Are residues in a protein folding nucleus evolutionarily conserved?

Protein is the working molecule of the cell, and evolution is the hallmark of life. It is important to understand how protein folding and evolution influence each other. Several studies correlating experimental measurement of residue participation in folding nucleus and sequence conservation have reached different conclusions. These studies are based on assessment of sequence conservation at folding nucleus sites using entropy or relative entropy measurement derived from multiple sequence alignment. Here we report analysis of conservation of folding nucleus using an evolutionary model alternative to entropy-based approaches. We employ a continuous time Markov model of codon substitution to distinguish mutation fixed by evolution and mutation fixed by chance. This model takes into account bias in codon frequency, bias-favoring transition over transversion, as well as explicit phylogenetic information. We measure selection pressure using the ratio omega of synonymous versus non-synonymous substitution at individual residue site. The omega-values are estimated using the PAML method, a maximum-likelihood estimator. Our results show that there is little correlation between the extent of kinetic participation in protein folding nucleus as measured by experimental phi-value and selection pressure as measured by omega-value. In addition, two randomization tests failed to show that folding nucleus residues are significantly more conserved than the whole protein, or the median omega value of all residues in the protein. These results suggest that at the level of codon substitution, there is no indication that folding nucleus residues are significantly more conserved than other residues. We further reconstruct candidate ancestral residues of the folding nucleus and suggest possible test tube mutation studies for testing folding behavior of ancient folding nucleus.     

H‐bond network optimization in protein–protein complexes: Are all‐atom force field scores enough?

Structural prediction of protein-protein complexes given the structures of the two interacting compounds in their unbound state is a key problem in biophysics. In addition to the problem of sampling of near-native orientations, one of the modeling main difficulties is to discriminate true from false positives. Here, we present a hierarchical protocol for docking refinement able to discriminate near native poses from a group of docking candidates. The main idea is to combine an efficient sampling of the full system hydrogen bond network and side chains, together with an all-atom force field and a surface generalized born implicit solvent. We tested our method on a set of twenty two complexes containing a near-native solution within the top 100 docking poses, obtaining a near native solution as the top pose in 70% of the cases. We show that all atom force fields optimized H-bond networks do improve significantly state of the art scoring functions.     

Triathlon for energy functions: Who is the winner for design of protein–protein interactions?

Computational prediction of stabilizing mutations into monomeric proteins has become an almost ordinary task. Yet, computational stabilization of protein–protein complexes remains a challenge. Design of protein–protein interactions (PPIs) is impeded by the absence of an energy function that could reliably reproduce all favorable interactions between the binding partners. In this work, we present three energy functions: one function that was trained on monomeric proteins, while the other two were optimized by different techniques to predict side-chain conformations in a dataset of PPIs. The performances of these energy functions are evaluated in three different tasks related to design of PPIs: predicting side-chain conformations in PPIs, recovering native binding-interface sequences, and predicting changes in free energy of binding due to mutations. Our findings show that both functions optimized on side-chain repacking in PPIs are more suitable for PPI design compared to the function trained on monomeric proteins. Yet, no function performs best at all three tasks. Comparison of the three energy functions and their performances revealed that (1) burial of polar atoms should not be penalized significantly in PPI design as in single-protein design and (2) contribution of electrostatic interactions should be increased several-fold when switching from single-protein to PPI design. In addition, the use of a softer van der Waals potential is beneficial in cases when backbone flexibility is important. All things considered, we define an energy function that captures most of the nuances of the binding energetics and hence, should be used in future for design of PPIs.     

Functional diversity of protein C-termini: more than zipcoding?

The carboxylated (C)-terminus of proteins, which includes the single terminal alpha-carboxyl group and preceding residues, is uniquely positioned to serve as a recognition signature for a variety of cell-biological processes, including protein targeting, subcellular anchoring and the static and dynamic formation of macromolecular complexes. The terminal sequence motifs can be processed by posttranslational modifications, thereby providing a means to increase sequence diversity and to regulate interactions. Several classes of protein domains have been identified that are either designed for or are capable of interacting with protein C-termini - these include PDZ and TPR domains. The interactions between these protein domains and various terminal epitopes play an important role in specifying cell-biological functions. The combination of diversity and the plasticity of the chemistry of C-termini provides mechanisms for spatial and temporal specificity that are exploited by a variety of biological processes, ranging from specifying prokaryotic protein degradation to nucleating mammalian neuronal signaling complexes. Understanding the diverse functions of protein C-termini might also provide an important indexing criterion for functional proteomics.     

Are human beings part of the rest of nature?

Unified explanations seek to situate the traits of human beings in a causal framework that also explains the trait values found in nonhuman species. Disunified explanations claim that the traits of human beings are due to causal processes not at work in the rest of nature. This paper outlines a methodology for testing hypotheses of these two types. Implications are drawn concerning evolutionary psychology, adaptationism, and anti-adaptationism. This revised version was published online in July 2006 with corrections to the Cover Date.     

Are men more promiscuous than women?

