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At least 451 records · Page 25Linked to original sources
PubMed1999

Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism.

We have determined two different structures of PcrA DNA helicase complexed with the same single strand tailed DNA duplex, providing snapshots of different steps on the catalytic pathway. One of the structures is of a complex with a nonhydrolyzable analog of ATP and is thus a "substrate" complex. The other structure contains a bound sulphate ion that sits in a position equivalent to that occupied by the phosphate ion produced after ATP hydrolysis, thereby mimicking a "product" complex. In both complexes, the protein is monomeric. Large and distinct conformational changes occur on binding DNA and the nucleotide cofactor. Taken together, these structures provide evidence against an "active rolling" model for helicase action but are instead consistent with an "inchworm" mechanism.

Adenylyl Imidodiphosphate↗
PubMed2003

An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins.

A computer program system was developed to predict carbohydrate-binding sites on three-dimensional (3D) protein structures. The programs search for binding sites by referring to the empirical rules derived from the known 3D structures of carbohydrate-protein complexes. A total of 80 non-redundant carbohydrate-protein complex structures were selected from the Protein Data Bank for the empirical rule construction. The performance of the prediction system was tested on 50 known complex structures to determine whether the system could detect the known binding sites. The known monosaccharide-binding sites were detected among the best three predictions in 59% of the cases, which covered 69% of the polysaccharide-binding sites in the target proteins, when the performance was evaluated by the overlap between residue patches of predicted and known binding sites.

Animals↗
PubMed1996

Simulation of a complex protein structural change: the T <--> R transition in the insulin hexamer.

The T <--> R transition in the insulin hexamer is an outstanding model for protein structural changes in terms of its extent and complexity: the limiting structures T(6), T(3)R(3) and R(6) have been defined by X-ray crystallography. The transition occurs cooperatively within trimers. It involves displacements of >30 A and a secondary structural rearrangement of 15% of the peptide chain between extended and helical conformations. Experimental data for the transition are plentiful. Theoretical methods to simulate pathways without constraints would never succeed with such substantial transitions. We have developed two approaches, targeted energy minimization (TEM) and targeted molecular dynamics (TMD). Previously successful in simulating the T <--> R transition of the insulin monomer, these procedures are also shown here to be effective in the hexamer. With TMD, more conformational space is explored and pathways are found at 500 kJ/mol lower energy than with TEM. Because the atoms have to meet distance constraints in sum rather than individually, a high degree of conformational freedom and independence is implied. T(6) --> T(3)R(3) and T(3)R(3) --> T(6) pathways do not coincide because the transformation is directed. One subunit enters a dead end pathway in one direction of the TMD simulation, which shows that constraint and freedom are critically balanced. The ensemble of productive pathways represents a plausible corridor for the transition. A video display of the transformations is available.

Crystallography, X-Ray↗
PubMed2001

Bimetallic cyanide-bridged complexes based on the photochromic nitroprusside anion and paramagnetic metal complexes. Syntheses, structures, and physical characterization of the coordination compounds [Ni(en)2]4[Fe(CN)5NO]2[Fe(CN)6]x5H2O, [Ni(en)2][Fe(CN)5NO]x3H2O, [Mn(3-MeOsalen)(H2O)]2[Fe(CN)5NO], and [Mn(5-Brsalen)]2[Fe(CN)5NO].

