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Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam...
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Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Biochemistry and Molecular Biology".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 32427

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

Special Issue Editors

Prof. Dr. Dmitri Davydov

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Guest Editor
Department of Chemistry, Washington State University, Fulmer 410, P.O. Box 644630, Pullman, WA 99164-4630, USA
Interests: enzymology; cytochromes P450; drug metabolism; allosteric enzymes; protein–protein interactions; effects of hydrostatic pressure on proteins; piezophilic enzymes
Special Issues, Collections and Topics in MDPI journals
PD Dr. Christiane Jung

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Guest Editor
KKS Ultraschall AG, Ultrasonic Technology & Surface Refinement, Frauholzring 29, CH-6422 SZ, Switzerland
Interests: protein biophysics; cytochromes P450; effects of hydrostatic pressure and ultrasound on biological materials; surface treatment, functionalizing, and ultrasonic cleaning of medical implants for traumatology; orthopedics; dentistry

Special Issue Information

Dear Colleagues,

This Special Issue is devoted to the effects of hydrostatic pressure on biological systems and the use of these effects for exploring the structure and function of biological macromolecules and their ensembles. Hydrostatic pressure, a fundamental thermodynamic parameter, profoundly affects the conformation of proteins and nucleic acids and biological membrane structure. It is widely used in protein biophysics and mechanistic enzymology as a tool for exploring protein conformational landscapes through displacing protein conformational equilibria and affecting protein–protein and protein–ligand interactions. Pressure perturbation spectroscopy and calorimetry complemented by ultrasound velocity measurements are indispensable for studying protein solvation and its role in enzyme functionality. Effects of hydrostatic pressure on proteins, nucleic acids, and biomembranes are also critical for understanding the mechanisms of piezophilic adaptation that allows deep-sea species (piezophiles) to survive at extreme pressures of ocean depth. In some sense, structural consequences of evolutionary adaptation to high hydrostatic pressure may be viewed as the effects of pressure perturbation imprinted in the structure of pressure-adapted biological systems. 

Despite a plethora of experimental papers and a dozen fundamental reviews devoted to the effects of pressure on biological systems, this important field appears to be severely underrepresented in modern literature. We hope that this Special Issue will bring together the most important new findings and new concepts in high-pressure biosciences and promote researchers’ interest in the unique exploratory potential of the pressure perturbation approach for biochemistry, biophysics, mechanistic enzymology, and evolutionary biology.

We would like to devote this Special Issue to the memory of Gaston Hui Bon Hoa, French biophysicist, our friend and colleague, who passed away in July 2020. Gaston was one of the pioneers studying the effects of hydrostatic pressure on proteins, nucleic acids, and their assemblies. He devoted over 40 years in his scientific career to establishing pressure perturbation approaches and applying them in studies of protein structure and function. Gaston was internationally recognized as a leading expert in high-pressure biophysics.

We welcome the submission of original research, either experimental or theoretical, and review manuscripts focusing on the effects of pressure on biological macromolecules and their use in exploring the structure and function of biological systems. Manuscripts devoted to the evolutionary adaptations of deep-sea species to high hydrostatic pressure and their use in structural biology, mechanistic enzymology, and protein biophysics are also welcome. 

Prof. Dr. Dmitri Davydov
PD Dr. Christiane Jung
Guest Editors

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. Biology 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

  • Hydrostatic pressure 
  • Thermodynamics 
  • Biochemical spectroscopy 
  • Conformational dynamics of biomolecules 
  • Protein-protein interactions
  • Protein-ligand interactions 
  • Piezophiles 
  • Evolutionary adaptation

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Published Papers (10 papers)

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Editorial

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7 pages, 1159 KiB  
Editorial
A Pathfinder in High-Pressure Bioscience: In Memoriam of Gaston Hui Bon Hoa
by Dmitri R. Davydov, Christiane Jung, Gregory A. Petsko, Stephen G. Sligar and Jack A. Kornblatt
Biology 2021, 10(8), 778; https://doi.org/10.3390/biology10080778 - 16 Aug 2021
Viewed by 2482
Abstract
On 26 July 2020, our colleague and friend Dr [...] Full article
(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)
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Research

