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Atabay M, Sardroodi JJ, Ebrahimzadeh AR, Avestan MS. Modeling the Interaction of Anticancer Protein Azurin with the Nanosheets for Medical Applications. ChemistrySelect 2022. [DOI: 10.1002/slct.202202633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Maryam Atabay
- Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
- Molecular Science and Engineering Research Group (MSERG) Azarbaijan Shahid Madani University Tabriz Iran
- Department of Chemistry Azarbaijan Shahid Madani University Tabriz Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
- Molecular Science and Engineering Research Group (MSERG) Azarbaijan Shahid Madani University Tabriz Iran
- Department of Chemistry Azarbaijan Shahid Madani University Tabriz Iran
| | - Alireza Rastkar Ebrahimzadeh
- Molecular Simulation Lab Azarbaijan Shahid Madani University Tabriz Iran
- Molecular Science and Engineering Research Group (MSERG) Azarbaijan Shahid Madani University Tabriz Iran
- Department of Physics Azarbaijan Shahid Madani University Tabriz Iran
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2
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Kontkanen OV, Biriukov D, Futera Z. Reorganization Free Energy of Copper Proteins in Solution, in Vacuum, and on Metal Surfaces. J Chem Phys 2022; 156:175101. [DOI: 10.1063/5.0085141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid QM/MM computational technique based on DFT to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Somewhat surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry, however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions.
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Affiliation(s)
| | - Denys Biriukov
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Czech Republic
| | - Zdenek Futera
- University of South Bohemia in Ceske Budejovice Faculty of Science, Czech Republic
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3
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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.
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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.
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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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5
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Schwaminger S, Blank‐Shim SA, Borkowska‐Panek M, Anand P, Fraga‐García P, Fink K, Wenzel W, Berensmeier S. Experimental characterization and simulation of amino acid and peptide interactions with inorganic materials. Eng Life Sci 2018; 18:84-100. [PMID: 32624891 PMCID: PMC6999452 DOI: 10.1002/elsc.201700019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/02/2017] [Accepted: 07/03/2017] [Indexed: 02/06/2023] Open
Abstract
Inspired by nature, many applications and new materials benefit from the interplay of inorganic materials and biomolecules. A fundamental understanding of complex organic-inorganic interactions would improve the controlled production of nanomaterials and biosensors to the development of biocompatible implants for the human body. Although widely exploited in applications, the interaction of amino acids and peptides with most inorganic surfaces is not fully understood. To date, precisely characterizing complex surfaces of inorganic materials and analyzing surface-biomolecule interactions remain challenging both experimentally and computationally. This article reviews several approaches to characterizing biomolecule-surface interactions and illustrates the advantages and disadvantages of the methods presented. First, we explain how the adsorption mechanism of amino acids/peptides to inorganic surfaces can be determined and how thermodynamic and kinetic process constants can be obtained. Second, we demonstrate how this data can be used to develop models for peptide-surface interactions. The understanding and simulation of such interactions constitute a basis for developing molecules with high affinity binding domains in proteins for bioprocess engineering and future biomedical technologies.
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Affiliation(s)
| | | | | | - Priya Anand
- Institute of NanotechnologyKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Paula Fraga‐García
- Bioseparation Engineering GroupTechnical University of MunichMünchenGermany
| | - Karin Fink
- Institute of NanotechnologyKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Wolfgang Wenzel
- Institute of NanotechnologyKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Sonja Berensmeier
- Bioseparation Engineering GroupTechnical University of MunichMünchenGermany
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6
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Bizzarri AR, Baldacchini C, Cannistraro S. Structure, Dynamics, and Electron Transfer of Azurin Bound to a Gold Electrode. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:9190-9200. [PMID: 28789529 DOI: 10.1021/acs.langmuir.7b01102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Blue copper redox protein azurin (AZ) constitutes an ideal active element for building bionano-optoelectronic devices based on the intriguing interplay among its electron transfer (ET), vibrational, and optical properties. A full comprehension of its dynamical and functional behavior is required for efficient applications. Here, AZ bound to gold electrode via its disulfide bridge was investigated by a molecular dynamics simulation approach taking into account for gold electron polarization which provides a more realistic description of the protein-gold interaction. Upon binding to gold, AZ undergoes slight changes in its secondary structure with the preservation of the copper-containing active site structure. Binding of AZ to gold promotes new collective motions, with respect to free AZ, as evidenced by essential dynamics. Analysis of the ET from the AZ copper ion to the gold substrate, performed by the Pathways model, put into evidence the main residues and structural motifs of AZ involved in the ET paths. During the dynamical evolution of the bionanosystem, transient contacts between some lateral protein atoms and the gold substrate occurred; concomitantly, the opening of additional ET channels with much higher rates was registered. These results provide new and detailed insights on the dynamics and ET properties of the AZ-gold system, by also helping to rationalize some imaging and conductive experimental evidences and also to design new bionanodevices with tailored features.
