1
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Vacek J, Zatloukalová M, Dorčák V, Cifra M, Futera Z, Ostatná V. Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field. Mikrochim Acta 2023; 190:442. [PMID: 37847341 PMCID: PMC10582152 DOI: 10.1007/s00604-023-05999-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.
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Affiliation(s)
- Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic.
| | - Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Vlastimil Dorčák
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, 18200, Prague, Czech Republic
| | - Zdeněk Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Sciences, v.v.i., Kralovopolska 135, 61200, Brno, Czech Republic
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2
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Kontkanen OV, Biriukov D, Futera Z. Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin. Phys Chem Chem Phys 2023; 25:12479-12489. [PMID: 37097130 DOI: 10.1039/d3cp00197k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
As the field of nanoelectronics based on biomolecules such as peptides and proteins rapidly grows, there is a need for robust computational methods able to reliably predict charge transfer properties at bio/metallic interfaces. Traditionally, hybrid quantum-mechanical/molecular-mechanical techniques are employed for systems where the electron hopping transfer mechanism is applicable to determine physical parameters controlling the thermodynamics and kinetics of charge transfer processes. However, these approaches are limited by a relatively high computational cost when extensive sampling of a configurational space is required, like in the case of soft biomatter. For these applications, semi-empirical approaches such as the perturbed matrix method (PMM) have been developed and successfully used to study charge-transfer processes in biomolecules. Here, we explore the performance of PMM on prototypical redox-active protein azurin in various environments, from solution to vacuum interfaces with gold surfaces and protein junction. We systematically benchmarked the robustness and convergence of the method with respect to the quantum-centre size, size of the Hamiltonian, number of samples, and level of theory. We show that PMM can adequately capture all the trends associated with the structural and electronic changes related to azurin oxidation at bio/metallic interfaces.
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Affiliation(s)
- Outi Vilhelmiina Kontkanen
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
| | - Denys Biriukov
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
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3
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Zanetti-Polzi L, Charchar P, Yarovsky I, Corni S. Origins of the pH-Responsive Photoluminescence of Peptide-Functionalized Au Nanoclusters. ACS NANO 2022; 16:20129-20140. [PMID: 36300936 DOI: 10.1021/acsnano.2c04335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ultrasmall peptide-protected gold nanoclusters are a promising class of bioresponsive material exhibiting pH-sensitive photoluminescence. We present a theoretical insight into the effect peptide-ligand environment has on pH-responsive fluorescence, with the aim of enhancing the rational design of gold nanoclusters for bioapplications. Employing a hybrid quantum/classical computational methodology, we systematically calculate deprotonation free energies of N-terminal cysteine amine groups in proximity to the inherently fluorescent core of Au25(Peptide)18 nanoclusters. We find that subtle changes in hexapeptide sequence alter the electrostatic environment and significantly shift the conventional N-terminal amine pKa expected for amino acids free-in-solution. Our findings provide an insight into how the deprotonation equilibrium of N-terminal amine and side chain carboxyl groups cooperatively respond to solution pH changes, explaining the experimentally observed, yet elusive, pH-responsive fluorescence of peptide-functionalized Au25 clusters.
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Affiliation(s)
- Laura Zanetti-Polzi
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125Modena, Italy
| | | | - Irene Yarovsky
- School of Engineering, RMIT University, Victoria3001, Australia
| | - Stefano Corni
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125Modena, Italy
- Dipartimento di Scienze Chimiche, Università di Padova, 35131Padova, Italy
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4
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Yu Y, Pan M, Peng J, Hu D, Hao Y, Qian Z. A review on recent advances in hydrogen peroxide electrochemical sensors for applications in cell detection. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.02.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Chen CG, Nardi AN, Amadei A, D’Abramo M. Theoretical Modeling of Redox Potentials of Biomolecules. Molecules 2022; 27:molecules27031077. [PMID: 35164342 PMCID: PMC8838479 DOI: 10.3390/molecules27031077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022] Open
Abstract
The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.