The synthesis, crystal structure, and physical characterization of the coordination compounds [Ni(en)2]4[Fe(CN)5NO]2[Fe(CN)6]x5H2O (1), [Ni(en)2][Fe(CN)5NO]x3H2O (2), [Mn(3-MeOsalen)(H2O)]2[Fe(CN)5NO] (3), and [Mn(5-Brsalen)]2[Fe(CN)5NO] (4) are presented. 1 crystallizes in the monoclinic space group P2(1)/n (a = 7.407(4) A, b = 28.963(6) A, c = 14.744(5) A, alpha = 90 degrees, beta = 103.26(4) degrees, gamma = 90 degrees, Z = 2). Its structure consists of branched linear chains formed by cis-[Ni(en)2]2+ cations and ferrocyanide and nitroprusside anions. The presence of two kinds of iron(II) sites has been demonstrated by Mössbauer spectroscopy. 2 crystallizes in the monoclinic space group P2(1)/c (a = 11.076(3) A, b = 10.983(2) A, c = 17.018(5) A, alpha = 90 degrees, beta = 107.25(2) degrees, gamma = 90 degrees, Z = 4). Its structure consists of zigzag chains formed by an alternated array of cis-[Ni(en)2]2+ cations and nitroprusside anions. 3 crystallizes in the triclinic space group P1 (a = 8.896(5) A, b = 10.430(5) A, c = 12.699(5) A, alpha = 71.110(5) degrees, beta = 79.990(5) degrees, gamma = 89.470(5) degrees, Z = 1). Its structure comprises neutral trinuclear bimetallic complexes in which a central [Fe(CN)5NO]2- anion is linked to two [Mn(3-MeOsalen)]+ cations. 4 crystallizes in the tetragonal space group P4/ncc (a = 13.630(5) A, c = 21.420(8) A, Z = 4). Its structure shows an extended 2D neutral network formed by cyclic octameric [-Mn-NC-Fe-CN-]4 units. The magnetic properties of these compounds indicate the presence of quasi-isolated paramagnetic Ni2+ and Mn3+. Irradiated samples of the four compounds have been studied by differential scanning calorimetry to detect the existence of the long-lived metastable states of nitroprusside.

Journal Article↗
PubMed2004

Differential arrangements of conserved building blocks among homologs of the Rad50/Mre11 DNA repair protein complex.

Structural maintenance of chromosomes (SMC) proteins have diverse cellular functions including chromosome segregation, condensation and DNA repair. They are grouped based on a conserved set of distinct structural motifs. All SMC proteins are predicted to have a bipartite ATPase domain that is separated by a long region predicted to form a coiled coil. Recent structural data on a variety of SMC proteins shows them to be arranged as long intramolecular coiled coils with a globular ATPase at one end. SMC proteins function in pairs as heterodimers or as homodimers often in complexes with other proteins. We expect the arrangement of the SMC protein domains in complex assemblies to have important implications for their diverse functions. We used scanning force microscopy imaging to determine the architecture of human, Saccharomyces cerevisiae, and Pyrococcus furiosus Rad50/Mre11, Escherichia coli SbcCD, and S.cerevisiae SMC1/SMC3 cohesin SMC complexes. Two distinct architectural arrangements are described, based on the way their components were connected. The eukaryotic complexes were similar to each other and differed from their prokaryotic and archaeal homologs. These similarities and differences are discussed with respect to their diverse mechanistic roles in chromosome metabolism.

Amino Acid Sequence↗
PubMed1999

Novel multi-dimensional heteronuclear NMR techniques for the study of 13C-O-acetylated oligosaccharides: expanding the dimensions for carbohydrate structures.

Complex carbohydrates have critical roles in a wide variety of biological processes. An understanding of the molecular mechanisms that underlie these processes is essential in the development of novel oligosaccharide-based therapeutic strategies. Unfortunately, obtaining detailed structural information for larger oligosaccharides (> 10 residues) can be exceedingly difficult, especially where the amount of sample available is limited. Here we demonstrate the application of 13C O-acetylation in combination with novel NMR experiments to obtain much of the information required to characterize the primary structure of oligosaccharides. (H)CMe COH-HEHAHA and H(CMe)COH-HEHAHA experiments are presented that use heteronuclear Hartmann-Hahn transfer to correlate the acetyl groups with sugar ring protons in peracetylated oligosaccharides. The in-phase, pure absorption nature of the correlation peaks in these experiments allows measurement of both chemical shifts and, importantly, 1H-1H coupling constants that are used to define the stereochemistry of the sugar ring. The (HCMe)COH and (HCMe)COH-RELAY experiments provide additional methods for obtaining chemical shift assignments for larger oligosaccharides to define the sites of glycosidic linkages from the patterns of acetylation.

