1
|
Nirmalraj PN, Rossell MD, Dachraoui W, Thompson D, Mayer M. In Situ Observation of Chemically Induced Protein Denaturation at Solvated Interfaces. ACS APPLIED MATERIALS & INTERFACES 2023; 15:48015-48026. [PMID: 37797325 PMCID: PMC10591235 DOI: 10.1021/acsami.3c10510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023]
Abstract
Proteins unfold in chaotropic salt solutions, a process that is difficult to observe at the single protein level. The work presented here demonstrates that a liquid-based atomic force microscope and graphene liquid-cell-based scanning transmission electron microscope make it possible to observe chemically induced protein unfolding. To illustrate this capability, ferritin proteins were deposited on a graphene surface, and the concentration-dependent urea- or guanidinium-induced changes of morphology were monitored for holo-ferritin with its ferrihydrite core as well as apo-ferritin without this core. Depending on the chaotropic agent the liquid-based imaging setup captured an unexpected transformation of natively folded holo-ferritin proteins into rings after urea treatment but not after guanidinium treatment. Urea treatment of apo-ferritin did not result in nanorings, confirming that nanorings are a specific signature of denaturation of holo-ferritins after exposture to sufficiently high urea concentrations. Mapping the in situ images with molecular dynamics simulations of ferritin subunits in urea solutions suggests that electrostatic destabilization triggers denaturation of ferritin as urea makes direct contact with the protein and also disrupts the water H-bonding network in the ferritin solvation shell. Our findings deepen the understanding of protein denaturation studied using label-free techniques operating at the solid-liquid interface.
Collapse
Affiliation(s)
- Peter Niraj Nirmalraj
- Transport
at Nanoscale Interfaces Laboratory, Swiss
Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Marta D. Rossell
- Electron
Microscopy Center, Swiss Federal Laboratories
for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Walid Dachraoui
- Electron
Microscopy Center, Swiss Federal Laboratories
for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Damien Thompson
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94T9PX, Ireland
| | - Michael Mayer
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| |
Collapse
|
2
|
Zhang L, Chu M, Ji C, Wei J, Yang Y, Huang Z, Tan W, Tan J, Yuan Q. In Situ Visualization of Epidermal Growth Factor Receptor Nuclear Translocation with Circular Bivalent Aptamer. Anal Chem 2022; 94:17413-17421. [PMID: 36469021 DOI: 10.1021/acs.analchem.2c02762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Epidermal growth factor receptor (EGFR) nuclear translocation correlates with the abnormal proliferation, migration, and anti-apoptosis of tumor cells. Monitoring EGFR nuclear translocation provides insights into the molecular mechanisms underlying cancers. EGFR nuclear translocation includes two processes, EGFR phosphorylation and phosphorylated EGFR translocation to the nucleus. With the help of aptamers, probes that can achieve the first step of anchoring phosphorylated EGFR have been developed. However, the EGFR nuclear translocation can last for hours, posing a challenge to monitor the entire nuclear translocation in living cells. Herein, we designed a circular bivalent aptamer-functionalized optical probe with greatly enhanced stability for long-term visualization of EGFR nuclear translocation in situ. The results of cell experiments show that the probe could monitor the entire nuclear translocation of EGFR. The findings of tissue and in vivo experiments demonstrate that the probe can evaluate the development and progression of tumors by imaging EGFR nuclear translocation in situ. The proposed approach allows us to monitor EGFR nuclear translocation in the long term, indicating its great potential in investigating the mechanisms of cancers and guiding for tumor treatment.