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Affiliation(s)
- Cheng Giuseppe Chen
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
| | | | - Andrea Amadei
- Department of Chemical and Technological Sciences, Tor Vergata University, 00133 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
- Correspondence:
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6
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Pantaleone S, Rimola A, Ugliengo P, Sodupe M. First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO 2 (101) Anatase Surface Adopting a Full Periodic Approach. J Chem Inf Model 2021; 61:5484-5498. [PMID: 34752107 DOI: 10.1021/acs.jcim.1c00689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO2 (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO2 surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, β-sheet, and α-helix) on the TiO2 surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C═O groups form Ti-O═C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the β-sheet because in the former, more Ti-O═C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed β-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain.,Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, Torino 10125, Italy.,Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, Perugia I-06123, Italy
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, Torino 10125, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
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7
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Zanetti-Polzi L, Smith MD, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design. J Phys Chem Lett 2021; 12:4195-4202. [PMID: 33900080 PMCID: PMC8097931 DOI: 10.1021/acs.jpclett.1c00425] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/21/2021] [Indexed: 05/03/2023]
Abstract
The catalytic reaction in SARS-CoV-2 main protease is activated by a proton transfer (PT) from Cys145 to His41. The same PT is likely also required for the covalent binding of some inhibitors. Here we use a multiscale computational approach to investigate the PT thermodynamics in the apo enzyme and in complex with two potent inhibitors, N3 and the α-ketoamide 13b. We show that with the inhibitors the free energy cost to reach the charge-separated state of the active-site dyad is lower, with N3 inducing the most significant reduction. We also show that a few key sites (including specific water molecules) significantly enhance or reduce the thermodynamic feasibility of the PT reaction, with selective desolvation of the active site playing a crucial role. The approach presented is a cost-effective procedure to identify the enzyme regions that control the activation of the catalytic reaction and is thus also useful to guide the design of inhibitors.
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Affiliation(s)
- Laura Zanetti-Polzi
- Center
S3, CNR Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
| | - Micholas Dean Smith
- Department
of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville, 309 Ken and Blaire Mossman Bldg., 1311 Cumberland
Avenue, Knoxville, Tennessee 37996, United States
| | - Chris Chipot
- UMR 7019, Université de Lorraine, Laboratoire
International Associé CNRS, 54506 Vandœuvre-lès-Nancy, France
- University
of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - James C. Gumbart
- School
of Physics, Georgia Institute of Technology, Atlanta Georgia 30332, United States
| | - Diane L. Lynch
- School
of Physics, Georgia Institute of Technology, Atlanta Georgia 30332, United States
| | - Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta Georgia 30332, United States
| | - Jeremy C. Smith
- Department
of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville, 309 Ken and Blaire Mossman Bldg., 1311 Cumberland
Avenue, Knoxville, Tennessee 37996, United States
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Isabella Daidone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, Via
Vetoio, I-67010 L’Aquila, Italy
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8
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Zanetti-Polzi L, Aschi M, Daidone I. Cooperative protein-solvent tuning of proton transfer energetics: carbonic anhydrase as a case study. Phys Chem Chem Phys 2021; 22:19975-19981. [PMID: 32857091 DOI: 10.1039/d0cp03652h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We investigate the coupling between the proton transfer (PT) energetics and the protein-solvent dynamics using the intra-molecular PT in wild type (wt) human carbonic anhydrase II and its ten-fold faster mutant Y7F/N67Q as a test case. We calculate the energy variation upon PT, and from that we also calculate the PT reaction free energy, making use of a hybrid quantum mechanics/molecular dynamics approach. In agreement with the experimental data, we obtain that the reaction free energy is basically the same in the two systems. Yet, we show that the instantaneous PT energy is on average lower in the mutant possibly contributing to the faster PT rate. Analysis of the contribution to the PT energetics of the solvent and of each protein residue, also not in the vicinity of the active site, provides evidence for electrostatic tuning of the PT energy arising from the combined effect of the solvent and the protein environment. These findings open up a way to the more general task of the rational design of mutants with either enhanced or reduced PT rate.
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Affiliation(s)
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy.
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy.
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9
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Zanetti-Polzi L, Smith MD, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:13200227. [PMID: 33200115 PMCID: PMC7668740 DOI: 10.26434/chemrxiv.13200227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 11/06/2020] [Indexed: 12/21/2022]
Abstract
In this comutational work a hybrid quantum mechanics/molecular mechanics approach, the MD-PMM approach, is used to investigate the proton transfer reaction the activates the catalytic activity of SARS-CoV-2 main protease. The proton transfer thermodynamics is investigated for the apo ensyme (i.e., without any bound substrate or inhibitor) and in the presence of a inhibitor, N3, which was previously shown to covalently bind SARS-CoV-2 main protease.
