Antônio F. Pereira de Araújo

Non‐native interactions, effective contact order, and protein folding: A mutational investigation with the energetically frustrated hydrophobic model

By Monte Carlo simulations, we explored the effect of single mutations on the thermodynamics and kinetics of the folding of a two‐dimensional, energetically frustrated, hydrophobic protein model. Φ‐Value analysis, corroborated by simulations beginning from given sets of judiciously chosen initial contacts, suggests that the transition state of the model consists of a limited region of the native structure, that is, a folding nucleus. It seems that the most important contacts in the transition state (large and positive Φ) are not the ones with the highest contact order, because in this case the entropic cost of their formation would be too high, but exactly the ones that decrease the entropic cost of difficult contacts, reducing their effective contact order. Mutations of internal monomers involved in high‐order contacts were actually the ones resulting in the fastest kinetics (and Φ < 0), indicating they tend to make low order, non‐native contacts of low entropic cost that stabilize the unfolded state with respect to the transition state. Folding acceleration by other non‐native interactions was also observed and a simple general mechanism is proposed according to which non‐native contacts can act indirectly over the folding nucleus, “chelating” out potentially harmful contacts. The polymer graph of our model, which facilitates the visualization of effective contact orders, successfully suggests the relative kinetic importance of different contacts and is reasonably consistent with analogous graphs for the well characterized family of SH3 domains. Proteins 2002;49:167–180.

Thermodynamics of Interactions between Amino Acid Side Chains: Experimental Differentiation of Aromatic-Aromatic, Aromatic-Aliphatic, and Aliphatic-Aliphatic Side-Chain Interactions in Water

A stationary phase for high-pressure liquid chromatography has been prepared by derivatizing microparticulate silica gel with functionality mimicking the side chain of isoleucine. The chromatographic retentions of a series of hydrophobic and amphiphilic amino acid analytes on this stationary phase (Ile MSP) using an aqueous mobile phase were measured as a function of temperature from 273 K to 323 K. Observed temperature dependencies are consistent with a constant change in heat capacity, DeltaC degrees P, upon binding of the analyte to the stationary phase. The curvatures of plots of retention data versus temperature (related to the magnitude of DeltaC degrees P) are distinctly different for retention of aromatic and aliphatic analytes, with retention of aliphatic analytes Val, Ile, and Leu exhibiting the characteristic signature of the hydrophobic effect, i.e., a large negative DeltaC degrees P upon desolvation from water and a maximum of retention around room temperature. Retention of aromatic analytes (Trp, Phe, and Tyr) involves smaller heat capacity changes and pronounced negative enthalpies of interaction with the stationary phase. Estimates of DeltaC degrees P for the interactions of analyte side chains with the Ile side chain were obtained by fitting the temperature dependence of retention to an expression derived from thermodynamic considerations and chromatographic theory. Similar estimates were made for interactions with the Phe side chain, using previously published data for a phenylalanine mimic stationary phase (Phe MSP) (. Protein Sci. 1:786-795). As with the Ile MSP, the retentions of aliphatic analytes show temperature dependencies markedly different from those of aromatic analytes. Data from both phases indicate that a realistic differentiation can be made between the interactions of various types of amino acid side chains tested (i.e., aliphatic/aliphatic, aliphatic/aromatic, and aromatic/aromatic) by comparison of the corresponding thermodynamic functions for pairwise interactions. The retention of leucine on the Phe MSP and that of phenylalanine on the Ile MSP showed similar DeltaC degrees P values, suggesting that the aromatic-aliphatic interaction is reasonably independent of the residue attached to the stationary phase. This result is consistent with a one-to-one interaction and suggests a simple way to estimate the column-dependent phase factor, making it possible to compare entropies and free energies of interaction obtained using different MSPs. The possibilities for using MSP-derived interaction potentials in folding simulations are discussed.

A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins.

Protein tertiary structures are known to be encoded in amino acid sequences, but the problem of structure prediction from sequence continues to be a challenge. With this question in mind, recent simulations have shown that atomic burials, as expressed by atom distances to the molecular geometrical center, are sufficiently informative for determining native conformations of small globular proteins. Here we use a simple computational experiment to estimate the amount of this required burial information and find it to be surprisingly small, actually comparable with the stringent limit imposed by sequence statistics. Atomic burials appear to satisfy, therefore, minimal requirements for a putative dominating property in the folding code because they provide an amount of information sufficiently large for structural determination but, at the same time, sufficiently small to be encodable in sequences. In a simple analogy with human communication, atomic burials could correspond to the actual “language” encoded in the amino acid “script” from which the complexity of native conformations is recovered during the folding process.

Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins

We investigate the possibility that atomic burials, as measured by their distances from the structural geometrical center, contain sufficient information to determine the tertiary structure of globular proteins. We report Monte Carlo simulated annealing results of all‐atom hard‐sphere models in continuous space for four small proteins: the all‐β WW‐domain 1E0L, the α/β protein‐G 1IGD, the all‐α engrailed homeo‐domain 1ENH, and the α + β engineered monomeric form of the Cro protein 1ORC. We used as energy function the sum over all atoms, labeled by i, of |Ri − R  i* |, where Ri is the atomic distance from the center of coordinates, or central distance, and R  i* is the “ideal” central distance obtained from the native structure. Hydrogen bonds were taken into consideration by the assignment of two ideal distances for backbone atoms forming hydrogen bonds in the native structure depending on the formation of a geometrically defined bond, independently of bond partner. Lowest energy final conformations turned out to be very similar to the native structure for the four proteins under investigation and a strong correlation was observed between energy and distance root mean square deviation (DRMS) from the native in the case of all‐β 1E0L and α/β 1IGD. For all α 1ENH and α + β 1ORC the overall correlation between energy and DRMS among final conformations was not as high because some trajectories resulted in high DRMS but low energy final conformations in which α‐helices adopted a non‐native mutual orientation. Comparison between central distances and actual accessible surface areas corroborated the implicit assumption of correlation between these two quantities. The Z‐score obtained with this native‐centric potential in the discrimination of native 1ORC from a set of random compact structures confirmed that it contains a much smaller amount of native information when compared to a traditional contact Go potential but indicated that simple sequence‐dependent burial potentials still need some improvement in order to attain a similar discriminability. Taken together, our results suggest that central distances, in conjunction to physically motivated hydrogen bond constraints, contain sufficient information to determine the native conformation of these small proteins and that a solution to the folding problem for globular proteins could arise from sufficiently accurate burial predictions from sequence followed by minimization of a burial‐dependent energy function. Proteins 2008.

Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions

We perform a statistical analysis of atomic distributions as a function of the distance R from the molecular geometrical center in a nonredundant set of compact globular proteins. The number of atoms increases quadratically for small R, indicating a constant average density inside the core, reaches a maximum at a size‐dependent distance Rmax, and falls rapidly for larger R. The empirical curves turn out to be consistent with the volume increase of spherical concentric solid shells and a Fermi‐Dirac distribution in which the distance R plays the role of an effective atomic energy ϵ(R) = R. The effective chemical potential μ governing the distribution increases with the number of residues, reflecting the size of the protein globule, while the temperature parameter β decreases. Interestingly, βμ is not as strongly dependent on protein size and appears to be tuned to maintain approximately half of the atoms in the high density interior and the other half in the exterior region of rapidly decreasing density. A normalized size‐independent distribution was obtained for the atomic probability as a function of the reduced distance, r = R/Rg, where Rg is the radius of gyration. The global normalized Fermi distribution, F(r), can be reasonably decomposed in Fermi‐like subdistributions for different atomic types τ, Fτ(r), with ΣτFτ(r) = F(r), which depend on two additional parameters μτ and hτ. The chemical potential μτ affects a scaling prefactor and depends on the overall frequency of the corresponding atomic type, while the maximum position of the subdistribution is determined by hτ, which appears in a type‐dependent atomic effective energy, ετ(r) = hτr, and is strongly correlated to available hydrophobicity scales. Better adjustments are obtained when the effective energy is not assumed to be necessarily linear, or ετ*(r) = hτ*rα,, in which case a correlation with hydrophobicity scales is found for the product ατhτ*. These results indicate that compact globular proteins are consistent with a thermodynamic system governed by hydrophobic‐like energy functions, with reduced distances from the geometrical center, reflecting atomic burials, and provide a conceptual framework for the eventual prediction from sequence of a few parameters from which whole atomic probability distributions and potentials of mean force can be reconstructed. Proteins 2007.

Folding pathway dependence on energetic frustration and interaction heterogeneity for a three‐dimensional hydrophobic protein model

Monte Carlo simulations of a hydrophobic protein model of 40 monomers in the cubic lattice are used to explore the effect of energetic frustration and interaction heterogeneity on its folding pathway. The folding pathway is described by the dependence of relevant conformational averages on an appropriate reaction coordinate, pfold, defined as the probability for a given conformation to reach the native structure before unfolding. We compare the energetically frustrated and heterogeneous hydrophobic potential, according to which individual monomers have a higher or lower tendency to form contacts unspecifically depending on their hydrophobicities, to an unfrustrated homogeneous Go‐type potential with uniformly attractive native interactions and neutral non‐native interactions (called Go1 in this study), and to an unfrustrated heterogeneous potential with neutral non‐native interactions and native interactions having the same energy as the hydrophobic potential (called Go2 in this study). Folding kinetics are slowed down dramatically when energetic frustration increases, as expected and previously observed in a two‐dimensional model. Contrary to our previous results in two dimensions, however, it appears that the folding pathway and transition state ensemble can be significantly dependent on the energy function used to stabilize the native structure. The sequence of events along the reaction coordinate, or the order along this coordinate in which different regions of the native conformation become structured, turns out to be similar for the hydrophobic and Go2 potentials, but with analogous events tending to occur at lower pfold values in the first case. In particular, the transition state obtained from the ensemble around pfold = 0.5 is more structured for the hydrophobic potential. For Go1, not only the transition state ensemble but the order of events itself is modified, suggesting that interaction heterogeneity, in addition to energetic frustration, can have significant effects on the folding mechanism, most likely by modifying the probability of different contacts in the unfolded state, the starting point for the folding reaction. Although based on a simple model, these results provide interesting insight into how sequence‐dependent switching between folding pathways might occur in real proteins. Proteins 2006.

