Contact Density Affects Protein Evolutionary Rate from Bacteria to Animals

The density of contacts or the fraction of buried sites in a protein structure is thought to be related to a protein’s designability, and genes encoding more designable proteins should evolve faster than other genes. Several recent studies have tested this hypothesis but have found conflicting results. Here, we investigate how a gene’s evolutionary rate is affected by its protein’s contact density, considering the four species Escherichia coli, Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We find for all four species that contact density correlates positively with evolutionary rate, and that these correlations do not seem to be confounded by gene expression level. The strength of this signal, however, varies widely among species. We also study the effect of contact density on domain evolution in multidomain proteins and find that a domain’s contact density influences the domain’s evolutionary rate. Within the same protein, a domain with higher contact density tends to evolve faster than a domain with lower contact density. Our study provides evidence that contact density can increase evolutionary rates, and that it acts similarly on the level of entire proteins and of individual protein domains. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Evolutionary Conservative and Species-Specific Antigenic Determinants of Mammalian Thyroglobulins

Evolutionary conservative and species-specific epitopes of thyroglobulins (Tg) from different mammalian species were studied using panel of 20 monoclonal antibodies (mAb) raised in our laboratory and recognizing 16 antigen determinants on human Tg molecule. Cross-reactivity of mAb with preparations of purified mammalian Tg from other species was studied by the method of indirect enzyme-linked immunosorbent assay (ELISA). Interaction of mAb with Tg in histological sections of thyroid gland tissue was studied by direct immunofluorescence assay using mAb conjugated with fluorescein isothiocyanate (FITC). Since certain Tg epitopes lose their ability to bind mAb after fixation and paraffin embedding, only 12 out of 20 mAb turned out to be suitable for detection of Tg in the tissue sections. The obtained data have allowed establishing that four human Tg epitopes are species-specific. Meanwhile, six human Tg epitopes are shared with bovine Tg epitopes, seven epitopes with porcine Tg, four with rat, and two with mouse Tg. Each Tg of two species (cat and dog) has three common epitopes with human Tg.     

Protein Determinants of SNARE-Mediated Lipid Mixing

Soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE)-mediated lipid mixing can be efficiently recapitulated in vitro by the incorporation of purified vesicle membrane (-v) SNARE and target membrane (t-) SNARE proteins into separate liposome populations. Despite the strong correlation between the observed activities in this system and the known SNARE physiology, some recent works have suggested that SNARE-mediated lipid mixing may be limited to circumstances where membrane defects arise from artifactual reconstitution conditions (such as nonphysiological high-protein concentrations or unrealistically small liposome populations). Here, we show that the previously published strategies used to reconstitute SNAREs into liposomes do not significantly affect either the physical parameters of the proteoliposomes or the ability of SNAREs to drive lipid mixing in vitro. The surface density of SNARE proteins turns out to be the most critical parameter, which controls both the rate and the extent of SNARE-mediated liposome fusion. In addition, the specific activity of the t-SNARE complex is significantly influenced by expression and reconstitution protocols, such that we only observe optimal lipid mixing when the t-SNARE proteins are coexpressed before purification.     

Evolutionary Rate Covariation Identifies New Members of a Protein Network Required for Drosophila melanogaster Female Post-Mating Responses

Seminal fluid proteins transferred from males to females during copulation are required for full fertility and can exert dramatic effects on female physiology and behavior. In Drosophila melanogaster, the seminal protein sex peptide (SP) affects mated females by increasing egg production and decreasing receptivity to courtship. These behavioral changes persist for several days because SP binds to sperm that are stored in the female. SP is then gradually released, allowing it to interact with its female-expressed receptor. The binding of SP to sperm requires five additional seminal proteins, which act together in a network. Hundreds of uncharacterized male and female proteins have been identified in this species, but individually screening each protein for network function would present a logistical challenge. To prioritize the screening of these proteins for involvement in the SP network, we used a comparative genomic method to identify candidate proteins whose evolutionary rates across the Drosophila phylogeny co-vary with those of the SP network proteins. Subsequent functional testing of 18 co-varying candidates by RNA interference identified three male seminal proteins and three female reproductive tract proteins that are each required for the long-term persistence of SP responses in females. Molecular genetic analysis showed the three new male proteins are required for the transfer of other network proteins to females and for SP to become bound to sperm that are stored in mated females. The three female proteins, in contrast, act downstream of SP binding and sperm storage. These findings expand the number of seminal proteins required for SP''s actions in the female and show that multiple female proteins are necessary for the SP response. Furthermore, our functional analyses demonstrate that evolutionary rate covariation is a valuable predictive tool for identifying candidate members of interacting protein networks.     