In spite of the unassailable logic that every new coital partner a man has is also a new partner for the woman concerned, men typically claim more sexual partners than women. If these claims are correct, can prostitutes and other hypersexual women account for this slippage? The present study examines whether the incidence of such women is sufficient to explain the discrepancy in number of lifetime partners claimed by men and women.     

How common is the funnel‐like energy landscape in protein‐protein interactions?

The goal of this study is to verify the concept of the funnel-like intermolecular energy landscape in protein-protein interactions by use of a series of computational experiments. Our preliminary analysis revealed the existence of the funnel in many protein-protein interactions. However, because of the uncertainties in the modeling of these interactions and the ambiguity of the analysis procedures, the detection of the funnels requires detailed quantitative approaches to the energy landscape analysis. A number of such approaches are presented in this study. We show that the funnel detection problem is equivalent to a problem of distinguishing between distributions of low-energy intermolecular matches in the funnel and in the low-frequency landscape fluctuations. If the fluctuations are random, the decision about whether the minimum is the funnel is equivalent to determining whether this minimum is significantly different from a would-be random one. A database of 475 nonredundant cocrystallized protein-protein complexes was used to re-dock the proteins by use of smoothed potentials. To detect the funnel, we developed a set of sophisticated models of random matches. The funnel was considered detected if the binding area was more populated by the low-energy docking predictions than by the matches generated in the random models. The number of funnels detected by use of different random models varied significantly. However, the results confirmed that the funnel may be the general feature in protein-protein association.     

Are more diverse parts of the mammalian skull more?labile?

Morphological variation is unevenly distributed within the mammalian skull; some of its parts have diversified more than others. It is commonly thought that this pattern of variation is mainly the result of the structural organization of the skull, as defined by the pattern and magnitude of trait covariation. Patterns of trait covariation can facilitate morphological diversification if they are aligned in the direction of selection, or these patterns can constrain diversification if oriented in a different direction. Within this theoretical framework, it is thought that more variable parts possess patterns of trait covariation that made them more capable of evolutionary change, that is, are more labile. However, differences in the degree of morphological variation among skull traits could arise despite variation in trait lability if, for example, some traits have evolved at a different rate and/or undergone stabilizing selection. Here, we test these hypotheses in the mammalian skull using 2D geometric morphometrics to quantify skull shape and estimating constraint, rates of evolution, and lability. Contrary to the expectations, more variable parts of the skull across mammalian species are less capable of evolutionary change than are less variable skull parts. Our results suggest that patterns of morphological variation in the skull could result from differences in rate of evolution and stabilizing selection.     

Cell surface protein kinases in Dictyostelium: Are they artifacts?

Evidence for cell surface protein kinases as possible regulatory factors of cell interaction in Dictyostelium discoideum was examined by incubating intact cells with gamma 32P-ATP in the presence and absence of histone. No significant incorporation of 32P was detected in the absence of histone. In its presence strong phosphorylation not only of the histone but also of endogenous proteins was obtained. This was due to the fact that histone made the cell membranes permeable for substrates and proteinkinases. Histone also preserved protein kinase activities which were otherwise lost during homogenization. The total protein kinase activity in histone treated cells was 5 fold higher than in sonicated cells.     

Is the surface area of the red cell membrane skeleton locally conserved?

The incompressibility of the lipid bilayer keeps the total surface area of the red cell membrane constant. Local conservation of membrane surface area requires that each surface element of the membrane skeleton keeps its area when its aspect ratio is changed. A change in area would require a flow of lipids past the intrinsic proteins to which the skeleton is anchored. in fast red cell deformations, there is no time for such a flow. Consequently, the bilayer provides for local area conservation. In quasistatic deformations, the extent of local change in surface area is the smaller the larger the isotropic modulus of the skeleton in relation to the shear modulus. Estimates indicate: (a) the velocity of relative flow between lipid and intrinsic proteins is proportional to the gradient in normal tension within the skeleton and inversely proportional to the viscosity of the bilayer; (b) lateral diffusion of lipids is much slower than this flow; (c) membrane tanktreading at frequencies prevailing in vivo as well as the release of a membrane tongue from a micropipette are fast deformations; and (d) the slow phase in micropipette aspiration may be dominated by a local change in skeleton surface.     

Are the conserved sequences in segment 1 of gelsolin important for binding actin?

The minimal region required for actin binding in the smallest of the three domains of gelsolin (termed Segment 1 or S1) was previously defined by deletion mutagenesis as residues 37-126. Further analysis of NH2-terminal deletions here redefines the minimal functional core as residues 41-126. Amino acid substitutions within this core further elucidate the nature of the interaction of segment 1 with actin. Of 26 point mutants analyzed, 14 reduced the affinity for actin. The charged residues His 119, Arg 120, Glu 121, and Gln 123 appear to be involved in direct interaction with actin. Substitutions of Leu 108, Leu 112, and Val 117 by polar groups all affect the structural stability of segment 1 and thereby reduce binding affinity. In addition replacement of Glu 126 by aspartic acid modifies the physical properties of segment 1 and weakens binding. We have further shown that changing charged residues within the highly conserved pentapeptide sequence LDDYL (residues 108-112) has no effect on actin binding. This sequence, found in a number of different actin binding proteins, does not therefore constitute part of the interaction site. Similarly, substitution of the two acidic residues by basic ones within the DESG motif of segment 1 (residues 96-99, but also found near the COOH terminus of actin) does not impair binding. These results show the dangers of predicting functional sites on the basis of conserved sequences.     

