arXiv subjects

Jorge A. Vila

Publications and source records attributed to Jorge A. Vila.

11 recordsLinked to original sources

arXiv2026

Analyzing \b{eta}-Lactamase Evolution from the Principle of Least Action Perspective

Protein sequences change over time due to the accumulation of mutations in the genes that encode them. Nonetheless, accurately identifying the most probable evolutionary pathways and more efficient trajectories between an ancestral and a derived sequence remains a challenge. This difficulty stems from a limited understanding of the critical factors that drive the evolutionary process. This study aims to address this issue by validating a newly proposed mechanistic model (grounded on the principle of least action) for analyzing protein evolution, using beta-lactamase as an empirically characterized evolutionary model. The initial findings indicate that, after accounting for how mutations and the context-dependent interactions between them (epistasis) affect protein stability and, hence, the kinetics of protein folding, a resort to the principle of least action allows us to simultaneously identify the most probable pathways and the most efficient trajectories swiftly and accurately. These findings also suggest that the most probable evolutionary protein pathways are the ones that exhibit the most efficient trajectories. All in all, our study addresses several unanswered questions regarding the main factors that govern how protein evolves at the molecular level (under constant selection pressure) and outlines directions for future research in key fields such as directed evolution and ancestral sequence reconstruction.

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arXiv2025

Factors controlling protein evolvability, at the molecular scale

This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an as-yet-unidentified epistatic force. Second, it seeks to ascertain the extent to which the principle of least action will enable us to identify which of all potential trajectories has the highest evolutionary efficiency, as well as how variations in factors such as protein robustness and folding rates, resulting from the unavoidability of destabilizing mutations, might influence this critical evolutionary process. The initial findings suggest that protein evolution, at a molecular level, may be more predictable than previously thought, as epistasis and the principle of least action collectively impose constraints on evolutionary paths and trajectories, and consequently, on protein evolvability. Thus, this work should advance our understanding of the main molecular mechanisms that underlie the evolution of mutation-driven proteins and also provide grounds to answer a fundamental evolutionary question: how does Darwinian selection regard all potential trajectories available?

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arXiv2024

The Origin of Mutational Epistasis

The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin (molecular basis) of epistasis (the non-additive interactions between mutations) is still, nonetheless, unknown. The existence of a new perspective on protein folding (a problem that needs to be conceived as an analytic whole) will enable us to shed light on the origin of mutational epistasis at the simplest level (within proteins) while also uncovering the reasons on why the genetic background in which they occur (a key component of molecular evolution) could foster changes in epistasis effects. Additionally, because mutations are the source of epistasis, more research is needed to determine the impact of posttranslational modifications (which have the potential to increase the diversity of the proteome by several orders of magnitude) on both mutational epistasis and protein evolvability. Finally, a protein evolution thermodynamic-based analysis that does not consider specific mutational steps or epistasis effects will be discussed. Our study explores the complex processes behind the evolution of proteins upon mutations, clearing up some previously unresolved issues and providing direction for further research in this area.

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arXiv2023

Analysis of proteins in the light of mutations

Proteins have evolved through mutations, amino acid substitutions, since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function, and structure. Three of the most recent findings in these areas deserve to be highlighted. First, an innovative method has made it feasible to massively determine the impact of mutations on protein stability. Second, a theoretical analysis showed how mutations impact the evolution of protein folding rates. Lastly, it has been shown that native-state structural changes brought on by mutations can be explained in detail by the amide hydrogen exchange protection factors. This study offers a new perspective on how those findings can be used to analyze proteins in the light of mutations. The preliminary results indicate that: (i) mutations can be viewed as sensitive probes to identify "typos" in the amino-acid sequence and also to assess the resistance of naturally occurring proteins to unwanted sequence alterations; (ii) the presence of "typos" in the amino acid sequence, rather than being an evolutionary obstacle, could promote faster evolvability and, in turn, increase the likelihood of higher protein stability; (iii) the mutation site is far more important than the substituted amino acid in terms of the protein's marginal stability changes, and (iv) the protein evolution unpredictability at the molecular level by mutations exists even in the absence of epistasis effects. Finally, the study results support the Darwinian concept of evolution as "descent with modification" by demonstrating that some regions of any protein sequence are susceptible to mutations while others are not.