Evolutionary Conservation of Protein Backbone Flexibility

Internal protein dynamics is essential for biological function. During evolution, protein divergence is functionally constrained: properties more relevant for function vary more slowly than less important properties. Thus, if protein dynamics is relevant for function, it should be evolutionary conserved. In contrast with the well-studied evolution of protein structure, the evolutionary divergence of protein dynamics has not been addressed systematically before, apart from a few case studies. X-Ray diffraction analysis gives information not only on protein structure but also on B-factors, which characterize the flexibility that results from protein dynamics. Here we study the evolutionary divergence of protein backbone dynamics by comparing the C_α flexibility (B-factor) profiles for a large dataset of homologous proteins classified into families and superfamilies. We show that C_α flexibility profiles diverge slowly, so that they are conserved at family and superfamily levels, even for pairs of proteins with nonsignificant sequence similarity. We also analyze and discuss the correlations among the divergences of flexibility, sequence, and structure. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. David Pollock]     

《基于三级营养水平的进化生态学:一支黄花、作瘿昆虫及其天敌》

该书由美国普林斯顿大学出版社 1 997年出版 ,作者为ＷａｒｒｅｎＧ .Ａｂｒａｈａｍｓｏｎ和ＡｒｔｈｕｒＥ .Ｗｅｉｓ。全书通过对一支黄花、作瘿昆虫及其天敌间的相互作用的研究 ,建立了田地生态和进化生态相互作用的系统模式 ,阐明了三级营养水平相互作用的关系。主要内容包括 :( 1 )进化生态学、植物及昆虫的相互关系 ;( 2 )茎杆作瘿昆虫的天敌和一支黄花 :三级营养水平互作的模式系统 ;( 3 )硕蝽Ｅｕｒｏｓｔａ对一支黄花的影响 ;( 4)寄主植物对作瘿昆虫的抗性 ;( 5)作瘿昆虫对寄主植物的选择 ;( 6)由硕蝽Ｅｕｒｏｓｔａ产生的虫瘿 ;(…     

蛋白质序列间进化距离的估计

本文考察了目前采用的估计同源蛋白质序列间进化距离的方法缺陷,并提出了几个新的计算公式,它们考虑了氨基酸位点间显然存在的替代速率的差异。另外,提出了一种考虑氨基酸间不同替代概率的最大似然估计方法。文中对这些公式进行了计算比较,并对它在实际中的运用提出了建议。     

Targeting Determinants and Proposed Evolutionary Basis for the Sec and the Delta pH Protein Transport Systems in Chloroplast Thylakoid Membranes

Transport of proteins to the thylakoid lumen is accomplished by two precursor-specific pathways, the Sec and the unique Delta pH transport systems. Pathway selection is specified by transient lumen-targeting domains (LTDs) on precursor proteins. Here, chimeric and mutant LTDs were used to identify elements responsible for targeting specificity. The results showed that: (a) minimal signal peptide motifs consisting of charged N, hydrophobic H, and cleavage C domains were both necessary and sufficient for pathway-specific targeting; (b) exclusive targeting to the Delta pH pathway requires a twin arginine in the N domain and an H domain that is incompatible with the Sec pathway; (c) exclusive targeting to the Sec pathway is achieved by an N domain that lacks the twin arginine, although the twin arginine was completely compatible with the Sec system. A dual-targeting signal peptide, constructed by combining Delta pH and Sec domains, was used to simultaneously compare the transport capability of both pathways when confronted with different passenger proteins. Whereas Sec passengers were efficiently transported by both pathways, Delta pH passengers were arrested in translocation on the Sec pathway. This finding suggests that the Delta pH mechanism evolved to accommodate transport of proteins incompatible with the thylakoid Sec machinery.     

Evolutionary Aspects of Protein Structure and Folding

Four basic stages of evolution of protein structure are described, basing on recent work of the authors aimed specifically to reconstruct the earliest events in the protein evolution. According to this reconstruction, the initial stage of short peptides comprising, probably, only a few amino acid residues had been followed by formation of closed loops of 25–30 residues, which corresponds to the polymer-statistically optimal ring closure size for mixed polypeptide chains. The next stage involved fusion of relatively small linear genes and formation of protein structures consisting of several closed loops of a nearly standard size, with 4–6 loops (100–200 amino acid residues) in a typical protein fold. The last, modern stage began with combinatorial fusion of the presumably circular 300–600 bp DNA units and, accordingly, formation of multidomain proteins.     

