Validation of the first step of the heuristic refinement method for the derivation of solution structures of proteins from NMR data

A new method for the analysis of NMR data in terms of the solution structure of proteins has been developed. The method consists of two steps: first a systematic search of the conformational space to define the region allowed by the initial set of experimental constraints, and second, the narrowing of this region by the introduction of additional constraints and optional refinement procedures. The search of the conformational space is guided by heuristics to make it computationally feasible. The method is therefore called the heuristic refinement method and is coded in an expert system called PROTEAN. The paper describes the validation of the first step of the method using an artificial NMR data set generated from the known crystal structure of sperm whale carbon monoxymyoglobin. It is shown that the initial search procedure yields a low-resolution structure of the myoglobin molecule, accurately reproducing its main topological features, and that the precision of the structure depends on the quality of the initial data set.     

PHYLOGENETIC ANALYSIS OF THE EVOLUTION OF ALTERNATIVE SOCIAL BEHAVIOR IN THE MANAKINS (AVES: PIPRIDAE)

Phylogenetic analyses of lekking, lek spatial organization, and cooperative and coordinated lek display in the manakins (Aves: Pipridae) demonstrate that variation in social behavior in the group has a strong, phylogenetic component. Two of the three classes of social behavior examined also show significant phylogenetic constraints. Current adaptive plasticity models are insufficient to explain the phylogenetic variation in these behaviors in the manakins. These findings support the conclusion that vertebrate reproductive social behavior has an evolutionary history, and that it is not determined solely by adaptive individual plasticity to current conditions. The evolution of social behavior, particularly through sexual selection, can have historical consequences that can limit subsequent behavioral adaptation.     

The bialaphos biosynthetic genes ofStreptomyces hygroscopicus: Molecular cloning and characterization of the gene cluster

Summary We have isolated and studied the organization ofStreptomyces hygroscopicus genes responsible for the biosynthesis of the antibiotic herbicide bialaphos. Bialaphos production genes were cloned from genomic DNA using a plasmid vector (pIJ702). Three plasmids were isolated which restored productivity toS. hygroscopicus mutants blocked at different steps of the biosynthetic pathway. Subcloning experiments using other nonproducing mutants showed that four additional bialaphos production genes were also contained on these plasmids. A gene conferring resistance to bialaphos, which was independently cloned using the plasmid vector pIJ61, and an antibiotic-sensitive host (S. lividans), was also linked to the production genes. Cosmids were isolated which defined the location of these genes in a 16 kb cluster.     

新型生物——人工复合血管研制的初步报告

本文设计一种由胶原和高分子聚合物组成的新型生物一人工复合血管。其研制过程是将包绕有聚酯网的硅胶棒埋入羊的皮下组织,再将形成的经聚酯网为支架的胶原管经醛化处理。作者通过肉眼和SEM观察提出了研制生物——人工复合血管的要点:聚酯网网孔要合适,其与硅胶棒的间隙要恰当,理化处理方法更要选择好。     

Energetic constraints and foraging efficiency

Previous research considers foraging options that differ interms of their gross rate of gain b and rate of energy expenditurec. This research argues that maximizing efficiency b/c willmaximize net energetic gain when there is an upper limit onthe amount of energy that can be assimilated. This analysisdoes not include the expenditure during the time for which theanimal is unable to forage because of this constraint. Whenthis expenditure is included, maximizing efficiency is no longeroptimal. Instead the best feeding option is the one with thehighest value of b/(c – c₁), where c, is the metabolicrate when the animal is not foraging.     

Divergence pattern and selective mode in protein evolution: The example of vertebrate myoglobins and hemoglobin chains