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Affiliation(s)
- Anna Rita Bizzarri
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia , Viterbo 01100, Italy
| | - Chiara Baldacchini
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia , Viterbo 01100, Italy
- IBAF-CNR , Porano 05010, Italy
| | - Salvatore Cannistraro
- Biophysics & Nanoscience Centre, DEB, Università della Tuscia , Viterbo 01100, Italy
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Atabay M, Jahanbin Sardroodi J, Rastkar Ebrahimzadeh A. Adsorption and immobilisation of human insulin on graphene monoxide, silicon carbide and boron nitride nanosheets investigated by molecular dynamics simulation. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1270452] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Maryam Atabay
- Molecular Simulation Lab, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Lab, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Alireza Rastkar Ebrahimzadeh
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Physics, Azarbaijan Shahid Madani University, Tabriz, Iran
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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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Baldacchini C, Bizzarri AR, Cannistraro S. Electron transfer, conduction and biorecognition properties of the redox metalloprotein Azurin assembled onto inorganic substrates. Eur Polym J 2016. [DOI: 10.1016/j.eurpolymj.2016.04.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Ramakrishnan SK, Zhu J, Gergely C. Organic-inorganic interface simulation for new material discoveries. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sathish Kumar Ramakrishnan
- Nanobiology Institute; Yale University; West Haven CT USA
- Laboratoire Charles Coulomb (L2C); UMR 5221 CNRS-Université de Montpellier; Montpellier France
| | - Jie Zhu
- Nanobiology Institute; Yale University; West Haven CT USA
| | - Csilla Gergely
- Laboratoire Charles Coulomb (L2C); UMR 5221 CNRS-Université de Montpellier; Montpellier France
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11
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Siwko ME, Corni S. Cytochrome C on a gold surface: investigating structural relaxations and their role in protein–surface electron transfer by molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:5945-56. [DOI: 10.1039/c3cp00146f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Bizzarri AR, Di Agostino S, Andolfi L, Cannistraro S. A combined atomic force microscopy imaging and docking study to investigate the complex between p53 DNA binding domain and Azurin. J Mol Recognit 2010; 22:506-15. [PMID: 19642109 DOI: 10.1002/jmr.975] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The tumor suppressor p53 interacts with the redox copper protein Azurin (AZ) forming a complex which is of some relevance in biomedicine and cancer therapy. To obtain information on the spatial organization of this complex when it is immobilized on a substrate, we have used tapping mode-atomic force microscopy (TM-AFM) imaging combined with computational docking. The vertical dimension and the bearing volume of the DNA binding domain (DBD) of p53, anchored to functionalized gold substrate through exposed lysine residues, alone and after deposing AZ, have been measured by TM-AFM. By a computational docking approach, a three-dimensional model for the DBD of p53, before and after addition of AZ, have been predicted. Then we have calculated the possible arrangements of these biomolecular systems on gold substrate by finding a good agreement with the related experimental distribution of the height. The potentiality of the approach combining TM-AFM imaging and computational docking for the study of biomolecular complexes immobilized on substrates is briefly discussed.
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Affiliation(s)
- Anna Rita Bizzarri
- Biophysics & Nanoscience Centre, CNISM, Facolta' di Scienze, Università della Tuscia, I-01100 Viterbo, Italy.
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Taranta M, Bizzarri AR, Cannistraro S. Modeling the interaction between the N-terminal domain of the tumor suppressor p53 and azurin. J Mol Recognit 2009; 22:215-22. [PMID: 19140135 DOI: 10.1002/jmr.934] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
It is known that the half life of the tumor suppressor p53 can be increased by the interaction with the bacterial protein azurin, resulting in an enhanced anti-tumoral activity. The understanding of the molecular mechanisms on the basis of this phenomenon can open the way to new anti-cancer strategies. Some experimental works have given evidence of an interaction between p53 and azurin (AZ); however the binding regions of the proteins are still unknown. Recently, fluorescence studies have shown that p53 partakes in the binding with the bacterial protein by its N-terminal (NT) domain. Here we have used a computational method to get insight into this interacting mode. The model that we propose for the best complex between AZ and p53 has been obtained from a rigid-body docking, coupled with a molecular dynamics (MD) simulation, a free energy calculation, and validated by mutagenesis analysis. We have found a high degree of geometric fit between the two proteins that are kept together by several hydrophobic interactions and numerous hydrogen bonds. Interestingly, it has emerged that AZ binds essentially to the helices H(I) and H(III) of the p53 NT domain, which are also interacting regions for the foremost inhibitor of p53, MDM2.