Are the molecular strategies that control apoptosis conserved in bacteria?

The Staphylococcus aureus cid and lrg operons have been shown to encode putative membrane proteins that are involved in the regulation of murein hydrolase activity and penicillin tolerance. Cid proteins enhance murein hydrolase activity and penicillin sensitivity, whereas Lrg proteins have an inhibitory effect on these processes. It has been proposed that the Cid and Lrg proteins function in a way analogous to bacteriophage-encoded holins and antiholins, respectively, which control the timing of bacteriophage-induced lysis. This article explores the possibility that the Cid-Lrg regulatory system controls bacterial programmed cell death using a molecular strategy that it is functionally analogous to that mediated by the eukaryotic Bcl-2 family of apoptosis regulatory proteins.     

Are tyrosine residues involved in the photoconversion of the water‐soluble chlorophyll‐binding protein of Chenopodium album?

Non‐photosynthetic and hydrophilic chlorophyll (Chl) proteins, called water‐soluble Chl‐binding proteins (WSCPs), are distributed in various species of Chenopodiaceae, Amaranthaceae, Polygonaceae and Brassicaceae. Based on their photoconvertibility, WSCPs are categorised into two classes: Class I (photoconvertible) and Class II (non‐photoconvertible). Chenopodium album WSCP (CaWSCP; Class I) is able to convert the chlorin skeleton of Chl a into a bacteriochlorin‐like skeleton under light in the presence of molecular oxygen. Potassium iodide (KI) is a strong inhibitor of the photoconversion. Because KI attacks tyrosine residues in proteins, tyrosine residues in CaWSCP are considered to be important amino acid residues for the photoconversion. Recently, we identified the gene encoding CaWSCP and found that the mature region of CaWSCP contained four tyrosine residues: Tyr13, Tyr14, Tyr87 and Tyr134. To gain insight into the effect of the tyrosine residues on the photoconversion, we constructed 15 mutant proteins (Y13A, Y14A, Y87A, Y134A, Y13‐14A, Y13‐87A, Y13‐134A, Y14‐87A, Y14‐134A, Y87‐134A, Y13‐14‐87A, Y13‐14‐134A, Y13‐87‐134A, Y14‐87‐134A and Y13‐14‐87‐134A) using site‐directed mutagenesis. Amazingly, all the mutant proteins retained not only chlorophyll‐binding activity, but also photoconvertibility. Furthermore, we found that KI strongly inhibited the photoconversion of Y13‐14‐87‐134A. These findings indicated that the four tyrosine residues are not essential for the photoconversion.     

An information-theoretic classification of amino acids for the assessment of interfaces in protein–protein docking

Docking represents a versatile and powerful method to predict the geometry of protein–protein complexes. However, despite significant methodical advances, the identification of good docking solutions among a large number of false solutions still remains a difficult task. We have previously demonstrated that the formalism of mutual information (MI) from information theory can be adapted to protein docking, and we have now extended this approach to enhance its robustness and applicability. A large dataset consisting of 22,934 docking decoys derived from 203 different protein–protein complexes was used for an MI-based optimization of reduced amino acid alphabets representing the protein–protein interfaces. This optimization relied on a clustering analysis that allows one to estimate the mutual information of whole amino acid alphabets by considering all structural features simultaneously, rather than by treating them individually. This clustering approach is fast and can be applied in a similar fashion to the generation of reduced alphabets for other biological problems like fold recognition, sequence data mining, or secondary structure prediction. The reduced alphabets derived from the present work were converted into a scoring function for the evaluation of docking solutions, which is available for public use via the web service score-MI: http://score-MI.biochem.uni-erlangen.de     

Are hybrid species more fit than ancestral parent species in the current hybrid species habitats?

Hybrid speciation is thought to be facilitated by escape of early generation hybrids into new habitats, subsequent environmental selection and adaptation. Here, we ask whether two homoploid hybrid plant species (Helianthus anomalus, H. deserticola) diverged sufficiently from their ancestral parent species (H. annuus, H. petiolaris) during hybrid speciation so that they are more fit than the parent species in hybrid species habitats. Hybrid and parental species were reciprocally transplanted into hybrid and parental habitats. Helianthus anomalus was more fit than parental species in the H. anomalus actively moving desert dune habitat. The abilities to tolerate burial and excavation and to obtain nutrients appear to be important for success in the H. anomalus habitat. In contrast, H. deserticola failed to outperform the parental species in the H. deserticola stabilized desert dune habitat, and several possible explanations are discussed. The home site advantage of H. anomalus is consistent with environmental selection having been a mechanism for adaptive divergence and hybrid speciation and supports the use of H. anomalus as a valuable system for further assessment of environmental selection and adaptive traits.