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Affiliation(s)
- Laura Zanetti-Polzi
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
| | - Micholas Dean Smith
- Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville. 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, TN 37996, United States
| | - Chris Chipot
- UMR 7019, Universite de Lorraine, Laboratoire International Associe CNRS
- University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, TN 37831, United States
- Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville. 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, TN 37996, United States
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy
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10
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Hitaishi VP, Mazurenko I, Vengasseril Murali A, de Poulpiquet A, Coustillier G, Delaporte P, Lojou E. Nanosecond Laser-Fabricated Monolayer of Gold Nanoparticles on ITO for Bioelectrocatalysis. Front Chem 2020; 8:431. [PMID: 32582633 PMCID: PMC7287402 DOI: 10.3389/fchem.2020.00431] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/24/2020] [Indexed: 11/13/2022] Open
Abstract
Redox enzymes can be envisioned as biocatalysts in various electrocatalytic-based devices. Among factors that play roles in bioelectrochemistry limitations, the effect of enzyme-enzyme neighboring interaction on electrocatalysis has rarely been investigated, although critical in vivo. We report in this work an in-depth study of gold nanoparticles prepared by laser ablation in the ultimate goal of determining the relationship between activity and enzyme density on electrodes. Nanosecond laser interaction with nanometric gold films deposited on indium tin oxide support was used to generate in situ gold nanoparticles (AuNPs) free from any stabilizers. A comprehensive analysis of AuNP size and coverage, as well as total geometric surface vs. electroactive surface is provided as a function of the thickness of the treated gold layer. Using microscopy and electrochemistry, the long-term stability of AuNP-based electrodes in the atmosphere and in the electrolyte is demonstrated. AuNPs formed by laser treatment are then modified by thiol chemistry and their electrochemical behavior is tested with a redox probe. Finally, enzyme adsorption and bioelectrocatalysis are evaluated in the case of two enzymes, i.e., the Myrothecium verrucaria bilirubin oxidase and the Thermus thermophilus laccase. Behaving differently on charged surfaces, they allow demonstrating the validity of laser treated AuNPs for bioelectrocatalysis.
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Affiliation(s)
- Vivek Pratap Hitaishi
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, UMR 7281, Marseille, France
| | - Ievgen Mazurenko
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, UMR 7281, Marseille, France
| | - Anjali Vengasseril Murali
- Aix Marseille Univ, CNRS, LP3, UMR 7341, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Anne de Poulpiquet
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, UMR 7281, Marseille, France
| | - Gaëlle Coustillier
- Aix Marseille Univ, CNRS, LP3, UMR 7341, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Philippe Delaporte
- Aix Marseille Univ, CNRS, LP3, UMR 7341, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Elisabeth Lojou
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, UMR 7281, Marseille, France
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11
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Zanetti-Polzi L, Daidone I, Amadei A. Fully Atomistic Multiscale Approach for p Ka Prediction. J Phys Chem B 2020; 124:4712-4722. [PMID: 32427481 DOI: 10.1021/acs.jpcb.0c01752] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The ionization state of titratable amino acids strongly affects proteins structure and functioning in a large number of biological processes. It is therefore essential to be able to characterize the pKa of ionizable groups inside proteins and to understand its microscopic determinants in order to gain insights into many functional properties of proteins. A big effort has been devoted to the development of theoretical approaches for the prediction of deprotonation free energies, yet the accurate theoretical/computational calculation of pKa values is recognized as a current challenge. A methodology based on a hybrid quantum/classical approach is here proposed for the computation of deprotonation free energies. The method is applied to calculate the pKa of formic acid, methylammonium, and methanethiol, providing results in good agreement with the corresponding experimental estimates. The pKa is also calculated for aspartic acid and lysine as single residues in solution and for three aspartic/glutamic acids inside a well-characterized protein: hen egg white lysozyme. While for small molecules the method is able to deal with multiple protonation states of all titratable groups, this becomes computationally very expensive for proteins. The calculated pKa values for the single amino acids (except for the zwitterionic aspartic acid) and inside the protein display a systematic shift with respect to the experimental values that suggests that the fine balance between hydrophobic and polar interactions might be not accurately reproduced by the usual classical force-fields, thus affecting the computation of deprotonation free energies. The calculated pKa shifts inside the protein are in good agreement with the corresponding experimental ones (within 1 pKa unit), well reproducing the pKa changes due to the protein environment even in the case of large pKa shifts.