Collapse
Affiliation(s)
- Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Mengge Chu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yanbing Yang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongnan Huang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.,The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.,College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| |
Collapse
|
3
|
Rawnaque FS, Simon JC. The effects of elastic modulus and impurities on bubble nuclei available for acoustic cavitation in polyacrylamide hydrogels. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2022; 152:3502. [PMID: 36586847 DOI: 10.1121/10.0016445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Safety of biomedical ultrasound largely depends on controlling cavitation bubbles in vivo, yet bubble nuclei in biological tissues remain unexplored compared to water. This study evaluates the effects of elastic modulus (E) and impurities on bubble nuclei available for cavitation in tissue-mimicking polyacrylamide (PA) hydrogels. A 1.5 MHz focused ultrasound transducer with f# = 0.7 was used to induce cavitation in 17.5%, 20%, and 22.5% v/v PA hydrogels using 10-ms pulses with pressures up to peak negative pressure (p-) = 35 MPa. Cavitation was monitored at 0.075 ms through high-speed photography at 40 000 fps. At p- = 29 MPa for all hydrogels, cavitation occurred at random locations within the -6 dB focal area [9.4 × 1.2 mm (p-)]. Increasing p- to 35 MPa increased bubble location consistency and caused shock scattering in the E = 282 MPa hydrogels; as the E increased to 300 MPa, bubble location consistency decreased (p = 0.045). Adding calcium phosphate or cholesterol at 0.25% w/v or bovine serum albumin at 5% or 10% w/v in separate 17.5% PA as impurities decreased the cavitation threshold from p- = 13.2 MPa for unaltered PA to p- = 11.6 MPa, p- = 7.3 MPa, p- = 9.7 MPa, and p- = 7.5 MPa, respectively. These results suggest that both E and impurities affect the bubble nuclei available for cavitation in tissue-mimicking hydrogels.
Collapse
Affiliation(s)
- Ferdousi Sabera Rawnaque
- Graduate Program in Acoustics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Julianna C Simon
- Graduate Program in Acoustics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
4
|
Kuten Pella O, Hornyák I, Horváthy D, Fodor E, Nehrer S, Lacza Z. Albumin as a Biomaterial and Therapeutic Agent in Regenerative Medicine. Int J Mol Sci 2022; 23:10557. [PMID: 36142472 PMCID: PMC9502107 DOI: 10.3390/ijms231810557] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 02/07/2023] Open
Abstract
Albumin is a constitutional plasma protein, with well-known biological functions, e.g., a nutrient for stem cells in culture. However, albumin is underutilized as a biomaterial in regenerative medicine. This review summarizes the advanced therapeutic uses of albumin, focusing on novel compositions that take advantage of the excellent regenerative potential of this protein. Albumin coating can be used for enhancing the biocompatibility of various types of implants, such as bone grafts or sutures. Albumin is mainly known as an anti-attachment protein; however, using it on implantable surfaces is just the opposite: it enhances stem cell adhesion and proliferation. The anticoagulant, antimicrobial and anti-inflammatory properties of albumin allow fine-tuning of the biological reaction to implantable tissue-engineering constructs. Another potential use is combining albumin with natural or synthetic materials that results in novel composites suitable for cardiac, neural, hard and soft tissue engineering. Recent advances in materials have made it possible to electrospin the globular albumin protein, opening up new possibilities for albumin-based scaffolds for cell therapy. Several described technologies have already entered the clinical phase, making good use of the excellent biological, but also regulatory, manufacturing and clinical features of serum albumin.