Jump to: Editorial, Review

27 pages, 3389 KiB  
Article
Conformational Rearrangements in the Redox Cycling of NADPH-Cytochrome P450 Reductase from Sorghum bicolor Explored with FRET and Pressure-Perturbation Spectroscopy
by Bixia Zhang, ChulHee Kang and Dmitri R. Davydov
Biology 2022, 11(4), 510; https://doi.org/10.3390/biology11040510 - 25 Mar 2022
Cited by 4 | Viewed by 2429
Abstract
NADPH-cytochrome P450 reductase (CPR) from Sorghum bicolor (SbCPR) serves as an electron donor for cytochrome P450 essential for monolignol and lignin production in this biofuel crop. The CPR enzymes undergo an ample conformational transition between the closed and open states in their functioning. [...] Read more.
NADPH-cytochrome P450 reductase (CPR) from Sorghum bicolor (SbCPR) serves as an electron donor for cytochrome P450 essential for monolignol and lignin production in this biofuel crop. The CPR enzymes undergo an ample conformational transition between the closed and open states in their functioning. This transition is triggered by electron transfer between the FAD and FMN and provides access of the partner protein to the electron-donating FMN domain. To characterize the electron transfer mechanisms in the monolignol biosynthetic pathway better, we explore the conformational transitions in SbCPR with rapid scanning stop-flow and pressure-perturbation spectroscopy. We used FRET between a pair of donor and acceptor probes incorporated into the FAD and FMN domains of SbCPR, respectively, to characterize the equilibrium between the open and closed states and explore its modulation in connection with the redox state of the enzyme. We demonstrate that, although the closed conformation always predominates in the conformational landscape, the population of open state increases by order of magnitude upon the formation of the disemiquinone state. Our results are consistent with several open conformation sub-states differing in the volume change (ΔV0) of the opening transition. While the ΔV0 characteristic of the oxidized enzyme is as large as −88 mL/mol, the interaction of the enzyme with the nucleotide cofactor and the formation of the double-semiquinone state of CPR decrease this value to −34 and −18 mL/mol, respectively. This observation suggests that the interdomain electron transfer in CPR increases protein hydration, while promoting more open conformation. In addition to elucidating the functional choreography of plant CPRs, our study demonstrates the high exploratory potential of a combination of the pressure-perturbation approach with the FRET-based monitoring of protein conformational transitions. Full article
(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)
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9 pages, 979 KiB  
Article
Proteins in Wonderland: The Magical World of Pressure
by Kazuyuki Akasaka and Akihiro Maeno
Biology 2022, 11(1), 6; https://doi.org/10.3390/biology11010006 - 21 Dec 2021
Cited by 6 | Viewed by 3678
Abstract
Admitting the “Native”, “Unfolded” and “Fibril” states as the three basic generic states of proteins in nature, each of which is characterized with its partial molar volume, here we predict that the interconversion among these generic states N, U, F may be performed [...] Read more.
Admitting the “Native”, “Unfolded” and “Fibril” states as the three basic generic states of proteins in nature, each of which is characterized with its partial molar volume, here we predict that the interconversion among these generic states N, U, F may be performed simply by making a temporal excursion into the so called “the high-pressure regime”, created artificially by putting the system under sufficiently high hydrostatic pressure, where we convert N to U and F to U, and then back to “the low-pressure regime” (the “Anfinsen regime”), where we convert U back to N (U→N). Provided that the solution conditions (temperature, pH, etc.) remain largely the same, the idea provides a general method for choosing N, U, or F of a protein, to a great extent at will, assisted by the proper use of the external perturbation pressure. A successful experiment is demonstrated for the case of hen lysozyme, for which the amyloid fibril state F prepared at 1 bar is turned almost fully back into its original native state N at 1 bar by going through the “the high-pressure regime”. The outstanding simplicity and effectiveness of pressure in controlling the conformational state of a protein are expected to have a wide variety of applications both in basic and applied bioscience in the future. Full article
(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)
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12 pages, 3196 KiB  
Article
Pressure Adaptations in Deep-Sea Moritella Dihydrofolate Reductases: Compressibility versus Stability
by Ryan W. Penhallurick and Toshiko Ichiye
Biology 2021, 10(11), 1211; https://doi.org/10.3390/biology10111211 - 20 Nov 2021
Cited by 8 | Viewed by 2413
Abstract
Proteins from “pressure-loving” piezophiles appear to adapt by greater compressibility via larger total cavity volume. However, larger cavities in proteins have been associated with lower unfolding pressures. Here, dihydrofolate reductase (DHFR) from a moderate piezophile Moritella profunda (Mp) isolated at ~2.9 km in [...] Read more.
Proteins from “pressure-loving” piezophiles appear to adapt by greater compressibility via larger total cavity volume. However, larger cavities in proteins have been associated with lower unfolding pressures. Here, dihydrofolate reductase (DHFR) from a moderate piezophile Moritella profunda (Mp) isolated at ~2.9 km in depth and from a hyperpiezophile Moritella yayanosii (My) isolated at ~11 km in depth were compared using molecular dynamics simulations. Although previous simulations indicate that MpDHFR is more compressible than a mesophile DHFR, here the average properties and a quasiharmonic analysis indicate that MpDHFR and MyDHFR have similar compressibilities. A cavity analysis also indicates that the three unique mutations in MyDHFR are near cavities, although the cavities are generally similar in size in both. However, while a cleft overlaps an internal cavity, thus forming a pathway from the surface to the interior in MpDHFR, the unique residue Tyr103 found in MyDHFR forms a hydrogen bond with Leu78, and the sidechain separates the cleft from the cavity. Thus, while Moritella DHFR may generally be well suited to high-pressure environments because of their greater compressibility, adaptation for greater depths may be to prevent water entry into the interior cavities. Full article
