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 why the genetic background in which they occur, a key component of molecular evolution, could foster changes in epistasis effects.

Analysis of proteins in the light of mutations.

Proteins have evolved through mutations-amino acid substitutions-since life appeared on Earth, some 10 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function, and structure. This study offers a new viewpoint on how the most recent findings in these areas can be used to explore the impact of mutations on protein sequence, stability, and evolvability.

Protein structure prediction from the complementary science perspective.

A comparative analysis between two problems-apparently unrelated-which are solved in a period of ~400 years, viz., the accurate prediction of both the planetary orbits and the protein structures, leads to inferred conjectures that go far beyond the existence of a common path in their resolution, i.e.

Protein folding rate evolution upon mutations.

Despite the spectacular success of cutting-edge protein fold prediction methods, many critical questions remain unanswered, including why proteins can reach their native state in a biologically reasonable time. A satisfactory answer to this simple question could shed light on the slowest folding rate of proteins as well as how mutations-amino-acid substitutions and/or post-translational modifications-might affect it. Preliminary results indicate that (i) Anfinsen's dogma validity ensures that proteins reach their native state on a reasonable timescale regardless of their sequence or length, and (ii) it is feasible to determine the evolution of protein folding rates without accounting for epistasis effects or the mutational trajectories between the starting and target sequences.

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, the thermodynamic hypothesis.

Proteins' Evolution upon Point Mutations.

As the reader must be already aware, state-of-the-art protein folding prediction methods have reached a smashing success in their goal of accurately determining the three-dimensional structures of proteins. Yet, a solution to simple problems such as the effects of protein point mutations on their (i) native conformation; (ii) marginal stability; (iii) ensemble of high-energy nativelike conformations; and (iv) metamorphism propensity and, hence, their evolvability, remains as an unsolved problem. As a plausible solution to the latter, some properties of the amide hydrogen-deuterium exchange, a highly sensitive probe of the structure, stability, and folding of proteins, are assessed from a new perspective.

Thoughts on the Protein's Native State.

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

Exploring the quality of protein structural models from a Bayesian perspective.

We explore how ideas and practices common in Bayesian modeling can be applied to help assess the quality of 3D protein structural models. The basic premise of our approach is that the evaluation of a Bayesian statistical model's fit may reveal aspects of the quality of a structure when the fitted data is related to protein structural properties. Therefore, we fit a Bayesian hierarchical linear regression model to experimental and theoretical C chemical shifts.

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 sequences, for a 100-residues polypeptide chain, to ~ 10 functional proteins and, secondly, estimate a robust average-mutation rate per amino acid (ξ ~ 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.

Thermodynamics of cell penetrating peptides on lipid membranes: sequence and membrane acidity regulate surface binding.

Cell-penetrating peptides (CPPs) are molecules that traverse cell membranes and facilitate the cellular uptake of nano-sized cargoes. In this work we characterize the adsorption of amphipathic and purely cationic CPPs on membranes containing acidic lipids. We describe how the peptide primary sequence, the location of amino-acids within the sequence, the membrane composition, and the pH of the environment, determine both the surface concentration of the peptides and the molecular organization of the interface.

Metamorphic Proteins in Light of Anfinsen's Dogma.

It is a common belief that metamorphic proteins challenge Anfinsen's thermodynamic hypothesis (or dogma). Here we argue against this view and aim to show that metamorphic proteins not only fulfill Anfinsen's dogma but also exhibit marginal stability comparable to that seen on biomolecules 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.

The Marginal Stability of Proteins: How the Jiggling and Wiggling of Atoms is Connected to Neutral Evolution.

Here we propose that the upper bound marginal stability of proteins is a universal property that includes macro-molecular complexes and is not affected by molecular changes such as mutations and post-translational modifications. We theorize that its existence is a consequence of Afinsen's thermodynamic hypothesis rather than a result of an evolutionary process. This result enables us to conjecture that neutral evolution should also be, with respect to protein stability, a universal phenomenon.

Assessing the One-Bond C-H Spin-Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches.

In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) in proteins: density functional theory (DFT) calculations, a Karplus-like equation, and Gaussian process regression. The main motivation of this work is to select the best method for fast and accurate computation of the SSCC, for its use in everyday applications in protein structure validation, refinement, and/or determination. Our initial results showed a poor agreement between the DFT-computed and observed SSCC values.

Classification of RNA backbone conformations into rotamers using C' chemical shifts: exploring how far we can go.

The conformational space of the ribose-phosphate backbone is very complex as it is defined in terms of six torsional angles. To help delimit the RNA backbone conformational preferences, 46 rotamers have been defined in terms of these torsional angles. In the present work, we use the ribose experimental and theoretical C' chemical shifts data and machine learning methods to classify RNA backbone conformations into rotamers and families of rotamers.