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arXiv2022

Rethinking the protein folding problem from a new perspective

One of the main concerns of Anfinsen was to reveal the connection between the amino acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins fold and how a sequence encodes its folding. As to the why, he proposes a plausible answer, namely, at a given milieu a protein folds into its functional form -- native state -- because such structure represents the lowest free-energy minimum among all feasible conformations -- the thermodynamic hypothesis or Anfinsen dogma. As to the how, this remains as an unsolved challenge and, hence, this inquiry is examined here from a new perspective of protein folding, namely, as an analytic whole -- a notion proposed by Leibnitz and Kant. This new perspective forces us to discuss in detail why the theoretical force-field-based approaches have failed in both their ability to predict the three-dimensional structure of a protein accurately and in their capacity to answer one of the most critical questions in structural biology: how a sequence encodes its folding.

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arXiv2022

Protein Folding: From Classical Issues to a New Perspective

The Levinthal paradox exposes many critical questions on the protein folding problem, among which we could point out why proteins can reach their native state in a biologically reasonable time. A proper answer to this question is of foremost importance for evolutive biology since it enables us to understand life as we know it. Preliminary results, based on the upper bound protein marginal-stability limit, together with transition state theory arguments, lead us to show that two-state proteins must reach their native state in, at most, seconds rather than ($\sim 10^{27}$) years -- as indicated by a naive solution of the Levinthal paradox. This outcome -- added to the amide hydrogen-exchange protection factors analysis -- makes it possible for us to suggest how a protein point mutations and/or post-translational modifications impact its folding time scales but not its upper bound limit that obeys the physics ruling the process. Noteworthy for almost 50 years, the protein folding problem --mas the Levinthal paradox -- has been a topic of passionate debate because Anfinsen's challenge -- how a sequence encodes its folding -- remains unsolved despite the smashing success of accurately predicting the protein tridimensional structures by state-of-the-art numerical-methods. Aimed to unlock this long-standing challenge, we propose a new perspective of protein folding, specifically, as a problem that should be devised as an 'analytic whole' -- a Leibniz & Kant's notion. This viewpoint might help us decode Anfinsen's challenge and, thus, open new avenues for future research in the protein folding field.

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arXiv2021

Thoughts on the Proteins Native State

The presence of metamorphism in the protein's native state is not yet fully understood. In an attempt to throw light on this issue here we present an assessment, in terms of the amide hydrogen exchange protection factor, that aims to determine the likely existence of structural fluctuations in the native-state consistent with both the upper bound marginal stability of proteins and the metamorphism presence. The preliminary results enable us to conclude that the native-state metamorphism is, indeed, more probable than thought.

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arXiv2020

About the Protein Space Vastness

An accurate estimation of the Protein Space size, in light of the factors that govern it, is a long-standing problem and of paramount importance in evolutionary biology, since it determines the nature of protein evolvability. A simple analysis will enable us to, firstly, reduce an unrealistic Protein Space size of ~10^130 sequences, for a 100-residues polypeptide chain, to ~10^9 functional proteins and, secondly, estimate a robust average-mutation rate per amino acid (x ~1.23) and infer from it, in light of the protein marginal stability, that only a fraction of the sequence will be available at any one time for a functional protein to evolve. Although this result does not solve the Protein Space vastness problem, frames it in a more rational one.

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arXiv2020

Metamorphic Proteins in light of the Anfinsen Dogma

It is a common belief that metamorphic proteins challenge the Anfinsen thermodynamic hypothesis (or dogma). Here we argue against this view aims to show that metamorphic proteins not just fulfill the Anfinsen dogma but also exhibit marginal stability comparable to that seen on macromolecules and macromolecular complexes. This work contributes to our general understanding of protein classification and may spur significant progress in our effort to analyze protein evolvability.

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arXiv2020

The Marginal Stability of Proteins: How Jiggling and Wiggling of Atoms are Connected to Neutral Evolution

Here we propose that the upper bound marginal stability of proteins (7.4 kcal/mol) is a universal property that includes macro-molecular complexes and is not affected by molecular changes such as mutations and Post-Translational Modifications. Its existence is, essentially, a consequence of the Anfinsen thermodynamic hypothesis rather than a result of an evolutive process. This result enables us to conjecture that neutral evolution should also be, with respect to protein stability, a universal phenomenon.

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arXiv2018

Guessing the upper bound free-energy difference between native-like structures

Use of a combination of statistical thermodynamics and the Gershgorin theorem enable us to guess, in the thermodynamic limit, a plausible value for the upper bound free-energy difference between native-like structures of monomeric globular proteins. Support to our result in light of both the observed free-energy change between the native and denatured states and the microstability free-energy values obtained from the observed micro-unfolding tendency of nine globular proteins, will be here discussed.

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