Summary The evolutionary relation of vertebrate myoglobin and the hemoglobin chains including the agnathan hemoglobin chain is investigated on the basis of a new view of amino acid changes that is developed by canonical discriminant analysis of amino acid residues at individual sites. In contrast to the clear discrimination of amino acid residues between myoglobin, hemoglobin a chain, and hemoglobin chain in warm-blood vertebrates, the three types of globins in the lower class of vertebrates show so much variation that they are not well discriminated. This is seen particularly at the sites that are ascertained in mammals to carry the amino acid residues participating in stabilizing the monomeric structure in myoglobin and the residues forming the subunit contacts in hemoglobin. At these sites, agnathan hemoglobin chains are evaluated to be intermediate between the myoglobin and hemoglobin chains of gnathostomes. The variation in the phylogenetically lower class of globins is also seen in the internal region; there the amino acid residues of myoglobin and hemoglobin chains in the phylogenetically higher class exhibit an example of parallel evolution at the molecular level. New quantities, the distance of sequence property between discriminated groups and the variation within each group, are derived from the values of discriminant functions along the peptide chain, and this set of quantities simply describes an overall feature of globins such that the distinction between the three types of globins has been clearer as the vertebrates have evolved to become jawed, landed, and warm-blooded. This result strongly suggests that the functional constraint on the amino acid sequence of a protein is changed by living conditions and that severe conditions constitute a driving force that creates a distinctive protein from a less-constrained protein.Offprint requests to: J. Otsuka     

Morphological differentiation in Carduelis finches: Adaptive vs. constraint models

In this study we show that morphological diversification in the avian genus Carduelis (Carduelinae) has to a large extent been conservative. Using multivariate methods, we found only minor deviations from the common (ancestral) body-plan. In particular, variation in bill morphology was found to be more conservative than variation in other parts of the body. We argue that constraint models of population differentiation can successfully account for the variation in bill morphology in this genus, but are less successful in accounting for variation in other traits. This can be interpreted as a result of long-term overall stabilizing selection for a certain bill morphology which is related to the way the birds open seeds. A trait combination that is adaptive on the evolutionary time scale may thus act as a constraint on changes in bill morphology on the microevolutionary scale. We conclude that the most parsimonious explanation for low divergence in bill morphology in this genus is that all species have retained the ancestral bill morphology. This may mean that each species chooses its environment rather than being moulded by it. This argument seems to apply to bill morphology, but other traits studied in this genus appear to have evolved in a less constrained fashion. A new index of morphometric integration is introduced to describe covariance structures.     

Backbone Cyclization of the C-terminal Part of Substance P. Part 1: The Important Role of the Sulphur in Position 11

Novel backbone-to-side chain and backbone-to-backbone cyclic analogues of substance P (SP) were prepared by solid-phase synthesis and screened for biological activity. An analogue containing a thioether- lactam ring between positions 9 and 11 showed an EC₅₀ value of 20nM toward the neurokinin 1 (NK-1) and was inactive toward the NK-2 and NK-3 receptors. On the other hand, in a multiple backbone cyclic peptide library of similar analogues, in which the sulphur was excluded from the ring, very low activity was detected. The activity was re-evaluated and was found to be even lower (EC₅₀=0.11 mM ) than the previously published data. These results indicate that the thioether moiety has a crucial role in receptor activation. The results also show tolerance of the NK-1 receptor, but not NK-2 or NK-3, to cyclization of the C-terminal portion of the SP_6–11 hexapeptide.     

Patterns of nucleotide substitutions inferred from the phylogenies of the class I major histocompatibility complex genes

Summary Patterns of nucleotide substitutions in human major histocompatibility complex (MHC) class I genes were estimated by using phylogenetic trees of DNA sequences. The pattern is defined as a set of 12 parameters, each of which represents the relative frequency of substitutions from a particular nucleotide to another. The pattern at the antigen recognition sites (ARS) in functional MHC genes was remarkably different from that at the remaining coding region (non-ARS). In particular, the proportion of transitions among all the nucleotide substitutions (P _s) was extremely low at the third codon positions of ARS. In the HLA-A genes, P _s at the third codon positions was only 6% in ARS, whereas it was 69% in non-ARS. In HLA-B, the corresponding values were 30% in ARS and 80% in non-ARS, respectively. On the other hand, P _s in a class I pseudogene (HLA-H) was 57%, which was in good agreement with P _s in other pseudogenes. Because pseudogenes are selectively neutral, the pattern in pseudogenes is regarded as the pattern of spontaneous substitution mutations. In general, the pattern in functional genes that are subject to selective forces deviates from the pattern in pseudogenes. At the third codon positions in coding regions, transitions scarcely cause amino acid replacements, whereas about half of transversions do cause replacements. Accordingly, P _s at the third codon positions decreases if amino acid replacements are accelerated by natural selection but increases if amino acids are conserved by functional constraint. Our observations imply that the ARS region is subject to natural selection favoring amino acid replacements, whereas the non-ARS region is subject to functional constraint. Offprint requests to: T. Gojobori