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Affiliation(s)
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Via della Ricerca Scientifica, I-00185 Rome, Italy
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12
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Paradisi A, Bellei M, Paltrinieri L, Bortolotti CA, Di Rocco G, Ranieri A, Borsari M, Sola M, Battistuzzi G. Binding of S. cerevisiae iso-1 cytochrome c and its surface lysine-to-alanine variants to cardiolipin: charge effects and the role of the lipid to protein ratio. J Biol Inorg Chem 2020; 25:467-487. [DOI: 10.1007/s00775-020-01776-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/06/2020] [Indexed: 11/30/2022]
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13
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Zanetti-Polzi L, Daidone I, Corni S. Evidence of a Thermodynamic Ramp for Hole Hopping to Protect a Redox Enzyme from Oxidative Damage. J Phys Chem Lett 2019; 10:1450-1456. [PMID: 30855973 DOI: 10.1021/acs.jpclett.9b00403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Redox proteins and enzymes are at risk of irreversible oxidative damage from highly oxidizing intermediates generated in the active site in the case of unsuccessful functional reaction. Chains of tyrosine and/or tryptophan residues have been recently proposed to provide protection to the active site and the whole protein by delivering oxidizing equivalents (holes) out of the protein via a multistep hopping mechanism. In the present work we use a hybrid quantum/classical theoretical-computational methodology based on the perturbed matrix method and on molecular dynamics simulations to calculate the oxidation potential difference along a chain of tyrosine and tryptophan residues in a human redox enzyme of major importance, a superoxide dismutase, which acts as antioxidant defense. We show that the hole hopping is thermodynamically favored along such a chain and that the hopping propensity is strongly affected by the protein environment and in particular by the active site and its second coordination sphere.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Stefano Corni
- Department of Chemical Sciences , University of Padova , I-35131 Padova , Italy
- Center S3 , CNR-Institute of Nanoscience , Via Campi 213/A , 41125 Modena , Italy
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14
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Davis CM, Zanetti-Polzi L, Gruebele M, Amadei A, Dyer RB, Daidone I. A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy. Chem Sci 2018; 9:9002-9011. [PMID: 30647892 PMCID: PMC6301204 DOI: 10.1039/c8sc03786h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/02/2018] [Indexed: 11/23/2022] Open
Abstract
We break the barrier between simulation and experiment by comparing identical computed and experimental infrared observables.
For small molecule reaction kinetics, computed reaction coordinates often mimic experimentally measured observables quite accurately. Although nowadays simulated and measured biomolecule kinetics can be compared on the same time scale, a gap between computed and experimental observables remains. Here we directly compared temperature-jump experiments and molecular dynamics simulations of protein folding dynamics using the same observable: the time-dependent infrared spectrum. We first measured the stability and folding kinetics of the fastest-folding β-protein, the GTT35 WW domain, using its structurally specific infrared spectrum. The relaxation dynamics of the peptide backbone, β-sheets, turn, and random coil were measured independently by probing the amide I′ region at different frequencies. Next, the amide I′ spectra along folding/unfolding molecular dynamics trajectories were simulated by accurate mixed quantum/classical calculations. The simulated time dependence and spectral amplitudes at the exact experimental probe frequencies provided relaxation and folding rates in agreement with experimental observations. The calculations validated by experiment yield direct structural evidence for a rate-limiting reaction step where an intermediate state with either the first or second hairpin is formed. We show how folding switches from a more homogeneous (apparent two-state) process at high temperature to a more heterogeneous process at low temperature, where different parts of the WW domain fold at different rates.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
| | - Martin Gruebele
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , IL 61801 , USA
| | - Andrea Amadei
- Department of Chemical and Technological Sciences , University of Rome "Tor Vergata" , 00133 Rome , Italy
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
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15