Collapse
Affiliation(s)
| | - István Hornyák
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary
| | - Dénes Horváthy
- Department of Interventional Radiology, Semmelweis University, 1122 Budapest, Hungary
| | - Eszter Fodor
- Institute for Sports and Health Sciences, Hungarian University of Sports Science, 1123 Budapest, Hungary
| | - Stefan Nehrer
- Center for Regenerative Medicine, Danube University Krems, 3500 Krems an der Donau, Austria
| | - Zsombor Lacza
- Orthosera GmbH, 3500 Krems an der Donau, Austria
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary
- Institute for Sports and Health Sciences, Hungarian University of Sports Science, 1123 Budapest, Hungary
| |
Collapse
|
5
|
Kadadou D, Tizani L, Wadi VS, Banat F, Naddeo V, Alsafar H, Yousef AF, Hasan SW. Optimization of an rGO-based biosensor for the sensitive detection of bovine serum albumin: Effect of electric field on detection capability. CHEMOSPHERE 2022; 301:134700. [PMID: 35469903 DOI: 10.1016/j.chemosphere.2022.134700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Despite significant progress in the field of biosensing, the impact of electric field on biosensor detection capability and the feasibility of the biosensor application in wastewater has yet to be investigated. The objective of this study was to develop a low-cost, highly sensitive, and selective reduced graphene oxide (rGO)-based biosensor. The constructed biosensor consists of an in-house prepared GO and a four-terminal Kelvin sensing. Spin-coating was chosen as the deposition technique and results revealed an optimal GO number of layers and concentration of 7 and 2 mg/mL, respectively. Experiments to determine the effects of electric field on the performance of the biosensor showed significant changes in the biosensor surface, also presenting a direct impact on the biosensor functionality, such that the biosensor showed an increase in limit of detection (LOD) from 1 to 106 fg/mL when the applied voltage was increased from 0.0008 to 0.2 V. Furthermore, this study successfully explores a pilot scale setup, mimicking wastewater flow through sewage pipelines. The demonstrated improvements in the detection capability and sensitivity of this biosensor at optimized testing conditions make it a promising candidate for further development and deployment for the detection of protein analytes present at very low concentrations in aqueous solutions. In addition, the application of this biosensor could be extended to the detection of protein analytes of interest (such as the spike protein of SARS-CoV-2) in much more complex solutions, like wastewater.
Collapse
Affiliation(s)
- Dana Kadadou
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates; Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Lina Tizani
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Vijay S Wadi
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates; Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Fawzi Banat
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates; Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II #132, 84084, Fisciano, SA, Italy
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates; Emirates Bio-research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates; Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed F Yousef
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates; Department of Biology, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Shadi W Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates; Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
6
|
Wu X, Wang C, Hao P, He F, Yao Z, Zhang X. Adsorption properties of albumin and fibrinogen on hydrophilic/hydrophobic TiO 2 surfaces: A molecular dynamics study. Colloids Surf B Biointerfaces 2021; 207:111994. [PMID: 34303996 DOI: 10.1016/j.colsurfb.2021.111994] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/06/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023]
Abstract
In serval experimental researches, UV-induced hydrophilicity enabled better hemocompatibility in the TiO2 surface, which was considered to be caused by the removal of the carboxylic acid contamination from the surface. In this paper, we altered the surface wetting property by applying the formate contamination on the rutile (110) surface, and systematically investigated the adsorption properties of albumin and fibrinogen on hydrophilic/hydrophobic TiO2 surface. Unique contacts were found between the charged residues and the hydrophilic surface, anchoring the protein on the surface. The small size and the heart shape of albumin make it easy to cross the stable water layers near the surface. Besides, albumin has a higher proportion of charged residues, so it can form more unique contacts on the hydrophilic surface. Therefore, the albumin tends to adsorb on the hydrophilic surface. For the hydrophobic surface, the water layers near the surface are weakened, which helps the fibrinogen diffusing to the surface and adjusting its orientation. Although the hydrophobic surface cannot form the unique contacts, the larger size of fibrinogen can provide more residues to form enough ordinary contacts after adjusting, and then achieves stable adsorption. Therefore, fibrinogen tends to adsorb on the hydrophobic surface.