Protein Determinants of Meiotic DNA Break Hot Spots

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Highlights? DSB hot spots for meiotic recombination are specified by largely unknown mechanisms ? Linear element proteins, required for most DSBs, are highly enriched at hot spots ? These proteins, the first known global hot spot determinants, bind without DSB formation ? Hot spot determination by these proteins provides a paradigm for crossover control     

Evolutionary Conserved Positions Define Protein Conformational Diversity

Conformational diversity of the native state plays a central role in modulating protein function. The selection paradigm sustains that different ligands shift the conformational equilibrium through their binding to highest-affinity conformers. Intramolecular vibrational dynamics associated to each conformation should guarantee conformational transitions, which due to its importance, could possibly be associated with evolutionary conserved traits. Normal mode analysis, based on a coarse-grained model of the protein, can provide the required information to explore these features. Herein, we present a novel procedure to identify key positions sustaining the conformational diversity associated to ligand binding. The method is applied to an adequate refined dataset of 188 paired protein structures in their bound and unbound forms. Firstly, normal modes most involved in the conformational change are selected according to their corresponding overlap with structural distortions introduced by ligand binding. The subspace defined by these modes is used to analyze the effect of simulated point mutations on preserving the conformational diversity of the protein. We find a negative correlation between the effects of mutations on these normal mode subspaces associated to ligand-binding and position-specific evolutionary conservations obtained from multiple sequence-structure alignments. Positions whose mutations are found to alter the most these subspaces are defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. These positions are shown to be evolutionary conserved, mostly buried aliphatic residues localized in regular structural regions of the protein like β-sheets and α-helix.     

ECOD: An Evolutionary Classification of Protein Domains

Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or “fold”). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies.     

Segregational Drift Constrains the Evolutionary Rate of Prokaryotic Plasmids

Plasmids are extrachromosomal genetic elements in prokaryotes that have been recognized as important drivers of microbial ecology and evolution. Plasmids are found in multiple copies inside their host cell where independent emergence of mutations may lead to intracellular genetic heterogeneity. The intracellular plasmid diversity is thus subject to changes upon cell division. However, the effect of plasmid segregation on plasmid evolution remains understudied. Here, we show that genetic drift during cell division—segregational drift—leads to the rapid extinction of novel plasmid alleles. We established a novel experimental approach to control plasmid allele frequency at the levels of a single cell and the whole population. Following the dynamics of plasmid alleles in an evolution experiment, we find that the mode of plasmid inheritance—random or clustered—is an important determinant of plasmid allele dynamics. Phylogenetic reconstruction of our model plasmid in clinical isolates furthermore reveals a slow evolutionary rate of plasmid-encoded genes in comparison to chromosomal genes. Our study provides empirical evidence that genetic drift in plasmid evolution occurs at multiple levels: the host cell and the population of hosts. Segregational drift has implications for the evolutionary rate heterogeneity of extrachromosomal genetic elements.     

Structural Determinants in Prion Protein Folding and Stability

Prions are responsible for a heterogeneous group of fatal neurodegenerative diseases, involving post-translational modifications of the cellular prion protein. Epidemiological studies on Creutzfeldt-Jakob disease, a prototype prion disorder, show a majority of cases being sporadic, while the remaining occurrences are either genetic or iatrogenic. The molecular mechanisms by which PrP^C is converted into its pathological isoform have not yet been established. While point mutations and seeds trigger the protein to cross the energy barriers, thus causing genetic and infectious transmissible spongiform encephalopathies, respectively, the mechanism responsible for sporadic forms remains unclear. Since prion diseases are protein-misfolding disorders, we investigated prion protein folding and stability as functions of different milieus. Using spectroscopic techniques and atomistic simulations, we dissected the contribution of major structural determinants, also defining the energy landscape of prion protein. In particular, we elucidated (i) the essential role of the octapeptide region in prion protein folding and stability, (ii) the presence of a very enthalpically stable intermediate in prion-susceptible species, and (iii) the role of the disulfide bridge in prion protein folding.