1
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Cho H, Shim S, Cho WW, Cho S, Baek H, Lee SM, Shin DS. Electrochemical Impedance-Based Biosensors for the Label-Free Detection of the Nucleocapsid Protein from SARS-CoV-2. ACS Sens 2022; 7:1676-1684. [PMID: 35653260 PMCID: PMC9211059 DOI: 10.1021/acssensors.2c00317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/19/2022] [Indexed: 02/06/2023]
Abstract
Diagnosis of coronavirus disease (COVID-19) is important because of the emergence and global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Real-time polymerase chain reaction (PCR) is widely used to diagnose COVID-19, but it is time-consuming and requires sending samples to test centers. Thus, the need to detect antigens for rapid on-site diagnosis rather than PCR is increasing. We quantified the nucleocapsid (N) protein in SARS-CoV-2 using an electro-immunosorbent assay (El-ISA) and a multichannel impedance analyzer with a 96-interdigitated microelectrode sensor (ToAD). The El-ISA measures impedance signals from residual detection antibodies after sandwich assays and thus offers highly specific, label-free detection of the N protein with low cross-reactivity. The ToAD sensor enables the real-time electrochemical detection of multiple samples in conventional 96-well plates. The limit of detection for the N protein was 0.1 ng/mL with a detection range up to 10 ng/mL. This system did not detect signals for the S protein. While this study focused on detecting the N protein in SARS-CoV-2, our system can also be widely applicable to detecting various biomolecules involved in antigen-antibody interactions.
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Affiliation(s)
- Hana Cho
- Department
of Chemical and Biological Engineering, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Republic of Korea
- Industry
Collaboration Center, Sookmyung Women’s
University, Yongsan-gu, Seoul 04310, Republic
of Korea
| | - Suhyun Shim
- Department
of Chemical and Biological Engineering, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Republic of Korea
| | - Won Woo Cho
- Cantis
Inc., Ansan-si, Gyeonggi-do 15588, Republic of Korea
| | - Sungbo Cho
- Department
of Electronics Engineering, Gachon University, Seongnam-si, Gyeonggi-do 13120, Republic of Korea
| | - Hanseung Baek
- Comprehensive
Dental Care Center, Purme Nexon Children
Rehabilitation Hospital, Mapo-gu, Seoul 03918, Republic
of Korea
| | - Sang-Myung Lee
- Cantis
Inc., Ansan-si, Gyeonggi-do 15588, Republic of Korea
| | - Dong-Sik Shin
- Department
of Chemical and Biological Engineering, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Republic of Korea
- Industry
Collaboration Center, Sookmyung Women’s
University, Yongsan-gu, Seoul 04310, Republic
of Korea
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2
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Kroutil O, Kabeláč M, Dorčák V, Vacek J. Structures of Peptidic H‐wires at Mercury Surface: Molecular Dynamics Study. ELECTROANAL 2019. [DOI: 10.1002/elan.201900314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ondřej Kroutil
- Institute of Physics and Biophysics, Faculty of ScienceUniversity of South Bohemia Branisovska 1760 370 05 Ceske Budejovice Czech Republic
| | - Martin Kabeláč
- Department of Chemistry, Faculty of ScienceUniversity of South Bohemia Branisovska 31 370 05 Ceske Budejovice Czech Republic
| | - Vlastimil Dorčák
- Institute of Biophysics of the CAS Kralovopolska 135 612 65 Brno Czech Republic
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and DentistryPalacky University Hnevotinska 3 775 15 Olomouc Czech Republic
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3
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Tang M, Gandhi NS, Burrage K, Gu Y. Interaction of gold nanosurfaces/nanoparticles with collagen-like peptides. Phys Chem Chem Phys 2019; 21:3701-3711. [PMID: 30361726 DOI: 10.1039/c8cp05191g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Nanotechnology has quickly emerged as a promising research field with potential effects in disease treatments. For example, gold nanoparticles (AuNPs) have been extensively used in diagnostics and therapeutics. When administrated into human tissues, AuNPs first encounter extracellular matrix (ECM) molecules. Amongst all the ECM components, collagen is the main tension-resisting constituent, whose biofunctional and mechanical properties are strongly dependent on its hierarchical structure. Therefore, an in-depth understanding of the structural response of collagen to the presence of gold nanosurfaces (AuNS) and AuNPs is crucial in terms of clinical applications of AuNPs. However, detailed understanding of the molecular-level and atomic-level interaction between AuNS/AuNPs and collagen in the ECM is elusive. In this study, comprehensive molecular dynamics (MD) simulations have been performed to investigate the molecular behaviour of a collagen molecule segment (CMS) in the presence of AuNS/AuNPs in explicit water, aiming to explore the interaction of AuNS/AuNPs with collagen triple helices at the molecular and atomic levels. The results show that the CMS forms a rapid association with AuNS/AuNPs and undergoes a severe unfolding upon adsorption on AuNS/AuNPs, indicating an unfolding propensity of gold surfaces. We conclude that collagen triple helices unfold readily on AuNS and bare AuNPs, due to the interaction of gold surfaces with the protein backbone. The revealed clear unfolding nature and the unravelled atomic-level unfolding mechanism of collagen triple helices onto AuNPs contribute to the development of AuNPs for biomedical and therapeutic applications, and the design of gold-binding proteins.