Collapse
Affiliation(s)
- Xiao Wu
- Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China
| | - Chenyang Wang
- Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China
| | - Pengfei Hao
- Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China
| | - Feng He
- Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China
| | - Zhaohui Yao
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiwen Zhang
- Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
7
|
Sitsanidis ED, Schirmer J, Lampinen A, Mentel KK, Hiltunen VM, Ruokolainen V, Johansson A, Myllyperkiö P, Nissinen M, Pettersson M. Tuning protein adsorption on graphene surfaces via laser-induced oxidation. NANOSCALE ADVANCES 2021; 3:2065-2074. [PMID: 36133099 PMCID: PMC9418809 DOI: 10.1039/d0na01028f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/11/2021] [Indexed: 06/14/2023]
Abstract
An approach for controlled protein immobilization on laser-induced two-photon (2P) oxidation patterned graphene oxide (GO) surfaces is described. Selected proteins, horseradish peroxidase (HRP) and biotinylated bovine serum albumin (b-BSA) were successfully immobilized on oxidized graphene surfaces, via non-covalent interactions, by immersion of graphene-coated microchips in the protein solution. The effects of laser pulse energy, irradiation time, protein concentration and duration of incubation on the topography of immobilized proteins and consequent defects upon the lattice of graphene were systemically studied by atomic force microscopy (AFM) and Raman spectroscopy. AFM and fluorescence microscopy confirmed the selective aggregation of protein molecules towards the irradiated areas. In addition, the attachment of b-BSA was detected by a reaction with fluorescently labelled avidin-fluorescein isothiocyanate (Av-FITC). In contrast to chemically oxidized graphene, laser-induced oxidation introduces the capability for localization on oxidized areas and tunability of the levels of oxidation, resulting in controlled guidance of proteins by light over graphene surfaces and progressing towards graphene microchips suitable for biomedical applications.
Collapse
Affiliation(s)
- Efstratios D Sitsanidis
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
| | - Johanna Schirmer
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
| | - Aku Lampinen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
| | - Kamila K Mentel
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
| | - Vesa-Matti Hiltunen
- Department of Physics, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
| | - Visa Ruokolainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
| | - Andreas Johansson
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
- Department of Physics, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
| | - Pasi Myllyperkiö
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
| | - Maija Nissinen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
| | - Mika Pettersson
- Department of Chemistry, Nanoscience Center, University of Jyväskylä P. O. Box 35, FI-40014 JYU Finland
| |
Collapse
|
8
|
Vilhena JG, Ortega M, Uhlig MR, Garcia R, Pérez R. Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G. ACS Sens 2021; 6:553-564. [PMID: 33503368 DOI: 10.1021/acssensors.0c02241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive-a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime-where the mechanical response is linked to the presence of the water environment- followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potential.
Collapse
Affiliation(s)
- J. G. Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Maria Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Manuel R. Uhlig
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Ricardo Garcia
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| |
Collapse
|
9
|
Ortega M, Vilhena JG, Zotti LA, Díez-Pérez I, Cuevas JC, Pérez R. Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations. Biomolecules 2019; 9:biom9100611. [PMID: 31618974 PMCID: PMC6843909 DOI: 10.3390/biom9100611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 12/15/2022] Open
Abstract
In the growing field of biomolecular electronics, blue-copper Azurin stands out as one of the most widely studied protein in single-molecule contacts. Interestingly, despite the paramount importance of the structure/dynamics of molecular contacts in their transport properties, these factors remain largely unexplored from the theoretical point of view in the context of single Azurin junctions. Here we address this issue using all-atom Molecular Dynamics (MD) of Pseudomonas Aeruginosa Azurin adsorbed to a Au(111) substrate. In particular, we focus on the structure and dynamics of the free/adsorbed protein and how these properties are altered upon single-point mutations. The results revealed that wild-type Azurin adsorbs on Au(111) along two well defined configurations: one tethered via cysteine groups and the other via the hydrophobic pocket surrounding the Cu 2 + . Surprisingly, our simulations revealed that single amino-acid mutations gave rise to a quenching of protein vibrations ultimately resulting in its overall stiffening. Given the role of amino-acid vibrations and reorientation in the dehydration process at the protein-water-substrate interface, we suggest that this might have an effect on the adsorption process of the mutant, giving rise to new adsorption configurations.
Collapse
Affiliation(s)
- Maria Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - J G Vilhena
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.
| | - Linda A Zotti
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Ismael Díez-Pérez
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.
| | - Juan Carlos Cuevas
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| |
Collapse
|