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Biophysica, Volume 2, Issue 2 (June 2022) – 7 articles

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19 pages, 6878 KiB  
Article
The Amyloidogenic Peptide Amyloid Beta(16–22) Displays Facet Dependent Conformation on Metal Surfaces
by Kieran P. Somers and David L. Cheung
Biophysica 2022, 2(2), 135-153; https://doi.org/10.3390/biophysica2020015 - 9 Jun 2022
Cited by 1 | Viewed by 2186
Abstract
Currently, it is not understood how metal nanoparticles influence the formation of protein fibrils, although recent literature highlights that the shape and chemical composition of such nanoparticles can strongly influence the process. Understanding this process at a fundamental level can potentially unlock routes [...] Read more.
Currently, it is not understood how metal nanoparticles influence the formation of protein fibrils, although recent literature highlights that the shape and chemical composition of such nanoparticles can strongly influence the process. Understanding this process at a fundamental level can potentially unlock routes to the development of new therapeutics, as well as novel materials for technological applications. This requires a microscopic picture of the behaviour of amyloidogenic proteins on metal surfaces. Using replica exchange molecular dynamics simulations, we investigate the conformation of the model amyloidogenic peptide, Aβ(16–22), on different gold and silver surfaces. The conformation of the peptide on gold surfaces also shows a strong facet dependence, with fibril-like conformations being promoted in the 100 surface and inhibited on the 111 surface. A smaller degree of facet dependence is seen for silver with the peptide behaving similar on both of these. The difference in the facet dependence can be related to the difference between direct adsorption onto the gold 111 surface, with a preference towards indirect (water mediated) adsorption onto the other surfaces. This new information on the behaviour of an amyloidogenic peptide on metal surfaces can give insight into the size-dependent effect of nanoparticles on fibril formation and the use of surfaces to control fibrillation. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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12 pages, 1630 KiB  
Review
Analysis of Enzyme Conformation Dynamics Using Single-Molecule Förster Resonance Energy Transfer (smFRET)
by Mai Huynh and Bhaswati Sengupta
Biophysica 2022, 2(2), 123-134; https://doi.org/10.3390/biophysica2020014 - 6 Jun 2022
Cited by 1 | Viewed by 2281
Abstract
Single-molecule Förster resonance energy transfer (smFRET) enables the deconvolution of various conformational substates of biomolecules. Over the past two decades, it has been widely used to understand the conformational dynamics of enzymes. Commonly, enzymes undergo reversible transitions between active and inactive states in [...] Read more.
Single-molecule Förster resonance energy transfer (smFRET) enables the deconvolution of various conformational substates of biomolecules. Over the past two decades, it has been widely used to understand the conformational dynamics of enzymes. Commonly, enzymes undergo reversible transitions between active and inactive states in solution. Using smFRET, the details of these transitions and the effect of ligands on these dynamics have been determined. In this mini-review, we discuss the various works focused on the investigation of enzyme conformational dynamics using smFRET. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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2 pages, 163 KiB  
Editorial
Recent Biophysical Advances in Drug Discovery
by Ho Leung Ng
Biophysica 2022, 2(2), 121-122; https://doi.org/10.3390/biophysica2020013 - 1 Jun 2022
Viewed by 1377
Abstract
In recent years, we have seen an explosion of technological progress related to drug discovery, including computing power, artificial intelligence, and electron microscopy [...] Full article
(This article belongs to the Special Issue Biophysical Advances in Structure-Based Drug Design)
8 pages, 836 KiB  
Article
The Relationship between Hydrophobicity and Drug-Protein Binding in Human Serum Albumin: A Quartz Crystal Microbalance Study
by Ahmad R. Alhankawi, Jacob K. Al-Husseini, Archie Spindler, Clark Baker, Tonderai T. Shoniwa, Mohammed Ahmed, Peter A. Chiarelli and Malkiat S. Johal
Biophysica 2022, 2(2), 113-120; https://doi.org/10.3390/biophysica2020012 - 23 May 2022
Cited by 3 | Viewed by 3417
Abstract
In this paper, the quartz crystal microbalance with dissipation monitoring (QCM-D) was used to investigate hydrophobicity and binding strength (KD) for 10 different drugs interacting with human serum albumin (HSA). Quantitative structure activity relationship (QSAR) analysis was used to determine the [...] Read more.