Increasing discrepancy between absolute and effective indexes of research output in a Brazilian academic department

We investigate possible effects from a strong encouragement for a large number of publications on the scientific production of a Brazilian cell biology department. An average increase in individual absolute production and a concomitant decrease in individual participation in each paper were detected by traditional bibliometric parameters, such as number of publications, citations, impact factors and h index, combined to their “effective” versions, in which co-authorship is taken into consideration. The observed situation, which might well represent a national trend, should be considered as a strong warning against current criteria of scientific evaluation heavily based on uncritical counting of publications.We investigate possible effects from a strong encouragement for a large number of publications on the scientific production of a Brazilian cell biology department. An average increase in individual absolute production and a concomitant decrease in individual participation in each paper were detected by traditional bibliometric parameters, such as number of publications, citations, impact factors and h index, combined to their “effective” versions, in which co-authorship is taken into consideration. The observed situation, which might well represent a national trend, should be considered as a strong warning against current criteria of scientific evaluation heavily based on uncritical counting of publications.

Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure

The three‐dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding. Proteins 2014; 82:1186–1199.

An experience of confluence between scientific and autobiographical narratives in biology teaching for young and adult students

This is an action-research developed among young and adult students of a public school in Dis-trito Federal, Brazil. The articulation between school-knowledge and experience-knowledge occurred during a workshop in which zoology contents were addressed from the standpoint of the relationship between students and other animals. Stories were shared in a circle and the texts produced were exhib-ited on a literary string at the school yard. Our proposal is based on Paulo Freire’s assumptions and on their links to other authors, according to which every teacher is a reading and writing teacher; the school is a legitimate instance for the construction of knowledge; every learning process is an exercise of re-reading one’s own experience. This research shows that it is possible to organize activities that value the personal life paths of subjects without failing to teach natural sciences, with the benefit of helping the construction of a personal and collective memory.This is an action-research developed among young and adult students of a public school in Dis-trito Federal, Brazil. The articulation between school-knowledge and experience-knowledge occurred during a workshop in which zoology contents were addressed from the standpoint of the relationship between students and other animals. Stories were shared in a circle and the texts produced were exhib-ited on a literary string at the school yard. Our proposal is based on Paulo Freire’s assumptions and on their links to other authors, according to which every teacher is a reading and writing teacher; the school is a legitimate instance for the construction of knowledge; every learning process is an exercise of re-reading one’s own experience. This research shows that it is possible to organize activities that value the personal life paths of subjects without failing to teach natural sciences, with the benefit of helping the construction of a personal and collective memory.

Uma experiência de encontro entre narrativas autobiográficas e narrativas científicas no en-sino de biologia para jovens e adultos

This is an action-research developed among young and adult students of a public school in Dis-trito Federal, Brazil. The articulation between school-knowledge and experience-knowledge occurred during a workshop in which zoology contents were addressed from the standpoint of the relationship between students and other animals. Stories were shared in a circle and the texts produced were exhib-ited on a literary string at the school yard. Our proposal is based on Paulo Freire’s assumptions and on their links to other authors, according to which every teacher is a reading and writing teacher; the school is a legitimate instance for the construction of knowledge; every learning process is an exercise of re-reading one’s own experience. This research shows that it is possible to organize activities that value the personal life paths of subjects without failing to teach natural sciences, with the benefit of helping the construction of a personal and collective memory.This is an action-research developed among young and adult students of a public school in Dis-trito Federal, Brazil. The articulation between school-knowledge and experience-knowledge occurred during a workshop in which zoology contents were addressed from the standpoint of the relationship between students and other animals. Stories were shared in a circle and the texts produced were exhib-ited on a literary string at the school yard. Our proposal is based on Paulo Freire’s assumptions and on their links to other authors, according to which every teacher is a reading and writing teacher; the school is a legitimate instance for the construction of knowledge; every learning process is an exercise of re-reading one’s own experience. This research shows that it is possible to organize activities that value the personal life paths of subjects without failing to teach natural sciences, with the benefit of helping the construction of a personal and collective memory.