Acetylation↗
PubMed2003

Horse hooves and bird feathers: Two model systems for studying the structure and development of highly adapted integumentary accessory organs--the role of the dermo-epidermal interface for the micro-architecture of complex epidermal structures.

Accessory organs of the integument are locally modified parts of the potentially feather-bearing skin in birds (e.g., the rhamphotheca, claws, or scales), and of the potentially hairy skin in mammals (e.g., the rhinarium, nails, claws, or hooves). These special parts of the integument are characterised by a modified structure of their epidermal, dermal and subcutaneous layers. The developmental processes of these various integumentary structures in birds and mammals show both similarities and differences. For example, the development of the specialised epidermal structures of both feathers and the hoof capsule is influenced by the local three-dimensional configuration of the dermis. However, in feathers, in contrast to hooves, the arrangement of the corneous cells is only partially a direct result of the particular arrangement and shape of the dermal surface of the papillary body. Whereas the diameter of the feather papilla, as well as the number, length, and width of dermal ridges on the surface of the feather papilla influence the three-dimensional architecture of the feather rami, there is no apparent direct correlation between the dermo-epidermal interface and the development of the highly ordered architecture of the radii and hamuli in the feather vane. In order to elucidate this morphogenic problem and the problem of locally different processes of keratinisation and cornification, the structure and development of feathers in birds are compared to those of the hoof capsule in horses. The equine hoof is the most complex mammalian integumentary structure, which is determined directly by the dermal surface of the papillary body. Perspectives for further research on the development of modified integumentary structures, such as the role of the dermal microangioarchitecture and the selective adhesion and various differentiation pathways of epidermal cells, are discussed.

Animals↗
PubMed1978

Size, technology, complexity, and structural differentiation: toward a theoretical synthesis.

This paper proposes a theoretical synthesis of the concepts of organizational size, technology, complexity, and structural differentiation. It suggests and finds that the most important determinant of differentiation in the division of labor is the scope of an organization's task, a technological dimension, and not organizational size. Neither horizontal nor vertical differentiation is thought to be determined by size while the scope of the task is proposed as a determinant of horizontal differentiation. The findings, however, support only the inference of a moderate causal connection between either size or task scope and either form of differentiation. Throughout the analysis and discussion the contrast between causal inference based on associations of levels and change rates is discussed. When dealing with the organizational processes addressed in this paper, both associations must be examined to adequately portray the complexity of the causal processes inferred.

Models, Theoretical↗
PubMed2003

Function and structure of complex II of the respiratory chain.

Complex II is the only membrane-bound component of the Krebs cycle and in addition functions as a member of the electron transport chain in mitochondria and in many bacteria. A recent X-ray structural solution of members of the complex II family of proteins has provided important insights into their function. One feature of the complex II structures is a linear electron transport chain that extends from the flavin and iron-sulfur redox cofactors in the membrane extrinsic domain to the quinone and b heme cofactors in the membrane domain. Exciting recent developments in relation to disease in humans and the formation of reactive oxygen species by complex II point to its overall importance in cellular physiology.

Animals↗
PubMed1988

Selectivity for harmonic structure in complex sounds by the green treefrog (Hyla cinerea).

1. A psychophysical technique based on reflex modification was used to study the detection of two-tone complexes in background noise by the green treefrog (Hyla cinerea). Three different two-tone complexes were synthesized and presented to measure detection thresholds--a harmonic complex of 900 + 3000 Hz (periodicity of 300 Hz, mimicking the structure of the natural advertisement call); an inharmonic complex of 830 + 3100 Hz; and a second harmonic complex of 828 + 2760 Hz (periodicity of 276 Hz). 2. Masked thresholds and 'critical ratios' (signal-to-noise ratios at threshold) were lowest for the two harmonic complexes (900 + 3000 Hz, mean 'critical ratio' of 16 dB; 828 + 2760 Hz, mean 'critical ratio' of 14 dB). For the inharmonic complex, for which there is no stable first-harmonic periodicity, the mean 'critical ratio' was 24 dB. These data suggest that the green treefrog is sensitive to the harmonic structure of complex sounds as a specific acoustic feature. 3. Because of the unique structure of the treefrog's inner ear, the heightened behavioral sensitivity to harmonic complexes must be due to processing in the central, rather than peripheral, auditory system.