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Affiliation(s)
- Ming Tang
- School of Chemistry Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, Australia.
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4
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Lee DJ, Park HS, Koo K, Lee JY, Nam YS, Lee W, Yang MY. Gold Binding Peptide Identified from Microfluidic Biopanning: An Experimental and Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:522-528. [PMID: 30592604 DOI: 10.1021/acs.langmuir.8b02563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biopanning refers to the processes of screening peptides with a high affinity to a target material. Microfluidic biopanning has advantages compared to conventional biopanning which requires large amounts of the target material and involves inefficient multiple pipetting steps to remove nonspecific or low-affinity peptides. Here, we fabricate a microfluidic biopanning system to identify a new gold-binding peptide (GBP). A polydimethylsiloxane microfluidic device is fabricated and bonded to a glass slide with a gold pattern that is deposited by electron-beam evaporation. The microfluidic biopanning system can provide high adjustability in the washing step during the biopanning process because the liquid flow rate and the resulting shear stress can be precisely controlled. The surface plasmon resonance analysis shows that the binding affinity of the identified GBP is comparable to previously reported GBPs. Moreover, molecular dynamics simulations are performed to understand its binding affinity against the gold surface in detail. Theoretical calculations suggest that the association and dissociation rates of the GBPs depend on their sequence-dependent conformations and interactions with the gold surface. These findings provide insight into designing efficient biopanning tools and peptides with a high affinity for various target materials.
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Affiliation(s)
| | | | - Kunmo Koo
- Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , 291 Daehak-ro, Yuseong-gu , Daejeon 34141 , Republic of Korea
| | - Jeong Yong Lee
- Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , 291 Daehak-ro, Yuseong-gu , Daejeon 34141 , Republic of Korea
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5
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Song M, Sun Y, Luo Y, Zhu Y, Liu Y, Li H. Exploring the Mechanism of Inhibition of Au Nanoparticles on the Aggregation of Amyloid-β(16-22) Peptides at the Atom Level by All-Atom Molecular Dynamics. Int J Mol Sci 2018; 19:ijms19061815. [PMID: 29925792 PMCID: PMC6032210 DOI: 10.3390/ijms19061815] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 01/01/2023] Open
Abstract
The abnormal self-assembly of the amyloid-β peptide into toxic β-rich aggregates can cause Alzheimer’s disease. Recently, it has been shown that small gold nanoparticles (AuNPs) inhibit Aβ aggregation and fibrillation by slowing down the nucleation process in experimental studies. However, the effects of AuNPs on Aβ oligomeric structures are still unclear. In this study, we investigate the conformation of Aβ(16-22) tetramers/octamers in the absence and presence of AuNPs using extensive all-atom molecular-dynamics simulations in explicit solvent. Our studies demonstrate that the addition of AuNPs into Aβ(16-22) solution prevents β-sheet formation, and the inhibition depends on the concentration of Aβ(16-22) peptides. A detailed analysis of the Aβ(16-22)/Aβ(16-22)/water/AuNPs interactions reveals that AuNPs inhibit the β-sheet formation resulting from the same physical forces: hydrophobic interactions. Overall, our computational study provides evidence that AuNPs are likely to inhibit Aβ(16-22) and full-length Aβ fibrillation. Thus, this work provides theoretical insights into the development of inorganic nanoparticles as drug candidates for treatment of AD.
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Affiliation(s)
- Menghua Song
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China.
- College of Energy and Mechanical Engineering, Shanghai University of Electric Power, Shanghai 200090, China.
| | - Yunxiang Sun
- State Key Laboratory of Surface Physics, Key Laboratory of Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Yin Luo
- State Key Laboratory of Surface Physics, Key Laboratory of Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Yanyan Zhu
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China.
| | - Yongsheng Liu
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China.
| | - Huiyu Li
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China.
- State Key Laboratory of Surface Physics, Key Laboratory of Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.