(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)
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14 pages, 2348 KiB  
Article
Pressure Perturbation Studies of Noncanonical Viral Nucleic Acid Structures
by Judit Somkuti, Orsolya Réka Molnár, Anna Grád and László Smeller
Biology 2021, 10(11), 1173; https://doi.org/10.3390/biology10111173 - 12 Nov 2021
Cited by 5 | Viewed by 2148
Abstract
G-quadruplexes are noncanonical structures formed by guanine-rich sequences of the genome. They are found in crucial loci of the human genome, they take part in the regulation of important processes like cell proliferation and cell death. Much less is known about the subjects [...] Read more.
G-quadruplexes are noncanonical structures formed by guanine-rich sequences of the genome. They are found in crucial loci of the human genome, they take part in the regulation of important processes like cell proliferation and cell death. Much less is known about the subjects of this work, the viral G-quadruplexes. We have chosen three potentially G-quadruplex-forming sequences of hepatitis B. We measured the stability and the thermodynamic parameters of these quadruplexes. We also investigated the potential stabilization of these G-quadruplexes by binding a special ligand that was originally developed for cancer therapy. Fluorescence and infrared spectroscopic measurements were performed over wide temperature and pressure ranges. Our experiments indicate the small unfolding volume change of all three oligos. We found a difference between the unfolding of the 2-quartet and the 3-quartet G-quadruplexes. All three G-quadruplexes were stabilized by TMPyP4, which is a cationic porphyrin developed for stabilizing the human telomere. Full article
(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)
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12 pages, 2542 KiB  
Article
Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth
by Hussein Kaddour, Honorine Lucchi, Guy Hervé, Jacques Vergne and Marie-Christine Maurel
Biology 2021, 10(8), 720; https://doi.org/10.3390/biology10080720 - 28 Jul 2021
Cited by 4 | Viewed by 2430
Abstract
A high pressure apparatus allowing one to study enzyme kinetics under pressure was used to study the self-cleavage activity of the avocado sunblotch viroid. The kinetics of this reaction were determined under pressure over a range up to 300 MPa (1–3000 bar). It [...] Read more.
A high pressure apparatus allowing one to study enzyme kinetics under pressure was used to study the self-cleavage activity of the avocado sunblotch viroid. The kinetics of this reaction were determined under pressure over a range up to 300 MPa (1–3000 bar). It appears that the initial rate of this reaction decreases when pressure increases, revealing a positive ΔV≠ of activation, which correlates with the domain closure accompanying the reaction and the decrease of the surface of the viroid exposed to the solvent. Although, as expected, temperature increases the rate of the reaction whose energy of activation was determined, it appeared that it does not significantly influence the ΔV≠ of activation and that pressure does not influence the energy of activation. These results provide information about the structural aspects or this self-cleavage reaction, which is involved in the process of maturation of this viroid. The behavior of ASBVd results from the involvement of the hammerhead ribozyme present at its catalytic domain, indeed a structural motif is very widespread in the ancient and current RNA world. Full article
(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)
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15 pages, 1761 KiB  
Article
The Effects of Temperature and Pressure on Protein-Ligand Binding in the Presence of Mars-Relevant Salts
by Nisrine Jahmidi-Azizi, Rosario Oliva, Stewart Gault, Charles S. Cockell and Roland Winter
Biology 2021, 10(7), 687; https://doi.org/10.3390/biology10070687 - 20 Jul 2021
Cited by 10 | Viewed by 4211
Abstract
Protein–ligand interactions are fundamental to all biochemical processes. Generally, these processes are studied at ambient temperature and pressure conditions. We investigated the binding of the small ligand 8-anilinonaphthalene-1-sulfonic acid (ANS) to the multifunctional protein bovine serum albumin (BSA) at ambient and low temperatures [...] Read more.
Protein–ligand interactions are fundamental to all biochemical processes. Generally, these processes are studied at ambient temperature and pressure conditions. We investigated the binding of the small ligand 8-anilinonaphthalene-1-sulfonic acid (ANS) to the multifunctional protein bovine serum albumin (BSA) at ambient and low temperatures and at high pressure conditions, in the presence of ions associated with the surface and subsurface of Mars, including the chaotropic perchlorate ion. We found that salts such as magnesium chloride and sulfate only slightly affect the protein–ligand complex formation. In contrast, magnesium perchlorate strongly affects the interaction between ANS and BSA at the single site level, leading to a change in stoichiometry and strength of ligand binding. Interestingly, both a decrease in temperature and an increase in pressure favor the ligand binding process, resulting in a negative change in protein–ligand binding volume. This suggests that biochemical reactions that are fundamental for the regulation of biological processes are theoretically possible outside standard temperature and pressure conditions, such as in the harsh conditions of the Martian subsurface. Full article
(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)
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13 pages, 2743 KiB  
Article
Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR
by Vincent Van Deuren, Yin-Shan Yang, Karine de Guillen, Cécile Dubois, Catherine Anne Royer, Christian Roumestand and Philippe Barthe
Biology 2021, 10(7), 656; https://doi.org/10.3390/biology10070656 - 12 Jul 2021
Cited by 6 | Viewed by 2827
Abstract
Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CαHα groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved [...] Read more.
Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CαHα groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CαHα, and CH3 groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CαHα when compared to amide groups. Full article
(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)
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Review