Acoustics↗
PubMed2000

The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster.

Jingwei (jgw) is the first gene found to be of sufficiently recent origin in Drosophila to offer insights into the origin of a gene. While its chimerical gene structure was partially resolved as including a retrosequence of alcohol dehydrogenase (ADH:), the structure of its non-ADH: parental gene, the donor of the N-terminal domain of jgw, is unclear. We characterized this non-ADH: parental locus, yellow emperor (ymp), by cloning it, mapping it onto the polytene chromosomes, sequencing the entire locus, and examining its expression patterns in Drosophila melanogaster. We show that ymp is located in the 96-E region; the N-terminal domain of ymp has donated the non-ADH: portion of jgw via a duplication. The similar 5' portions of the gene and its regulatory sequences give rise to similar testis-specific expression patterns in ymp and jgw in Drosophila teissieri. Furthermore, between-species comparison of ymp revealed purifying selection in the protein sequence, suggesting a functional constraint in ymp. While the structure of ymp provides clear information for the molecular origin of the new gene jgw, it unexpectedly casts a new light on the concept of genes. We found, for the first time, that the single locus of the ymp gene encompasses three major molecular mechanisms determining structure of eukaryotic genes: (1) the 5' exons of ymp are involved in an exon-shuffling event that has created the portion recruited by jgw; (2) using alternative cleavage sites and alternative splicing sites, the 3' exon groups of ymp produce two proteins with nonhomologous C-terminal domains, both exclusively in the testis; and (3) in the opposite strand of the third intron of ymp is an essential gene, musashi (msi), which encodes an RNA-binding protein. The composite gene structure of ymp manifests the complexity of the gene concept, which should be considered in genomic research, e.g., gene finding.

Alternative Splicing↗
PubMed1992

Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Deoxyribonuclease I footprinting of defined complexes.

The structure and properties of ternary complexes of RNA polymerase are of central importance in understanding the mechanisms of transcriptional elongation and termination, and the regulation of these primary steps in gene expression. However, there has been no systematic study of the structure and properties of such complexes along a single transcription unit. Recently, we have described the isolation of a collection of halted ternary complexes of Escherichia coli RNA polymerase bearing transcripts from 11 to 35 nucleotides in length along two different transcription units (accompanying paper). Here, we report structural studies of these complexes using DNase I footprinting. Surprisingly, nearly all of the different ternary complexes have distinctly different footprints along the two DNA strands, and the position of the footprint relative to the 3' end of the transcript also varies for most complexes. Halted complexes bearing transcripts of comparable size do not have identical footprints; hence, DNA sequence as well as transcript length plays a role in determining the size and position of the footprint. These differences in structure are consistent with our earlier findings that ternary complexes can differ considerably in stability and gel mobility. The downstream boundary of the RNA polymerase in ternary complexes does not move forward regularly as successive nucleotide residues are added to the RNA chain. In contrast, the upstream boundary moves forward more or less in concert with the movement of the 3' terminus of the transcript. These factors lead to a general compression of the overall footprint as transcription proceeds, together with a steady movement of the 3' terminus of the RNA toward the downstream boundary of the polymerase. Ultimately, after the length of the RNA transcript has increased from eight to ten nucleotides, the downstream boundary of the complex is found to move downstream along the DNA, suggesting a translocation event. We suggest that RNA chain elongation, like RNA chain initiation, may involve a saltatory process in which net translocation of the complex along the DNA occurs only after addition of a number of ribonucleotides to the RNA chain.

Base Sequence↗
PubMed2001

The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel.

