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Biophysica
Special Issues
State-of-the-Art Biophysics in Spain 2.0
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State-of-the-Art Biophysics in Spain 2.0

A special issue of Biophysica (ISSN 2673-4125).

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 8331

Special Issue Editor

Prof. Dr. Jaume Casademunt

E-Mail Website
Guest Editor
1. Departament de Física de la Matèria Condensada, Universitat de Barcelona, 08028 Barcelona, Spain
2. Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Spain
Interests: molecular motors; cell motility; collective cell migration; tissue mechanics; morphogenesis; development; active matter; hydrodynamics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biophysics is one of the most promising and innovative areas of multidisciplinary research. Spain has actively participated in its development during the last decades, from the original concept of biophysics as a branch of biology that involved physical concepts and instruments, to the current status as a consolidated area of research where Biology and Physics meet and cross-fertilize. Many Spanish groups have pioneered a physical approach to biological systems, both contributing to a deeper understanding of the physical mechanisms that underlay biological phenomena and to the pursuit of new physics in living matter. This Special Issue aims to provide a comprehensive overview of the state-of-the-art of Biophysics in Spain, ranging from the more traditional and established areas to the most innovative approaches. We invite researchers in the Spanish research system to submit full research articles or comprehensive reviews. Potential topics include but are not limited to the following research areas:

  • Structure and Dynamics of Biomolecules and Their Assemblies Biomolecular Machines;
  • Biomembranes;
  • Genetics and Gene Expression Mechanisms;
  • Cell Biophysics;
  • Tissue Biophysics;
  • Developmental Biophysics;
  • Biophysical Techniques and Instrumentation;
  • Theory and Modeling of Biological Systems;
  • Systems Biology;
  • Neuronal networks;
  • Synthetic Biology;
  • Physics of Evolution.

Prof. Dr. Jaume Casademunt
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. Biophysica is an international peer-reviewed open access quarterly 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 1000 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

  • self-assembly
  • self-organization
  • living matter
  • molecular biophysics
  • protein folding
  • protein aggregation
  • single-molecule physics
  • molecular motors
  • ion channels
  • membrane dynamics
  • signaling
  • gene expression
  • cell biophysics
  • cell mechanics
  • tissue mechanics
  • mechanobiology
  • cell motility
  • cell migration
  • development
  • embryogenesis
  • morphogenesis
  • pattern formation
  • neuron physics
  • neuronal networks
  • systems biology
  • synthetic biology
  • evolution
  • computational biology

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Published Papers (5 papers)

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Research

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12 pages, 1619 KiB  
Article
Gibbs Free Energy and Enthalpy–Entropy Compensation in Protein–Ligand Interactions
by Juan S. Jiménez and María J. Benítez
Biophysica 2024, 4(2), 298-309; https://doi.org/10.3390/biophysica4020021 - 14 Jun 2024
Viewed by 1331
Abstract
The thermodynamics of protein–ligand interactions seems to be associated with a narrow range of Gibbs free energy. As a consequence, a linear enthalpy–entropy relationship showing an apparent enthalpy–entropy compensation (EEC) is frequently associated with protein–ligand interactions. When looking for the most negative values [...] Read more.
The thermodynamics of protein–ligand interactions seems to be associated with a narrow range of Gibbs free energy. As a consequence, a linear enthalpy–entropy relationship showing an apparent enthalpy–entropy compensation (EEC) is frequently associated with protein–ligand interactions. When looking for the most negative values of ∆H to gain affinity, the entropy compensation gives rise to a barely noticeable increase in affinity, therefore negatively affecting the design and discovery of new and more efficient drugs capable of binding protein targets with a higher affinity. Originally attributed to experimental errors, compensation between ∆H and T∆S values is an observable fact, although its molecular origin has remained obscure and controversial. The thermodynamic parameters of a protein–ligand interaction can be interpreted in terms of the changes in molecular weak interactions as well as in vibrational, rotational, and translational energy levels. However, a molecular explanation to an EEC rendering a linear enthalpy–entropy relationship is still lacking. Herein, we show the results of a data search of ∆G values of 3025 protein–ligand interactions and 2558 “in vivo” ligand concentrations from the Protein Data Bank database and the Metabolome Database (2020). These results suggest that the EEC may be plausibly explained as a consequence of the narrow range of ∆G associated with protein–ligand interactions. The Gaussian distribution of the ∆G values matches very well with that of ligands. These results suggest the hypothesis that the set of ∆G values for the protein–ligand interactions is the result of the evolution of proteins. The conformation versatility of present proteins and the exchange of thousands (even millions) of minute amounts of energy with the environment may have functioned as a homeostatic mechanism to make the ∆G of proteins adaptive to changes in the availability of ligands and therefore achieve the maximum regulatory capacity of the protein function. Finally, plausible strategies to avoid the EEC consequences are suggested. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain 2.0)
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9 pages, 1749 KiB  
Article
Detecting Molecular Folding from Noise Measurements
by Marc Rico-Pasto and Felix Ritort
Biophysica 2023, 3(3), 539-547; https://doi.org/10.3390/biophysica3030036 - 5 Sep 2023
Viewed by 1023
Abstract
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We consider cases where Brownian force fluctuations are large, masking the force rips and [...] Read more.
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We consider cases where Brownian force fluctuations are large, masking the force rips and jumps characteristics of conformational transitions. We compare unfolding and folding data for DNA hairpin systems of loop sizes 4, 8, and 20 and the 110-amino acid protein barnase, finding conditions that facilitate the detection of folding events at low forces where the signal-to-noise ratio is low. In particular, we discuss the role of temperature as a useful parameter to improve the detection of folding transitions in entropically driven processes where folding forces are temperature independent. The force variance approach might be extended to detect the elusive intermediate states in RNA and protein folding. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain 2.0)
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Review