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Zanetti-Polzi L, Del Galdo S, Daidone I, D'Abramo M, Barone V, Aschi M, Amadei A. Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory. Phys Chem Chem Phys 2018; 20:24369-24378. [PMID: 30215645 DOI: 10.1039/c8cp04190c] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some years ago we developed a theoretical-computational hybrid quantum/classical methodology, the Perturbed Matrix Method (PMM), to be used in conjunction with molecular dynamics simulations for the investigation of chemical processes in complex systems, that proved to be a valuable tool for the simulation of relevant experimental observables, e.g., spectroscopic signals, reduction potentials, kinetic constants. In typical PMM calculations the quantum sub-part of the system, the quantum centre, is embedded into an external perturbing field providing a perturbation operator explicitly calculated up to the dipolar terms. In this paper we further develop the PMM approach, beyond the dipolar terms in the perturbation operator expansion, by including explicitly the quadrupolar terms and/or by expanding the perturbation operator on each atom of the quantum centre. These different levels of the perturbation operator expansion, providing different levels of theory, have been tested by calculating three different spectroscopic observables: the spectral signal of liquid water and aqueous benzene due to the lowest energy electronic excitation and the infrared amide I band of aqueous trans-N-methylacetamide. All the systems tested show that, even though the previous PMM level of theory is already capable of reproducing the main features of the spectral signal, the higher levels of theory improve the quantitative reproduction of the spectral details.
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Affiliation(s)
- Laura Zanetti-Polzi
- Dipartimento di Scienze Fisiche e Chimiche, University of L'Aquila, via Vetoio (Coppito 1), 67010 L'Aquila, Italy
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16
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Abstract
Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.
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17
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Carrillo-Parramon O, Del Galdo S, Aschi M, Mancini G, Amadei A, Barone V. Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code. J Chem Theory Comput 2017; 13:5506-5514. [DOI: 10.1021/acs.jctc.7b00341] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
| | - Massimiliano Aschi
- Dipartimento
di Scienze Fisiche e Chimiche, Universitá di L’Aquila, Via
Vetoio s.n.c.67100, L’Aquila, Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Andrea Amadei
- Dipartimento
di Scienze e Tecnologie Chimiche, Universitá di Roma ’Tor Vergata’, Via Della Ricerca Scientifica, 00100 Roma, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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18
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Zanetti Polzi L, Battistuzzi G, Borsari M, Pignataro M, Paltrinieri L, Daidone I, Bortolotti CA. Computational investigation of the electron transfer complex between neuroglobin and cytochrome c. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1377342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Laura Zanetti Polzi
- Department of Physical and Chemical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Gianantonio Battistuzzi
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Marco Borsari
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Marcello Pignataro
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Licia Paltrinieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L’Aquila, L’Aquila, Italy
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19
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Zanetti-Polzi L, Aschi M, Amadei A, Daidone I. Alternative Electron-Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Excited States in Riboflavin Binding Protein. J Phys Chem Lett 2017; 8:3321-3327. [PMID: 28665138 DOI: 10.1021/acs.jpclett.7b01575] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Flavoproteins, containing flavin chromophores, are enzymes capable of transferring electrons at very high speeds. The ultrafast photoinduced electron-transfer (ET) kinetics of riboflavin binding protein to the excited riboflavin was studied by femtosecond spectroscopy and found to occur within a few hundred femtoseconds [ Zhong and Zewail, Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11867-11872 ]. This ultrafast kinetics was attributed to the presence of two aromatic rings that could transfer the electron to riboflavin: the side chains of tryptophan 156 and tyrosine 75. However, the underlying ET mechanism remained unclear. Here, using a hybrid quantum mechanical-molecular dynamics approach, we perform ET dynamics simulations taking into account the motion of the protein and the solvent upon ET. This approach reveals that ET occurs via a major reaction channel involving tyrosine 75 (83%) and a minor one involving tryptophan 156 (17%). We also show that the protein environment is designed to ensure the fast quenching of the riboflavin excited state.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00185 Rome, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
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20
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Lee HK, Heo J, Myung S, Shin IS, Kim TH. Homogeneous Electrochemical Assay for Real-time Monitoring of Exonuclease III Activity Based on a Graphene Monolayer. ELECTROANAL 2017. [DOI: 10.1002/elan.201700006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Heon-Kyu Lee
- Department of Chemistry; Soonchunhyang University; Asan 31538 Republic of Korea
| | - Jihye Heo
- Department of Chemistry; Soonchunhyang University; Asan 31538 Republic of Korea
| | - Sung Myung