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6
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Yagi S, Akanuma S, Kaji A, Niiro H, Akiyama H, Uchida T, Yamagishi A. Selection of a platinum-binding sequence in a loop of a four-helix bundle protein. J Biosci Bioeng 2017; 125:192-198. [PMID: 29050803 DOI: 10.1016/j.jbiosc.2017.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/01/2017] [Accepted: 09/20/2017] [Indexed: 10/18/2022]
Abstract
Protein-metal hybrids are functional materials with various industrial applications. For example, a redox enzyme immobilized on a platinum electrode is a key component of some biofuel cells and biosensors. To create these hybrid materials, protein molecules are bound to metal surfaces. Here, we report the selection of a novel platinum-binding sequence in a loop of a four-helix bundle protein, the Lac repressor four-helix protein (LARFH), an artificial protein in which four identical α-helices are connected via three identical loops. We created a genetic library in which the Ser-Gly-Gln-Gly-Gly-Ser sequence within the first inter-helical loop of LARFH was semi-randomly mutated. The library was then subjected to selection for platinum-binding affinity by using the T7 phage display method. The majority of the selected variants contained the Tyr-Lys-Arg-Gly-Tyr-Lys (YKRGYK) sequence in their randomized segment. We characterized the platinum-binding properties of mutant LARFH by using quartz crystal microbalance analysis. Mutant LARFH seemed to interact with platinum through its loop containing the YKRGYK sequence, as judged by the estimated exclusive area occupied by a single molecule. Furthermore, a 10-residue peptide containing the YKRGYK sequence bound to platinum with reasonably high affinity and basic side chains in the peptide were crucial in mediating this interaction. In conclusion, we have identified an amino acid sequence, YKRGYK, in the loop of a helix-loop-helix motif that shows high platinum-binding affinity. This sequence could be grafted into loops of other polypeptides as an approach to immobilize proteins on platinum electrodes for use as biosensors among other applications.
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Affiliation(s)
- Sota Yagi
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan
| | - Asumi Kaji
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hiroya Niiro
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hayato Akiyama
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Tatsuya Uchida
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
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7
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Hughes ZE, Wei G, Drew KLM, Colombi Ciacchi L, Walsh TR. Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10193-10204. [PMID: 28885033 DOI: 10.1021/acs.langmuir.7b02480] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
| | - Gang Wei
- Hybrid Materials Interface Group, Faculty of Production Engineering, University of Bremen , D-28359 Bremen, Germany
| | - Kurt L M Drew
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interface Group, Faculty of Production Engineering, University of Bremen , D-28359 Bremen, Germany
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
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8
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Walsh TR. Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures. Acc Chem Res 2017; 50:1617-1624. [PMID: 28665581 DOI: 10.1021/acs.accounts.7b00065] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face challenges in their successful application to model the biotic-abiotic interface, related to several factors. For instance, simulations require a plausible description of the chemistry and the physics of the interface, which comprises two very different states of matter, in the presence of liquid water. Also, it is essential that the conformational ensemble be comprehensively characterized under these conditions; this is especially challenging because intrinsically disordered peptides do not typically admit one single structure or set of structures. Moreover, a plausible structural model of the substrate is required, which may require a high level of detail, even for single-element materials such as Au surfaces or graphene. Developing and applying strategies to make credible predictions of the conformational ensemble of adsorbed peptides and using these to construct structure-property relationships of these interfaces have been the goals of our efforts. We have made substantial progress in developing interatomic potentials for these interfaces and adapting advanced conformational sampling approaches for these purposes. This Account summarizes our progress in the development and deployment of interfacial force fields and molecular simulation techniques for the purpose of elucidating these insights at biomolecule-materials interfaces, using examples from our laboratories ranging from noble-metal interfaces to graphitic substrates (including carbon nanotubes and graphene) and oxide materials (such as titania). In addition to the well-established application areas of plasmonic materials, biosensing, and the production of medical implant materials, we outline new directions for this field that have the potential to bring new advances in areas such as energy materials and regenerative medicine.
