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Protein Adsorption and Conformational Changes
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Protein Adsorption and Conformational Changes

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Bioorganic Chemistry".

Deadline for manuscript submissions: closed (31 July 2021) | Viewed by 21222

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Prof. Dr. Michael Assfalg

E-Mail Website
Guest Editor
Department of Biotechnology, University of Verona, Verona, Italy
Interests: biomolecular structure and dynamics; protein–surface interactions; misfolding; molecular recognition; biomolecular NMR spectroscopy; protein chemical modifications
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein adsorption to solids, nanomaterials, and biological surfaces is of central interest in many fields, including biomedicine, bioanalytical chemistry, materials engineering, bio-nanotechnology, as well as basic biomolecular research. Although protein adsorption may sometimes occur with little consequence on molecular structure, interactions with surfaces frequently cause changes in local or global conformations and dynamics, perturbations to secondary structures or tertiary folds, eventually resulting in dramatically altered protein function. Importantly, surfaces may trigger protein misfolding and self-aggregation, or, conversely, promote protein structure formation. The use of nanoscale surfaces to remodel the conformational landscape and the aggregation pathways of amyloidogenic peptides and proteins has been proposed as a promising strategy against several severe human diseases. The rapid growth of applications and technological innovation which is based on or concerned with protein adsorption necessitates renewed efforts to provide molecular level insight into adsorption-induced protein structural perturbations.

In this Special Issue, we aim to gather the most recent findings of experimental and computational investigations that contribute novel insight into protein adsorption with a focus on structural and dynamic aspects. Special emphasis will be placed on observations obtained with advanced technologies and approaches, on integrated experimental measurements/computational methods, submolecular level and biomolecular exchange studies, theoretical modeling, novel features of protein conformational landscapes, and the molecular basis of surface-mediated protein conformational transitions.

We welcome submissions of original research and reviews that address some aspect of the Special Issue’s theme.

Prof. Dr. Michael Assfalg
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. Molecules is an international peer-reviewed open access semimonthly 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 adsorption
  • Protein–surface interactions
  • Conformational landscape
  • Protein structure and dynamics
  • Misfolding
  • Nano–bio interface

Published Papers (6 papers)

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Editorial

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3 pages, 169 KiB  
Editorial
Protein Adsorption and Conformational Changes
by Michael Assfalg
Molecules 2021, 26(23), 7079; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26237079 - 23 Nov 2021
Cited by 5 | Viewed by 1489
Abstract
Protein adsorption onto surfaces of diverse materials of both natural and artificial origin is of utmost relevance in many areas of research and technology: medicine, pharmaceutical sciences, analytical sciences, biotechnology, nanotechnology, and cell biology, among others [...] Full article
(This article belongs to the Special Issue Protein Adsorption and Conformational Changes)

Research

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14 pages, 1670 KiB  
Article
Understanding the Adsorption of Peptides and Proteins onto PEGylated Gold Nanoparticles
by Yasiru Randika Perera, Joanna Xiuzhu Xu, Dhanush L. Amarasekara, Alex C. Hughes, Ibraheem Abbood and Nicholas C. Fitzkee
Molecules 2021, 26(19), 5788; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26195788 - 24 Sep 2021
Cited by 18 | Viewed by 3753
Abstract
Polyethylene glycol (PEG) surface conjugations are widely employed to render passivating properties to nanoparticles in biological applications. The benefits of surface passivation by PEG are reduced protein adsorption, diminished non-specific interactions, and improvement in pharmacokinetics. However, the limitations of PEG passivation remain an [...] Read more.
Polyethylene glycol (PEG) surface conjugations are widely employed to render passivating properties to nanoparticles in biological applications. The benefits of surface passivation by PEG are reduced protein adsorption, diminished non-specific interactions, and improvement in pharmacokinetics. However, the limitations of PEG passivation remain an active area of research, and recent examples from the literature demonstrate how PEG passivation can fail. Here, we study the adsorption amount of biomolecules to PEGylated gold nanoparticles (AuNPs), focusing on how different protein properties influence binding. The AuNPs are PEGylated with three different sizes of conjugated PEG chains, and we examine interactions with proteins of different sizes, charges, and surface cysteine content. The experiments are carried out in vitro at physiologically relevant timescales to obtain the adsorption amounts and rates of each biomolecule on AuNP-PEGs of varying compositions. Our findings are relevant in understanding how protein size and the surface cysteine content affect binding, and our work reveals that cysteine residues can dramatically increase adsorption rates on PEGylated AuNPs. Moreover, shorter chain PEG molecules passivate the AuNP surface more effectively against all protein types. Full article
(This article belongs to the Special Issue Protein Adsorption and Conformational Changes)
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14 pages, 1194 KiB  
Article
Insights into a Protein-Nanoparticle System by Paramagnetic Perturbation NMR Spectroscopy
by Yamanappa Hunashal, Cristina Cantarutti, Sofia Giorgetti, Loredana Marchese, Federico Fogolari and Gennaro Esposito
Molecules 2020, 25(21), 5187; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25215187 - 07 Nov 2020
Cited by 5 | Viewed by 5215
Abstract
Background: The interaction between proteins and nanoparticles is a very relevant subject because of the potential applications in medicine and material science in general. Further interest derives from the amyloidogenic character of the considered protein, β2-microglobulin (β2m), which may be regarded as a [...] Read more.
Background: The interaction between proteins and nanoparticles is a very relevant subject because of the potential applications in medicine and material science in general. Further interest derives from the amyloidogenic character of the considered protein, β2-microglobulin (β2m), which may be regarded as a paradigmatic system for possible therapeutic strategies. Previous evidence showed in fact that gold nanoparticles (AuNPs) are able to inhibit β2m fibril formation in vitro. Methods: NMR (Nuclear Magnetic Resonance) and ESR (Electron Spin Resonance) spectroscopy are employed to characterize the paramagnetic perturbation of the extrinsic nitroxide probe Tempol on β2m in the absence and presence of AuNPs to determine the surface accessibility properties and the occurrence of chemical or conformational exchange, based on measurements conducted under magnetization equilibrium and non-equilibrium conditions. Results: The nitroxide perturbation analysis successfully identifies the protein regions where protein-protein or protein-AuNPs interactions hinder accessibility or/and establish exchange contacts. These information give interesting clues to recognize the fibrillation interface of β2m and hypothesize a mechanism for AuNPs fibrillogenesis inhibition. Conclusions: The presented approach can be advantageously applied to the characterization of the interface in protein-protein and protein-nanoparticles interactions. Full article
(This article belongs to the Special Issue Protein Adsorption and Conformational Changes)
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Review