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Affiliation(s)
- Monia Taranta
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell'Università 01100, Viterbo, Italy
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Hagiwara T, Sakiyama T, Watanabe H. Molecular simulation of bovine beta-lactoglobulin adsorbed onto a positively charged solid surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:226-234. [PMID: 19032076 DOI: 10.1021/la8024149] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To obtain detailed insight into the mechanism of beta-lactoglobulin (beta-Lg) adsorption to a stainless steel surface at acidic pH, the adsorption of positively charged beta-Lg to a positively charged surface (Au (100) surface with virtual positive charge) was simulated using classical molecular dynamics. The initial orientation and position of beta-Lg on the surface were determined using Monte Carlo simulation using the implicit water system. Molecular dynamics simulation with the explicit water system was conducted for a 5 ns simulation time to monitor beta-Lg adsorption. To investigate surface charge density effects on adsorption of beta-Lg, the positive charge number per Au atom on the (100) surface, C, was varied from 0 to +0.0250|e|. Stable adsorption occurred in MD simulations when C was equal to or less than +0.0200|e|. Among these surface Au charge conditions, no large difference was observed in the vertical separation distance between the surface and the protein's center of mass, and the orientation angle. This fact indicates that the main interactions contributing to the adsorption were van der Waals interactions. The protein domain contacting the surface was near Thr125, agreeing with previous experimental studies. Considering simulation results and those previous experimental studies suggests a detailed adsorption mechanism of beta-Lg at acidic pH: beta-Lg molecule is adsorbed initially with the specific part of 125-135th residues close to the surface by van der Waals interactions. Simultaneously or subsequently, side carboxylic groups of acidic amino acid residues near the surface in 125-135th residues dissociate, leading to firmer adsorption by attractive electrostatic residue-surface interaction.
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Affiliation(s)
- Tomoaki Hagiwara
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan.
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15
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Optical investigation of the electron transfer protein azurin–gold nanoparticle system. Biophys Chem 2009; 139:1-7. [DOI: 10.1016/j.bpc.2008.09.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 09/19/2008] [Accepted: 09/19/2008] [Indexed: 11/15/2022]
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Bizzarri A, Andolfi L, Taranta M, Cannistraro S. Optical and electronic coupling of the redox copper Azurin on ITO-coated quartz substrate. Biosens Bioelectron 2008; 24:204-9. [DOI: 10.1016/j.bios.2008.03.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2008] [Revised: 03/19/2008] [Accepted: 03/25/2008] [Indexed: 10/22/2022]
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17
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Iori F, Corni S. Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces. J Comput Chem 2008; 29:1656-66. [DOI: 10.1002/jcc.20928] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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De Grandis V, Bizzarri AR, Cannistraro S. Docking study and free energy simulation of the complex between p53 DNA-binding domain and azurin. J Mol Recognit 2007; 20:215-26. [PMID: 17703463 DOI: 10.1002/jmr.840] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Molecular interaction between p53 tumor suppressor and the copper protein azurin (AZ) has been demonstrated to enhance p53 stability and hence antitumoral function, opening new perspectives in cancer treatment. While some experimental work has provided evidence for AZ binding to p53, no crystal structure for the p53-AZ complex was solved thus far. In this work the association between AZ and the p53 DNA-binding domain (DBD) was investigated by computational methods. Using a combination of rigid-body protein docking, experimental mutagenesis information, and cluster analysis 10 main p53 DBD-AZ binding modes were generated. The resulting structures were further characterized by molecular dynamics (MD) simulations and free energy calculations. We found that the highest scored docking conformation for the p53 DBD-AZ complex also yielded the most favorable free energy value. This best three-dimensional model for the complex was validated by using a computational mutagenesis strategy. In this structure AZ binds to the flexible L(1) and s(7)-s(8) loops of the p53 DBD and stabilizes them through protein-protein tight packing interactions, resulting in high degree of both surface matching and electrostatic complementarity.
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Affiliation(s)
- Valentina De Grandis
- Biophysics and Nanoscience Centre, CNISM, Facoltà di Scienze, Università della Tuscia, Largo dell'Università-I-01100 Viterbo, Italy
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Venkat AS, Corni S, Di Felice R. Electronic coupling between azurin and gold at different protein/substrate orientations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2007; 3:1431-7. [PMID: 17591735 DOI: 10.1002/smll.200700001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
By means of constrained classical molecular dynamics simulations, we have computed the structure of azurin deposited on a Au(111) surface at different possible orientations and the azimuthal forces acting on the protein at each sampled conformation. We have then evaluated the effect of the angular variation on the speed of electron tunneling between the protein redox site and the metal surface. We find that the azurin/gold electronic coupling has a strong dependence on the molecular orientation and is greatly enhanced by inclining the protein to lie as flat as possible on the surface. We discuss the implications of our results for scanning probe microscopy experiments in which tunneling currents are measured while the protein is subjected to mechanical forces exerted by the tip of the instrument.
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Affiliation(s)
- Anurag Setty Venkat
- National Research Center on nanoStructures and bioSystems at Surfaces S3 of INFM-CNR, Modena, Italy
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