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16 pages, 1971 KiB  
Review
Mathematical Models of the Arabidopsis Circadian Oscillator
by Lucas Henao, Saúl Ares and Pablo Catalán
Biophysica 2024, 4(2), 267-282; https://doi.org/10.3390/biophysica4020019 - 28 May 2024
Viewed by 877
Abstract
We review the construction and evolution of mathematical models of the Arabidopsis circadian clock, structuring the discussion into two distinct historical phases of modeling strategies: extension and reduction. The extension phase explores the bottom-up assembly of regulatory networks, introducing as many components and [...] Read more.
We review the construction and evolution of mathematical models of the Arabidopsis circadian clock, structuring the discussion into two distinct historical phases of modeling strategies: extension and reduction. The extension phase explores the bottom-up assembly of regulatory networks, introducing as many components and interactions as possible to capture the oscillatory nature of the clock. The reduction phase deals with functional decomposition, distilling complex models to their essential dynamical repertoire. Current challenges in this field, including the integration of spatial considerations and environmental influences like light and temperature, are also discussed. The review emphasizes the ongoing need for models that balance molecular detail with practical simplicity. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain 2.0)
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22 pages, 4283 KiB  
Review
Physical Virology in Spain
by David Reguera, Pedro J. de Pablo, Nicola G. A. Abrescia, Mauricio G. Mateu, Javier Hernández-Rojas, José R. Castón and Carmen San Martín
Biophysica 2023, 3(4), 598-619; https://doi.org/10.3390/biophysica3040041 - 31 Oct 2023
Viewed by 1699
Abstract
Virus particles consist of a protein coat that protects their genetic material and delivers it to the host cell for self-replication. Understanding the interplay between virus structure and function is a requirement for understanding critical processes in the infectious cycle such as entry, [...] Read more.
Virus particles consist of a protein coat that protects their genetic material and delivers it to the host cell for self-replication. Understanding the interplay between virus structure and function is a requirement for understanding critical processes in the infectious cycle such as entry, uncoating, genome metabolism, capsid assembly, maturation, and propagation. Together with well-established techniques in cell and molecular biology, physical virology has emerged as a rapidly developing field, providing detailed, novel information on the basic principles of virus assembly, disassembly, and dynamics. The Spanish research community contains a good number of groups that apply their knowledge on biology, physics, or chemistry to the study of viruses. Some of these groups got together in 2010 under the umbrella of the Spanish Interdisciplinary Network on Virus Biophysics (BioFiViNet). Thirteen years later, the network remains a fertile ground for interdisciplinary collaborations geared to reveal new aspects on the physical properties of virus particles, their role in regulating the infectious cycle, and their exploitation for the development of virus-based nanotechnology tools. Here, we highlight some achievements of Spanish groups in the field of physical virology. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain 2.0)
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13 pages, 8969 KiB  
Review
Developmental Pattern Formation: Spanish Contributions from a Biophysical Perspective
by Javier Buceta and Léna Guitou
Biophysica 2023, 3(2), 335-347; https://doi.org/10.3390/biophysica3020022 - 6 May 2023
Viewed by 2451
Abstract
During the last few decades, developmental pattern formation has evolved from being a descriptive discipline to a quantitative one. That process has been possible due to the implementation of multidisciplinary approaches where biophysicists and mathematicians have played a key role. In this review, [...] Read more.
During the last few decades, developmental pattern formation has evolved from being a descriptive discipline to a quantitative one. That process has been possible due to the implementation of multidisciplinary approaches where biophysicists and mathematicians have played a key role. In this review, we highlight relevant Spanish contributions and stress their biophysical approaches, as well as provide some historical context. Finally, this work also aimed at bridging the concepts from biology to physics/math (and back) and at shedding light on some directions for future research. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain 2.0)
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