa D, Garrain PA, Diawara B, Marcus P. Biomolecule-biomaterial interaction: a DFT-D study of glycine adsorption and self-assembly on hydroxylated Cr2O3 surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:2747-60. [PMID: 21338116 DOI: 10.1021/la104317j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The adsorption of glycine, the building block of amino acids, on hydroxylated (0001)-Cr2O3 model surfaces, representing the stainless steel passive film surface, was modeled by means of the GGA + U method. The roles of glycine coverage and surface termination (hydroxylated Cr- and O-terminated surfaces) on the adsorption mode and self-assembly properties were explored. The hydroxylated Cr-terminated Cr2O3 surface, which presents two types of (H)OH groups exhibiting different acidic character, is more reactive than the hydroxylated O-terminated surface, where one single type of OH group is present, for all adsorption modes and coverages considered. Outer sphere adsorption occurs in the zwitterion form, stabilized at low coverage through H-bond formation with coadsorbed water molecules, and at the monolayer coverage by glycine self-assembling. The OH substitution by glycinate is favored on the hydroxylated Cr-terminated surface and not on the O-terminated one. The inclusion of dispersion forces does not change the observed tendencies. An atomistic thermodynamics approach suggests that outer sphere adsorption is thermodynamically favored over inner sphere adsorption in the whole domain of glycine concentration. The obtained SAM's free energies of formation are rationalized in a model considering the balance between sublimation and solvation free energies, and extrapolated to other amino acids, to predict the SAMs formation above hydroxylated surfaces. It is found that hydrophobic AA tend to self-assemble at the surface, whereas hydrophilic ones do not.
Collapse
Affiliation(s)
- D Costa
- Laboratoire de Physico-Chimie des Surfaces, CNRS-ENSCP (UMR 7045) , Ecole Nationale Supérieure de Chimie de Paris, Chimie-Paristech, 11 rue Pierre et Marie Curie, 75005 France
| | | | | | | |
Collapse
|
226
|
Curtis SB, MacGillivray RTA, Dunbar WS. Effects of bacteriophage on the surface properties of chalcopyrite (CuFeS₂), and phage-induced flocculation of chalcopyrite, glacial till, and oil sands tailings. Biotechnol Bioeng 2011; 108:1579-90. [PMID: 21337331 DOI: 10.1002/bit.23097] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/27/2011] [Accepted: 02/04/2011] [Indexed: 11/08/2022]
Abstract
The binding of mineral-specific phage to the surface of chalcopyrite (CuFeS(2)) was investigated by using X-ray photoelectron spectroscopy and scanning Auger microscopy. These studies confirmed the elemental composition of the minerals and confirmed that bacteriophage were bound to the mineral surface. These techniques also revealed that the phage were not forming a continuous film over the entire surface of the CuFeS(2) particles, but selectively bound to the slimes coating the particles. In addition, the effect of mineral-specific phage binding to the surface of CuFeS(2) was investigated using induction time and zeta potential measurements. Bacteriophage (10(12) /mL) increased the induction time (contact time resulting in 50% particle attachment to a bubble) from ∼7.5 to ∼17 ms and reversed the zeta potential from negative to positive. In the course of performing the zeta potential measurements on particles <45 µm in diameter, phage-induced aggregation was observed. The mechanism of aggregation was explored using a range of pH (3-11) and cation concentrations. Aggregation was observed across the tested pH range and with all cations. Phage also mediated aggregation of glacial till and oil sands tailings in a dose-dependent and particle size-dependent manner. We conclude that binding of bacteriophage to the surface of CuFeS(2) does alter its surface properties.
