Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation

Bizzarri, Anna Rita

doi:10.1016/j.bpc.2006.03.012

Cited by 21 publications

(31 citation statements)

References 51 publications

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“…Accordingly, the outlined preservation of the shape of the emission spectrum upon AuNP addition in our experiments is an indication that Az molecules participating to the signal (and, thus, also the molecules bound to AuNP surface) remain presumably in their native configuration. This is in agreement with both experimental results [15,41] and molecular dynamics simulation of an Az molecule near a gold surface showing that the protein undergoes only small configurational changes even when it is covalently bound to the surface [42]. is obviously due to the sum of signal of quenched and not quenched sources.…”

supporting

confidence: 91%

“…Moreover, the hypothesis of aggregation caused by Az addition has link gold surfaces, as also theoretically described by means of molecular dynamics simulations [15,[40][41][42]. Whatever the link is, if a monolayer is formed, an estimate of the theoretical number of Az proteins (N Az ) that each spherical particle can accomodate on its surface may be derived from steric considerations using the following expression [43]:…”

mentioning

confidence: 99%

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Optical investigation of the electron transfer protein azurin–gold nanoparticle system

Delfino

Cannistraro

2009

Biophysical Chemistry

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To cite this version:Ines Delfino, Salvatore Cannistraro.Optical investigation of the electron transfer protein azurin -gold nanoparticle system. Biophysical Chemistry, Elsevier, 2008, 139 (1), pp. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. delfino@unitus.it A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT ABSTRACTThe hybrid system obtained by conjugating the protein azurin, which is a very stable and well-described The fluorescence quenching of azurin bound molecules is explained by an energy transfer from protein to metal surface and it is discussed in terms of the involvement of the Az electron transfer route in the interaction of the protein with the nanoparticle.

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supporting

confidence: 91%

mentioning

confidence: 99%

Optical investigation of the electron transfer protein azurin–gold nanoparticle system

Delfino

Cannistraro

2009

Biophysical Chemistry

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“…Along with well-known applications of metal surfaces, such as biosensors and implants (Liu et al 2004), metal surfaces are also used in bioelectronics as electrodes as they allow controlled exchange of electrons with metalloproteins immobilized on them (Alessandrini et al 2005;Andolfi et al 2004). The interactions of proteins with bare metal surfaces have been the subject of many computational studies, which cover a wide range of different elemental and alloy surfaces, such as Cu(100) (Chen & Wang, 2010), Au(111) (Bizzarri, 2006;Hoefling et al 2011;Siwko & Corni, 2013;Venkat et al 2007;Zanetti-Polzi et al 2014), Au(100) (Hagiwara et al 2009), Au nanoparticle (Todorova et al 2014), Fe (Zhang et al 2009b), Ni (Yang & Zhao, 2006), Pd (Coppage et al 2011), Pt (Kantarci et al 2005, Ag (Aliaga et al 2011;Ghosh et al 2012) and steel (Imamura et al 2003).…”

Section: Elemental Metals and Alloysmentioning

confidence: 99%

“…They provide two sets of parameters for metal atoms (Ag, Al, Au, Cu, Ni, Pb, Pd, Pt); one set suited for 12-6 Lennard-Jones functions to be used in AMBER, CHARMM, CVFF and OPLS-AA force-fields, and another for 9-6 Lennard-Jones functions to be used in the COMPASS (Sun, 1998) In addition to polarization, surface charges should be taken into account when modeling a surface. Bizzarri (2006) investigated the dynamics and electron transfer (ET) properties of the bacterial ET protein, azurin, anchored to neutral, positively and negatively charged gold surfaces using classical MD simulations. They calculated the ET rate between the azurin copper atom and the sulfur atom of the cysteine surface anchor using classical Marcus theory (Marcus & Sutin, 1985).…”

Section: Metal Surfacesmentioning

confidence: 99%

“…Examples include simulations for structural refinement of docked complexes (Aliaga et al 2011;Alvarez-Paggi et al 2013;Brancolini et al 2012Brancolini et al , 2015Imamura et al 2007), and for the investigation of the binding orientations of proteins on surfaces (Alvarez-Paggi et al 2010;Boughton et al 2010;Coppage et al 2013); the kinetic mechanisms of adsorption (Raffaini & Ganazzoli, 2010); the ET pathways and properties of adsorbed proteins (Bizzarri, 2006;Siwko & Corni, 2013;Utesch et al 2012;Zanetti-Polzi et al 2014;Zhou et al 2004); the effects of pH (Emami et al 2014b;Imamura et al 2003;Tosaka et al 2010;Utesch et al 2013) and ionic strength (Bizzarri, 2006) on adsorption; the role of ions in mediating adsorption ; and structural and energetic aspects of adsorption of proteins on surfaces (Apicella et al 2013;Jose & Sengupta, 2013;Hoefling et al 2011;Hung et al 2011;Kubiak-Ossowska & Mulheran, 2010a, b;O'Mahony et al 2013;Vila Verde et al 2009Wang et al 2010a, b;Yu et al 2012a;Steckbeck et al 2014;Sun et al 2014a;Sun et al 2014b). Further, conventional MD can be used to simulate physical perturbations, such as mechanical or electrical forces exerted on molecules in experiments.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

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Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

193

199

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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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Structures of Peptidic H‐wires at Mercury Surface: Molecular Dynamics Study

et al. 2019

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Biopolymer immobilization strategies, self‐assembly systems and adsorption phenomenon in general are crucial for the development of methods that work on the basis of the surface‐detection principle, including electrochemistry. A mechanistic view into the interaction of biopolymers with electrode surfaces is also important for studying fundamental and dynamic processes such as electron/proton transport. In this sense, the utilization of new approaches for investigating the interfacial behavior of immobilized biomolecular architectures is a permanent focus. Here we use a molecular dynamics (MD) approach to simulate the structural changes and metallic surface interactions of a model 21‐mer peptide of His (H) and Ala (A), A3(HA2)6, a peptidic proton wire (H‐wire). This H‐wire was previously proposed for the electrochemical study of proton transfer at mercury electrodes (Langmuir, 2018, 34, 6997). The rigid solid mercury mono‐atomic layer (α‐mercury lattice model) was used systematically in all our simulations. The calculations were performed in a simulation box with 1, 16 and 32 H‐wire strands attached covalently to the mercury layer via the thiol group of a cysteinamide residue appended to the H‐wire C‐terminus. The internal alpha‐helical configuration of H‐wires was maintained by the presence of 2,2,2‐trifluoroethanol. It was shown that both the surface density of H‐wires and the protonation state of His residues play a decisive role in the structural stability and orientation of the peptide to the surface, whereas the applied voltage only has a mild effect on it, especially in case of 16 and 32 H‐wire strand configurations. The MD simulations presented here could be used for the further investigation of other peptides at metallic surfaces and for electrochemical analyses of structural changes of surface‐attached peptides that depend on their protonation states and other external factors.

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Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation

Cited by 21 publications

References 51 publications

Optical investigation of the electron transfer protein azurin–gold nanoparticle system

Optical investigation of the electron transfer protein azurin–gold nanoparticle system

Modeling and simulation of protein–surface interactions: achievements and challenges

Structures of Peptidic H‐wires at Mercury Surface: Molecular Dynamics Study

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