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Affiliation(s)
- Tiffany R. Walsh
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
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9
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Yaakov N, Chaikin Y, Wexselblatt E, Tor Y, Vaskevich A, Rubinstein I. Application of Surface Click Reactions to Localized Surface Plasmon Resonance (LSPR) Biosensing. Chemistry 2017; 23:10148-10155. [DOI: 10.1002/chem.201701511] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Noga Yaakov
- Department of Materials and Interfaces Weizmann Institute of Science Rehovot 7610001 Israel
| | - Yulia Chaikin
- Department of Materials and Interfaces Weizmann Institute of Science Rehovot 7610001 Israel
| | - Ezequiel Wexselblatt
- Department of Chemistry and Biochemistry University of California San Diego, La Jolla California 92093 USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry University of California San Diego, La Jolla California 92093 USA
| | - Alexander Vaskevich
- Department of Materials and Interfaces Weizmann Institute of Science Rehovot 7610001 Israel
| | - Israel Rubinstein
- Department of Materials and Interfaces Weizmann Institute of Science Rehovot 7610001 Israel
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10
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Hughes ZE, Kochandra R, Walsh TR. Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3742-3754. [PMID: 28358489 DOI: 10.1021/acs.langmuir.6b04558] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The adsorption of three homo-tripeptides, HHH, YYY, and SSS, at the aqueous Au interface is investigated, using molecular dynamics simulations. We find that consideration of surface facet effects, relevant to experimental conditions, opens up new questions regarding interpretations of current experimental findings. Our well-tempered metadynamics simulations predict the rank ordering of the tripeptide binding affinities at aqueous Au(111) to be YYY > HHH > SSS. This ranking differs with that obtained from existing experimental data which used surface-immobilized Au nanoparticles as the target substrate. The influence of Au facet on these experimental findings is then considered, via our binding strength predictions of the relevant amino acids at aqueous Au(111) and Au(100)(1 × 1). The Au(111) interface supports an amino acid ranking of Tyr > HisA ≃ HisH > Ser, matching that of the tripeptides on Au(111), while the ranking on Au(100) is HisA > Ser ≃ Tyr ≃ HisH, with only HisA showing non-negligible binding. The substantial reduction in Tyr amino acid affinity for Au(100) vs Au(111) offers one possible explanation for the experimentally observed weaker adsorption of YYY on the nanoparticle-immobilized substrate compared with HHH. In a separate set of simulations, we predict the structures of the adsorbed tripeptides at the two aqueous Au facets, revealing facet-dependent differences in the adsorbed conformations. Our findings suggest that Au facet effects, where relevant, may influence the adsorption structures and energetics of biomolecules, highlighting the possible influence of the structural model used to interpret experimental binding data.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia
| | - Raji Kochandra
- Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia
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11
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Abstract
Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
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12
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Ozboyaci M, Martinez M, Wade RC. An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association. J Chem Theory Comput 2016; 12:4563-77. [DOI: 10.1021/acs.jctc.6b00350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Musa Ozboyaci
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Heidelberg University, INF 205, 69120 Heidelberg, Germany
| | - Michael Martinez
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C. Wade
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, INF 282, 69120 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120 Heidelberg, Germany
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13
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Ozboyaci M, Kokh DB, Wade RC. Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations. Phys Chem Chem Phys 2016; 18:10191-200. [PMID: 27021898 DOI: 10.1039/c6cp00201c] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The addition of three N-terminal histidines to β-lactamase inhibitor protein was shown experimentally to increase its binding potency to an Au(111) surface substantially but the binding mechanism was not resolved. Here, we propose a complete adsorption mechanism for this fusion protein by means of a multi-scale simulation approach and free energy calculations. We find that adsorption is a three-step process: (i) recognition of the surface predominantly by the histidine fusion peptide and formation of an encounter complex facilitated by a reduced dielectric screening of water in the interfacial region, (ii) adsorption of the protein on the surface and adoption of a specific binding orientation, and (iii) adaptation of the protein structure on the metal surface accompanied by induced fit. We anticipate that the mechanistic features of protein adsorption to an Au(111) surface revealed here can be extended to other inorganic surfaces and proteins and will therefore aid the design of specific protein-surface interactions.