- Thin Film Materials Research Center; Korea Research Institute of Chemical Technology; Daejeon 34114 Republic of Korea
| | - Ik-Soo Shin
- Department of Chemistry; Soongsil University; Seoul 06978 Republic of Korea
| | - Tae Hyun Kim
- Department of Chemistry; Soonchunhyang University; Asan 31538 Republic of Korea
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21
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Computational evidence support the hypothesis of neuroglobin also acting as an electron transfer species. J Biol Inorg Chem 2017; 22:615-623. [DOI: 10.1007/s00775-017-1455-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/28/2017] [Indexed: 12/31/2022]
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22
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Bellucci L, Bussi G, Di Felice R, Corni S. Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface. NANOSCALE 2017; 9:2279-2290. [PMID: 28124697 DOI: 10.1039/c6nr06010b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins in the proximity of inorganic surfaces and nanoparticles may undergo profound adjustments that trigger biomedically relevant processes, such as protein fibrillation. The mechanisms that govern protein-surface interactions at the molecular level are still poorly understood. In this work, we investigate the adsorption onto a gold surface, in water, of an amyloid-β (Aβ) peptide, which is the amyloidogenic peptide involved in Alzheimer's disease. The entire adsorption process, from the peptide in bulk water to its conformational relaxation on the surface, is explored by large-scale atomistic molecular dynamics (MD) simulations. We start by providing a description of the conformational ensemble of Aβ in solution by a 22 μs temperature replica exchange MD simulation, which is consistent with previous results. Then, we obtain a statistical description of how the peptide approaches the gold surface by multiple MD simulations, identifying the preferential gold-binding sites and giving a kinetic picture of the association process. Finally, relaxation of the Aβ conformations at the gold/water interface is performed by a 19 μs Hamiltonian-temperature replica exchange MD simulation. We find that the conformational ensemble of Aβ is strongly perturbed by the presence of the surface. In particular, at the gold/water interface the population of the conformers akin to amyloid fibrils is significantly enriched, suggesting that this extended contact geometry may promote fibrillation.
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Affiliation(s)
- Luca Bellucci
- Center S3, CNR Institute of Nanoscience, via Campi 213/A, 41125 Modena, Italy.
| | - Giovanni Bussi
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
| | - Rosa Di Felice
- Center S3, CNR Institute of Nanoscience, via Campi 213/A, 41125 Modena, Italy. and Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Stefano Corni
- Center S3, CNR Institute of Nanoscience, via Campi 213/A, 41125 Modena, Italy.
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23
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Stan RC, Kros A, Akkilic N, Sanghamitra NJ, Appel J. Direct wiring of the azurin redox center to gold electrodes investigated by protein film voltammetry. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.01.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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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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25
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Zhang L, Vogel YB, Noble BB, Gonçales VR, Darwish N, Brun AL, Gooding JJ, Wallace GG, Coote ML, Ciampi S. TEMPO Monolayers on Si(100) Electrodes: Electrostatic Effects by the Electrolyte and Semiconductor Space-Charge on the Electroactivity of a Persistent Radical. J Am Chem Soc 2016; 138:9611-9. [PMID: 27373457 DOI: 10.1021/jacs.6b04788] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work demonstrates the effect of electrostatic interactions on the electroactivity of a persistent organic free radical. This was achieved by chemisorption of molecules of 4-azido-2,2,6,6-tetramethyl-1-piperdinyloxy (4-azido-TEMPO) onto monolayer-modified Si(100) electrodes using a two-step chemical procedure to preserve the open-shell state and hence the electroactivity of the nitroxide radical. Kinetic and thermodynamic parameters for the surface electrochemical reaction are investigated experimentally and analyzed with the aid of electrochemical digital simulations and quantum-chemical calculations of a theoretical model of the tethered TEMPO system. Interactions between the electrolyte anions and the TEMPO grafted on highly doped, i.e., metallic, electrodes can be tuned to predictably manipulate the oxidizing power of surface nitroxide/oxoammonium redox couple, hence showing the practical importance of the electrostatics on the electrolyte side of the radical monolayer. Conversely, for monolayers prepared on the poorly doped electrodes, the electrostatic interactions between the tethered TEMPO units and the semiconductor-side, i.e., space-charge, become dominant and result in drastic kinetic changes to the electroactivity of the radical monolayer as well as electrochemical nonidealities that can be explained as an increase in the self-interaction "a" parameter that leads to the Frumkin isotherm.