Collapse
Affiliation(s)
- Susan B Curtis
- Norman B. Keevil Institute of Mining Engineering, 517-6350 Stores Road, Vancouver, BC, Canada V6T1Z4
| | | | | |
Collapse
|
227
|
Date T, Sekine J, Matsuno H, Serizawa T. Polymer-binding peptides for the noncovalent modification of polymer surfaces: effects of peptide density on the subsequent immobilization of functional proteins. ACS APPLIED MATERIALS & INTERFACES 2011; 3:351-359. [PMID: 21288050 DOI: 10.1021/am100970w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Peptides that specifically bind to polyetherimide (PEI) were selected, characterized, and used for the noncovalent modification of the PEI surface. The peptides were successfully identified from a phage-displayed peptide library. A chemically-synthesized peptide composed of the Thr-Gly-Ala-Asp-Leu-Asn-Thr sequence showed an extremely high binding constant for the PEI films (5.6 × 10(8) M(-1)), which was more than three orders of magnitude greater than that for the reference polystyrene films. The peptide was biotinylated and immobilized onto the PEI films to further immobilize streptavidin (SAv). The amount of SAv bound depended on the density of immobilized peptide. It gradually increased with an increasing density of immobilized peptide and achieved a maximum (2.1 pmol cm(-2)) at a peptide density of 19.8 pmol cm(-2). The ratio of peptide used for immobilizing SAv at the maximum value was only 11%, and was partially due to the low accessibility of SAv to the biotin moieties on the PEI films. Moreover, the amount of SAv bound gradually decreased at higher peptide densities, suggesting that the clustering of the peptides also inhibited the binding of SAv. Furthermore, peptides on the PEI films promoted the uniform immobilization of SAv with less structural denaturing. The immobilized SAv was able to further immobilize probe DNA to hybridize with its complementary DNA. These present results suggest that the density of immobilized peptide has a great impact on the surface modifications using polymer-binding peptides.
Collapse
Affiliation(s)
- Takaaki Date
- Graduate School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | | | | | | |
Collapse
|
228
|
Shen L, Bao N, Zhou Z, Prevelige PE, Gupta A. Materials design using genetically engineered proteins. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm12238j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
229
|
Vreuls C, Genin A, Zocchi G, Boschini F, Cloots R, Gilbert B, Martial J, Van De Weerdt C. Genetically engineered polypeptides as a new tool for inorganic nano-particles separation in water based media. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm12440d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
230
|
Oguzie EE, Li Y, Wang SG, Wang F. Understanding corrosion inhibition mechanisms—experimental and theoretical approach. RSC Adv 2011. [DOI: 10.1039/c1ra00148e] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
231
|
Zhang MX, Cui R, Zhao JY, Zhang ZL, Pang DW. Synthesis of sub-5 nm Au–Ag alloy nanoparticles using bio-reducing agent in aqueous solution. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm13120f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
232
|
Abufager PN, Solano Canchaya JG, Wang Y, Alcamí M, Martín F, Alvarez Soria L, Martiarena ML, Reuter K, Busnengo HF. Theoretical study of the structure of self-assembled monolayers of short alkylthiolates on Au(111) and Ag(111): the role of induced substrate reconstruction and chain–chain interactions. Phys Chem Chem Phys 2011; 13:9353-62. [DOI: 10.1039/c0cp02490b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
233
|
Laref S, Li Y, Bocquet ML, Delbecq F, Sautet P, Loffreda D. Nature of adhesion of condensed organic films on platinum by first-principles simulations. Phys Chem Chem Phys 2011; 13:11827-37. [DOI: 10.1039/c0cp02285c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
234
|
Shen L, Bao N, Prevelige PE, Gupta A. Fabrication of ordered nanostructures of sulfide nanocrystal assemblies over self-assembled genetically engineered P22 coat protein. J Am Chem Soc 2010; 132:17354-7. [PMID: 21090711 DOI: 10.1021/ja107080b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Ordered ZnS and CdS nanocrystal assemblies have been synthesized by a facile bioinspired approach consisting of an initial self-assembly of engineered proteins into spherical biotemplates and a subsequent protein-directed nucleation and growth of ZnS and CdS nanocrystals symmetrically distributed over the self-assembled biotemplates.