Outline of an experimental design aimed to detect a protein A mirror image in solution.

There is abundant theoretical evidence indicating that a mirror image of may occur during the protein folding process. However, as to whether such mirror image exists in solution is an unsolved issue. Here we provide outline of an experimental design aimed to detect the mirror image of in solution.

Adsorption and insertion of polyarginine peptides into membrane pores: The trade-off between electrostatics, acid-base chemistry and pore formation energy.

The mechanism that arginine-rich cell penetrating peptides (ARCPPs) use to translocate lipid membranes is not entirely understood. In the present work, we develop a molecular theory that allows to investigate the adsorption and insertion of ARCPPs on membranes bearing hydrophilic pores. This method accounts for size, shape, conformation, protonation state and charge distribution of the peptides; it also describes the state of protonation of acidic membrane lipids.

Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH.

Assessment of the relative amounts of the forms of the imidazole ring of Histidine (His), namely the protonated (H) and the tautomeric N-H and N-H forms, respectively, is a challenging task in NMR spectroscopy. Indeed, their determination by direct observation of the N and C chemical shifts or the one-bond C-H, , Spin-Spin Coupling Constants (SSCC) requires knowledge of the "canonical" limiting values of these forms in which each one is present to the extent of 100%. In particular, at high-pH, an accurate determination of these "canonical" limiting values, at which the tautomeric forms of His coexist, is an elusive problem in NMR spectroscopy.

A comprehensive analysis of the computed tautomer fractions of the imidazole ring of histidines in Loligo vulgaris.

A recently introduced electrostatic-based method to determine the pKa values of ionizable residues and fractions of ionized and tautomeric forms of histidine (His) and acid residues in proteins, at a given fixed pH, is applied here to the analysis of a His-rich protein, namely Loligo vulgaris (pdb id 1E1A), a 314-residue all-β protein. The average tautomeric fractions for the imidazole ring of each of the six histidines in the sequence were computed using an approach that includes, but is not limited to, molecular dynamic simulations coupled with calculations of the ionization states for all 94 ionizable residues of protein 1E1A in water at pH 6.5 and 300 K.

Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins.

A computational method, to predict the pKa values of the ionizable residues Asp, Glu, His, Tyr, and Lys of proteins, is presented here. Calculation of the electrostatic free-energy of the proteins is based on an efficient version of a continuum dielectric electrostatic model. The conformational flexibility of the protein is taken into account by carrying out molecular dynamics simulations of 10 ns in implicit water.

Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules.

Glycans are key molecules in many physiological and pathological processes. As with other molecules, like proteins, visualization of the 3D structures of glycans adds valuable information for understanding their biological function. Hence, here we introduce Azahar, a computing environment for the creation, visualization and analysis of glycan molecules.

Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study.

Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using (13)C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the (13)C chemical shifts from the expected (mean) experimental value of the non-modified residue.

Factors affecting the computation of the 13C shielding in disaccharides.

Knowledge of the three-dimensional structures of glycans and glycoproteins is useful for a full understanding of molecular processes in which glycans are involved, such as antigen-recognition and virus infection, to name a few. Among the ubiquitous nuclei in glycan molecules, the (13)C nucleus is an attractive candidate for computation of theoretical chemical shifts at the quantum chemical level of theory to validate and determine glycan structures. For this purpose, it is important to determine, first, which carbons can be used as probes to sense conformational changes and, second, all factors that affect the computation of the shielding, at the density functional theory (DFT) level of theory, of those carbons.

Accounting for a mirror-image conformation as a subtle effect in protein folding.

By using local (free-energy profiles along the amino acid sequence and (13)C(α) chemical shifts) and global (principal component) analyses to examine the molecular dynamics of protein-folding trajectories, generated with the coarse-grained united-residue force field, for the B domain of staphylococcal protein A, we are able to (i) provide the main reason for formation of the mirror-image conformation of this protein, namely, a slow formation of the second loop and part of the third helix (Asp29-Asn35), caused by the presence of multiple local conformational states in this portion of the protein; (ii) show that formation of the mirror-image topology is a subtle effect resulting from local interactions; (iii) provide a mechanism for how protein A overcomes the barrier between the metastable mirror-image state and the native state; and (iv) offer a plausible reason to explain why protein A does not remain in the metastable mirror-image state even though the mirror-image and native conformations are at least energetically compatible.

Are accurate computations of the 13C' shielding feasible at the DFT level of theory?

The goal of this study is twofold. First, to investigate the relative influence of the main structural factors affecting the computation of the (13)C' shielding, namely, the conformation of the residue itself and the next nearest-neighbor effects. Second, to determine whether calculation of the (13)C' shielding at the density functional level of theory (DFT), with an accuracy similar to that of the (13)C(α) shielding, is feasible with the existing computational resources.