The complex structure of hunter-gatherer social networks

In nature, many different types of complex system form hierarchical, self-similar or fractal-like structures that have evolved to maximize internal efficiency. In this paper, we ask whether hunter-gatherer societies show similar structural properties. We use fractal network theory to analyse the statistical structure of 1189 social groups in 339 hunter-gatherer societies from a published compilation of ethnographies. We show that population structure is indeed self-similar or fractal-like with the number of individuals or groups belonging to each successively higher level of organization exhibiting a constant ratio close to 4. Further, despite the wide ecological, cultural and historical diversity of hunter-gatherer societies, this remarkable self-similarity holds both within and across cultures and continents. We show that the branching ratio is related to density-dependent reproduction in complex environments and hypothesize that the general pattern of hierarchical organization reflects the self-similar properties of the networks and the underlying cohesive and disruptive forces that govern the flow of material resources, genes and non-genetic information within and between social groups. Our results offer insight into the energetics of human sociality and suggest that human social networks self-organize in response to similar optimization principles found behind the formation of many complex systems in nature.     

The probable structure of the protamine-DNA complex

A detailed molecular structure is proposed for the human protamine-DNA complex, which has hitherto been largely a mystery. The structure was created with virtual modeling software (AmiraMol), employing logical deduction as the primary investigative tool. A beta-sheet structure for the protein component is essentially mandated, as the alternatives can be decisively excluded. A dimeric structure too is essentially mandated, since the cysteine residues of protamines P1 and P2 are invariably aligned in all species having both chains. The cross-sectional and axial spacings of arginine guanidinium groups in this protein structure can be perfectly aligned with those of phosphate groups in DNA according to the DNA structure proposed by Wu. This is a non-helical structure, whose possible occurrence in certain plasmids has been suggested by experimental observations. The unit cell of this protamine-DNA complex is essentially devoid of steric hindrances, and heavily favored by a multitude of ionic and hydrogen bonds. The packing of adjacent "unit cells" of the protamine-DNA structure is based on a complex array of salt bridges, the mere existence of which is so fortuitous that it is virtually inconceivable that it comes about through a mere modeling "coincidence". The possible significance of the structure beyond the sperm cell is discussed.     

The structure of the iron complex in metaquohemerythrin

The novel binuclear iron complex in metaquohemerythrin is described. One of the two iron atoms is octahedrally coordinated, the other being penta-coordinate. A number of questions concerning the structure of the metal complex in different forms of this nonheme iron oxygen transport protein have been clarified. The structure of the complex presented here differs from that of metazidohemerythrin in that the Fe atom providing the binding locus for azide ion is five-coordinate with no small molecule ligand bound to it. The coordination polyhedron of this Fe is best described as a trigonal bipyramid.     

The structure of eukaryotic and prokaryotic complex I

The structures of the NADH dehydrogenases from Bos taurus and Aquifex aeolicus have been determined by 3D electron microscopy, and have been analyzed in comparison with the previously determined structure of Complex I from Yarrowia lipolytica. The results show a clearly preserved domain structure in the peripheral arm of complex I, which is similar in the bacterial and eukaryotic complex. The membrane arms of both eukaryotic complexes show a similar shape but also significant differences in distinctive domains. One of the major protuberances observed in Y. lipolytica complex I appears missing in the bovine complex, while a protuberance not found in Y. lipolytica connects in bovine complex I a domain of the peripheral arm to the membrane arm. The structural similarities of the peripheral arm agree with the common functional principle of all complex Is. The differences seen in the membrane arm may indicate differences in the regulatory mechanism of the enzyme in different species.     

The structure of a Michaelis serpin-protease complex.

Serine protease inhibitors (serpins) regulate the activities of circulating proteases. Serpins inhibit proteases by acylating the serine hydroxyl at their active sites. Before deacylation and complete proteolysis of the serpin can occur, massive conformational changes are triggered in the serpin while maintaining the covalent linkage between the protease and serpin. Here we report the structure of a serpin-trypsin Michaelis complex, which we visualized by using the S195A trypsin mutant to prevent covalent complex formation. This encounter complex reveals a more extensive interaction surface than that present in small inhibitor-protease complexes and is a template for modeling other serpin-protease pairs. Mutations of several serpin residues at the interface reduced the inhibitory activity of the serpin. The serine residue C-terminal to the scissile peptide bond is found in a closer than usual interaction with His 57 at the active site of trypsin.     

The emerging structure of the Agrobacterium T-DNA transfer complex

Single-stranded DNA-protein complex (T-complex) is proposed to mediate T-DNA transfer from Agrobacterium to plant cells. A novel model for transfer is presented which incorporates features of both bacterial conjugation and viral infection. Specific protein components of the T-complex, its ultrastructure and possible functions in the plant cell are discussed.     

The complex structure and dynamic evolution of human subtelomeres

Subtelomeres are extraordinarily dynamic and variable regions near the ends of chromosomes. They are defined by their unusual structure: patchworks of blocks that are duplicated near the ends of multiple chromosomes. Duplications among subtelomeres have spawned small gene families, making inter-individual variation in subtelomeres a potential source of phenotypic diversity. The ectopic recombination that occurs between subtelomeres might also have a role in reconstituting telomeres in the absence of telomerase. However, the propensity for subtelomeres to interchange is a double-edged sword, as extensive subtelomeric homology can mediate deleterious rearrangements of the ends of chromosomes to cause human disease.     