Collapse
Affiliation(s)
- Liming Shen
- Center for Materials for Information Technology, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | | | | | | |
Collapse
|
235
|
Feng J, Wang W, Li JH, Fu LX, Zhao JX, Qiao YT, Sun PC, Yuan Z. Effects of oligopeptide's conformational changes on its adsorption. Colloids Surf B Biointerfaces 2010; 83:229-36. [PMID: 21145711 DOI: 10.1016/j.colsurfb.2010.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 11/11/2010] [Accepted: 11/11/2010] [Indexed: 11/16/2022]
Abstract
We report the effects of peptide adsorption to cross-linked polymers (adsorbents) by its conformational changes. Two adsorbents, APhe and ALeu, were prepared and expected to show high affinity to the oligopeptide VW-8 (NH(2)-Val-Val-Arg-Gly-Cys-Thr-Trp-Trp-COOH) according to our previous studies. These absorbents bared the residues of phenylalanine and leucine, respectively, and carried both hydrophobic and electrical groups. The adsorbent AAsp, which carried only the electrostatic groups, was also prepared as a reference. Both APhe and ALeu were found to exhibit higher VW-8 capacity than AAsp, in which APhe showed the highest VW-8 capacity (13.6 mg/g). The VW-8 adsorption to ALeu and APhe was analyzed using a variety of techniques, including the surface plasmon resonance (SPR) technology, nuclear magnetic resonance (NMR) spectra and isothermal titration calorimetry (ITC). The comprehensive experimental data together indicated that APhe could induce a conformational change of VW-8 from a random-coil to a β-strand structure due to its ability to provide the strong ring stacking and electrostatic interactions, which is believed to be responsible for its highest adsorption affinity (K(a)=2.59×10(7) M(-1)). In contrast, the hydrophobic interactions provided by ALeu were not strong enough to induce a VW-8 conformational change to a regular structure, and therefore it exhibited a relatively lower affinity to VW-8 (K(a)=6.23×10(5) M(-1)). The results presented in this work showed that peptide adsorption can be influenced by its conformational changes induced by suitable adsorbents via strong non-covalent interactions.
Collapse
Affiliation(s)
- Jing Feng
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, PR China
| | | | | | | | | | | | | | | |
Collapse
|
236
|
Zareh SK, Wang YM. Single-molecule imaging of protein adsorption mechanisms to surfaces. Microsc Res Tech 2010; 74:682-7. [DOI: 10.1002/jemt.20954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 09/19/2010] [Indexed: 11/09/2022]
|
237
|
Heinz H. Computational screening of biomolecular adsorption and self-assembly on nanoscale surfaces. J Comput Chem 2010; 31:1564-8. [PMID: 19862812 DOI: 10.1002/jcc.21421] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer-scale surfaces is often difficult experimentally and a recurring challenge in molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface-solute-solvent system, the solute-solvent system, the solvent system, and the surface-solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution.
Collapse
Affiliation(s)
- Hendrik Heinz
- Department of Polymer Engineering, University of Akron, Akron, Ohio 44325, USA.
| |
Collapse
|
238
|
Yu J, Becker ML, Carri GA. A molecular dynamics simulation of the stability-limited growth mechanism of peptide-mediated gold-nanoparticle synthesis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:2242-2245. [PMID: 20853372 DOI: 10.1002/smll.201000889] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Jing Yu
- Department of Polymer Science, The University of Akron, Akron, OH 44325-3909, USA
| | | | | |
Collapse
|
239
|
Sethi M, Pacardo DB, Knecht MR. Biological surface effects of metallic nanomaterials for applications in assembly and catalysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:15121-15134. [PMID: 20297781 DOI: 10.1021/la100034q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Recent experimental evidence has suggested that bioinspired techniques represent promising avenues toward the production of functional nanomaterials that possess a high degree of activity. These materials are prepared under synthetically simple and efficient conditions, thus making them attractive alternatives to many traditional methods that employ hazardous and harsh conditions. Many biomimetic methods employ peptide and amino acid binding events on the surfaces of nanostructures to generate materials that are stable in solution. The basis of both the stability and activity of these materials is likely to be controlled by the biotic/abiotic interface, which is mediated by the bioligand binding process. Unfortunately, most readily available techniques are unable to be used to study this intrinsic process; however, very recent studies have begun to shed light on this important event. In this feature article, an overview of the understanding of peptide and amino acid binding events to nanomaterials and how these motifs can be exploited for activities in nanoparticle assembly and catalytic reactivity is discussed. From both 2D surface studies and computational modeling analyses, different biomolecule binding characteristics have been elucidated. These results indicate that the amino acid sequence and peptide secondary structure play important roles in the binding capability. Furthermore, these studies suggest that the peptides are able to form specific patterns and motifs once bound to the nanoparticle surface. This attribute could affect the nanoparticle electronics and can play a significant role in their activities to generate functional materials. From these binding motifs, the ability of reagents to interact with the metallic surface is possible, thus affecting many of the properties of these materials.