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Affiliation(s)
- M Ozboyaci
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
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14
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Kyrychenko A. NANOGOLD decorated by pHLIP peptide: comparative force field study. Phys Chem Chem Phys 2016; 17:12648-60. [PMID: 25903421 DOI: 10.1039/c5cp01136a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The potential of gold nanoparticles (AuNPs) in therapeutic and diagnostic cancer applications is becoming increasingly recognized, which focuses on their efficient and specific delivery from passive accumulation in tumour tissue to directly targeting tumor-specific biomarkers. AuNPs functionalized by pH low insertion peptide (pHLIP) have recently revealed the capability of targeting acidic tissues and inserting into cell membranes. However, the structure of AuNP-pHLIP conjugates and fundamental gold-peptide interactions still remain unknown. In this study, we have developed a series of molecular dynamics (MD) models reproducing a small gold nanoparticle coupled to pHLIP. We focus on Au135 nanoparticles that comprise a nearly spherical Au core (diameter ∼ 1.4 nm) functionalized with a monomaleimide moiety, mimicking a commercially available monomaleimido NANOGOLD® labelling agent. To probe the structure and folding of pHLIP, which is attached covalently to the maleimide NANOGOLD particle, we have benchmarked the performances of a series of popular, all-atom force fields (FF), including those of OPLS-AA, AMBER03, three variations of CHARMM FFs, as well as united-atom GROMOS G53A6 FF. We found that CHARMMs and OPLSAA FFs predict that in an aqueous salt solution at a neutral pH, pHLIP is partially bound onto the gold surface through some short hydrophobic peptide stretches, while at the same time, a large portion of peptide remains in solution. In contrast, AMBER03 and G53A6 FFs revealed the formation of compact, tightly bound peptide configurations adsorbed onto the nanoparticle core. To reproduce the experimental physical picture of the peptide adsorption onto gold in unfolded and unstructured conformations, our study suggests CHARMM36 and OPLS-AA FFs as a tool of choice for the computational studies of NANOGOLD decorated by pHLIP.
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Affiliation(s)
- A Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody square, Kharkiv 61022, Ukraine.
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15
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Guerreiro JRL, Bochenkov VE, Runager K, Aslan H, Dong M, Enghild JJ, De Freitas V, Ferreira Sales MG, Sutherland DS. Molecular Imprinting of Complex Matrices at Localized Surface Plasmon Resonance Biosensors for Screening of Global Interactions of Polyphenols and Proteins. ACS Sens 2016. [DOI: 10.1021/acssensors.5b00054] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Joana Rafaela Lara Guerreiro
- BioMark Sensor
Research-CINTESIS, Instituto Superior de Engenharia do Porto, Porto 4200-072, Portugal
- REQUIMTE/LAQV,
Departamento de Química e Bioquímica, Faculdade de Ciências
da Universidade do Porto, Porto 4169-007, Portugal
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus 8000, Denmark
| | - Vladimir E. Bochenkov
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus 8000, Denmark
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Kasper Runager
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus 8000, Denmark
| | - Hüsnü Aslan
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus 8000, Denmark
| | - Mingdong Dong
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus 8000, Denmark
| | - Jan J. Enghild
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus 8000, Denmark
- Department
of Molecular Biology and Genetics, Aarhus University, Aarhus 8000, Denmark
| | - Victor De Freitas
- REQUIMTE/LAQV,
Departamento de Química e Bioquímica, Faculdade de Ciências
da Universidade do Porto, Porto 4169-007, Portugal
| | | | - Duncan S. Sutherland
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Aarhus 8000, Denmark
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16
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Wright LB, Palafox-Hernandez JP, Rodger PM, Corni S, Walsh TR. Facet selectivity in gold binding peptides: exploiting interfacial water structure. Chem Sci 2015; 6:5204-5214. [PMID: 29449926 PMCID: PMC5669244 DOI: 10.1039/c5sc00399g] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/20/2015] [Indexed: 11/21/2022] Open
Abstract
Peptide sequences that can discriminate between gold facets under aqueous conditions offer a promising route to control the growth and organisation of biomimetically-synthesised gold nanoparticles. Knowledge of the interplay between sequence, conformations and interfacial properties is essential for predictable manipulation of these biointerfaces, but the structural connections between a given peptide sequence and its binding affinity remain unclear, impeding practical advances in the field. These structural insights, at atomic-scale resolution, are not easily accessed with experimental approaches, but can be delivered via molecular simulation. A current unmet challenge lies in forging links between predicted adsorption free energies derived from enhanced sampling simulations with the conformational ensemble of the peptide and the water structure at the surface. To meet this challenge, here we use an in situ combination of Replica Exchange with Solute Tempering with Metadynamics simulations to predict the adsorption free energy of a gold-binding peptide sequence, AuBP1, at the aqueous Au(111), Au(100)(1 × 1) and Au(100)(5 × 1) interfaces. We find adsorption to the Au(111) surface is stronger than to Au(100), irrespective of the reconstruction status of the latter. Our predicted free energies agree with experiment, and correlate with trends in interfacial water structuring. For gold, surface hydration is predicted as a chief determining factor in peptide-surface recognition. Our findings can be used to suggest how shaped seed-nanocrystals of Au, in partnership with AuBP1, could be used to control AuNP nanoparticle morphology.
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Affiliation(s)
- Louise B Wright
- Dept. of Chemistry , University of Warwick , Coventry , CV4 7AL , UK
| | | | - P Mark Rodger
- Dept. of Chemistry , University of Warwick , Coventry , CV4 7AL , UK
- Centre for Scientific Computing , University of Warwick , Coventry , CV4 7AL , UK .
| | - Stefano Corni
- Centro S3 CNR Istituto Nanoscienze , Modena , Italy .
| | - Tiffany R Walsh
- Institute for Frontier Materials , Deakin University , Geelong , 3216 , VIC , Australia .