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Affiliation(s)
- Long Zhang
- ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, University of Wollongong , Wollongong, New South Wales 2500, Australia
| | - Yan Boris Vogel
- ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, University of Wollongong , Wollongong, New South Wales 2500, Australia
| | - Benjamin B Noble
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Vinicius R Gonçales
- School of Chemistry, Australian Centre for NanoMedicine and ARC Centre of Excellence for Convergent Bio-Nano Science and Technology, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Nadim Darwish
- Institut de Bioenginyeria de Catalunya (IBEC) , Baldiri Reixac 15-21, Barcelona 08028, Catalonia Spain
| | - Anton Le Brun
- Bragg Institute, Australian Nuclear Science and Technology Organisation (ANSTO) , Locked Bag 2001, Kirrawee DC, New South Wales 2232, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine and ARC Centre of Excellence for Convergent Bio-Nano Science and Technology, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Gordon G Wallace
- ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, University of Wollongong , Wollongong, New South Wales 2500, Australia
| | - Michelle L Coote
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Simone Ciampi
- ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, University of Wollongong , Wollongong, New South Wales 2500, Australia
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26
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Zanetti-Polzi L, Corni S, Daidone I, Amadei A. Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteins. Phys Chem Chem Phys 2016; 18:18450-9. [PMID: 27339768 DOI: 10.1039/c6cp03394f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here, a methodology is proposed to investigate the collective fluctuation modes of an arbitrary set of observables, maximally contributing to the fluctuation of another functionally relevant observable. The methodology, based on the analysis of fully classical molecular dynamics (MD) simulations, exploits the essential dynamics (ED) method, originally developed to analyse the collective motions in proteins. We apply this methodology to identify the residues that are more relevant for determining the reduction potential (E(0)) of a redox-active protein. To this aim, the fluctuation modes of the single-residue electrostatic potentials mostly contributing to the fluctuations of the total electrostatic potential (the main determinant of E(0)) are investigated for wild-type azurin and two of its mutants with a higher E(0). By comparing the results here obtained with a previous study on the same systems [Zanetti-Polzi et al., Org. Biomol. Chem., 2015, 13, 11003] we show that the proposed methodology is able to identify the key sites that determine E(0). This information can be used for a general deeper understanding of the molecular mechanisms on the basis of the redox properties of the proteins under investigation, as well as for the rational design of mutants with a higher or lower E(0). From the results of the present analysis we propose a new azurin mutant that, according to our calculations, shows a further increase of E(0).
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy.
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27
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Gunawan CA, Nam EV, Marquis CP, Gooding JJ, Thordarson P, Zhao C. Scanning Electrochemical Microscopy of Cytochrome
c
Peroxidase through the Orientation‐Controlled Immobilisation of Cytochrome
c. ChemElectroChem 2016. [DOI: 10.1002/celc.201600195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Ekaterina V. Nam
- School of Chemistry The University of New South Wales Sydney 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemistry The University of New South Wales Sydney 2052 Australia
| | - Christopher P. Marquis
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney 2052 Australia
| | - J. Justin Gooding
- School of Chemistry The University of New South Wales Sydney 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemistry The University of New South Wales Sydney 2052 Australia
| | - Pall Thordarson
- School of Chemistry The University of New South Wales Sydney 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemistry The University of New South Wales Sydney 2052 Australia
| | - Chuan Zhao
- School of Chemistry The University of New South Wales Sydney 2052 Australia
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28
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Charchar P, Christofferson AJ, Todorova N, Yarovsky I. Understanding and Designing the Gold-Bio Interface: Insights from Simulations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2395-418. [PMID: 27007031 DOI: 10.1002/smll.201503585] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/01/2016] [Indexed: 05/20/2023]
Abstract
Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.