Collapse
Affiliation(s)
- Manish Sethi
- Department of Chemistry, University of Kentucky, 101 Chemistry-Physics Building, Lexington, Kentucky 40506-0055, USA
| | | | | |
Collapse
|
240
|
Pandey RB, Heinz H, Farmer BL, Drummy LF, Jones SE, Vaia RA, Naik RR. Layer of clay platelets in a peptide matrix: Binding, encapsulation, and morphology. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/polb.22140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
241
|
Ding Y, Fan F, Tian Z, Wang ZL. Atomic Structure of Au−Pd Bimetallic Alloyed Nanoparticles. J Am Chem Soc 2010; 132:12480-6. [DOI: 10.1021/ja105614q] [Citation(s) in RCA: 205] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yong Ding
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, and Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Fengru Fan
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, and Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Zhongqun Tian
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, and Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Zhong Lin Wang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, and Department of Chemistry, Xiamen University, Xiamen 361005, China
| |
Collapse
|
242
|
Exploitation of peptide motif sequences and their use in nanobiotechnology. Curr Opin Biotechnol 2010; 21:412-25. [DOI: 10.1016/j.copbio.2010.07.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/13/2010] [Accepted: 07/15/2010] [Indexed: 12/18/2022]
|
243
|
Heinz H, Jha KC, Luettmer-Strathmann J, Farmer BL, Naik RR. Polarization at metal-biomolecular interfaces in solution. J R Soc Interface 2010; 8:220-32. [PMID: 20630881 DOI: 10.1098/rsif.2010.0318] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Metal surfaces in contact with water, surfactants and biopolymers experience attractive polarization owing to induced charges. This fundamental physical interaction complements stronger epitaxial and covalent surface interactions and remains difficult to measure experimentally. We present a first step to quantify polarization on even gold (Au) surfaces in contact with water and with aqueous solutions of peptides of different charge state (A3 and Flg-Na3) by molecular dynamics simulation in all-atomic resolution and a posteriori computation of the image potential. Attractive polarization scales with the magnitude of atomic charges and with the length of multi-poles in the aqueous phase such as the distance between cationic and anionic groups. The polarization energy per surface area is similar on aqueous Au {1 1 1} and Au {1 0 0} interfaces of approximately -50 mJ m(-2) and decreases to -70 mJ m(-2) in the presence of charged peptides. In molecular terms, the polarization energy corresponds to -2.3 and -0.1 kJ mol(-1) for water in the first and second molecular layers on the metal surface, and to between -40 and 0 kJ mol(-1) for individual amino acids in the peptides depending on the charge state, multi-pole length and proximity to the surface. The net contribution of polarization to peptide adsorption on the metal surface is determined by the balance between polarization by the peptide and loss of polarization by replaced surface-bound water. On metal surfaces with significant epitaxial attraction of peptides such as Au {1 1 1}, polarization contributes only 10-20% to total adsorption related to similar polarity of water and of amino acids. On metal surfaces with weak epitaxial attraction of peptides such as Au {1 0 0}, polarization is a major contribution to adsorption, especially for charged peptides (-80 kJ mol(-1) for peptide Flg-Na(3)). A remaining water interlayer between the metal surface and the peptide then reduces losses in polarization energy by replaced surface-bound water. Computed polarization energies are sensitive to the precise location of the image plane (within tenths of Angstroms near the jellium edge). The computational method can be extended to complex nanometre and micrometer-size surface topologies.
