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Biomolecules
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Biomolecular Electronics
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Biomolecular Electronics

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (30 August 2019) | Viewed by 19473

Special Issue Editor

Prof. Dr. Stuart Lindsay

E-Mail Website
Guest Editor
Biodesign Institute, Arizona State University, Tempe, AZ, USA
Interests: single-molecule measurements; charge transport in proteins; electron tunneling; quantum effects in biology; protein electronics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

DNA-based electronics has become quite advanced, with a good agreement between theory and experiment in some cases and sophisticated proposals for self-assembled devices based on DNA origami. The same is not true of proteins, where there seems to be no agreement at all between theories based on the coupling of redox centers by electron tunneling and molecular device measurements in which proteins are contacted by electrodes. In the latter case, there are reports of nS conductance over distances of many nm. Multilayers of protein appear to conduct as well as monolayers and large conductances have been observed in long filaments. Strikingly, bacterial pili have been shown to have conductivities that can exceed s/m. Even redox-active proteins, which should be textbook examples of Marcus-like hopping transport, have been measured as having temperature-independent conductances.

Long-range, temperature-independent transport would appear to require quantum coherence, which seems unlikely in a water bath at 300K. However, if these systems are not quantum coherent, how can we accommodate the reports of electron spin polarization in transport through chiral proteins?

One focus of this Special Issue of Biomolecules is examining these fundamental problems, or at least exposing them to a wider audience. However, the technological implications of biomolecular electronics are far-reaching. This is particularly true for the simpler case of DNA. DNA "circuits" are one example; sequencing by means of electron tunneling is another. As we approach an age where VLSI and nanotechnology merge with molecular medicine and biology based on massive data sets, this field will become central in the integration of computing and biology.

Prof. Stuart Lindsay
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Protein electronics
  • Molecular electronics
  • Single-Molecule conductance
  • Protein detection
  • Protein sensing
  • Label-free detection
  • Conductance gating in proteins
  • Electron transport mechanisms in proteins
  • Coherence and dephasing in proteins
  • Role of water in protein conductance
  • Extended electronic states in proteins
  • Hopping conductance in proteins
  • Long-range hopping in proteins
  • Electrode-protein interfaces
  • Charge injection barriers at protein-electrode interfaces
  • Proteins as electronic devices
  • Protein assemblies as electronic devices
  • DNA electronics
  • Electron transport in DNA
  • DNA-electrode interfaces
  • Charge injection at a DNA-electrode interface
  • Barrier to charge injection at a DNA-electrode interface

Published Papers (5 papers)