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Affiliation(s)
- Patrick Charchar
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | | | - Nevena Todorova
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
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29
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Schön JC, Oligschleger C, Cortes J. Prediction and clarification of structures of (bio)molecules on surfaces. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/znb-2015-0222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The design of future materials for biotechnological applications via deposition of molecules on surfaces will require not only exquisite control of the deposition procedure, but of equal importance will be our ability to predict the shapes and stability of individual molecules on various surfaces. Furthermore, one will need to be able to predict the structure patterns generated during the self-organization of whole layers of (bio)molecules on the surface. In this review, we present an overview over the current state of the art regarding the prediction and clarification of structures of biomolecules on surfaces using theoretical and computational methods.
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Affiliation(s)
- J. Christian Schön
- Max-Planck-Institute for Solid State Research , Heisenbergstr. 1, D-70569 Stuttgart, Germany
| | - Christina Oligschleger
- University of Applied Sciences Bonn-Rhein-Sieg , Von-Liebigstr. 20, D-53359 Rheinbach, Germany
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30
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Zanetti-Polzi L, Corni S. A dynamical approach to non-adiabatic electron transfers at the bio-inorganic interface. Phys Chem Chem Phys 2016; 18:10538-49. [DOI: 10.1039/c6cp00044d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A methodology is proposed to investigate the role of the energy fluctuations, determined by the dynamical evolution of a system, and the role of non-adiabaticity in affecting the kinetic rate of electron transfer reactions at the bio-inorganic interface.
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31
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Zanetti-Polzi L, Bortolotti CA, Daidone I, Aschi M, Amadei A, Corni S. A few key residues determine the high redox potential shift in azurin mutants. Org Biomol Chem 2015; 13:11003-13. [PMID: 26381463 DOI: 10.1039/c5ob01819f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The wide range of variability of the reduction potential (E(0)) of blue-copper proteins has been the subject of a large number of studies in the past several years. In particular, a series of azurin mutants have been recently rationally designed tuning E(0) over a very broad range (700 mV) without significantly altering the redox-active site [Marshall et al., Nature, 2009, 462, 113]. This clearly suggests that interactions outside the primary coordination sphere are relevant to determine E(0) in cupredoxins. However, the molecular determinants of the redox potential variability are still undisclosed. Here, by means of atomistic molecular dynamics simulations and hybrid quantum/classical calculations, the mechanisms that determine the E(0) shift of two azurin mutants with high potential shifts are unravelled. The reduction potentials of native azurin and of the mutants are calculated obtaining results in good agreement with the experiments. The analysis of the simulations reveals that only a small number of residues (including non-mutated ones) are relevant in determining the experimentally observed E(0) variation via site-specific, but diverse, mechanisms. These findings open the path to the rational design of new azurin mutants with different E(0).
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Affiliation(s)
- Laura Zanetti-Polzi
- Center S3, CNR-Institute of Nanoscience, Via Campi 213/A, 41125, Modena, Italy.
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32
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Hilaire MR, Abaskharon RM, Gai F. Biomolecular Crowding Arising from Small Molecules, Molecular Constraints, Surface Packing, and Nano-Confinement. J Phys Chem Lett 2015; 6:2546-53. [PMID: 26266732 PMCID: PMC4610718 DOI: 10.1021/acs.jpclett.5b00957] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The effect of macromolecular crowding on the structure, dynamics, and reactivity of biomolecules is well established and the relevant research has been extensively reviewed. Herein, we focus our discussion on crowding effects arising from small cosolvent molecules and densely packed surface conditions. In addition, we highlight recent efforts that capitalize on the excluded volume effect for various tailored biochemical and biophysical applications. Specifically, we discuss how a targeted increase in local mass density can be exploited to gain insight into the folding dynamics of the protein of interest and how confinement via reverse micelles can be used to study a range of biophysical questions, from protein hydration dynamics to amyloid formation.
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Affiliation(s)
| | | | - Feng Gai
- To whom correspondence should be addressed; ; Phone: 215-573-6256; Fax: 215-573-2112
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