Collapse
Affiliation(s)
- Hendrik Heinz
- Department of Polymer Engineering, University of Akron, Akron, OH 44325, USA.
| | | | | | | | | |
Collapse
|
244
|
Di Profio G, Curcio E, Drioli E. Supersaturation Control and Heterogeneous Nucleation in Membrane Crystallizers: Facts and Perspectives. Ind Eng Chem Res 2010. [DOI: 10.1021/ie100418z] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gianluca Di Profio
- Institute on Membrane Technology, ITM-CNR, Rende, Italy, and Department of Chemical and Materials Engineering, University of Calabria, Rende, Italy
| | - Efrem Curcio
- Institute on Membrane Technology, ITM-CNR, Rende, Italy, and Department of Chemical and Materials Engineering, University of Calabria, Rende, Italy
| | - Enrico Drioli
- Institute on Membrane Technology, ITM-CNR, Rende, Italy, and Department of Chemical and Materials Engineering, University of Calabria, Rende, Italy
| |
Collapse
|
245
|
Zhang J, Liu X, Guo X, Wu S, Wang S. A General Approach to Fabricate Diverse Noble-Metal (Au, Pt, Ag, Pt/Au)/Fe2O3Hybrid Nanomaterials. Chemistry 2010; 16:8108-16. [DOI: 10.1002/chem.201000096] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
246
|
Feyer V, Plekan O, Tsud N, Cháb V, Matolín V, Prince KC. Adsorption of histidine and histidine-containing peptides on Au(111). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:8606-8613. [PMID: 20337409 DOI: 10.1021/la904684e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The adsorption of histidine (His) and three His-derived peptides on Au(111) has been studied by soft X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectroscopy (NEXAFS) at the nitrogen and oxygen K edges. The peptides were glycyl-histidine (Gly-His), glycyl-histidine-glycine (Gly-His-Gly), and glycyl-glycyl-histidine (Gly-Gly-His) and were adsorbed at saturated coverage on the Au(111) surface from aqueous solution. Coverages of 1 and 0.5 monolayers (ML) of His were adsorbed by evaporation in vacuum and compared with 1 ML deposited from solution. There were no significant chemical differences between the monolayers deposited in vacuum or from solution. The Au 4f core level shift indicates that a chemisorption rather than a physisorption bond is formed. In both deposited phases, His bonds to the gold surface in anionic form via the imino nitrogen atom of the imidazole ring and the oxygen atoms of the carboxylate group. N and O K-edge NEXAFS indicate that the ring and carboxylate triangle of adsorbed His are tilted at approximately 35 degrees and approximately 27 degrees, respectively, with respect to the Au(111) surface. The peptides bond to the gold surface in a mode similar to the single His molecule, via the imino and carboxylate groups, while the peptide group is at a steep angle to the surface. However, the peptides adsorb with a higher atomic density, consistent with the peptide groups being above the surface. There are also differences between Gly-His-Gly and Gly-Gly-His, implying that the sequence within the peptide has a significant influence on the bonding geometry.