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17
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Canoa P, Simón-Vázquez R, Popplewell J, González-Fernández Á. A quantitative binding study of fibrinogen and human serum albumin to metal oxide nanoparticles by surface plasmon resonance. Biosens Bioelectron 2015; 74:376-83. [PMID: 26162328 DOI: 10.1016/j.bios.2015.05.070] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 05/27/2015] [Accepted: 05/31/2015] [Indexed: 10/23/2022]
Abstract
The interaction of plasma proteins with metal oxide nanoparticles (NPs) is important due to the potential biomedical application of these NPs. In this study, new approaches were applied to measure quantitatively the kinetics and affinities of fibrinogen and human serum albumin (HSA) for TiO2, CeO2, Al2O3 and ZnO NPs immobilized on a sensor chip. Real-time surface plasmon resonance (SPR) measurements showed that fibrinogen interacted with TiO2 and CeO2 NPs with high affinity (135 and 40 pM, respectively) and to Al2O3 NPs with moderate affinity (15 nM). The data fitted well to the Langmuir model describing a 1:1 interaction. In contrast, HSA interacted with TiO2, CeO2 and Al2O3 NPs with lower affinity (80 nM, 37 nM and 2 µM, respectively) with the data fitting better to the conformational change model. TiO2 and CeO2 NPs had fast association rate constants with fibrinogen (1×10(6) M(-1) s(-1)) and Al2O3 NPs had a slower association rate constant (1×10(4) M(-1) s(-1)). By contrast, HSA had markedly slower association rate constants (1×10(3)-1×10(4) M(-1) s(-1)). The binding of the proteins was reversible, thus allowing the rapid capture of data for replicates. The occurrence of matrix effects was evaluated by using surfaces with different chemistries to capture the NPs, namely alginate, NeutrAvidin and bare gold. The affinity values determined for the NP-protein interactions were largely independent of the underlying surface used to capture the NPs.
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Affiliation(s)
- Pilar Canoa
- Departamento de Química Orgánica, Facultad de Química, Universidad de Vigo, 36310 Vigo, Spain.
| | - Rosana Simón-Vázquez
- Immunology, Biomedical Research Center (CINBIO) and Institute of Biomedical Research of Vigo (IBIV), University of Vigo, Campus Lagoas Marcosende, 36310 Vigo, Pontevedra, Spain
| | - Jonathan Popplewell
- Bio-Rad Laboratories Ltd, Bio-Rad House, Maxted Road, Hemel Hempstead, Hertfordshire HP2 7DX, UK
| | - África González-Fernández
- Immunology, Biomedical Research Center (CINBIO) and Institute of Biomedical Research of Vigo (IBIV), University of Vigo, Campus Lagoas Marcosende, 36310 Vigo, Pontevedra, Spain
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18
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Limo MJ, Perry CC. Thermodynamic Study of Interactions Between ZnO and ZnO Binding Peptides Using Isothermal Titration Calorimetry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6814-6822. [PMID: 26037020 DOI: 10.1021/acs.langmuir.5b01347] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
While material-specific peptide binding sequences have been identified using a combination of combinatorial methods and computational modeling tools, a deep molecular level understanding of the fundamental principles through which these interactions occur and in some instances modify the morphology of inorganic materials is far from being fully realized. Understanding the thermodynamic changes that occur during peptide-inorganic interactions and correlating these to structural modifications of the inorganic materials could be the key to achieving and mastering control over material formation processes. This study is a detailed investigation applying isothermal titration calorimetry (ITC) to directly probe thermodynamic changes that occur during interaction of ZnO binding peptides (ZnO-BPs) and ZnO. The ZnO-BPs used are reported sequences G-12 (GLHVMHKVAPPR), GT-16 (GLHVMHKVAPPR-GGGC), and alanine mutants of G-12 (G-12A6, G-12A11, and G-12A12) whose interaction with ZnO during solution synthesis studies have been extensively investigated. The interactions of the ZnO-BPs with ZnO yielded biphasic isotherms comprising both an endothermic and an exothermic event. Qualitative differences were observed in the isothermal profiles of the different peptides and ZnO particles studied. Measured ΔG values were between -6 and -8.5 kcal/mol, and high adsorption affinity values indicated the occurrence of favorable ZnO-BP-ZnO interactions. ITC has great potential in its use to understand peptide-inorganic interactions, and with continued development, the knowledge gained may be instrumental for simplification of selection processes of organic molecules for the advancement of material synthesis and design.