In this paper, the quartz crystal microbalance with dissipation monitoring (QCM-D) was used to investigate hydrophobicity and binding strength (KD) for 10 different drugs interacting with human serum albumin (HSA). Quantitative structure activity relationship (QSAR) analysis was used to determine the relationship between drug hydrophobicity (ClogP) and HSA binding strength log(1/KD). The results are compared to prior knowledge on bovine serum albumin (BSA) binding. We demonstrate a positive correlation between drug hydrophobicity and the strength of ligand-protein binding to HSA and show a statistically significant similarity with the trend reported in BSA. The findings presented in this work provide insight into the role that bound water plays in ligand-protein interactions. Further, the comparison between HSA and BSA provides quantitative justification for the use of these proteins interchangeably in the analysis of drug-based binding kinetics. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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2 pages, 182 KiB  
Editorial
Protein Engineering: The Present and the Future
by Javier Sancho
Biophysica 2022, 2(2), 111-112; https://doi.org/10.3390/biophysica2020011 - 29 Apr 2022
Viewed by 2508
Abstract
Yes, we are made of proteins, and yes, we can profit from them [...] Full article
(This article belongs to the Special Issue Protein Engineering: The Present and the Future)
20 pages, 1370 KiB  
Review
Amyloid-β Oligomers: Multiple Moving Targets
by Dylan Shea and Valerie Daggett
Biophysica 2022, 2(2), 91-110; https://doi.org/10.3390/biophysica2020010 - 28 Apr 2022
Cited by 18 | Viewed by 6621
Abstract
Alzheimer’s Disease (AD) is a neurodegenerative disorder that is characterized clinically by progressive cognitive decline and pathologically by the β-sheet rich fibril plaque deposition of the amyloid-β (Aβ) peptide in the brain. While plaques are a hallmark of AD, plaque burden is not [...] Read more.
Alzheimer’s Disease (AD) is a neurodegenerative disorder that is characterized clinically by progressive cognitive decline and pathologically by the β-sheet rich fibril plaque deposition of the amyloid-β (Aβ) peptide in the brain. While plaques are a hallmark of AD, plaque burden is not correlated with cognitive impairment. Instead, Aβ oligomers formed during the aggregation process represent the main agents of neurotoxicity, which occurs 10–20 years before patients begin to show symptoms. These oligomers are dynamic in nature and represented by a heterogeneous distribution of aggregates ranging from low- to high-molecular weight, some of which are toxic while others are not. A major difficulty in determining the pathological mechanism(s) of Aβ, developing reliable diagnostic markers for early-stage detection, as well as effective therapeutics for AD are the differentiation and characterization of oligomers formed throughout disease propagation based on their molecular features, effects on biological function, and relevance to disease propagation and pathology. Thus, it is critical to methodically identify the mechanisms of Aβ aggregation and toxicity, as well as describe the roles of different oligomers and aggregates in disease progression and molecular pathology. Here, we describe a variety of biophysical techniques used to isolate and characterize a range of Aβ oligomer populations, as well as discuss proposed mechanisms of toxicity and therapeutic interventions aimed at specific assemblies formed during the aggregation process. The approaches being used to map the misfolding and aggregation of Aβ are like what was done during the fundamental early studies, mapping protein folding pathways using combinations of biophysical techniques in concert with protein engineering. Such information is critical to the design and molecular engineering of future diagnostics and therapeutics for AD. Full article
(This article belongs to the Special Issue Protein Engineering: The Present and the Future)
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2 pages, 162 KiB  
Editorial
First Year of Biophysica
by Matthias Buck and Victor Muñoz
Biophysica 2022, 2(2), 89-90; https://doi.org/10.3390/biophysica2020009 - 30 Mar 2022
Viewed by 1713
Abstract
“I can’t believe another year has passed already” is what most of us think when another birthday is upon us or when we see our children grow [...] Full article
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