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23 pages, 1969 KiB  
Review
Alpha-Synuclein—Nanoparticle Interactions: Understanding, Controlling and Exploiting Conformational Plasticity
by Mariapina D’Onofrio, Francesca Munari and Michael Assfalg
Molecules 2020, 25(23), 5625; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25235625 - 29 Nov 2020
Cited by 14 | Viewed by 3751
Abstract
Alpha-synuclein (αS) is an extensively studied protein due to its involvement in a group of neurodegenerative disorders, including Parkinson′s disease, and its documented ability to undergo aberrant self-aggregation resulting in the formation of amyloid-like fibrils. In dilute solution, the protein is intrinsically disordered [...] Read more.
Alpha-synuclein (αS) is an extensively studied protein due to its involvement in a group of neurodegenerative disorders, including Parkinson′s disease, and its documented ability to undergo aberrant self-aggregation resulting in the formation of amyloid-like fibrils. In dilute solution, the protein is intrinsically disordered but can adopt multiple alternative conformations under given conditions, such as upon adsorption to nanoscale surfaces. The study of αS-nanoparticle interactions allows us to better understand the behavior of the protein and provides the basis for developing systems capable of mitigating the formation of toxic aggregates as well as for designing hybrid nanomaterials with novel functionalities for applications in various research areas. In this review, we summarize current progress on αS-nanoparticle interactions with an emphasis on the conformational plasticity of the biomolecule. Full article
(This article belongs to the Special Issue Protein Adsorption and Conformational Changes)
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17 pages, 2082 KiB  
Review
Protein Conformational Dynamics upon Association with the Surfaces of Lipid Membranes and Engineered Nanoparticles: Insights from Electron Paramagnetic Resonance Spectroscopy
by Elka R. Georgieva
Molecules 2020, 25(22), 5393; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25225393 - 18 Nov 2020
Cited by 5 | Viewed by 2857
Abstract
Detailed study of conformational rearrangements and dynamics of proteins is central to our understanding of their physiological functions and the loss of function. This review outlines the applications of the electron paramagnetic resonance (EPR) technique to study the structural aspects of proteins transitioning [...] Read more.
Detailed study of conformational rearrangements and dynamics of proteins is central to our understanding of their physiological functions and the loss of function. This review outlines the applications of the electron paramagnetic resonance (EPR) technique to study the structural aspects of proteins transitioning from a solution environment to the states in which they are associated with the surfaces of biological membranes or engineered nanoobjects. In the former case these structural transitions generally underlie functional protein states. The latter case is mostly relevant to the application of protein immobilization in biotechnological industries, developing methods for protein purification, etc. Therefore, evaluating the stability of the protein functional state is particularly important. EPR spectroscopy in the form of continuous-wave EPR or pulse EPR distance measurements in conjunction with protein spin labeling provides highly versatile and sensitive tools to characterize the changes in protein local dynamics as well as large conformational rearrangements. The technique can be widely utilized in studies of both protein-membrane and engineered nanoobject-protein complexes. Full article
(This article belongs to the Special Issue Protein Adsorption and Conformational Changes)
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17 pages, 1644 KiB  
Review
Protein Adsorption on Solid Supported Membranes: Monitoring the Transport Activity of P-Type ATPases
by Francesco Tadini-Buoninsegni
Molecules 2020, 25(18), 4167; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25184167 - 11 Sep 2020
Cited by 6 | Viewed by 3256
Abstract
P-type ATPases are a large family of membrane transporters that are found in all forms of life. These enzymes couple ATP hydrolysis to the transport of various ions or phospholipids across cellular membranes, thereby generating and maintaining crucial electrochemical potential gradients. P-type ATPases [...] Read more.
P-type ATPases are a large family of membrane transporters that are found in all forms of life. These enzymes couple ATP hydrolysis to the transport of various ions or phospholipids across cellular membranes, thereby generating and maintaining crucial electrochemical potential gradients. P-type ATPases have been studied by a variety of methods that have provided a wealth of information about the structure, function, and regulation of this class of enzymes. Among the many techniques used to investigate P-type ATPases, the electrical method based on solid supported membranes (SSM) was employed to investigate the transport mechanism of various ion pumps. In particular, the SSM method allows the direct measurement of charge movements generated by the ATPase following adsorption of the membrane-bound enzyme on the SSM surface and chemical activation by a substrate concentration jump. This kind of measurement was useful to identify electrogenic partial reactions and localize ion translocation in the reaction cycle of the membrane transporter. In the present review, we discuss how the SSM method has contributed to investigate some key features of the transport mechanism of P-type ATPases, with a special focus on sarcoplasmic reticulum Ca2+-ATPase, mammalian Cu+-ATPases (ATP7A and ATP7B), and phospholipid flippase ATP8A2. Full article
(This article belongs to the Special Issue Protein Adsorption and Conformational Changes)
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