Collapse
Affiliation(s)
- Vitaliy Feyer
- Sincrotrone Trieste S.C.p.A., in Area Science Park, Strada Statale 14, km 163.5, I-34012 Basovizza, Trieste, Italy.
| | | | | | | | | | | |
Collapse
|
247
|
Hoefling M, Iori F, Corni S, Gottschalk KE. Interaction of amino acids with the Au(111) surface: adsorption free energies from molecular dynamics simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:8347-8351. [PMID: 20426434 DOI: 10.1021/la904765u] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Interactions of proteins with inorganic surfaces are of high importance in biological events and in modern biotechnological applications. Therefore, peptides have been engineered to recognize inorganic surfaces with high specificity. However, the underlying interactions are still not well understood. Here, we investigated the adsorption of amino acids as protein building blocks onto a Au(111) surface. In particular, using molecular dynamics simulations, we calculated the potential of mean force between all the 20 amino acids and the gold surface. We found a strong dependence of the binding affinities on the chemical character of the amino acids. Additionally, the interaction free energy is correlated with the propensity of amino acids to form beta-sheets, hinting at design principles for gold binding peptides and induction of beta-sheet formation near surfaces.
Collapse
Affiliation(s)
- Martin Hoefling
- Ludwig-Maximilians University, Amalienstr. 54, 80799 Munich, Germany
| | | | | | | |
Collapse
|
248
|
Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, Wade RC. ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent. J Chem Theory Comput 2010; 6:1753-68. [DOI: 10.1021/ct100086j] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daria B. Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| | - Stefano Corni
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| | - Peter J. Winn
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| | - Martin Hoefling
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| | - Kay E. Gottschalk
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German
| |
Collapse
|
249
|
Calzolari A, Cicero G, Cavazzoni C, Di Felice R, Catellani A, Corni S. Hydroxyl-Rich β-Sheet Adhesion to the Gold Surface in Water by First-Principle Simulations. J Am Chem Soc 2010; 132:4790-5. [DOI: 10.1021/ja909823n] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Arrigo Calzolari
- Centro S3, CNR-Istituto di Nanoscienze, Modena, Italy, Department of Material Science and Chemical Engineering, Politecnico of Torino, Torino, Italy, CNR-IMEM Institute of Materials for Electronics and Magnetisms, Parma, Italy, and CINECA, Interuniversity Computing Center, Bologna, Italy
| | - Giancarlo Cicero
- Centro S3, CNR-Istituto di Nanoscienze, Modena, Italy, Department of Material Science and Chemical Engineering, Politecnico of Torino, Torino, Italy, CNR-IMEM Institute of Materials for Electronics and Magnetisms, Parma, Italy, and CINECA, Interuniversity Computing Center, Bologna, Italy
| | - Carlo Cavazzoni
- Centro S3, CNR-Istituto di Nanoscienze, Modena, Italy, Department of Material Science and Chemical Engineering, Politecnico of Torino, Torino, Italy, CNR-IMEM Institute of Materials for Electronics and Magnetisms, Parma, Italy, and CINECA, Interuniversity Computing Center, Bologna, Italy
| | - Rosa Di Felice
- Centro S3, CNR-Istituto di Nanoscienze, Modena, Italy, Department of Material Science and Chemical Engineering, Politecnico of Torino, Torino, Italy, CNR-IMEM Institute of Materials for Electronics and Magnetisms, Parma, Italy, and CINECA, Interuniversity Computing Center, Bologna, Italy
| | - Alessandra Catellani
- Centro S3, CNR-Istituto di Nanoscienze, Modena, Italy, Department of Material Science and Chemical Engineering, Politecnico of Torino, Torino, Italy, CNR-IMEM Institute of Materials for Electronics and Magnetisms, Parma, Italy, and CINECA, Interuniversity Computing Center, Bologna, Italy
| | - Stefano Corni
- Centro S3, CNR-Istituto di Nanoscienze, Modena, Italy, Department of Material Science and Chemical Engineering, Politecnico of Torino, Torino, Italy, CNR-IMEM Institute of Materials for Electronics and Magnetisms, Parma, Italy, and CINECA, Interuniversity Computing Center, Bologna, Italy
| |
Collapse
|
250
|
Chen CL, Rosi N. Peptide-Based Methods for the Preparation of Nanostructured Inorganic Materials. Angew Chem Int Ed Engl 2010; 49:1924-42. [DOI: 10.1002/anie.200903572] [Citation(s) in RCA: 389] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|