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15 pages, 1700 KiB  
Review
Molecular Responses to High Hydrostatic Pressure in Eukaryotes: Genetic Insights from Studies on Saccharomyces cerevisiae
by Fumiyoshi Abe
Biology 2021, 10(12), 1305; https://doi.org/10.3390/biology10121305 - 9 Dec 2021
Cited by 14 | Viewed by 4639
Abstract
High hydrostatic pressure is common mechanical stress in nature and is also experienced by the human body. Organisms in the Challenger Deep of the Mariana Trench are habitually exposed to pressures up to 110 MPa. Human joints are intermittently exposed to hydrostatic pressures [...] Read more.
High hydrostatic pressure is common mechanical stress in nature and is also experienced by the human body. Organisms in the Challenger Deep of the Mariana Trench are habitually exposed to pressures up to 110 MPa. Human joints are intermittently exposed to hydrostatic pressures of 3–10 MPa. Pressures less than 50 MPa do not deform or kill the cells. However, high pressure can have various effects on the cell’s biological processes. Although Saccharomyces cerevisiae is not a deep-sea piezophile, it can be used to elucidate the molecular mechanism underlying the cell’s responses to high pressures by applying basic knowledge of the effects of pressure on industrial processes involving microorganisms. We have explored the genes associated with the growth of S. cerevisiae under high pressure by employing functional genomic strategies and transcriptomics analysis and indicated a strong association between high-pressure signaling and the cell’s response to nutrient availability. This review summarizes the occurrence and significance of high-pressure effects on complex metabolic and genetic networks in eukaryotic cells and how the cell responds to increasing pressure by particularly focusing on the physiology of S. cerevisiae at the molecular level. Mechanosensation in humans has also been discussed. Full article
(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)
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18 pages, 2216 KiB  
Review
Volumetric Properties of Four-Stranded DNA Structures
by Tigran V. Chalikian and Robert B. Macgregor, Jr.
Biology 2021, 10(8), 813; https://doi.org/10.3390/biology10080813 - 22 Aug 2021
Cited by 10 | Viewed by 3244
Abstract
Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic instability, and regulation of transcription and translation events. [...] Read more.
Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic instability, and regulation of transcription and translation events. To gain an understanding of the molecular determinants underlying the biological role of four-stranded DNA structures, their biophysical properties have been extensively studied. The limited libraries on volume, expansibility, and compressibility accumulated to date have begun to provide insights into the molecular origins of helix-to-coil and helix-to-helix conformational transitions involving four-stranded DNA structures. In this article, we review the recent progress in volumetric investigations of G-quadruplexes and i-motifs, emphasizing how such data can be used to characterize intra-and intermolecular interactions, including solvation. We describe how volumetric data can be interpreted at the molecular level to yield a better understanding of the role that solute–solvent interactions play in modulating the stability and recognition events of nucleic acids. Taken together, volumetric studies facilitate unveiling the molecular determinants of biological events involving biopolymers, including G-quadruplexes and i-motifs, by providing one more piece to the thermodynamic puzzle describing the energetics of cellular processes in vitro and, by extension, in vivo. Full article
(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)
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