The X-ray structure of the pyochelin Fe3+ complex

By X-ray structure analysis it could be shown that from the solution equilibrium of pyochelin I and II, differing in the stereochemistry at C-2" (1a and 1b), crystals of the Fe3+ complex of the steroisomer 1a are formed with a 1:1 metal-to-ligand ratio. Ligand sites are the carboxylate and the phenolate anions and the two nitrogen atoms. Two equivalent ferri-pyochelin moieties are held together by a hydroxy and an acetate unit which satisfy the remaining two coordination sites of Fe3+.     

The structure of the metal-nucleotide complex substrate for yeast hexokinase

A comparison has been made of the kinetic parameters obtained with yeast hexokinase using Mg²⁺ or Ni²⁺ as metal ion activator and ATP or tubercidin-5′-triphosphate as nucleotide substrate. It is concluded that the relative specificity of the enzyme for MgATP^2? does not involve a contribution arising from an interaction of the metal ion with the purine ring of the nucleotide.     

The subunit structure of the cytochrome c oxidase complex.

The subunit structure of the cytochrome c oxidase complex has been obtained for three preparations each isolated by a different detergent procedure. Six polypeptides were present in all samples with the following molecular weights: subunits I, 36000; II, 22500, III, 17100; IV, 12500; V, 9700; and VI, 5300. These subunits have been purified by gel filtration in sodium dodecyl sulfate or in 6 M guanidine hydrochloride and their amino acid compositions have been determined. Subunit I is hydrophobic in character with a polarity of 35.7%. Subunits II through VI are more hydrophilic with polarities of 45.5, 48.6, 47.8, 49.7, and 53.7%, respectively.     

The SecY translocation complex: convergence of genetics and structure

All organisms share a requirement for translocation of proteins across membranes. The major mechanism for this process is the universally conserved SecY/Sec61 pathway. Many years of extensive genetic and biochemical analyses identified the components of the SecY/Sec61 pathway, demonstrated that most exported proteins use this route for translocation, and led to understanding of many functions of the components. Recently, structural predictions based on genetic analyses in Escherichia coli were confirmed, in a striking and satisfying manner, by the solution of an X-ray crystal structure from an archaeal SecY complex. This review discusses the genetic background that led to those hypotheses and the convergence of genetic studies with structural data.     

The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex

Acarbose is a naturally occurring pseudo-tetrasaccharide. It has been used in conjunction with other drugs in the treatment of diabetes where it acts as an inhibitor of intestinal glucosidases. To probe the interactions of acarbose with other carbohydrate recognition enzymes, the crystal structure of E. coli maltodextrin phosphorylase (MalP) complexed with acarbose has been determined at 2.95 A resolution and refined to crystallographic R-values of R (Rfree) = 0.241 (0.293), respectively. Acarbose adopts a conformation that is close to its major minimum free energy conformation in the MalP-acarbose structure. The acarviosine moiety of acarbose occupies sub-sites +1 and +2 and the disaccharide sub-sites +3 and +4. (The site of phosphorolysis is between sub-sites -1 and +1.) This is the first identification of sub-sites +3 and +4 of MalP. Interactions of the glucosyl residues in sub-sites +2 and +4 are dominated by carbohydrate stacking interactions with tyrosine residues. These tyrosines (Tyr280 and Tyr613, respectively, in the rabbit muscle phosphorylase numbering scheme) are conserved in all species of phosphorylase. A glycerol molecule from the cryoprotectant occupies sub-site -1. The identification of four oligosaccharide sub-sites, that extend from the interior of the phosphorylase close to the catalytic site to the exterior surface of MalP, provides a structural rationalization of the substrate selectivity of MalP for a pentasaccharide substrate. Crystallographic binding studies of acarbose with amylases, glucoamylases, and glycosyltranferases and NMR studies of acarbose in solution have shown that acarbose can adopt two different conformations. This flexibility allows acarbose to target a number of different enzymes. The two alternative conformations of acarbose when bound to different carbohydrate enzymes are discussed.     

The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex

Polygalacturonases hydrolyze the alpha-(1-4) glycosidic bonds of de-esterified pectate in the smooth region of the plant cell wall. Crystal structures of polygalacturonase from Aspergillus aculeatus were determined at pH 4.5 and 8.5 both to 2.0 A resolution. A. aculeatus polygalacturonase is a glycoprotein with one N and ten O-glycosylation sites and folds into a right-handed parallel beta-helix. The structures of the three independent molecules are essentially the same, showing no dependency on pH or crystal packing, and are very similar to that of Aspergillus niger polygalacturonase. However, the structures of the long T1 loop containing a catalytic tyrosine residue are significantly different in the two proteins. A three-dimensional model showing the substrate binding mode for a family 28 hydrolase was obtained by a combined approach of flexible docking, molecular dynamics simulations, and energy minimization. The octagalacturonate substrate was modeled as an unbent irregular helix with the -1 ring in a half-chair ((4)H(3)) form that approaches the transition state conformation. A comparative modeling of the three polygalacturonases with known structure shows that six subsites ranging from -4 to +2 are clearly defined but subsites -5 and +3 may or may not be shaped depending on the nearby amino acid residues. Both distal subsites are mostly exposed to the solvent region and have weak binding affinity even if they exist. The complex model provides a clear explanation for the functions, either in catalysis or in substrate binding, of all conserved amino acid residues in the polygalacturonase family of proteins. Modeling suggests that the role of the conserved Asn157 and Tyr270, which had previously been unidentified, may be in transition state stabilization. In A. niger polygalacturonase, the long T1 loop may have to undergo conformational change upon binding of the substrate to bring the tyrosine residue close to subsite -1.