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Affiliation(s)
- Marion J Limo
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - Carole C Perry
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
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19
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Ramezani F, Habibi M, Rafii-Tabar H, Amanlou M. Effect of peptide length on the conjugation to the gold nanoparticle surface: a molecular dynamic study. ACTA ACUST UNITED AC 2015; 23:9. [PMID: 25630230 PMCID: PMC4312466 DOI: 10.1186/s40199-014-0085-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 12/17/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Gold nanoparticles now command a great deal of attention for medical applications. Despite the importance of nano-bio interfaces, interaction between peptides and proteins with gold surfaces is not still fully understood, especially in a molecular level. METHODS In the present study computational simulation of adsorption of 20 amino acids, in three forms of mono-amino acid, homo di-peptide and homo tri-peptide, on the gold nanoparticles was performed by Gromacs using OPLSAA force field. The flexibility, stability, and size effect of the peptides on the gold nanoparticles were studied as well as the molecular structure of them. RESULTS According to our results, adsorbed homo tri-peptides on the gold surface had more flexibility, more gyration, and the farthest distance from the GNP in comparison with homo di-peptides and mono-amino acids. CONCLUSION Our findings provide new insights into the precise control of interactions between amino acids anchored on the GNPs.
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Affiliation(s)
| | | | | | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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20
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Niide T, Goto M, Kamiya N. Enzymatic self-sacrificial display of an active protein on gold nanoparticles. RSC Adv 2014. [DOI: 10.1039/c3ra46384b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Niide T, Shimojo K, Wakabayashi R, Goto M, Kamiya N. Enzymatic fabrication of protein-decorated gold nanoparticles by the aid of artificial peptides with gold-binding affinity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:15596-15605. [PMID: 24274699 DOI: 10.1021/la401327h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Here, we report a new approach for the biofabrication of protein-immobilized gold nanoparticles (Au NPs), using oxidoreductase with gold-binding peptide-tagged recombinant proteins. The reduction of Au ions to Au(0) was achieved using a natural electron-donating cofactor, nicotinamide adenine dinucleotide, which was regenerated by the glycerol dehydrogenase (GLD) enzyme. First, we selected the A3 peptide (AYSSGAPPMPPF) as a gold binding moiety. The A3 peptide was introduced to the C-terminus of fusion proteins of immunoglobulin G (IgG)-binding domains of protein G and protein A. In the presence of the recombinant protein, the GLD-catalyzed cofactor reduction resulted in the efficient in situ fabrication of Au NPs immobilized with the fusion protein. Moreover, the protein-immobilized Au NPs were shown to have IgG binding activity. Although the A3 peptide had the ability to stabilize Au NPs, the results suggested that its binding affinity for Au NPs was unexpectedly weaker than that of His-tag. A cysteine residue was thus introduced to a recombinant protein adjacent to the A3 peptide. Finally, an artificial peptide, comprising A3 sequence with the C-terminal single cysteine residue, enabled the stable display of a fusion protein while maintaining its IgG binding activity through the Au-S bond. This enzyme-assisted one-pot methodology for protein-Au NPs conjugation offers one potent route for the facile fabrication of biomolecule-decorated metal NPs.
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Affiliation(s)
- Teppei Niide
- Department of Applied Chemistry, Graduate School of Engineering , 744 Motooka, Fukuoka 819-0395, Japan
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22
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Tang Z, Palafox-Hernandez JP, Law WC, Hughes ZE, Swihart MT, Prasad PN, Knecht MR, Walsh TR. Biomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors. ACS NANO 2013; 7:9632-46. [PMID: 24124916 DOI: 10.1021/nn404427y] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Bionanocombinatorics is an emerging field that aims to use combinations of positionally encoded biomolecules and nanostructures to create materials and devices with unique properties or functions. The full potential of this new paradigm could be accessed by exploiting specific noncovalent interactions between diverse palettes of biomolecules and inorganic nanostructures. Advancement of this paradigm requires peptide sequences with desired binding characteristics that can be rationally designed, based upon fundamental, molecular-level understanding of biomolecule-inorganic nanoparticle interactions. Here, we introduce an integrated method for building this understanding using experimental measurements and advanced molecular simulation of the binding of peptide sequences to gold surfaces. From this integrated approach, the importance of entropically driven binding is quantitatively demonstrated, and the first design rules for creating both enthalpically and entropically driven nanomaterial-binding peptide sequences are developed. The approach presented here for gold is now being expanded in our laboratories to a range of inorganic nanomaterials and represents a key step toward establishing a bionanocombinatorics assembly paradigm based on noncovalent peptide-materials recognition.