Replicative helicases are motor proteins that unwind DNA at replication forks. Escherichia coli DnaB is the best characterized member of this family of enzymes. We present the 26 A resolution three-dimensional structure of the DnaB hexamer in complex with its loading partner, DnaC, obtained from cryo-electron microscopy. Analysis of the volume brings insight into the elaborate way the two proteins interact, and provides a structural basis for control of the symmetry state and inactivation of the helicase by DnaC. The complex is arranged on the basis of interactions among DnaC and DnaB dimers. DnaC monomers are observed for the first time to arrange as three dumb-bell-shaped dimers that interlock into one of the faces of the helicase. This could be responsible for the freezing of DnaB in a C(3) architecture by its loading partner. The central channel of the helicase is almost occluded near the end opposite to DnaC, such that even single-stranded DNA could not pass through. We propose that the DnaB N-terminal domain is located at this face.

Bacterial Proteins↗
PubMed1996

Synthesis, Spectroscopic Characterization, and Structural Studies of Bis(&mgr;-sulfido)bis[{O,O-dialkyl (alkylene) dithiophosphato}oxomolybdenum(V)] Complexes. Crystal Structures of Mo(2)O(2)S(2)[S(2)P(OEt)(2)](2), Mo(2)O(2)S(2)[S(2)P(OEt)(2)](2).2NC(5)H(5), and Mo(2)O(3)[S(2)P(OPh)(2)](4).

A series of new complexes, Mo(2)O(2)S(2)[S(2)P(OR)(2)](2) (where R = Et, n-Pr, i-Pr) and Mo(2)O(2)S(2)[S(2)POGO](2) (where G = -CH(2)CMe(2)CH(2)-, -CMe(2)CMe(2)-) have been prepared by the dropwise addition of an ethanolic solution of the ammonium or sodium salt of the appropriate O,O-dialkyl or -alkylene dithiophosphoric acid, or the acid itself, to a hot aqueous solution of molybdenum(V) pentachloride. The complexes were also formed by heating solutions of Mo(2)O(3)[S(2)P(OR)(2)](4) or Mo(2)O(3)[S(2)POGO](4) species in glacial acetic acid. The Mo(2)O(2)S(2)[S(2)P(OR)(2)](2) and Mo(2)O(2)S(2)[S(2)POGO](2) compounds were characterized by elemental analyses, (1)H, (13)C, and (31)P NMR, and infrared and Raman spectroscopy, as were the 1:2 adducts formed on reaction with pyridine. The crystal structures of Mo(2)O(2)S(2)[S(2)P(OEt(2))](2), Mo(2)O(2)S(2)[S(2)P(OEt)(2)](2).2NC(5)H(5), and Mo(2)O(3)[S(2)P(OPh)(2)](4) were determined. Mo(2)O(2)S(2)[S(2)P(OEt)(2)](2) (1) crystallizes in space group C2/c, No. 15, with cell parameters a = 15.644(3) Å, b = 8.339(2) Å, c = 18.269(4) Å, beta = 103.70(2) degrees, V = 2315.4(8) Å(3), Z = 4, R = 0.0439, and R(w) = 0.0353. Mo(2)O(2)S(2)[S(2)P(OEt)(2)](2).2NC(5)H(5) (6) crystallizes in space group P&onemacr;, No. 2, with the cell parameters a = 12.663(4) Å,b = 14.291(5) Å, c = 9.349(3) Å, alpha = 100.04(3) degrees, beta = 100.67(3) degrees, gamma = 73.03(3) degrees V = 1557(1) Å(3), Z = 2, R = 0.0593, and R(w) = 0.0535. Mo(2)O(3)[S(2)P(OPh)(2)](4) (8) crystallizes in space group P2(1)/n, No. 14, with cell parameters a = 15.206(2)Å, b = 10.655(3)Å, c = 19.406(3)Å, beta = 111.67(1) degrees, V = 2921(1)Å(3), Z = 2, R = 0.0518, R(w) = 0.0425. The immediate environment about the molybdenum atoms in 1 is essentially square pyramidal if the Mo-Mo interaction is ignored. The vacant positions in the square pyramids are occupied by two pyridine molecules in 6, resulting in an octahedral environment with very long Mo-N bonds. The terminal oxygen atoms in both 1 and 6 are in the syn conformation. In 8, which also has a distorted octahedral environment about molybdenum, two of the dithiophosphate groups are bidentate as in 1 and 6, but the two others have one normal Mo-S bond and one unusually long Mo-S bond.