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Research

10 pages, 2189 KiB  
Article
Spin-Polarized Electron Transmission in DNA-Like Systems
by Miguel A. Sierra, David Sánchez, Rafael Gutierrez, Gianaurelio Cuniberti, Francisco Domínguez-Adame and Elena Díaz
Biomolecules 2020, 10(1), 49; https://0-doi-org.brum.beds.ac.uk/10.3390/biom10010049 - 28 Dec 2019
Cited by 12 | Viewed by 3168
Abstract
The helical distribution of the electronic density in chiral molecules, such as DNA and bacteriorhodopsin, has been suggested to induce a spin–orbit coupling interaction that may lead to the so-called chirality-induced spin selectivity (CISS) effect. Key ingredients for the theoretical modelling are, in [...] Read more.
The helical distribution of the electronic density in chiral molecules, such as DNA and bacteriorhodopsin, has been suggested to induce a spin–orbit coupling interaction that may lead to the so-called chirality-induced spin selectivity (CISS) effect. Key ingredients for the theoretical modelling are, in this context, the helically shaped potential of the molecule and, concomitantly, a Rashba-like spin–orbit coupling due to the appearance of a magnetic field in the electron reference frame. Symmetries of these models clearly play a crucial role in explaining the observed effect, but a thorough analysis has been largely ignored in the literature. In this work, we present a study of these symmetries and how they can be exploited to enhance chiral-induced spin selectivity in helical molecular systems. Full article
(This article belongs to the Special Issue Biomolecular Electronics)
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22 pages, 12561 KiB  
Article
Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations
by Maria Ortega, J. G. Vilhena, Linda A. Zotti, Ismael Díez-Pérez, Juan Carlos Cuevas and Rubén Pérez
Biomolecules 2019, 9(10), 611; https://0-doi-org.brum.beds.ac.uk/10.3390/biom9100611 - 15 Oct 2019
Cited by 15 | Viewed by 4364
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Biomolecular Electronics)
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22 pages, 414 KiB  
Article
A Landauer Formula for Bioelectronic Applications
by Eszter Papp, Dávid P. Jelenfi, Máté T. Veszeli and Gábor Vattay
Biomolecules 2019, 9(10), 599; https://0-doi-org.brum.beds.ac.uk/10.3390/biom9100599 - 11 Oct 2019
Cited by 15 | Viewed by 3422
Abstract
Recent electronic transport experiments using metallic contacts attached to proteins identified some “stylized facts”, which contradict conventional wisdom that increasing either the spatial distance between the electrodes or the temperature suppresses conductance exponentially. These include nearly temperature-independent conductance over the protein in the [...] Read more.
Recent electronic transport experiments using metallic contacts attached to proteins identified some “stylized facts”, which contradict conventional wisdom that increasing either the spatial distance between the electrodes or the temperature suppresses conductance exponentially. These include nearly temperature-independent conductance over the protein in the 30 to 300 K range, distance-independent conductance within a single protein in the 1 to 10 nm range and an anomalously large conductance in the 0.1 to 10 nS range. In this paper, we develop a generalization of the low temperature Landauer formula, which can account for the joint effects of tunneling and decoherence and can explain these new experimental findings. We use novel approximations, which greatly simplify the mathematical treatment and allow us to calculate the conductance in terms of a handful macroscopic parameters, instead of the myriads of microscopic parameters describing the details of an atomic level quantum chemical computation. The new approach makes it possible to get predictions for the outcomes of new experiments without relying solely on high performance computing and can distinguish important and unimportant details of the protein structures from the point of view of transport properties. Full article
(This article belongs to the Special Issue Biomolecular Electronics)
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13 pages, 4003 KiB  
Article
Can One Define the Conductance of Amino Acids?
by Linda A. Zotti, Beatrice Bednarz, Juan Hurtado-Gallego, Damien Cabosart, Gabino Rubio-Bollinger, Nicolas Agrait and Herre S.J. van der Zant
Biomolecules 2019, 9(10), 580; https://0-doi-org.brum.beds.ac.uk/10.3390/biom9100580 - 07 Oct 2019
Cited by 28 | Viewed by 4333
Abstract
We studied the electron-transport properties of ten different amino acids and one dimer (di-methionine) using the mechanically controlled break-junction (MCBJ) technique. For methionine and cysteine, additional measurements were performed with the scanning tunneling microscope break-junction (STM-BJ) technique. By means of a statistical clustering [...] Read more.
We studied the electron-transport properties of ten different amino acids and one dimer (di-methionine) using the mechanically controlled break-junction (MCBJ) technique. For methionine and cysteine, additional measurements were performed with the scanning tunneling microscope break-junction (STM-BJ) technique. By means of a statistical clustering technique, we identified several conductance groups for each of the molecules considered. Ab initio calculations revealed that the observed broad conductance distribution stems from the possibility of various binding geometries which can be formed during stretching combined with a multitude of possible conformational changes. The results suggest that it would be helpful to explore different experimental techniques such as recognition tunneling and conditions to help identify the nature of amino-acid-based junctions even further, for example, with the goal to establish a firm platform for their unambiguous recognition by tunneling break-junction experiments. Full article
(This article belongs to the Special Issue Biomolecular Electronics)
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12 pages, 2249 KiB  
Article
Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction
by Carlos Romero-Muñiz, María Ortega, J. G. Vilhena, Ismael Diéz-Pérez, Juan Carlos Cuevas, Rubén Pérez and Linda A. Zotti
Biomolecules 2019, 9(9), 506; https://0-doi-org.brum.beds.ac.uk/10.3390/biom9090506 - 19 Sep 2019
Cited by 16 | Viewed by 3556
Abstract
Protein-based electronics is an emerging field which has attracted considerable attention over the past decade. Here, we present a theoretical study of the formation and electronic structure of a metal-protein-metal junction based on the blue-copper azurin from pseudomonas aeruginosa. We focus on the [...] Read more.
Protein-based electronics is an emerging field which has attracted considerable attention over the past decade. Here, we present a theoretical study of the formation and electronic structure of a metal-protein-metal junction based on the blue-copper azurin from pseudomonas aeruginosa. We focus on the case in which the protein is adsorbed on a gold surface and is contacted, at the opposite side, to an STM (Scanning Tunneling Microscopy) tip by spontaneous attachment. This has been simulated through a combination of molecular dynamics and density functional theory. We find that the attachment to the tip induces structural changes in the protein which, however, do not affect the overall electronic properties of the protein. Indeed, only changes in certain residues are observed, whereas the electronic structure of the Cu-centered complex remains unaltered, as does the total density of states of the whole protein. Full article
(This article belongs to the Special Issue Biomolecular Electronics)
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