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Affiliation(s)
- Zhenghua Tang
- Department of Chemistry, University of Miami , 1301 Memorial Drive, Coral Gables, Florida 33146 United States
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23
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Sapsford KE, Algar WR, Berti L, Gemmill KB, Casey BJ, Oh E, Stewart MH, Medintz IL. Functionalizing nanoparticles with biological molecules: developing chemistries that facilitate nanotechnology. Chem Rev 2013; 113:1904-2074. [PMID: 23432378 DOI: 10.1021/cr300143v] [Citation(s) in RCA: 818] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kim E Sapsford
- Division of Biology, Department of Chemistry and Materials Science, Office of Science and Engineering Laboratories, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
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24
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Wright LB, Rodger PM, Corni S, Walsh TR. GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100). J Chem Theory Comput 2013; 9:1616-30. [DOI: 10.1021/ct301018m] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Louise B. Wright
- University of Warwick, Dept.
of Chemistry and Centre for Scientific Computing, Coventry, CV4 7AL,
United Kingdom
| | - P. Mark Rodger
- University of Warwick, Dept.
of Chemistry and Centre for Scientific Computing, Coventry, CV4 7AL,
United Kingdom
| | | | - Tiffany R. Walsh
- Deakin University,
Institute for
Frontier Materials, Geelong, Vic. 3216, Australia
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25
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Evolutionary screening and adsorption behavior of engineered M13 bacteriophage and derived dodecapeptide for selective decoration of gold interfaces. J Colloid Interface Sci 2013; 389:220-9. [DOI: 10.1016/j.jcis.2012.08.046] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/02/2012] [Accepted: 08/03/2012] [Indexed: 11/19/2022]
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26
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Bellucci L, Brancolini G, Calzolari A, Carrillo Parramon O, Corni S, Di Felice R. Proteins and Peptides at Gold Surfaces: Insights from Atomistic Simulations. ACTA ACUST UNITED AC 2012. [DOI: 10.1021/bk-2012-1120.ch010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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27
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Brancolini G, Kokh DB, Calzolai L, Wade RC, Corni S. Docking of ubiquitin to gold nanoparticles. ACS NANO 2012; 6:9863-78. [PMID: 23033917 DOI: 10.1021/nn303444b] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Protein-nanoparticle associations have important applications in nanoscience and nanotechnology such as targeted drug delivery and theranostics. However, the mechanisms by which proteins recognize nanoparticles and the determinants of specificity are still poorly understood at the microscopic level. Gold is a promising material in nanoparticles for nanobiotechnology applications because of the ease of its functionalization and its tunable optical properties. Ubiquitin is a small, cysteine-free protein (ubiquitous in eukaryotes) whose binding to gold nanoparticles has been characterized recently by nuclear magnetic resonance (NMR). To reveal the molecular basis of these protein-nanoparticle interactions, we performed simulations at multiple levels (ab initio quantum mechanics, classical molecular dynamics and Brownian dynamics) and compared the results with experimental data (circular dichroism and NMR). The results provide a model of the ensemble of structures constituting the ubiquitin-gold surface complex, and insights into the driving forces for the binding of ubiquitin to gold nanoparticles, the role of nanoparticle surfactants (citrate) in the association process, and the origin of the perturbations in the NMR chemical shifts.
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Affiliation(s)
- Giorgia Brancolini
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy.
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28
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Mereghetti P, Kokh D, McCammon JA, Wade RC. Diffusion and association processes in biological systems: theory, computation and experiment. BMC BIOPHYSICS 2011; 4:2. [PMID: 21595997 PMCID: PMC3093674 DOI: 10.1186/2046-1682-4-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 03/02/2011] [Indexed: 12/17/2022]
Abstract
Macromolecular diffusion plays a fundamental role in biological processes. Here, we give an overview of recent methodological advances and some of the challenges for understanding how molecular diffusional properties influence biological function that were highlighted at a recent workshop, BDBDB2, the second Biological Diffusion and Brownian Dynamics Brainstorm.
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Affiliation(s)
- Paolo Mereghetti
- Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
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29
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Tighilt FZ, Subramanian P, Belhaneche-Bensemra N, Boukherroub R, Gabouze N, Sam S, Szunerits S. Localized surface plasmon resonance interfaces coated with poly[3-(pyrrolyl)carboxylic acid] for histidine-tagged peptide sensing. Analyst 2011; 136:4211-6. [DOI: 10.1039/c1an15535k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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