Journal Article↗
PubMed1992

Modelling and simulation of complex control structures in cell biology.

Biological and biomedical tissues and organs represent very complex and highly dynamic systems. The problem to model such complex systems is twofold. First, it is necessary to identify and describe the biological properties and the connecting control mechanisms of the studied system and its subparts. Here, biological knowledge is often missing. Secondly, we are confronted with the problem to formulate the model of the control structure in a form that allows model analysis. Here, a normal mathematical formalism is often inadequate. To solve these modelling problems and to develop methods for building models of complex control structures that will enable the formulation of dynamic systems in biology, a framework for building such models is presented. The model framework is here mainly used for studies of dynamic cell structures, but the possible application areas are more general. An example is given for modelling cell structures of epithelial tissues in the intestine.

Cell Physiological Phenomena↗
PubMed1995

In vivo assembly of the proteasomal complexes, implications for antigen processing.

The multicatalytic and multisubunit proteasomal complexes have been implicated in the processing of antigens to peptides presented by class I major histocompatibility complex molecules. Two structural complexes of this proteinase, 20 S and 26 S proteasomes, have been isolated from cells. By analyzing in vivo assembly of the proteasomal complexes we show that the 20 S proteasomal complexes are irreversibly assembled via 15 S assembly intermediates containing unprocessed beta-type subunits. The 20 S proteasomes further associate reversibly with proteasome activators PA28 or pre-existing ATPase complexes to form 26 S proteasomal complexes. Our findings that not all of the 20 S proteasomal complexes are assembled into 26 S proteasomal complexes within cells and that all of PA28 and ATPase complexes are associated with 20 S proteasomes strongly suggest that all proteasomal complexes coexist within cells. We further demonstrate that 26 S proteasomal complexes are predominantly present in the cytoplasm and a significant portion of the 20 S proteasomal complexes is associated with the endoplasmic reticulum membrane. Taken together, our findings suggest that depending upon their associated regulatory components, 26 S and 20 S-PA28 proteasomal complexes serve different housekeeping functions within the cells, while they degrade antigens in a cooperative manner in antigen processing.

Animals↗
PubMedDate not supplied

Isolation and preliminary characterization of a structural glycoprotein complex from bovine corneal stroma.

After extraction of bovine corneal stroma with 1M CaC1(2) and subsequent digestion of the insoluble residue with purified bacterial collagenase, two crude structural glycoprotein (SPG) fractions were obtained; one which precipitated upon dialysis against water of the collagenase solubilized material and the other which was extracted by 8M urea from the collagenase insoluble material. Amino acid analyses of these crude SGP fractions indicated that they were primarily non-collagenous but that very small amounts of collagen-derived amino acids were present. Upon gel filtration of these SGP fractions on Sepharose 4B-CL, void volume fractions were isolated from each of the crude fractions which were enriched, relative to the original crude fractions, in the collagen-derived amino acids. Carbohydrate analysis indicated that the void volume fractions had the properties of glycoproteins rather than proteoglycans. Upon disulfide reduction and SDS-PAGE, each of these fractions was resolved into five major protein bands with molecular weights of 155,000, 137,000, 117,000 82,000 and 34,000. Only the three largest bands contained the collagen derived amino acids. These data are consistent with the presence within bovine corneal stroma of a large structural glycoprotein complex comprised of at least five protein components associated through disulfide bonds. Collagen apparently is associated with three of these, either through covalent crosslinkage, or as part of the primary structure.

Amino Acids↗